Wikidata:WikiCite/Wikidata lists/Items about RNA-Seq

Article	publication date	author	author name string	published in
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.	2023-05-18	Jürg Bähler Ian Goodhead Valerie Wood	Brian T Wilhelm Samuel Marguerat Stephen Watt Falk Schubert Christopher J Penkett Jane Rogers Jürg Bähler	Nature
The transcriptional landscape of the yeast genome defined by RNA sequencing	2023-06-06	Mark Bender Gerstein	Ugrappa Nagalakshmi Zhong Wang Karl Waern Chong Shou Debasish Raha Michael Snyder	Science
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome	2023-07-03	Stefan Haas	Marc Sultan Marcel H Schulz Hugues Richard Alon Magen Andreas Klingenhoff Matthias Scherf Martin Seifert Tatjana Borodina Aleksey Soldatov Dmitri Parkhomchuk Dominic Schmidt Sean O'Keeffe Martin Vingron Hans Lehrach Marie-Laure Yaspo	Science
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays	2008-09	Yoav Gilad John C Marioni	Christopher E Mason Shrikant M Mane Matthew Stephens	Genome Research
Transcript length bias in RNA-seq data confounds systems biology	2009	Alicia Oshlack Matthew Wakefield		Biology Direct
RNA-Seq: a revolutionary tool for transcriptomics	2009-01	Mark Bender Gerstein	Zhong Wang Michael Snyder	Nature Reviews Genetics
Estimating accuracy of RNA-Seq and microarrays with proteomics	2009-04-16	Wei Chen	Xing Fu Ning Fu Song Guo Zheng Yan Ying Xu Hao Hu Corinna Menzel Yixue Li Rong Zeng Philipp Khaitovich	BMC Genomics
TopHat: discovering splice junctions with RNA-Seq	2009-05-01	Steven Salzberg Lior Pachter	Cole Trapnell	Bioinformatics
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.	2009-07-17	Julian Parkhill Paul P. Gardner Jyoti Choudhary Nicholas Thomson	Timothy T Perkins Robert A Kingsley Maria C Fookes Keith D James Lu Yu Samuel A Assefa Miao He Nicholas J Croucher Derek J Pickard Duncan J Maskell Gordon Dougan	PLOS Genetics
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.	2009-09-01	Simon J van Heeringen Gert Jan C Veenstra	Robert C Akkers Ulrike G Jacobi Eva M Janssen-Megens Kees-Jan Françoijs Hendrik G Stunnenberg	Developmental Cell
Identifiability of isoform deconvolution from junction arrays and RNA-Seq.	2009-09-16	Hui Jiang	David Hiller Weihong Xu Wing Hung Wong	Bioinformatics
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.	2009-10-16	Chad Nusbaum	Joshua Z Levin Michael F Berger Xian Adiconis Peter Rogov Alexandre Melnikov Timothy Fennell Levi A Garraway Andreas Gnirke	Genome Biology
Transcript quantification with RNA-Seq data.	2009-10-19	Gunnar Rätsch	Regina Bohnert Jonas Behr	BMC Bioinformatics
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.	2009-10-24	Likun Wang Xi Wang	Zhixing Feng Xiaowo Wang Xuegong Zhang	Bioinformatics
RNA-seq: from technology to biology.	2009-10-27 2010-02-01	Jürg Bähler	Samuel Marguerat Jürg Bähler	Cellular and Molecular Life Sciences
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.	2009-11-12	M Boutros	Moritz Gilsdorf Thomas Horn Zeynep Arziman Oliver Pelz Evgeny Kiner	Nucleic Acids Research
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.	2009-11-18	Cynthia Sharma Jörg Vogel Richard Reinhardt	Marco Albrecht Thomas Rudel	Nucleic Acids Research
H-DBAS: human-transcriptome database for alternative splicing: update 2010	2009-12-07	Takashi Gojobori Tadashi Imanishi	Jun-ichi Takeda Yutaka Suzuki Ryuichi Sakate Yoshiharu Sato Sumio Sugano	Nucleic Acids Research
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data	2009-12-11	Daniel Ramsköld Rickard Sandberg	Eric T Wang Christopher B Burge	PLOS Computational Biology
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.	2009-12-30	Kathryn J Boor Martin Wiedmann Uri Keich	Haley F Oliver Renato H Orsi Lalit Ponnala Wei Wang Qi Sun Samuel W Cartinhour Melanie J Filiatrault	BMC Genomics
Differential expression analysis for sequence count data	2010	Simon Anders Wolfgang Huber		Genome Biology
Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements	2010	Sandro Banfi Elia Stupka Vincenzo Alessandro Gennarino Remo Sanges	Danilo Licastro Francesca Petrera	BMC Genomics
From RNA-seq reads to differential expression results	2010 2010-12-22	Alicia Oshlack Mark D. Robinson	Matthew D Young	Genome Biology
A scaling normalization method for differential expression analysis of RNA-seq data	2010	Alicia Oshlack Mark D. Robinson		Genome Biology
Global and unbiased detection of splice junctions from RNA-seq data	2010	Ulf Gyllensten Adam Ameur	Anna Wetterbom Lars Feuk	Genome Biology
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.	2010-01-01	Vincent Plagnol Graham Heap Charles Mein David A van Heel Richard Dobson Lude Franke	Jennie H M Yang Kate Downes Barry C Healy Karen A Hunt Nicholas Bockett Patrick C Dubois Thomas J Albert Matthew J Rodesch David G Clayton John A Todd	Human Molecular Genetics
Next-generation sequencing	2010-01-01	Jonathan Arnold	Momiao Xiong Zhongming Zhao Fuli Yu	Journal of Biomedicine and Biotechnology
Defining transcribed regions using RNA-seq.	2010-01-21	Jürg Bähler	Brian T Wilhelm Samuel Marguerat Ian Goodhead Jürg Bähler	Nature Protocols
Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life	2010-01-26	Mark Johnston Antonis Rokas	Chris Todd Hittinger John T Tossberg	Proceedings of the National Academy of Sciences of the United States of America
Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq.	2010-01-29	Luciano Xumerle Giovanni Malerba Diana Bellin	Sara Zenoni Alberto Ferrarini Enrico Giacomelli Marianna Fasoli Mario Pezzotti Massimo Delledonne	Plant Physiology
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.	2010-02-04	Thomas D Otto Arnab Pain Chris Newbold Matthew Berriman Ulrike Böhme	Daniel Wilinski Sammy Assefa Thomas M Keane Louis R Sarry Jacob Lemieux Bart Barrell Manuel Llinás	Molecular Microbiology
Gene ontology analysis for RNA-seq: accounting for selection bias.	2010-02-04	Alicia Oshlack Matthew Wakefield Gordon K Smyth	Matthew D Young	Genome Biology
Close association of RNA polymerase II and many transcription factors with Pol III genes	2010-02-05	Mark Bender Gerstein	Debasish Raha Zhong Wang Zarmik Moqtaderi Linfeng Wu Guoneng Zhong Kevin Struhl Michael Snyder	Proceedings of the National Academy of Sciences of the United States of America
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.	2010-02-11	Marie-Laure Yaspo Stefan Haas Hans Lehrach Martin Vingron	Hugues Richard Marcel H Schulz Marc Sultan Asja Nürnberger Sabine Schrinner Daniela Balzereit Emilie Dagand Axel Rasche Marie-Laure Yaspo	Nucleic Acids Research
RNA-Seq analysis to capture the transcriptome landscape of a single cell.	2010-02-25	Azim Surani	Fuchou Tang Catalin Barbacioru Ellen Nordman Bin Li Nanlan Xu Vladimir I Bashkirov Kaiqin Lao	Nature Protocols
The primary transcriptome of the major human pathogen Helicobacter pylori	2010-03-11	Peter F. Stadler Jörg Vogel Kristin Reiche Fabien Darfeuille Cynthia Sharma Jörg Hackermüller Richard Reinhardt	Steve Hoffmann Jérémy Reignier Sven Findeiss Alexandra Sittka Sandrine Chabas	Nature
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.	2010-03-19	Qiye Li Guojie Zhang Jun Wang Karsten Kristiansen Huanming Yang Jian Wang Xiuqing Zhang	Guangwu Guo Xueda Hu Yong Zhang Ruiqiang Li Ruhong Zhuang Zhike Lu Zengquan He Xiaodong Fang Li Chen Wei Tian Yong Tao Songgang Li	Genome Research
In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines	2010-03-25	Daniel Klevebring	Magnus Bjursell Olof Emanuelsson Joakim Lundeberg	PLOS ONE
Integrative analysis of the melanoma transcriptome	2010-04	Eric Lander Chad Nusbaum Carrie Sougnez Andreas Gnirke Gad Getz Kristian Cibulskis Wendy Winckler Reinhard Dummer Liuda Ziaugra Jordi Barretina Matthew Meyerson Stacey Gabriel	Michael F Berger Joshua Z Levin Krishna Vijayendran Andrey Sivachenko Xian Adiconis Jared Maguire Laura A Johnson James Robinson Roel G Verhaak Robert C Onofrio Elisabeth Laine David E Fisher David B Jaffe Levi A Garraway	Genome Research
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus	2010-04-01	Stéphane Audic Chantal Abergel Jean-Michel Claverie Julie Poulain Pascal Hingamp	Matthieu Legendre Olivier Poirot Virginie Seltzer Deborah Byrne Audrey Lartigue Magali Lescot Alain Bernadac	Genome Research
Detection of splice junctions from paired-end RNA-seq data by SpliceMap.	2010-04-05	Hui Jiang	Kin Fai Au Lan Lin Yi Xing Wing Hung Wong	Nucleic Acids Research
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites	2010-04-12	Tim Nicolai Siegel	Doeke R Hekstra Xuning Wang Scott Dewell George A M Cross	Nucleic Acids Research
Supersplat--spliced RNA-seq alignment.	2010-04-21	Weng-Keen Wong	Douglas W Bryant Rongkun Shen Henry D Priest Todd C Mockler	Bioinformatics
Bacillus anthracis genome organization in light of whole transcriptome sequencing	2010-04-29	Karla D Passalacqua	Jeffrey Martin Wenhan Zhu Nicholas Bergman Mark Borodovsky	BMC Bioinformatics
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation	2010-05	Steven Salzberg Lior Pachter	Cole Trapnell Brian A Williams Geo Pertea Ali Mortazavi Gordon Kwan Marijke J van Baren Barbara J Wold	Nature Biotechnology
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.	2010-05-01	Azim Surani	Fuchou Tang Catalin Barbacioru Siqin Bao Caroline Lee Ellen Nordman Xiaohui Wang Kaiqin Lao	Cell Stem Cell
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs	2010-05-02	J Z Levin Magdalena J Koziol John L. Rinn	Mitchell Guttman Manuel Garber Julie Donaghey James Robinson Xian Adiconis Lin Fan Andreas Gnirke Chad Nusbaum Eric S Lander Aviv Regev	Nature Biotechnology
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling	2010-05-05	James R. Bradford Crispin J. Miller	Yvonne Hey Tim Yates Yaoyong Li Stuart D Pepper	BMC Genomics
Modeling non-uniformity in short-read rates in RNA-Seq data	2010-05-11	Jun Li	Hui Jiang Wing Hung Wong	Genome Biology
Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.	2010-05-28	Elizabeth T Cirulli	Abanish Singh Kevin V Shianna Dongliang Ge Jason P Smith Jessica M Maia Erin L Heinzen James J Goedert David B Goldstein Center for HIV/AIDS Vaccine Immunology (CHAVI)	Genome Biology
rQuant.web: a tool for RNA-Seq-based transcript quantitation	2010-06-15	Gunnar Rätsch	Regina Bohnert	Nucleic Acids Research
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.	2010-06-17	Andrea Sboner Joel Rozowsky Mark Bender Gerstein Valerie Reinke	Ashish Agarwal David Koppstein Lukas Habegger Ladeana W Hillier Rajkumar Sasidharan Robert H Waterston	BMC Genomics
A probabilistic framework for aligning paired-end RNA-seq data	2010-06-23	Derek Y Chiang	Yin Hu Kai Wang Xiaping He Jan F Prins Jinze Liu	Bioinformatics
Uncovering the complexity of transcriptomes with RNA-Seq.	2010-06-27	Valerio Costa Claudia Angelini Italia DeFeis	Alfredo Ciccodicola	Journal of Biomedicine and Biotechnology
Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq	2010-06-28	Dale Hedges Erik K Flemington	Guorong Xu Claire Fewell Christopher Taylor Nan Deng Dale Hedges Xia Wang Kun Zhang Michelle Lacey Haitao Zhang Qinyan Yin Jennifer Cameron Zhen Lin Dongxiao Zhu	RNA
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.	2010-06-29	David Casero Sabeeha Merchant Matteo Pellegrini	David González-Ballester Shawn Cokus Arthur R Grossman	The Plant Cell
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.	2010-07-01	Mehmet Somel Wei Chen Augix Guohua Xu Svante Pääbo	Liu He Zhongshan Li Ying Xu Mingfeng Li Xing Fu Zheng Yan Yuan Yuan Corinna Menzel Na Li Hao Hu Philipp Khaitovich	PLOS Computational Biology
Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice.	2010-07-01	Timofey Skvortsov	D V Ignatov K B Majorov A S Apt T L Azhikina	Acta naturae
Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.	2010-07-02	Minou Nowrousian	Minou Nowrousian	Eukaryotic Cell
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.	2010-07-13	Guojun Lu Bin Han	Tingting Lu Danlin Fan Chuanrang Zhu Wei Li Qiang Zhao Qi Feng Yan Zhao Yunli Guo Wenjun Li Xuehui Huang	Genome Research
An integrative approach to genomic introgression mapping.	2010-07-23	David L. Hyten	Andrew J Severin Gregory A Peiffer Wayne W Xu Bruna Bucciarelli Jamie A O'Rourke Yung-Tsi Bolon David Grant Andrew D Farmer Gregory D May Carroll P Vance Randy C Shoemaker Robert M Stupar	Plant Physiology
Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro.	2010-08-01	Paul Klenerman	Stephen D Woodhouse Ramamurthy Narayan Sally Latham Sheena Lee Robin Antrobus Bevin Gangadharan Shujun Luo Gary P Schroth Nicole Zitzmann	Hepatology
RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome	2010-08-05	Michelle Graham Gary J Muehlbauer	Andrew J Severin Jenna L Woody Yung-Tsi Bolon Bindu Joseph Brian W Diers Andrew D Farmer Rex T Nelson David Grant James E Specht Steven B Cannon Gregory D May Carroll P Vance Randy C Shoemaker	BMC Plant Biology
Recent advances in RNA sequence analysis	2010-08-19	Steven Salzberg		F1000 biology reports
Transcribed dark matter: meaning or myth?	2010-08-25	Chris Ponting	T Grant Belgard	Human Molecular Genetics
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.	2010-08-27	Charles M. Perou Piotr A Mieczkowski Derek Y Chiang	Kai Wang Darshan Singh Zheng Zeng Stephen J Coleman Yan Huang Gleb L Savich Xiaping He Sara A Grimm James N MacLeod Jan F Prins Jinze Liu	Nucleic Acids Research
Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.	2010-09-01	Lauren McIntyre	Alison M Morse Valentina Carballo Donald A Baldwin Christopher G Taylor	Journal of Biomolecular Techniques
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.	2010-09-01	Gavin Sherlock Sadie L Marjani	Vincent M Bruno Zhong Wang Ghia M Euskirchen Jeffrey Martin Michael Snyder	Genome Research
High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.	2010-09-16	Nicholas J Loman Mark Pallen	Charles W Penn	Current Opinion in Microbiology
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.	2010-09-19	Christoph Bock Peggy Farnham David Haussler Junchen Gu Mattia Pelizzola Ryan Lister Alexander Meissner	R Alan Harris Ting Wang Cristian Coarfa Raman P Nagarajan Chibo Hong Sara L Downey Brett E Johnson Shaun D Fouse Allen Delaney Yongjun Zhao Adam Olshen Tracy Ballinger Xin Zhou Kevin J Forsberg Lorigail Echipare Henriette O'Geen Yuanxin Xi Charles B Epstein Bradley E Bernstein R David Hawkins Bing Ren Wen-Yu Chung Hongcang Gu Andreas Gnirke Michael Q Zhang Joseph R Ecker Wei Li Robert A Waterland Marco A Marra Martin Hirst Aleksandar Milosavljevic Joseph F Costello	Nature Biotechnology
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data.	2010-09-27	Zhaohui Steve Qin	Debashis Ghosh	Genes
Studying bacterial transcriptomes using RNA-seq.	2010-09-29 2010-10-01	Nicholas Thomson	Nicholas J Croucher	Current Opinion in Microbiology
Single molecule sequencing with a HeliScope genetic analysis system	2010-10-01	John F Thompson	Kathleen E Steinmann	Current protocols in molecular biology
De novo assembly and analysis of RNA-seq data.	2010-10-10	Shaun Jackman Malachi Griffith Timothee Cezard Steven Jones Pamela A. Hoodless Inanc Birol	Gordon Robertson Jacqueline Schein Readman Chiu Richard Corbett Matthew Field Karen Mungall Sam Lee Hisanaga Mark Okada Jenny Q Qian Anthony Raymond Nina Thiessen Yaron S Butterfield Richard Newsome Simon K Chan Rong She Richard Varhol Baljit Kamoh Anna-Liisa Prabhu Angela Tam YongJun Zhao Richard A Moore Martin Hirst Marco A Marra	Nature Methods
Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells.	2010-10-13	Erik K Flemington	Zhen Lin Guorong Xu Nan Deng Christopher Taylor Dongxiao Zhu	Journal of Virology
Analysis of next-generation genomic data in cancer: accomplishments and challenges	2010-10-15	Elaine Mardis	Li Ding Michael C Wendl Daniel C Koboldt	Human Molecular Genetics
The RNA-Seq approach to studying the expression of mosquito mitochondrial genes.	2010-10-19	Gareth J Lycett	M Neira-Oviedo A Tsyganov-Bodounov V Kokoza A S Raikhel J Krzywinski	Insect Molecular Biology
RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity.	2010-10-27	Geneviève Boucher	Brian T Wilhelm Mathieu Briau Pamela Austin Amélie Faubert Pierre Chagnon Kristin Hope Simon Girard Nadine Mayotte Josette-Renee Landry Josée Hébert Guy Sauvageau	Blood
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.	2010-10-29	Andrea Sboner Stéphane Terry Francesca Demichelis Mark Rubin Mark Bender Gerstein	Dorothee Pflueger Lukas Habegger Raquel Esgueva Pei-Chun Lin Maria A Svensson Naoki Kitabayashi Benjamin J Moss Theresa Y MacDonald Xuhong Cao Terrence Barrette Ashutosh K Tewari Mark S Chee Arul M Chinnaiyan David S Rickman	Genome Research
SNP discovery in the bovine milk transcriptome using RNA-Seq technology	2010-11-06	Alma Islas-Trejo	Angela Cánovas Gonzalo Rincon Saumya Wickramasinghe Juan F Medrano	Mammalian Genome
Analysis and design of RNA sequencing experiments for identifying isoform regulation	2010-11-07	Edoardo M Airoldi	Yarden Katz Eric T Wang Christopher B Burge	Nature Methods
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads	2010-11-24	Gavin Sherlock Matthew Blow	Jeffrey Martin Vincent M Bruno Zhide Fang Xiandong Meng Tao Zhang Michael Snyder Zhong Wang	BMC Genomics
Scaffolding a Caenorhabditis nematode genome with RNA-seq	2010-12	Erich M Schwarz Paul W. Sternberg	Ali Mortazavi Brian Williams Lorian Schaeffer Igor Antoshechkin Barbara J Wold	Genome Research
RNA-Seq Read Alignments with PALMapper	2010-12	Gunnar Rätsch	Géraldine Jean André Kahles Vipin T. Sreedharan Fabio De Bona
Defining the transcriptome and proteome in three functionally different human cell lines.	2010-12-01	Cajsa Algenäs Daniel Klevebring Linn Fagerberg Ivan Matic Mathias Uhlén	Emma Lundberg Tamar Geiger Juergen Cox Cajsa Algenäs Joakim Lundeberg Matthias Mann	Molecular Systems Biology
A high-resolution comparative map of porcine chromosome 4 (SSC4).	2010-12-01	Lawrence B. Schook Craig W. Beattie	J-G Ma T-C Chang H Yasue A D Farmer J A Crow K Eyer H Hiraiwa T Shimogiri S N Meyers J E Beever E F Retzel W-S Liu	Animal Genetics
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.	2010-12-01	Xi Wang	Zhengpeng Wu Xuegong Zhang	Journal of Bioinformatics and Computational Biology
De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology	2010-12-02	Jacob E. Crawford	Wamdaogo M Guelbeogo Antoine Sanou Alphonse Traoré Kenneth D Vernick N'Fale Sagnon Brian P Lazzaro	PLOS ONE
Analysis of transcript and protein overlap in a human osteosarcoma cell line.	2010-12-02	Mathias Uhlén Daniel Klevebring Linn Fagerberg	Emma Lundberg Olof Emanuelsson Joakim Lundeberg	BMC Genomics
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.	2010-12-05	Andrea Sboner Joel Rozowsky Mark Bender Gerstein	Lukas Habegger Tara A Gianoulis Ashish Agarwal Michael Snyder	Bioinformatics
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment.	2010-12-14	Alexey I Nesvizhskii	Kang Ning	BMC Bioinformatics
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology	2010-12-14	Aziz A. Aboobaker	Martin J Blythe Damian Kao Sunir Malla Joanna Rowsell Ray Wilson Deborah Evans Jamie Jowett Amy Hall Virginie Lemay Sabrina Lam	PLOS ONE
H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3	2010-12-16	Richard Bartfai Arne H Smits Moritz Treeck	Wieteke A M Hoeijmakers Adriana M Salcedo-Amaya Eva Janssen-Megens Anita Kaan Tim-Wolf Gilberger Kees-Jan Françoijs Hendrik G Stunnenberg	PLOS Pathogens
Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq	2010-12-17	Wen Huang	Hasan Khatib	BMC Genomics
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.	2010-12-17	Xi Wang	Zhengpeng Wu Xuegong Zhang	Bioinformatics
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome	2010-12-22	Ayelet T. Lamm	Michael R Stadler Huibin Zhang Jonathan I Gent Andrew Z Fire	Genome Research
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts	2010-12-22	Moritz Gerstung	Daniel Enderle Christian Beisel Michael B Stadler Prashanth Athri Renato Paro	Genome Research
miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1.	2010-12-31	Johan Flygare Harvey Lodish	Lingbo Zhang Piu Wong Bing Lim	Genes & Development
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples	2011	Celina Sanchez Rivers Zora Modrusan Brock A Peters	Serban Nacu Wenlin Yuan Zhengyan Kan Deepali Bhatt Jeremy Stinson Kenneth Jung Somasekar Seshagiri Thomas D Wu	BMC Medical Genomics
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing	2011	Songnian Hu	Wanfei Liu Yuhui Zhao Peng Cui Qiang Lin Feng Ding Chengqi Xin Xinyu Tan Shuhui Song Jun Yu	Frontiers in Genetics
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti	2011	Mariangela Bonnizoni Osvaldo Marinotti	W Augustine Dunn Corey L Campbell Ken E Olson Michelle T Dimon Anthony A James	BMC Genomics
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans	2011	Matthew Berriman Karen Mungall Gary Saunders Anna V Protasio Martin Hunt Roz Laing Michael Andrew Quail	Steven Laing Frank Jackson Robin Beech John S Gilleard	PLOS ONE
The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair	2011	Benjamin Yu	Gloria K Lefkowitz Anandaroop Mukhopadhyay Christopher Cowing-Zitron	PLOS ONE
A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq	2011	Thomas Brutnell	Lin Wang Yaqing Si Lauren K Dedow Ying Shao Peng Liu	PLOS ONE
ENCODE whole-genome data in the UCSC genome browser (2011 update)	2011-01	David Haussler Venkat S Malladi Angie S. Hinrichs Donna Karolchik Hiram Clawson Ann S Zweig	Brian J Raney Melissa S Cline Kate R Rosenbloom Timothy R Dreszer Katrina Learned Galt P Barber Laurence R Meyer Cricket A Sloan Krishna M Roskin Bernard B Suh Vanessa Kirkup Pauline A Fujita Brooke Rhead Kayla E Smith Andy Pohl Robert M Kuhn W James Kent	Nucleic Acids Research
Insights into global mechanisms and disease by gene expression profiling.	2011-01-01	Hubert Hackl Johannes Rainer Ana Dopazo	Fátima Sánchez-Cabo Zlatko Trajanoski	Methods in Molecular Biology
Identifying mRNA editing deaminase targets by RNA-Seq.	2011-01-01	Nina Papavasiliou	Brad R Rosenberg Scott Dewell F Nina Papavasiliou	Methods in Molecular Biology
The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq	2011-01-12	Jeff H. Chang	Yanming Di Daniel W Schafer Jason S Cumbie	Statistical Applications in Genetics and Molecular Biology
A pipeline for RNA-seq data processing and quality assessment	2011-01-13	Alvis Brazma Angela Goncalves	Andrew Tikhonov Misha Kapushesky	Bioinformatics
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts	2011-01-17	Katherine Lontok	Michelle T Dimon Joseph L DeRisi	Nucleic Acids Research
Length bias correction for RNA-seq data in gene set analyses	2011-01-19	Xiangqin Cui	Liyan Gao Zhide Fang Kui Zhang Degui Zhi	Bioinformatics
Identification of fusion genes in breast cancer by paired-end RNA-sequencing.	2011-01-19	Olli-Pekka Kallioniemi Anne-Lise Børresen-Dale Sara Kangaspeska Vesa Hongisto Kristine Kleivi	Henrik Edgren Astrid Murumagi Sara Kangaspeska Daniel Nicorici Vesa Hongisto Inga H Rye Sandra Nyberg Maija Wolf	Genome Biology
Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics?	2011-01-19	Greg T. Sutherland Jillian J. Kril	Michal Janitz	Journal of Neurochemistry
Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array	2011-01-21	Shikai Liu Eric Peatman Huseyin Kucuktas Ludmilla Kaltenboeck Shaolin Wang Zhanjiang Liu	Zunchun Zhou Jianguo Lu Fanyue Sun Hong Liu Yanliang Jiang	BMC Genomics
Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.	2011-01-26	Agnes Grallert Valerie Wood Iain M. Hagan Crispin J. Miller	Danny A Bitton Paul J Scutt Tim Yates Duncan L Smith	Genetics
In vitro culture and characterization of putative porcine embryonic germ cells derived from domestic breeds and Yucatan mini pig embryos at Days 20-24 of gestation.	2011-01-31	Hendrik Marks Yu Gao Poul Hyttel	Stoyan G Petkov Tino Klein Rodrigo S Garcia Henk Stunnenberg	Stem Cell Research
Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs	2011-02	Nina Papavasiliou	Brad R Rosenberg Claire E Hamilton Michael M Mwangi Scott Dewell F Nina Papavasiliou	Nature Structural & Molecular Biology
General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq	2011-02-01	Jochen Wolf Jarosław Bryk	Jochen Bw Wolf	BMC Genomics
The next generation: using new sequencing technologies to analyse gene regulation.	2011-02-01	Olivia Alder Pamela A. Hoodless	Rebecca Cullum	Respirology
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.	2011-02-08	Michael Eisen S E Lott	Jacqueline E Villalta Gary P Schroth Shujun Luo Leath A Tonkin	PLOS Biology
Identification and optimization of small molecules that restore E-cadherin expression and reduce invasion in colorectal carcinoma cells.	2011-02-09	Robert Daniel Beauchamp Craig W Lindsley	Sydney L Stoops A Scott Pearson Connie Weaver Alex G Waterson Emily Days Chris Farmer Suzanne Brady C David Weaver	ACS Chemical Biology
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.	2011-02-10	Ernest Turro Angela Goncalves Lachlan Coin Sylvia Richardson Alexandra M. Lewin	Shu-Yi Su	Genome Biology
Isoform-level microRNA-155 target prediction using RNA-seq	2011-02-11	Erik K Flemington	Nan Deng Adriane Puetter Kun Zhang Kristen Johnson Zhiyu Zhao Christopher Taylor Dongxiao Zhu	Nucleic Acids Research
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.	2011-02-15	Peggy Farnham	Kimberly R Blahnik Lei Dou Lorigail Echipare Sushma Iyengar Henriette O'Geen Erica Sanchez Yongjun Zhao Marco A Marra Martin Hirst Joseph F Costello Ian Korf	PLOS ONE
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.	2011-02-16	Vineet Bafna Olivier Harismendy	Marcus Kinsella Masakazu Nakano Kelly A Frazer	Bioinformatics
Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.	2011-02-17	Thomas D Otto Arnab Pain Anthony A Holder Rita Tewari	Solabomi A Ogun Steven A Howell Ellen Knuepfer Deirdre A Cunningham Zhengyao Xu	PLOS Pathogens
RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture	2011-02-17	Avigdor Eldar	Adam Z Rosenthal Eric G Matson Jared R Leadbetter	The ISME Journal
ACT: aggregation and correlation toolbox for analyses of genome tracks.	2011-02-23	Joel Rozowsky Kevin Y Yip Lucas Lochovsky	Justin Jee Robert Bjornson Guoneng Zhong Zhengdong Zhang Yutao Fu Jie Wang Zhiping Weng Mark Gerstein	Bioinformatics
Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.	2011-03-01	Traver Hart	Steven R Head H Kiyomi Komori John Shimashita Lana Schaffer Daniel R Salomon Phillip T Ordoukhanian	BioTechniques
Accurate estimation of expression levels of homologous genes in RNA-seq experiments.	2011-03-01	Bogdan Pasaniuc Noah Zaitlen	Eran Halperin	Journal of Computational Biology
The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles.	2011-03-02	Bratati Mukherjee	James V Moroney Yunbing Ma Wesley D Frey Katelyn A Fusilier Trang T Pham Tiffany A Simms Robert J DiMario Jing Yang	Photosynthesis Research
Improving RNA-Seq expression estimates by correcting for fragment bias.	2011-03-16	Lior Pachter John L. Rinn	Adam Roberts Cole Trapnell Julie Donaghey	Genome Biology
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers	2011-03-17	Louis M Staudt Ujunwa C Okoye Pedro Farinha Anke van den Berg Steven Jones	Christian Steidl Sohrab P Shah Bruce W Woolcock Lixin Rui Masahiro Kawahara Nathalie A Johnson Yongjun Zhao Adele Telenius Susana Ben Neriah Andrew McPherson Barbara Meissner Arjan Diepstra Mark Sun Gillian Leung Joseph M Connors David G Huntsman Kerry J Savage Lisa M Rimsza Douglas E Horsman Ulrich Steidl Marco A Marra Randy D Gascoyne	Nature
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii.	2011-03-21	Sabeeha Merchant Matteo Pellegrini David Casero	Janette Kropat Anne Hong-Hermesdorf Petr Ent Madeli Castruita Davin Malasarn	The Plant Journal
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.	2011-03-22	Graziano Pesole Ernesto Picardi	Mattia D'Antonio Danilo Carrabino Tiziana Castrignanò	Bioinformatics
Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing	2011-03-24	Peter Robinson Stefan Mundlos	Marten Jäger Claus-Eric Ott Johannes Grünhagen Jochen Hecht Hanna Schell Stefan Mundlos Georg N Duda Jasmin Lienau	BMC Genomics
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays	2011-03-24	Nicole A Walter Jessica Ezzell Hunter Michael A Mooney Shannon K McWeeney	Daniel Bottomly Priscila Darakjian Sunita Kawane Kari J Buck Robert P Searles Robert Hitzemann	PLOS ONE
Effects of nickel treatment on H3K4 trimethylation and gene expression.	2011-03-24	Stuart M. Brown Phillip R Smith	Kam-Meng Tchou-Wong Kathrin Kiok Zuojian Tang Thomas Kluz Adriana Arita Max Costa	PLOS ONE
Developmental changes in transcriptional profiles.	2011-03-30	Gad Shaulsky	William F Loomis	Development, Growth and Differentiation
RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation.	2011-04-05	Vladimir Benes Gunnar Rätsch	Tanja Dorothe Rösel Lee-Hsueh Hung Jan Medenbach Katrin Donde Stefan Starke Albrecht Bindereif	The EMBO Journal
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.	2011-04-08	Stylianos Antonarakis Christian Iseli Carlo Rivolta Ioannis Xenarios Jacques S. Beckmann Armand Valsesia	Donata Rimoldi Danielle Martinet Mark Ibberson Paola Benaglio Manfredo Quadroni Patrice Waridel Muriel Gaillard Mireille Pidoux Blandine Rapin Andrew J G Simpson C Victor Jongeneel Brian J Stevenson	PLOS ONE
Genome-wide analysis of the 5' and 3' ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts.	2011-04-13	Bernard Moss	Zhilong Yang Daniel P Bruno Craig A Martens Stephen F Porcella	Journal of Virology
A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.	2011-04-15	Jeremy Davis-Turak Yu Zhou	Kristi Fox-Walsh Hairi Li Xiang-Dong Fu	Genomics
Design and validation issues in RNA-seq experiments.	2011-04-15	Xiangqin Cui	Zhide Fang	Briefings in Bioinformatics
Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.	2011-04-15	David Casero Sabeeha Merchant Matteo Pellegrini Astrid Vieler Christoph Benning	Madeli Castruita Steven J Karpowicz Janette Kropat Scott I Hsieh Weihong Yan Shawn Cokus Joseph A Loo	The Plant Cell
Estimation of alternative splicing isoform frequencies from RNA-Seq data	2011-04-19	Ion I. Mandoiu Alexander Zelikovsky	Marius Nicolae Serghei Mangul	Algorithms for Molecular Biology
Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.	2011-04-20	Luciana D'Apice Aldo Donizetti Monica Rienzo Paola Salvatore Stefania Crispi Valerio Costa Piergiuseppe De Berardinis Teresa Infante Claudia Angelini Marco Picardi Berardo Sarubbi Raffaele Calabrò Claudio Napoli Amelia Casamassimi	Margherita Mutarelli Linda Sommese Maria Assunta Gallo Marianna Aprile Roberta Esposito Luigi Leone Alfredo Ciccodicola	PLOS ONE
BM-map: Bayesian mapping of multireads for next-generation sequencing data.	2011-04-22	Yuan Yuan Han Liang	Yuan Ji Yanxun Xu Qiong Zhang Kam-Wah Tsui Clift Norris Shoudan Liang	Biometrics
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.	2011-04-27	Cynthia Sharma Jörg Vogel Gabriele Klug	Bork A Berghoff Jens Glaeser Monica Zobawa Friedrich Lottspeich	Molecular Microbiology
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.	2011-05-05	Jeremy Chien Jian Ma	Yang Li David I Smith	Bioinformatics
Protocol dependence of sequencing-based gene expression measurements	2011-05-06	John F Thompson	Tal Raz Philipp Kapranov Doron Lipson Stan Letovsky Patrice M Milos	PLOS ONE
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.	2011-05-11	Antonella Bacchiocchi	Fabio Parisi Stephan Ariyan Deepak Narayan Kathleen Hoyt Elaine Cheng Fang Xu Peining Li Ruth Halaban Yuval Kluger	BMC Genomics
The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue	2011-05-13	Curtis A. Suttle Julia A Gustavsen Jan M Friedman Robert A Holt	Richard A Moore René L Warren J Douglas Freeman Caroline Chénard Yongjun Zhao	PLOS ONE
NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.	2011-05-16	Zheng Xia	Jianguo Wen Chung-Che Chang Xiaobo Zhou	BMC Bioinformatics
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.	2011-05-18	Wolfgang Hoeck	Huanying Ge Kejun Liu Todd Juan Fang Fang Matthew Newman	Bioinformatics
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.	2011-05-19	Malachi Griffith Gavin Ha	Andrew McPherson Fereydoun Hormozdiari Abdalnasser Zayed Ryan Giuliany Mark G F Sun Alireza Heravi Moussavi Janine Senz Nataliya Melnyk Marina Pacheco Marco A Marra Martin Hirst Torsten O Nielsen S Cenk Sahinalp David Huntsman Sohrab P Shah	PLOS Computational Biology
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.	2011-05-19	A S Weyrich	Jesse W Rowley Andrew J Oler Neal D Tolley Benjamin N Hunter Elizabeth N Low David A Nix Christian C Yost Guy A Zimmerman	Blood
The zebrafish transcriptome during early development.	2011-05-24	Juha Kere Outi Hovatta Liselotte Vesterlund	Hong Jiao Per Unneberg Outi Hovatta	BMC Developmental Biology
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding	2011-05-27	Antonis Rokas Laurence J. Zwiebel	R Jason Pitts David C Rinker Patrick L Jones	BMC Genomics
Pyrosequencing-based expression profiling and identification of differentially regulated genes from Manduca sexta, a lepidopteran model insect.	2011-05-27	Haobo Jiang	Shuguang Zhang Ramesh T Gunaratna Xiufeng Zhang Fares Najar Yang Wang Bruce Roe	Insect Biochemistry and Molecular Biology
Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events.	2011-05-31	Loredana Bury A S Weyrich Paolo Gresele	Luca Cecchetti Neal D Tolley Noemi Michetti	Blood
Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq	2011-06	Frank Schembri Jennifer Beane Yuriy O Alekseyev Avrum Spira Marc E Lenburg Shawn Levy	Jessica Vick Christina Anderlind Adam Gower Joshua Campbell Lingqi Luo Xiao Hui Zhang Ji Xiao Shenglong Wang Pierre P Massion	Cancer Prevention Research
RNA-seq: technical variability and sampling.	2011-06-06	Lauren McIntyre	Kenneth K Lopiano Alison M Morse Victor Amin Ann L Oberg Linda J Young Sergey V Nuzhdin	BMC Genomics
Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics.	2011-06-07	Tracy L Bergemann	Jason Wilson	BMC Bioinformatics
RNA sequencing reveals two major classes of gene expression levels in metazoan cells.	2011-06-07	Sarah Teichmann Alexander van Oudenaarden Muxin Gu Varodom Charoensawan Daniel Hebenstreit	Miaoqing Fang	Molecular Systems Biology
PR-domain-containing Mds1-Evi1 is critical for long-term hematopoietic stem cell function.	2011-06-10	Subhash Juneja	Yi Zhang Sandra Stehling-Sun Kimberly Lezon-Geyda Lucie Coillard Gouri Chatterjee Charles A Wuertzer Fernando Camargo Archibald S Perkins	Blood
Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.	2011-06-22	Dirce Carraro Emmanuel Dias-Neto Helena Brentani Renata Pasqualini	Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Ricardo Renzo Brentani	PLOS ONE
Deterministic and stochastic allele specific gene expression in single mouse blastomeres	2011-06-23	Azim Surani	Fuchou Tang Catalin Barbacioru Ellen Nordman Siqin Bao Caroline Lee Xiaohui Wang Brian B Tuch Edith Heard Kaiqin Lao	PLOS ONE
Transcription factor TEAD4 regulates expression of myogenin and the unfolded protein response genes during C2C12 cell differentiation	2011-06-24	Gabrielle Mengus Irwin Davidson	A Benhaddou C Keime T Ye A Morlon I Michel B Jost	Cell Death & Differentiation
Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation.	2011-06-28	Filip Van Nieuwerburgh James W Golden	Britt L Flaherty Steven R Head	BMC Genomics
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq	2011-07	Sten Linnarsson Peter Lönnerberg	Saiful Islam Una Kjällquist Annalena Moliner Pawel Zajac Jian-Bing Fan	Genome Research
Full-length transcriptome assembly from RNA-Seq data without a reference genome	2011-07	Kerstin Lindblad-Toh Aviv Regev Chad Nusbaum Andreas Gnirke Evan Mauceli Nir Friedman Nicholas Rhind Nir Hacohen Raktima Raychowdhury	Manfred G Grabherr Brian J Haas Moran Yassour Joshua Z Levin Dawn A Thompson Ido Amit Xian Adiconis Lin Fan Raktima Raychowdhury Qiandong Zeng Zehua Chen Federica di Palma Bruce W Birren	Nature Biotechnology
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.	2011-07-01	Paweł P Łabaj Steven Wiley D Kreil	Germán G Leparc Bryan E Linggi Lye Meng Markillie	Bioinformatics
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus.	2011-07-01	Antonis Rokas	John G Gibbons Anne Beauvais Remi Beau Kriston L McGary Jean-Paul Latgé	Eukaryotic Cell
Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq.	2011-07-02	Ricardo DeMarco Sergio Verjovski-Almeida	Giulliana Tessarin Almeida Murilo Sena Amaral Felipe Cesar Ferrarezi Beckedorff João Paulo Kitajima	Experimental Parasitology
An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.	2011-07-05	Iain W Wilson	Qi Tang Xiaojun Ma Changming Mo Cai Song Huan Zhao Yanfang Yang Wei Fu Deyou Qiu	BMC Genomics
A comparative analysis of DNA methylation across human embryonic stem cell lines.	2011-07-06	Matteo Pellegrini	Pao-Yang Chen Suhua Feng Jong Wha Joanne Joo Steve E Jacobsen	Genome Biology
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data	2011-07-07	Tak-Wah Lam	Songbo Huang Jinbo Zhang Ruiqiang Li Wenqian Zhang Zengquan He Zhiyu Peng Siu-Ming Yiu	Frontiers in Genetics
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.	2011-07-12	David Casero Matteo Pellegrini Sabeeha Merchant	David Lopez Shawn J Cokus	BMC Bioinformatics
De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome.	2011-07-19	Ya-Ting Chao	Chun-lin Su Yao-Chien Alex Chang Wan-Chieh Chen Chun-Yi Chen Ann-Ying Lee Kee Tuan Hwa Ming-Che Shih	Plant and Cell Physiology
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).	2011-07-19	Angel Pizarro Gregory R Grant Eric A Pierce	Michael H Farkas Nicholas F Lahens Jonathan Schug Brian P Brunk Christian J Stoeckert John B Hogenesch	Bioinformatics
RseqFlow: workflows for RNA-Seq data analysis.	2011-07-27	Ewa Deelman	Ying Wang Gaurang Mehta Rajiv Mayani Jingxi Lu Tade Souaiaia Yangho Chen Andrew Clark Hee Jae Yoon Lin Wan Oleg V Evgrafov James A Knowles Ting Chen	Bioinformatics
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length	2011-07-27	Jing Woei Li Stephen Kwok-Wing Tsui T F Chan	Shao-Ke Lou Hao Qin Aldrin Kay-Yuen Yim Leung-Yau Lo Bing Ni Kwong-Sak Leung	BMC Bioinformatics
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.	2011-07-28	Tom Maniatis Brad Friedman		Genome Biology
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.	2011-07-29	Mikhail Matz	E Meyer G V Aglyamova	Molecular Ecology
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression	2011-07-31	John R. Prensner Qi Cao Irfan Asangani Nallasivam Palanisamy	Matthew K Iyer O Alejandro Balbin Saravana M Dhanasekaran J Chad Brenner Bharathi Laxman Catherine S Grasso Hal D Kominsky Xuhong Cao Xiaojun Jing Xiaoju Wang Javed Siddiqui John T Wei Daniel Robinson Hari K Iyer Christopher A Maher Arul M Chinnaiyan	Nature Biotechnology
RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.	2011-08-01	Jennifer M Ritchie	Anjali Mandlik Jonathan Livny William P Robins John J Mekalanos Matthew K Waldor	Cell Host & Microbe
AlleleSeq: analysis of allele-specific expression and binding in a network framework.	2011-08-02	Yong Kong Alexej Abyzov Joel Rozowsky Mark Rubin Mark Bender Gerstein	Jing Wang Pedro Alves Debasish Raha Arif Harmanci Jing Leng Robert Bjornson Naoki Kitabayashi Nitin Bhardwaj Michael Snyder	Molecular Systems Biology
Synthetic spike-in standards for RNA-seq experiments.	2011-08-04	Thomas R. Gingeras	Lichun Jiang Felix Schlesinger Carrie A Davis Yu Zhang Renhua Li Marc Salit Brian Oliver	Genome Research
Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome	2011-08-04	Paul P. Gardner Roy R Chaudhuri Jyoti Choudhary	Lu Yu Alpa Kanji Timothy T Perkins Duncan J Maskell Andrew J Grant	Microbiology
RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes	2011-08-05	Eran Pichersky	Petra M Bleeker Eleni A Spyropoulou Paul J Diergaarde Hanne Volpin Michiel T J De Both Philipp Zerbe Joerg Bohlmann Vasiliki Falara Yuki Matsuba Eran Pichersky Michel A Haring Robert C Schuurink	Plant Molecular Biology
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.	2011-08-08	Derek Y Chiang	Darshan Singh Christian F Orellana Yin Hu Corbin D Jones Yufeng Liu Jinze Liu Jan F Prins	Bioinformatics
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts	2011-08-11	Steven Salzberg	Daehwan Kim	Genome Biology
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.	2011-08-11	Jason Gertz Katherine E Varley Timothy E Reddy	Kevin M Bowling Florencia Pauli Stephanie L Parker Katerina S Kucera Huntington F Willard Richard M Myers	PLOS Genetics
Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing	2011-08-12	Robert W. Williams	Hao Chen Zhimin Liu Suzhen Gong Xingjun Wu William L Taylor Shannon G Matta Burt M Sharp	Frontiers in Neuroscience
Local and global factors affecting RNA sequencing analysis.	2011-08-16	Graham D Johnson	Edward Sendler Stephen A Krawetz	Analytical Biochemistry
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma	2011-08-18	Martin Hirst Yaron Butterfield Angela Brooks-Wilson Eric Y Zhao Malachi Griffith Andrew Mungall	Ryan D Morin Maria Mendez-Lago Rodrigo Goya Karen L Mungall Richard D Corbett Nathalie A Johnson Tesa M Severson Readman Chiu Matthew Field Shaun Jackman Martin Krzywinski David W Scott Diane L Trinh Jessica Tamura-Wells Sa Li Marlo R Firme Sanja Rogic Susanna Chan Oleksandr Yakovenko Irmtraud M Meyer Duane Smailus Michelle Moksa Suganthi Chittaranjan Lisa Rimsza John J Spinelli Susana Ben-Neriah Barbara Meissner Bruce Woolcock Merrill Boyle Helen McDonald Angela Tam Yongjun Zhao Allen Delaney Thomas Zeng Kane Tse Inanç Birol Rob Holt Jacqueline Schein Douglas E Horsman Richard Moore Steven J M Jones Joseph M Connors Randy D Gascoyne Marco A Marra	Nature
An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype	2011-08-18	Michele Balsamo	Irina M Shapiro Albert W Cheng Nicholas C Flytzanis John S Condeelis Maja H Oktay Christopher B Burge Frank B Gertler	PLOS Genetics
Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes.	2011-08-18	Ali Jabbari	Mayte Suárez-Fariñas Scott Dewell James G Krueger	Journal of Investigative Dermatology
The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression	2011-08-19	Songnian Hu	Peng Cui Qiang Lin Lingfang Zhang Feng Ding Chengqi Xin Daoyong Zhang Fanglin Sun Jun Yu	PLOS ONE
Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry.	2011-08-23	Daojun Yuan Xianlong Zhang	Li Xu Longfu Zhu Lili Tu Linlin Liu Li Jin Lu Long	Journal of Experimental Botany
Bioaccumulation and effects of CdTe/CdS quantum dots on Chlamydomonas reinhardtii - nanoparticles or the free ions?	2011-08-25	Rute F. Domingos Kevin J Wilkinson	Dana F Simon Charles Hauser	Environmental Science & Technology
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.	2011-08-26	Daniel A Skelly	Marnie Johansson Jennifer Madeoy Jon Wakefield Joshua M Akey	Genome Research
Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system.	2011-09-01	Deborah Charlesworth	Roberta Bergero	Current Biology
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses	2011-09-02	Loyal Goff Magdalena J Koziol John L. Rinn	Moran N Cabili Cole Trapnell Barbara Tazon-Vega Aviv Regev	Genes & Development
Wnt gene loss in flatworms.	2011-09-03	Nick Riddiford	Peter D Olson	Development Genes and Evolution
SpliceTrap: a method to quantify alternative splicing under single cellular conditions.	2011-09-06	W. Richard McCombie Adrian Robert Krainer	Jie Wu Martin Akerman Shuying Sun Michael Q Zhang	Bioinformatics
Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation.	2011-09-06	Ross C Hardison James C Mullikin	Andre M Pilon Subramanian S Ajay Swathi Ashok Kumar Laurie A Steiner Praveen F Cherukuri Stephen Wincovitch Stacie M Anderson NISC Comparative Sequencing Center Patrick G Gallagher Elliott H Margulies David M Bodine	Blood
wapRNA: a web-based application for the processing of RNA sequences.	2011-09-06	Songnian Hu	Wenming Zhao Wanfei Liu Dongmei Tian Bixia Tang Yanqing Wang Caixia Yu Rujiao Li Yunchao Ling Jiayan Wu Shuhui Song	Bioinformatics
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.	2011-09-07	Deyou Zheng	Mingyan Lin Erika Pedrosa Abhishek Shah Anastasia Hrabovsky Shahina Maqbool Herbert M Lachman	PLOS ONE
Differential expression in RNA-seq: a matter of depth.	2011-09-08	Joaquín Dopazo Ana Conesa Sonia Tarazona Alberto Ferrer	Fernando García-Alcalde	Genome Research
Proteomic and phosphoproteomic comparison of human ES and iPS cells.	2011-09-11	Justin Brumbaugh	Douglas H Phanstiel Craig D Wenger Shulan Tian Mitchell D Probasco Derek J Bailey Danielle L Swaney Mark A Tervo Jennifer M Bolin Victor Ruotti Ron Stewart James A Thomson Joshua J Coon	Nature Methods
Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.	2011-09-12	Elia Stupka Christiaan V. Henkel Herman P Spaink	Yanju Zhang Hans J Jansen Fons J Verbeek	Journal of integrative bioinformatics
Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.	2011-09-13	Jurian Schuijers Michal Mokry	Pantelis Hatzis Nico Lansu Frans-Paul Ruzius Hans Clevers Edwin Cuppen	Nucleic Acids Research
Integrative approach involving RNA-Seq, foliar traits and growth measurements revealed genotype-specific plasticity on Eucalyptus subjected to seasonal water shortage.	2011-09-13	Christophe Plomion	Emilie Villar Jean-Marc Gion	BMC Proceedings
Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant.	2011-09-15	Daniel L Kiss	Sarah B Smith Edward Turk Alan M Tartakoff Erik D Andrulis	Yeast
RNA-Seq methods for imperfect samples: development, evaluation and applications	2011-09-19 2011	Aviv Regev Chad Nusbaum Gad Getz	Xian Adiconis Lin Fan David DeLuca Andrey Sivachenko Nathalie Pochet Aaron Berlin Sarah Young Andreas Gnirke Joshua Z Levin	Genome Biology
Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design	2011-09-22	Davis J McCarthy Alicia Oshlack Gordon K Smyth	Matthew D. Young Matthew J. Wakefield Mark D. Robinson
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.	2011-09-25	Vincent Lynch Gunter P Wagner	Robert D Leclerc Gemma May	Nature Genetics
From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).	2011-09-28	Thomas Schmutzer Martin Mascher Uwe Scholz Nils Stein Klaus Mayer Eva Bauer	Grit Haseneyer Michael Seidel Ruonan Zhou Chris-Carolin Schön Stefan Taudien	BMC Plant Biology
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.	2011-09-29	Jae-Hyung Lee Guangdun Peng Xinshu Xiao	Jae Hoon Bahn Gang Li Christopher Greer	Genome Research
Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing.	2011-10-01	Ece D. Gamsiz Eric M. Morrow	Qing Ouyang Michael Schmidt Shailender Nagpal	Genomics
RNA-Seq analysis in MeV.	2011-10-05	John Quackenbush	Eleanor A Howe Raktim Sinha Daniel Schlauch	Bioinformatics
RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs	2011-10-05	Tirza Doniger	Shulamit Michaeli Sachin Kumar Gupta Omri Wurtzel Mali Romano Damian Visnovezky Rotem Sorek Ron Unger Elisabetta Ullu	Nucleic Acids Research
GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.	2011-10-06	Jeff H. Chang Jeffrey A Kimbrel James C. Carrington	Jason S Cumbie Yanming Di Daniel W Schafer Larry J Wilhelm Samuel E Fox Christopher M Sullivan Aron D Curzon Todd C Mockler	PLOS ONE
S-MART, a software toolbox to aid RNA-Seq data analysis	2011-10-06	Hadi Quesneville	Matthias Zytnicki	PLOS ONE
Nonrandom gene loss from the Drosophila miranda neo-Y chromosome.	2011-10-10	Doris Bachtrog	Vera B Kaiser Qi Zhou	Genome Biology and Evolution
The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction.	2011-10-13	Gaedigk R Steven N. Hart	Dan Li J Steven Leeder Xiao-bo Zhong	Molecular Pharmacology
RNA-Seq for Plant Pathogenic Bacteria.	2011-10-13	Jeffrey A Kimbrel Jeff H. Chang	Yanming Di Jason S Cumbie	Genes
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.	2011-10-18	Charles D. Johnson Ulisses Braga Neto	Ying Wang Noushin Ghaffari Hui Wang Rui Chen Huaijun Zhou	BMC Bioinformatics
The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity	2011-10-21	Paulo José Pereira Lima Teixeira Joan Barau Antonio Costa-filho	Gustavo Zaparoli Mario Ramos de Oliveira Barsottini Juliana Ferreira de Oliveira Fabio Dyszy Odalys Garcia Andre Luis Berteli Ambrosio Gonçalo Amarante Guimarães Pereira Sandra Martha Gomes Dias	Biochemistry
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.	2011-10-23	Thomas R. Gingeras Jay Shendure David Sturgill	Xinxian Deng Joseph B Hiatt Di Kim Nguyen Sevinc Ercan LaDeana W Hillier Felix Schlesinger Carrie A Davis Valerie J Reinke Robert H Waterston Brian Oliver Jason D Lieb Christine M Disteche	Nature Genetics
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines	2011-10-27	Anne Vincent-Salomon William D Foulkes Jorge Reis-Filho Rachael Natrajan Alan Ashworth	Kevin C H Ha Emilie Lalonde Lili Li Luca Cavallone Maryou B Lambros Costas Mitsopoulos Jarle Hakas Iwanka Kozarewa Kerry Fenwick Chris J Lord Mark Basik Jacek Majewski	BMC Medical Genomics
RNA-Seq reveals an integrated immune response in nucleated erythrocytes.	2011-10-27	Nerea Roher Laia Ribas Joan C Balasch Sebastian Boltana Steven B. Roberts Simon Mackenzie	Davinia Morera Carmen Doñate Agnes Callol Giles Goetz Frederick W Goetz	PLOS ONE
The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.	2011-10-28	Giovanni Giuliano Kevin L. Childs	Alicia N Massa Haining Lin Glenn J Bryan C Robin Buell	PLOS ONE
RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus	2011-11-02	Christophe Plomion Evandro Novaes	Emilie Villar Christophe Klopp Céline Noirot Matias Kirst Jean-Marc Gion	BMC Genomics
RNA-Seq improves annotation of protein-coding genes in the cucumber genome.	2011-11-02	Zhen Li Sanwen Huang	Zhonghua Zhang Pengcheng Yan Zhangjun Fei Kui Lin	BMC Genomics
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.	2011-11-03	Peter F. Stadler Jan Gorodkin David Langenberger Claus T. Ekstrøm Sachin Pundhir	Steve Hoffmann	Bioinformatics
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.	2011-11-06	Adam Ameur Ulf Gyllensten	Ammar Zaghlool Jonatan Halvardson Anna Wetterbom Lucia Cavelier Lars Feuk	Nature Structural & Molecular Biology
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq	2011-11-08	Giovanni Bussotti Robert Kofler Cedric Notredame Miguel Perez-Enciso Anna Esteve-Codina	Nicola Palmieri	BMC Genomics
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.	2011-11-08	Ming Hu Zhaohui Steve Qin	Yu Zhu Jeremy M G Taylor Jun S Liu	Bioinformatics
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.	2011-11-10	Andreas Sommer Irena Vlatkovic Hendrik Marks Robert Kralovics	Ru Huang Markus Jaritz Philipp Guenzl Ido M Tamir Thorsten Klampfl Hendrik G Stunnenberg Denise P Barlow Florian M Pauler	PLOS ONE
Non-laser capture microscopy approach for the microdissection of discrete mouse brain regions for total RNA isolation and downstream next-generation sequencing and gene expression profiling.	2011-11-13	Norman Atkins	Charlie M Miller Joseph R Owens Fred W Turek	Journal of Visualized Experiments
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.	2011-11-16	Jeffrey T. Leek Ben Langmead	Alyssa C Frazee	BMC Bioinformatics
Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq.	2011-11-16	Melody Baddoo Dale Hedges Erik K Flemington	Monica Concha Xia Wang Subing Cao Melody Baddoo Claire Fewell Zhen Lin William Hulme Dale Hedges Jane McBride	Journal of Virology
Genetic variation of pre-mRNA alternative splicing in human populations	2011-11-17	Zhi-xiang Lu	Peng Jiang Yi Xing	Wiley interdisciplinary reviews. RNA
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.	2011-11-22	Aviv Regev Eivind Valen Albin Sandelin John L. Rinn	Andrea Pauli Michael F Lin Manuel Garber Nadine L Vastenhouw Joshua Z Levin Lin Fan Alexander F Schier	Genome Research
RNA-Seq and find: entering the RNA deep field.	2011-11-22	Lior Pachter	Adam Roberts	Genome Medicine
Estimation of alternative splicing variability in human populations.	2011-11-23	Roderic Guigó i Serra Michael Sammeth	Mar Gonzàlez-Porta Miquel Calvo	Genome Research
RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.	2011-11-24	Blake Meyers	Sridhara G Kunjeti Thomas A Evans Adam G Marsh Nancy F Gregory Saritha Kunjeti Venugopal S Kalavacharla Nicole M Donofrio	Molecular Plant Pathology
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.	2011-11-28	Robert Tibshirani	Jun Li	Statistical Methods in Medical Research
Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.	2011-11-28	Paola Tosi J Paul Knox Jackie Freeman	Till K Pellny Alison Lovegrove Christopher G Love Peter R Shewry Rowan A C Mitchell	Plant Physiology
Transposase mediated construction of RNA-seq libraries.	2011-11-29	Jason Gertz Katherine E Varley	Nicholas S Davis Bradley J Baas Igor Y Goryshin Ramesh Vaidyanathan Scott Kuersten Richard M Myers	Genome Research
Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.	2011-11-30	Jian Luo Mingyao Liu	Geng Chen Kangping Yin Leming Shi Yuanzhang Fang Ya Qi Peng Li Bing He Tieliu Shi	PLOS ONE
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120	2011-11-30	Agustín Vioque Fabian Haas Wolfgang R Hess Alicia María Muro-Pastor	Jan Mitschke	Proceedings of the National Academy of Sciences of the United States of America
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.	2011-12-01	Jingyi Jessica Li	Ci-Ren Jiang James B Brown Haiyan Huang Peter J Bickel	Proceedings of the National Academy of Sciences of the United States of America
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.	2011-12-01	Jing Qin Junwen Wang	Lily Yan Wang Panwen Wang Mulin Jun Li Xiaowo Wang Michael Q Zhang	Epigenetics
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).	2011-12-02	Jérôme Salse	Caroline Pont Florent Murat Carole Confolent Sandrine Balzergue	Genome Biology
X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription	2011-12-04	Ruslan I Sadreyev	Eda Yildirim Stefan F Pinter Jeannie T Lee	Nature Structural & Molecular Biology
Isoform diversity and its importance for axon regeneration.	2011-12-13	John L. Bixby Vance P. Lemmon	Jessica K Lerch	Neuropathology
Protein identification using customized protein sequence databases derived from RNA-Seq data.	2011-12-14	David Tabb Daniel C. Liebler	Xiaojing Wang Robbert J C Slebos Dong Wang Patrick J Halvey Bing Zhang	Journal of Proteome Research
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.	2011-12-14	Qiong-Yi Zhao	Yi Wang Yi-Meng Kong Da Luo Xuan Li Pei Hao	BMC Bioinformatics
GC-content normalization for RNA-Seq data	2011-12-17	Gavin Sherlock Davide Risso	Katja Schwartz Sandrine Dudoit	BMC Bioinformatics
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis	2011-12-22	Desmond G. Higgins Geraldine Butler Sarah L Maguire Matthew Berriman	Alessandro Guida Claudia Lindstädt Chen Ding Nicola J Corton	BMC Genomics
Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses.	2011-12-22	Laurence Florens Swaminathan Venkatesh Michael P. Washburn	Joshua M Gilmore Mihaela E Sardiu Brent Stutzman Allison Peak Chris W Seidel Jerry L Workman	Molecular & Cellular Proteomics
Statistical methods on detecting differentially expressed genes for RNA-seq data.	2011-12-23	Saralees Nadarajah	Zhongxue Chen Jianzhong Liu Hon Keung Tony Ng Saralees Nadarajah Howard L Kaufman Jack Y Yang Youping Deng	BMC Systems Biology
Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders	2011-12-27	Jordan L Meier Peter Dervan	Jevgenij A Raskatov James W Puckett Fei Yang Parameswaran Ramakrishnan	Proceedings of the National Academy of Sciences of the United States of America
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.	2011-12-28	Fangqing Zhao	Qi Liu Chong Chen Enjian Shen Zhongsheng Sun Jinyu Wu	Genomics
Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection.	2011-12-28	Steven G Schroeder	Robert W Li	Functional and Integrative Genomics
Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.	2011-12-29	Steven B. Roberts	Mackenzie R Gavery	Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms	2012	Christina A Cuomo	Kelly L Robertson Anahita Mostaghim Carissa M Soto Nikolai Lebedev Robert F Bailey Zheng Wang	PLOS ONE
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq	2012	John L. Bixby Vance P. Lemmon Dario Motti	Jessica K Lerch Frank Kuo Richard Morris	PLOS ONE
Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers	2012	Jacqueline Salit	Guoqing Wang Zhibo Xu Rui Wang Mohammed Al-Hijji Yael Strulovici-Barel Ann E Tilley Jason G Mezey Ronald G Crystal	BMC Medical Genomics
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain	2012	Andrea Telatin Stefano Campanaro Giorgio Valle	Fabio De Pascale Riccardo Schiavon Douglas H Bartlett	BMC Genomics
Computational analysis of noncoding RNAs	2012	Manolis Kellis Stefan Washietl Bonnie Berger John L. Rinn	Sebastian Will David A. Hendrix Loyal A. Goff	Wiley interdisciplinary reviews. RNA
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea	2012	Brenton R. Graveley	Alissa M Resch Dasaradhi Palakodeti Yi-Chien Lu Michael Horowitz	PLOS ONE
RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi	2012	Tae Sung Jung	Ho Bin Jang Young Kyu Kim Carmelo S Del Castillo Seong Won Nho In Seok Cha Seong Bin Park Mi Ae Ha Jun-Ichi Hikima Sung Jong Hong Takashi Aoki	PLOS ONE
GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats	2012	David Goldman	Mary-Anne Enoch Zhifeng Zhou Mitsuru Kimura Deborah C Mash Qiaoping Yuan	PLOS ONE
Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line	2012	Mark Bender Gerstein Vincent Schulz	Jia Qian Wu Montrell Seay Manoj Hariharan David Tuck Jin Lian Jiang Du Minyi Shi Zhijia Ye Michael P Snyder Sherman Weissman	PLOS Genetics
Gene expression profiling of liver cancer stem cells by RNA-sequencing	2012	Timothy Wan	David W Y Ho Zhen Fan Yang Kang Yi Chi Tat Lam Michael N P Ng Wan Ching Yu Joyce Lau Xiaoqi Wang Zhixiang Yan Hang Liu Yong Zhang Sheung Tat Fan	PLOS ONE
Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene	2012	Feng Gao Abdul B Abou-Samra	Ren Zhang Fayi Yao	PLOS ONE
RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells	2012	Sten Linnarsson	Kersti Jääger Saiful Islam Pawel Zajac Toomas Neuman	PLOS ONE
Stable gene targeting in human cells using single-strand oligonucleotides with modified bases	2012	George M. Church	Xavier Rios Adrian W Briggs Danos Christodoulou Josh M Gorham Jonathan G Seidman	PLOS ONE
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data	2012	Jean-Baptiste Veyrieras Daniel J Gaffney	Jean-Baptiste Veyrieras Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard	PLOS ONE
Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment	2012	Honghuang Lin	N. Medina-Medina A. Broka S. Lacey E. S. Klings C. T. Baldwin M. H. Steinberg P. Sebastiani	Advances in Intelligent and Soft Computing
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012	2012-01	Sumio Sugano	Riu Yamashita Yutaka Suzuki Kenta Nakai	Nucleic Acids Research
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes	2012-01-01	Andreas Gnirke Georgia Giannoukos Ashlee Earl Chad Nusbaum Dirk Gevers	Dawn M Ciulla Katherine Huang Brian J Haas Jacques Izard Joshua Z Levin Jonathan Livny Doyle V Ward Bruce W Birren	Genome Biology
How to analyze gene expression using RNA-sequencing data.	2012-01-01	Daniel Ramsköld Rickard Sandberg	Ersen Kavak	Methods in Molecular Biology
Detection and quantification of alternative splicing variants using RNA-seq.	2012-01-01	Henry D Priest	Douglas W Bryant Todd C Mockler	Methods in Molecular Biology
Retinal transcriptome profiling by directional next-generation sequencing using 100 ng of total RNA.	2012-01-01	Anand Swaroop	Matthew J Brooks Harsha Karur Rajasimha	Methods in Molecular Biology
Sex-biased transcriptome evolution in Drosophila.	2012-01-01	Doris Bachtrog	Raquel Assis Qi Zhou	Genome Biology and Evolution
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach.	2012-01-01	Jordi Solana Aziz A. Aboobaker	Damian Kao Yuliana Mihaylova Farah Jaber-Hijazi Sunir Malla Ray Wilson	Genome Biology
Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.	2012-01-01	Gangqing Hu	Gang Wei Kairong Cui Keji Zhao	Methods in Enzymology
Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells.	2012-01-01	Yasuyuki Ohkawa Kazu Kobayakawa Seiji Okada Hideyuki Okano	Hiromi Kumamaru Hirokazu Saiwai Hisakata Yamada Kensuke Kubota Koichi Akashi Yukihide Iwamoto	Nature Communications
Computational analysis of RNA-seq.	2012-01-01	Scott A. Givan	Christopher A Bottoms William G Spollen	Methods in Molecular Biology
Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.	2012-01-03	Robert K. Bradley	Jason Merkin Nicole J Lambert Christopher B Burge	PLOS Biology
Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.	2012-01-03	Baojin Yao	Yu Zhao Haishan Zhang Mei Zhang Meichen Liu Hailong Liu Juan Li	Biotechnology Letters
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.	2012-01-04	Zemin Ning Peter A.C. 't Hoen Pieternella E Slagboom	Yanju Zhang Eric-Wubbo Lameijer Kai Ye	Bioinformatics
IQSeq: integrated isoform quantification analysis based on next-generation sequencing.	2012-01-06	Andrea Sboner Mark Bender Gerstein	Jiang Du Jing Leng Lukas Habegger Drew McDermott	PLOS ONE
Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.	2012-01-11	Melody Baddoo Erik K Flemington	Zhen Lin Adriane Puetter Joseph Coco Guorong Xu Michael J Strong Xia Wang Claire Fewell Melody Baddoo Christopher Taylor	Journal of Virology
Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.	2012-01-13	Andrew C. Allan Xue-ren Yin	Chao Feng Ming Chen Chang-jie Xu Lin Bai Xian Li Ian B Ferguson Kun-song Chen	BMC Genomics
Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy	2012-01-14	Peadar Ó Gaora Helen M Roche	Eoin P Brennan Melissa J Morine David W Walsh Sarah A Roxburgh Maja T Lindenmeyer Derek P Brazil Denise M Sadlier Clemens D Cohen GENIE Consortium Catherine Godson Finian Martin	Biochimica et Biophysica Acta
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression.	2012-01-17	Cynthia Sharma	Vinoy K Ramachandran Neil Shearer Jobin J Jacob Arthur Thompson	BMC Genomics
FX: an RNA-Seq analysis tool on the cloud.	2012-01-17	Young Seok Ju Thomas Bleazard	Dongwan Hong Arang Rhie Sung-Soo Park Jongkeun Lee Sujung Kim Saet-Byeol Yu Hyun-Seok Park Hwanseok Rhee Hyonyong Chong Kap-Seok Yang Yeon-Su Lee In-Hoo Kim Jin Soo Lee Jong-Il Kim Jeong-Sun Seo	Bioinformatics
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.	2012-01-20	Zhi-xiang Lu Jian Huang	Shihao Shen Juw Won Park Kimberly A Dittmar Qing Zhou Russ P Carstens Yi Xing	Nucleic Acids Research
Application of RNA-Seq transcriptome analysis: CD151 is an Invasion/Migration target in all stages of epithelial ovarian cancer.	2012-01-24	Sergio Marchini Robert Fruscio Maurizio D'Incalci	Rebecca A Mosig Li Lin Emir Senturk Hardik Shah Fei Huang Peter Schlosshauer Samantha Cohen Ravi Sachidanandam Peter Dottino John A Martignetti	Journal of Ovarian Research
A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.	2012-01-26	Philip Rosenstiel Ueli Grossniklaus Marc W Schmid	Anja Schmidt Ulrich C Klostermeier Matthias Barann	PLOS ONE
Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.	2012-01-26	Robert Ekblom Jon Slate Terry Burke	Gavin J Horsburgh Tim Birkhead	Comparative and Functional Genomics
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.	2012-01-27	David Tabb	Surendra Dasari Matthew C Chambers Misti A Martinez Kristin L Carpenter Amy-Joan L Ham Lorenzo J Vega-Montoto	Journal of Proteome Research
Removing technical variability in RNA-seq data using conditional quantile normalization.	2012-01-27	Kasper D. Hansen Zhijin Wu	Rafael A Irizarry	Biostatistics
The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.	2012-01-27	Lars Kraemer Philip Rosenstiel	E E R Philipp D Mountfort M Schilhabel S Schreiber	Bioinformatics
A new approach to bias correction in RNA-Seq	2012-01-28	Walter L. Ruzzo	Daniel C Jones Xinxia Peng Michael G Katze	Bioinformatics
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.	2012-01-28	Davis J McCarthy Gordon K Smyth	Yunshun Chen	Nucleic Acids Research
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.	2012-01-31	Asa Ben-Hur	Mark F Rogers Julie Thomas Anireddy Sn Reddy	Genome Biology
Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).	2012-02-01	W. Richard McCombie Norman J Wickett Mark W. Chase	Michael R McKain Yeting Zhang Saravanaraj Ayyampalayam J Chris Pires Claude W dePamphilis Jim Leebens-Mack	American Journal of Botany
Spt4 is selectively required for transcription of extended trinucleotide repeats.	2012-02-01	Yijuang Chern	Chia-Rung Liu Chuang-Rung Chang Tzu-Han Wang Wen-Chieh Hsieh Wen-Chuan Shen Chi-Yuan Chang I-Chieh Chu Ning Deng Stanley N Cohen Tzu-Hao Cheng	Cell
The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.	2012-02-03	Andreas Dötsch Denitsa Eckweiler Susanne Häussler	Monika Schniederjans Ariane Zimmermann Vanessa Jensen Maren Scharfe Robert Geffers	PLOS ONE
Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.	2012-02-07	Miao Tian	Jie Xiong Xingyi Lu Zhemin Zhou Yue Chang Dongxia Yuan Zhigang Zhou Lei Wang Chengjie Fu Eduardo Orias Wei Miao	PLOS ONE
Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae.	2012-02-09	Nick Talbot	Darren M Soanes Apratim Chakrabarti Konrad H Paszkiewicz Angus L Dawe	PLOS Pathogens
Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation.	2012-02-09	Jie Huang Yu Zhou Changwei Shao Yi Zhang	Rui Xiao Peng Tang Bo Yang Hairi Li Hui Sun Xiang-Dong Fu	Molecular Cell
Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.	2012-02-09	Andrew Paul Hutchins Stéphane Poulain	Diego Miranda-Saavedra	Blood
Specific and sensitive mRNA biomarkers for the identification of skin in 'touch DNA' evidence.	2012-02-09	Cordula Haas	E Hanson R Jucker J Ballantyne	Forensic Science International: Genetics
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.	2012-02-12	Jun Wang Bertrand Chin-Ming Tan Zhiyu Peng	Yanbing Cheng Lin Kang Zhijian Tian Yuankun Zhu Wenwei Zhang Yu Liang Xueda Hu Xuemei Tan Jing Guo Zirui Dong Yan Liang Li Bao	Nature Biotechnology
Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms	2012-02-14	Dan L. Warren Michael B Thompson Gunter P Wagner	Matthew C Brandley Rebecca L Young	Genome Biology and Evolution
RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.	2012-02-17	Jens U Marquardt Ugur Sahin	Markus Krupp Peter R Galle John Castle Andreas Teufel	Bioinformatics
RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus.	2012-02-17	Eric Peatman	Chao Li Yu Zhang Ruijia Wang Jianguo Lu Samiran Nandi Sriprakash Mohanty Jeffery Terhune Zhanjiang Liu	Fish and Shellfish Immunology
RNA-seq analysis of the functional compartments within the rat placentation site.	2012-02-21	Kartik Shankar	Ying Zhong Ping Kang Michael L Blackburn Michael J Soares Thomas M Badger Horacio Gomez-Acevedo	Endocrinology
RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.	2012-02-21	Jian-Hua Mao Jun Wang Huanming Yang	Shancheng Ren Zhiyu Peng Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun	Cell Research
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.	2012-02-29	Alexey I Nesvizhskii	Kang Ning Damian Fermin	Journal of Proteome Research
RNA-Seq quantification of the human small airway epithelium transcriptome	2012-02-29	Juan L Rodriguez-Flores	Neil R Hackett Marcus W Butler Renat Shaykhiev Jacqueline Salit Larsson Omberg Jason G Mezey Yael Strulovici-Barel Guoqing Wang Lukas Didon Ronald G Crystal	BMC Genomics
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.	2012-02-29	Angelo Valleriani	Gong Zhang Ivan Fedyunin Sebastian Kirchner Chuanle Xiao Zoya Ignatova	Nucleic Acids Research
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks	2012-03	Loyal Goff Steven Salzberg Lior Pachter Harold Pimentel John L. Rinn	Cole Trapnell Adam Roberts Geo Pertea Daehwan Kim David R Kelley	Nature Protocols
Characterization and differential expression analysis of complete coding sequences of Vitis vinifera L. sirtuin genes.	2012-03-03	Giacomo Morreale Matteo Busconi Luigi Bavaresco	M Cucurachi A Zanetti C Fogher	Plant Physiology and Biochemistry
A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.	2012-03-04	Franck Tirode Olivier Delattre	Gaëlle Pierron Carlo Lucchesi Stéphanie Reynaud Stelly Ballet Sarah Cohen-Gogo Virginie Perrin Jean-Michel Coindre	Nature Genetics
The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.	2012-03-08	Gerton Lunter Izortze Santin Michael Sammeth Miriam Cnop Lorella Marselli Piero Marchetti Fernanda Ortis Mark McCarthy	Décio L Eizirik Thomas Bouckenooghe Guy Bottu Giorgia Sisino Mariana Igoillo-Esteve Maikel L Colli Jenny Barthson Luc Bouwens Linda Hughes Lorna Gregory	PLOS Genetics
HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.	2012-03-08	Vladimir Benes Gunnar Rätsch Hans-Martin Jäck	Marco Preussner Silke Schreiner Lee-Hsueh Hung Martina Porstner Albrecht Bindereif	Nucleic Acids Research
Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia.	2012-03-09	Annalisa Lonetti Giovanni Malerba Alberto Ferrarini Luciano Xumerle Anna Ferrari Cristina Papayannidis Simona Soverini	I Iacobucci M Sazzini E Giacomelli D Luiselli A Boattini P Garagnani A Vitale F Pane M Baccarani M Delledonne G Martinelli	Blood Cancer Journal
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells.	2012-03-12	Sascha Brunke Karl Kuchler Reinhard Guthke	Lanay Tierney Jörg Linde Sebastian Müller Juan Camilo Molina Bernhard Hube Ulrike Schöck	Frontiers in Microbiology
A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.	2012-03-19	Effie Mutasa-Göttgens Berthold Gottgens	Anagha Joshi Helen F Holmes Peter Hedden	BMC Genomics
Transcriptome landscape of the human placenta	2012-03-27	Zhi-xiang Lu Jin-kai Wang	Jinsil Kim Keyan Zhao Peng Jiang Jeffrey C Murray Yi Xing	BMC Genomics
Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers.	2012-03-27	Jennifer Thomson Cong-Jun Li	Ransom L Baldwin Robert W Li Brian J Bequette	Physiological Genomics
Alternative splicing networks regulated by signaling in human T cells.	2012-03-27	Nicole M Martinez	Qun Pan Brian S Cole Christopher A Yarosh Grace A Babcock Florian Heyd William Zhu Sandya Ajith Benjamin J Blencowe Kristen W Lynch	RNA
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts	2012-03-28	Francisco Peñagaricano	Ashley M Driver Wen Huang Khawaja R Ahmad Katie S Hackbart Milo C Wiltbank Hasan Khatib	BMC Genomics
A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis	2012-03-28	Paolo Miotto Alessandro Ambrosi	Danilo Pellin Daniela Maria Cirillo Clelia Di Serio	PLOS ONE
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.	2012-03-29	Jae-Hyung Lee Guangdun Peng Xinshu Xiao	Gang Li Jae Hoon Bahn Zugen Chen Stanley F Nelson	Nucleic Acids Research
Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis.	2012-04-01	Songnian Hu	Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Daoyong Zhang Feng Ding Chengqi Xin Zhang Zhang Shuhui Song Fanglin Sun Jun Yu	Genomics Proteomics and Bioinformatics
Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.	2012-04-01	Ellen V. Rothenberg	Jingli A Zhang Ali Mortazavi Brian A Williams Barbara J Wold	Cell
A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola.	2012-04-01	Igor V Grigoriev	Akhil Srivastava Robin A Ohm Lindsay Oxiles Fred Brooks Christopher B Lawrence Yangrae Cho	Molecular Plant-Microbe Interactions
Identification of shortened 3' untranslated regions from expression arrays.	2012-04-01	Andrei Zinovyev Loredana Martignetti Emmanuel Barillot		Journal of Bioinformatics and Computational Biology
Improving RNA-Seq Precision with MapAl.	2012-04-02	D Kreil	Paweł P Labaj Bryan E Linggi H Steven Wiley	Frontiers in Genetics
RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis	2012-04-02	Alex Schultink Jacob K Jensen Markus Pauly	Kenneth Keegstra Curtis G Wilkerson	Plant Physiology Journal
Deep sequencing the circadian and diurnal transcriptome of Drosophila brain	2012-04-03	Gregory R Grant	Michael E Hughes Christina Paquin Jack Qian Michael N Nitabach	Genome Research
The clonal and mutational evolution spectrum of primary triple-negative breast cancers	2012-04-04	Gavin Ha D Yap Daniel Lai Inanc Birol Malachi Griffith Gregg B Morin Suet-feung Chin Christina Curtis Mackey JR Wyeth W Wasserman Steven Jones	Sohrab P Shah Andrew Roth Rodrigo Goya Arusha Oloumi Yongjun Zhao Gulisa Turashvili Jiarui Ding Kane Tse Gholamreza Haffari Ali Bashashati Leah M Prentice Jaswinder Khattra Angela Burleigh Virginie Bernard Andrew McPherson Karey Shumansky Anamaria Crisan Ryan Giuliany Alireza Heravi-Moussavi Jamie Rosner Richard Varhol Angela Tam Noreen Dhalla Thomas Zeng Kevin Ma Simon K Chan Annie Moradian S-W Grace Cheng Peter Watson Karen Gelmon Stephen Chia Oscar M Rueda Paul D Pharoah Sambasivarao Damaraju Kelly Hoon Timothy Harkins Vasisht Tadigotla Mahvash Sigaroudinia Philippe Gascard Thea Tlsty Joseph F Costello Irmtraud M Meyer Connie J Eaves David Huntsman Martin Hirst Carlos Caldas Marco A Marra Samuel Aparicio	Nature
Spatial proximity and similarity of the epigenetic state of genome domains.	2012-04-04	Ekaterina E Khrameeva Gennady G Fedonin Mikhail S Gelfand	Andrey A Mironov Philipp Khaitovich	PLOS ONE
Computational inference of mRNA stability from histone modification and transcriptome profiles	2012-04-10	Yong Zhang	Chengyang Wang Rui Tian Qian Zhao Han Xu Clifford A Meyer Cheng Li X Shirley Liu	Nucleic Acids Research
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.	2012-04-12	J Duitama	Pramod K Srivastava Ion I Măndoiu	BMC Genomics
Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes.	2012-04-17	Niklaus Zemp	Aline Muyle Clothilde Deschamps Sylvain Mousset Alex Widmer Gabriel A B Marais	PLOS Biology
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data	2012-04-19	Pierre Peterlongo Marie-France Sagot	Gustavo A T Sacomoto Janice Kielbassa Rayan Chikhi Raluca Uricaru Pavlos Antoniou Vincent Lacroix	BMC Bioinformatics
A context-based approach to identify the most likely mapping for RNA-seq experiments.	2012-04-19	Ralf Zimmer	Thomas Bonfert Gergely Csaba Caroline C Friedel	BMC Bioinformatics
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy	2012-04-24	Daniel S. Rokhsar Kranthi Varala	Kankshita Swaminathan Won Byoung Chae Therese Mitros Liang Xie Adam Barling Katarzyna Glowacka Megan Hall Stanislaw Jezowski Ray Ming Matthew Hudson John A Juvik Stephen P Moose	BMC Genomics
RNA-SeQC: RNA-seq metrics for quality control and process optimization	2012-04-25	Gad Getz Wendy Winckler	David S DeLuca Joshua Z Levin Andrey Sivachenko Timothy Fennell Marc-Danie Nazaire Chris Williams Michael Reich	Bioinformatics
Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin	2012-04-25	Ana Conesa Diana Huestis Jeffrey A Fabrick Juan Luis Jurat-Fuentes	Brenda Oppert Scot E Dowd Pascal Bouffard Lewyn Li Marcé D Lorenzen Michelle Toutges Jeremy Marshall Cris Oppert	PLOS ONE
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.	2012-04-26	Ralf Zimmer	Lukas Windhager Thomas Bonfert Kaspar Burger Zsolt Ruzsics Stefan Krebs Stefanie Kaufmann Georg Malterer Anne L'Hernault Markus Schilhabel Stefan Schreiber Philip Rosenstiel Dirk Eick Caroline C Friedel Lars Dölken	Genome Research
Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.	2012-04-27	Jingqin Wu Xi Wang Murray J Cairns	Natalie J Beveridge Paul A Tooney Rodney J Scott Vaughan J Carr	PLOS ONE
Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq	2012-05	John Quackenbush Naftali Kaminski	Rebecca L. Kusko John Brothers II Gang Liu Lingqi Luo Brenda J. Guardela John R. Tedrow Yuriy Aleksyev Ivana V. Yang Mick Correll Mark Geraci Frank C. Sciurba Marc Lenburg David A. Schwartz Jennifer Beane Avrum Spira
Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease	2012-05-01	Olivier Elemento	Seema Gollamudi Ashu Johri Noel Y Calingasan Lichuan Yang M Flint Beal	PLOS ONE
Utilizing RNA-Seq data for de novo coexpression network inference	2012-05-03	Shannon K McWeeney	Ovidiu D Iancu Sunita Kawane Daniel Bottomly Robert Searles Robert Hitzemann	Bioinformatics
Identifying differentially expressed transcripts from RNA-seq data with biological variation.	2012-05-03	Magnus Rattray Antti Honkela	Peter Glaus Antti Honkela	Bioinformatics
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.	2012-05-04	Douwe Molenaar	Jumamurat R Bayjanov Vesela Tzeneva Roland J Siezen Sacha A F T van Hijum	BMC Genomics
RNA-Seq identifies SNP markers for growth traits in rainbow trout	2012-05-04	Timothy D Leeds	Mohamed Salem Roger L Vallejo Yniv Palti Sixin Liu Annas Sabbagh Caird E Rexroad Jianbo Yao	PLOS ONE
Gene mapping via bulked segregant RNA-Seq (BSR-Seq).	2012-05-07	Cheng-Ting Yeh Dan Nettleton Patrick S Schnable	Sanzhen Liu Ho Man Tang	PLOS ONE
A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.	2012-05-15	Marie-Laure Yaspo Hans Lehrach	Marc Sultan Simon Dökel Vyacheslav Amstislavskiy Daniela Wuttig Holger Sültmann Marie-Laure Yaspo	Biochemical and Biophysical Research Communications
Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.	2012-05-15	Weizhong Li	Sitao Wu Robert W Li Cong-Jun Li	PLOS ONE
Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions	2012-05-18	Lars K. Nielsen Robin William Palfreyman Quan Nguyen	Leslie C L Chan Steven Reid	PLOS ONE
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance.	2012-05-20	David J. Lynn Christopher J. Creevey David A Kenny	Matthew McCabe Sinéad Waters Dermot Morris	BMC Genomics
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns	2012-05-24	Anders Krogh Jun Wang Johannes Waage Joachim Weischenfeldt Bo Torben Porse Janus Schou Jakobsen Karsten Kristiansen	Geng Tian Jing Zhao Inge Damgaard	Genome Biology
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer	2012-05-25	Gavin Ha Daniel Lai Suet-feung Chin	Andrew Roth Ali Bashashati Jiarui Ding Rodrigo Goya Ryan Giuliany Jamie Rosner Arusha Oloumi Karey Shumansky Gulisa Turashvili Martin Hirst Marco A Marra Samuel Aparicio Sohrab P Shah Carlos Caldas	Genome Research
Dissect: detection and characterization of novel structural alterations in transcribed sequences	2012-06-01	Inanc Birol	Deniz Yorukoglu Faraz Hach Lucas Swanson Colin C Collins S Cenk Sahinalp	Bioinformatics
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.	2012-06-01	Piero Carninci Yukihiko Noro	Alka Saxena Akiko Wagatsuma Takenobu Kuji Atsuko Asaka-Oba Akira Watahiki Cecile Gurnot Michela Fagiolini Takao K Hensch	BioTechniques
Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection.	2012-06-02	Eric Peatman Shikai Liu	Fanyue Sun Chao Li Yanliang Jiang Zunchun Zhou Zhanjiang Liu	Developmental and Comparative Immunology
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics	2012-06-08	John E. Lunn Björn Usadel Alisdair R Fernie Mark Stitt	Marc Lohse Anthony M Bolger Axel Nagel	Nucleic Acids Research
Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites	2012-06-08	Gabriel Kreiman Nicole Cloonan Sean M. Grimmond	Martin Hemberg Jesse M Gray Scott Kuersten Michael E Greenberg	Nucleic Acids Research
Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.	2012-06-10	Marek Żywicki Marcel Scheideler Mathieu Rederstorff	Konstantinia Skreka Michael Karbiener Alexander Hüttenhofer	Journal of Nucleic Acids
Modeling gene expression using chromatin features in various cellular contexts	2012-06-13	Roderic Guigó i Serra Mark Bender Gerstein Ewan Birney Sarah Djebali Xianjun Dong Anshul Kundaje Thomas R. Gingeras	Melissa C Greven James B Brown Chao Cheng Zhiping Weng	Genome Biology
Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma.	2012-06-13	Stephanie Ma Li Fu Xin-Yuan Guan Xin-Yuan Guan	Jessie Y J Bao Pak Shing Kwan Yuen Piu Chan Carol M Tong Na Zhang Amy H Y Tong Yan-Ru Qin Sai Wah Tsao Kwok Wah Chan Si Lok	Gastroenterology
Alternative splicing regulated by butyrate in bovine epithelial cells.	2012-06-14	Wen Huang Weizhong Li	Sitao Wu Congjun Li Robert W Li	PLOS ONE
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.	2012-06-17	Alberto Ferrarini Elisa Ficarra Simona Soverini Giovanni Martinelli Ilaria Iacobucci	Francesco Abate Andrea Acquaviva Giulia Paciello Carmelo Foti Massimo Delledonne Enrico Macii	Bioinformatics
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.	2012-06-18	Sean Doyle David J. Lynn Bernadette Earley	Aran O'Loughlin Mark McGee Matthew McCabe	BMC Genomics
Detecting differential usage of exons from RNA-seq data	2012-06-21	Alejandro Reyes Simon Anders Wolfgang Huber		Genome Research
PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification	2012-06-21	Zhaohui Steve Qin	Han Wu Yu Zhu	Statistics in biosciences
Expressed pseudogenes in the transcriptional landscape of human cancers	2012-06-22	John R. Prensner Shanker Kalyana-Sundaram Chandan Kumar-Sinha Irfan Asangani Nallasivam Palanisamy	Sunita Shankar Dan R Robinson Yi-Mi Wu Xuhong Cao Vishal Kothari Robert J Lonigro Matthew K Iyer Terrence Barrette Achiraman Shanmugam Saravana M Dhanasekaran Arul M Chinnaiyan	Cell
RNA-Seq and human complex diseases: recent accomplishments and future perspectives.	2012-06-27	Valerio Costa	Marianna Aprile Roberta Esposito Alfredo Ciccodicola	European Journal of Human Genetics
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.	2012-06-27	Richard W Francis Kim Carter Denise Anderson Alex H. Beesley	Katherine Thompson-Wicking Ursula R Kees	PLOS ONE
A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.	2012-06-29	Gregory J. Kato	Nalini Raghavachari Jennifer Barb Yanqin Yang Poching Liu Kimberly Woodhouse Daniel Levy Christopher J O'Donnell Peter J Munson	BMC Medical Genomics
SAVoR: a server for sequencing annotation and visualization of RNA structures	2012-07	Otto Valladares Fan Li	Paul Ryvkin Daniel M Childress Brian D Gregory Li-San Wang	Nucleic Acids Research
Digging in the RNA-seq Garbage: Evaluating the Characteristics of Unmapped RNA-seq Reads in Normal Tissues	2012-07	Federica Cavallo	Matteo Carrara Maddalena Arigoni Raffaele A. Calogero
Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks	2012-07-01	Catherine L Peichel	Anna K Greenwood Jennifer N Cech	Evolution & Development
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions	2012-07-01	Iros Barozzi Gioacchino Natoli	Dev M Bhatt Amy Pandya-Jones Ann-Jay Tong Michelle M Lissner Douglas L Black Stephen T Smale	Cell
RNA-seq analysis of the C. briggsae transcriptome.	2012-07-06	Bora Uyar	Jeffrey S C Chu Ismael A Vergara Shu Yi Chua Martin R Jones Tammy Wong David L Baillie Nansheng Chen	Genome Research
Incorporating RNA-seq data into the zebrafish Ensembl genebuild	2012-07-12	Simon White	John E Collins Stephen M J Searle Derek L Stemple	Genome Research
Paired-end sequencing of Fosmid libraries by Illumina.	2012-07-16	Gad Getz Chad Nusbaum Yotam Drier	Louise J S Williams Diana G Tabbaa Na Li Aaron M Berlin Terrance P Shea Iain Maccallum Michael S Lawrence Sarah K Young David B Jaffe Andreas Gnirke	Genome Research
Inflammatory priming predisposes mice to age-related retinal degeneration.	2012-07-17	Krzysztof Palczewski	Debarshi Mustafi Tadao Maeda Hideo Kohno Joseph H Nadeau	Journal of Clinical Investigation
RNA processing in the minimal organism Nanoarchaeum equitans	2012-07-18	L Randau	Lennart Randau	Genome Biology
Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton	2012-07-20	Daojun Yuan	Xiyan Yang Xianlong Zhang Fangyan Jin Yunchao Zhang Jiao Xu	BMC Plant Biology
Genomic imprinting absent in Drosophila melanogaster adult females.	2012-07-20	C Joel McManus Brenton R. Graveley	Joseph D Coolon Kraig R Stevenson Patricia J Wittkopp	Cell Reports
Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data	2012-07-23	Willard M. Freeman Kent Vrana	Kathryn J Huber-Keener Xiuping Liu Zhong Wang Yaqun Wang Song Wu Maricarmen D Planas-Silva Xingcong Ren Yan Cheng Yi Zhang Chang-Gong Liu Jin-Ming Yang Rongling Wu	PLOS ONE
Metabolic Regulation of "Ca. Methylacidiphilum Fumariolicum" SolV Cells Grown Under Different Nitrogen and Oxygen Limitations.	2012-07-25	Huub J.M. Op den Camp	Ahmad F Khadem Arjan Pol Adam S Wieczorek Mike S M Jetten	Frontiers in Microbiology
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq.	2012-07-26	Akshay Kakumanu Andy Pereira	Madana M R Ambavaram Curtis Klumas Arjun Krishnan Utlwang Batlang Elijah Myers Ruth Grene	Plant Physiology
Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells.	2012-07-27	Guoping Fan	Ganlu Hu Kevin Huang Juehua Yu Sailesh Gopalakrishna-Pillai Jun Kong He Xu Zhenshan Liu Kunshan Zhang Jun Xu Yuping Luo Siguang Li Yi E Sun Linda E Iverson Zhigang Xue	PLOS ONE
Identification of novel transcripts deregulated in buccal cancer by RNA-seq.	2012-07-27	Ajai K. Tripathi Subhash J Jakhesara Chaitanya G. Joshi	Manisha R Sajnani Amrutlal K Patel Vaibhav D Bhatt Viral B Ahir Vangipuram Shankar Siddharth Shah Tejas M Shah Prakash G Koringa	Gene
Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis	2012-07-29	Anastassios Vourekas Panagiotis Alexiou Manolis Maragkakis Yohei Kirino Zissimos Mourelatos	Qi Zheng Brian D Gregory	Nature Structural & Molecular Biology
A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin.	2012-07-30	Karla D Passalacqua	Sarah W Satola Emily K Crispell Timothy D Read	Antimicrobial Agents and Chemotherapy
easyRNASeq: a bioconductor package for processing RNA-Seq data	2012-07-30	Eileen E. M. Furlong Lars M Steinmetz	Nicolas Delhomme Ismaël Padioleau	Bioinformatics
RNASeq profiling of UTR expression during neuronal plasticity.	2012-07-31	Robert M. Flight Jeffrey C. Petruska	Benjamin J Harrison Abdallah Eteleeb Eric C Rouchka	BMC Bioinformatics
Recurrent R-spondin fusions in colon cancer.	2012-08-01	Robert Gentleman	Somasekar Seshagiri Eric W Stawiski Steffen Durinck Zora Modrusan Elaine E Storm Caitlin B Conboy Subhra Chaudhuri Yinghui Guan Vasantharajan Janakiraman Bijay S Jaiswal Joseph Guillory Connie Ha Gerrit J P Dijkgraaf Jeremy Stinson Florian Gnad Melanie A Huntley Jeremiah D Degenhardt Peter M Haverty Richard Bourgon Weiru Wang Hartmut Koeppen Timothy K Starr Zemin Zhang David A Largaespada Thomas D Wu Frederic J de Sauvage	Nature
Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.	2012-08-04	Stéphane Poulain Andrew Paul Hutchins Hodaka Fujii	Diego Miranda-Saavedra	Genomics
Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.	2012-08-05	Altus Viljoen	Chun-Yu Li Gui-Ming Deng Jing Yang Yan Jin Rui-Bin Kuang Cun-Wu Zuo Zhi-Cheng Lv Qiao-Song Yang Ou Sheng Yue-Rong Wei Chun-Hua Hu Tao Dong Gan-Jun Yi	BMC Genomics
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.	2012-08-08	Vincent Lynch	Günter P Wagner Koryu Kin	Theory in Biosciences
RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.	2012-08-13	Stan Gaj Hans Lehrach Ralf Herwig Jos Kleinjans	Joost van Delft Stan Gaj Matthias Lienhard Marcus W Albrecht Alexander Kirpiy Karen Brauers Sandra Claessen Daneida Lizarraga	Toxicological Sciences
Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish.	2012-08-13	Ian A Johnston	Graham R Scott	Proceedings of the National Academy of Sciences of the United States of America
Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.	2012-08-16	Peter A. DiMaggio Barry M Zee	Gary LeRoy Iouri Chepelev Mario A Blanco Keji Zhao Benjamin A Garcia	Genome Biology
Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.	2012-08-16	Marilyn Renfree Anthony T. Papenfuss Emily S Wong Camilla M Whittington Glenn F King	David Morgenstern Ehtesham Mofiz Sara Gombert Katrina M Morris Peter Temple-Smith Wesley C Warren Katherine Belov	Molecular & Cellular Proteomics
RNA-seq transcriptome analysis of male and female zebra finch cell lines	2012-08-21	Christopher N. Balakrishnan Ya-Chi Lin Sarah E London David F. Clayton	Christopher N Balakrishnan Ya-Chi Lin Sarah E London David F Clayton	Genomics
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data	2012-08-21	Shaojie Zhang	Peter Tonner Vinodh Srinivasasainagendra Degui Zhi	BMC Genomics
Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome.	2012-08-21	Michael McManus Hail Kim	Gregory M Ku Ian W Vaughn Matthew J Hangauer Chang Myung Oh Michael S German	Molecular Endocrinology
shortran: a pipeline for small RNA-seq data analysis.	2012-08-22	Stig Uggerhøj Andersen Jens Stougaard	Vikas Gupta Katharina Markmann Christian N S Pedersen	Bioinformatics
Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis	2012-08-22	Karla D Passalacqua	Anjana Varadarajan Charlotte Weist Brian D Ondov Benjamin Byrd Timothy D Read Nicholas H Bergman	PLOS ONE
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.	2012-08-24	Yong Zhang	Jianxing Feng Clifford A Meyer Qian Wang Jun S Liu X Shirley Liu	Bioinformatics
An injury-response mechanism conserved across kingdoms determines entry of the fungus Trichoderma atroviride into development.	2012-08-27	Miguel Hernández-Oñate Alfredo Herrera-Estrella	Edgardo U Esquivel-Naranjo Artemio Mendoza-Mendoza Alison Stewart	Proceedings of the National Academy of Sciences of the United States of America
A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.	2012-08-28	Anna Terry Niall G. Campbell Charles Mein	Scott Brouilette Scott Kuersten Monika Bozek Kerith-Rae Dias Leena Bhaw-Rosun Yasunori Shintani Steven Coppen Chiho Ikebe Vinit Sawhney Masahiro Kaneko Nobuko Tano Hidekazu Ishida Ken Suzuki Kenta Yashiro	Developmental Dynamics
A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq.	2012-08-30	Winfriede Weschke	Stefan Kohl Julien Hollmann Frank R Blattner Volodymyr Radchuk Franka Andersch Burkhard Steuernagel Thomas Schmutzer Uwe Scholz Karin Krupinska Hans Weber	BMC Plant Biology
Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders	2012-08-30	Deyou Zheng	Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Tao Wang Herbert M Lachman	PLOS ONE
RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter	2012-08-30	Nicolas Rouhier Julie Poulain Benjamin Petre Sébastien Duplessis Corinne Da Silva Francis Martin Emmanuelle Morin Annegret Kohler	Emilie Tisserant Stéphane Hacquard Christine Delaruelle	PLOS ONE
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs	2012-09	Roderic Guigó i Serra Sarah Djebali Rory Johnson Thomas R. Gingeras	Hagen Tilgner David G Knowles Carrie A Davis Sudipto Chakrabortty João Curado Michael Snyder	Genome Research
Dual RNA-seq of pathogen and host.	2012-09-01	Alexander Westermann Jörg Vogel	Stanislaw A Gorski	Nature Reviews Microbiology
Long noncoding RNAs are rarely translated in two human cell lines	2012-09-01	Yanbao Yu Anshul Kundaje Brian D Strahl Krzysztof Krajewski	Balázs Bánfai Hui Jia Jainab Khatun Emily Wood Brian Risk William E Gundling Harsha P Gunawardena Ling Xie Xian Chen Peter Bickel Morgan C Giddings James B Brown Leonard Lipovich	Genome Research
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.	2012-09-01	Andrea Tanzer Jose M Gonzalez Bronwen Aken Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Cédric Howald Thibaut Hourlier Thomas Derrien Alexandre Reymond Simon White Adam Frankish	Jacqueline Chrast Nathalie Walters Jan-Hinnerk Vogel Stephen Searle	Genome Research
Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes.	2012-09-03	Xiaohan Yang Gerald A Tuskan Sara S Jawdy Lee Gunter Stan D Wullschleger	Abhijit A Karve Sara M Allen David J Weston	New Phytologist
The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.	2012-09-04	Silvia Dal Santo Giovanni Battista Tornielli Vittorio Murino Luca Venturini Lorenzo Farina	Marianna Fasoli Sara Zenoni Anita Zamboni Andrea Porceddu Manuele Bicego Alberto Ferrarini Massimo Delledonne Mario Pezzotti	The Plant Cell
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue	2012-09-05	Graziano Pesole Angela Gallo Ernesto Picardi	Federica Galeano Sara Tomaselli	PLOS ONE
Modelling and simulating generic RNA-Seq experiments with the flux simulator.	2012-09-07	Roderic Guigó i Serra Michael Sammeth	Thasso Griebel Benedikt Zacher Paolo Ribeca Emanuele Raineri Vincent Lacroix	Nucleic Acids Research
Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-Seq	2012-09-07	Mariangela Bonnizoni Guiyun Yan	Yaw Afrane William Augustine Dunn Francis K Atieli Goufa Zhou Daibin Zhong Jun Li Andrew Githeko	PLOS ONE
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.	2012-09-08	Taejoon Kwon Rosa A Uribe Jeffrey M Gross		Developmental Biology
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.	2012-09-10	Jens Nielsen Natapol Pornputtapong Linn Fagerberg Intawat Nookaew	Marta Papini Gionata Scalcinati Matthias Uhlén	Nucleic Acids Research
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.	2012-09-11	Todd P Michael	Chongyuan Luo David J Sidote Yi Zhang Randall A Kerstetter Eric Lam	The Plant Journal
The bench scientist's guide to statistical analysis of RNA-Seq data.	2012-09-14	Craig R Yendrek	Elizabeth A Ainsworth Jyothi Thimmapuram	BMC Research Notes
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.	2012-09-17	Georgi K Marinov Peter Dervan	Jevgenij A Raskatov Nicholas G Nickols Amanda E Hargrove Barbara Wold	Proceedings of the National Academy of Sciences of the United States of America
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells	2012-09-18	Harri Lähdesmäki Vivek Anantharaman Lakshminarayanan Aravind Tarmo Aijö John Gagnon Xing Chang	Micah J Benson Tarmo Aijö Utz J Pape Juha-Pekka Pursiheimo Shalini Oberdoerffer X Shirley Liu Riitta Lahesmaa Anjana Rao	Proceedings of the National Academy of Sciences of the United States of America
Functional transcriptomics of a migrating cell in Caenorhabditis elegans.	2012-09-18	Erich M Schwarz Paul W. Sternberg	Mihoko Kato	Proceedings of the National Academy of Sciences of the United States of America
Differential Expression Analysis for RNA-Seq Data.	2012-09-20	Alok Bhattacharya	Rashi Gupta Isha Dewan Richa Bharti	ISRN bioinformatics
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters	2012-09-20	Yi Zheng	Yun-Ru Chen Bao Liu Silin Zhong Jim Giovannoni Zhangjun Fei	Plant Methods
High-resolution transcriptome of human macrophages.	2012-09-21	Joachim Schultze Andrea Nino-Castro	Marc Beyer Michael R Mallmann Jia Xue Andrea Staratschek-Jox Daniela Vorholt Wolfgang Krebs Daniel Sommer Jil Sander Christina Mertens Susanne V Schmidt	PLOS ONE
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.	2012-09-22	Hao Wu Zhijin Wu	Chi Wang	Biostatistics
Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.	2012-09-24	Axel Künstner	Nagarjun Vijay Jelmer W Poelstra Jochen B W Wolf	Molecular Ecology
RNA-Seq Assembly - Are We There Yet?	2012-09-25	Andrea Bräutigam	Simon Schliesky Udo Gowik Andreas P M Weber	Frontiers in Plant Science
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.	2012-09-26	Peggy Farnham	Seth Frietze Rui Wang Lijing Yao Yu Gyoung Tak Zhenqing Ye Malaina Gaddis Heather Witt Victor X Jin	Genome Biology
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level.	2012-10-01	Israel Barrantes Jeremy Leipzig	Wolfgang Marwan	Gene Regulation and Systems Biology
The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation	2012-10-01	Sen-Lin Lai	Michael R Miller Kristin J Robinson Chris Q Doe	Developmental Cell
Dual lineage-specific expression of Sox17 during mouse embryogenesis.	2012-10-01	Momoko Yoshimoto Mark A. Magnuson Elisabetta Manduchi Anne Grapin-Botton	Eunyoung Choi Marine R C Kraus Laurence A Lemaire Sasidhar Vemula Leah A Potter Christian J Stoeckert	Stem Cells
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq.	2012-10-01	Jennifer Beane John Quackenbush Naftali Kaminski	Rebecca L Kusko John Brothers Gang Liu Lingqi Luo Brenda Juan Guardela John Tedrow Yuriy Aleksyev Ivana V Yang Mick Correll Mark Geraci Frank Sciurba Marc Lenburg David A Schwartz Avrum Spira	BMC Proceedings
SERE: single-parameter quality control and sample comparison for RNA-Seq.	2012-10-03	Rahul Kanwar	Stefan K Schulze Meike Gölzenleuchter Terry M Therneau Andreas S Beutler	BMC Genomics
Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.	2012-10-03	Anton Suvorov	Nicola Palmieri Viola Nolte Carolin Kosiol Christian Schlötterer	PLOS ONE
Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage.	2012-10-05	David Casero Eugen Urzica Crysten E Blaby-Haas Matteo Pellegrini Sabeeha Merchant	Hiroaki Yamasaki Scott I Hsieh Lital N Adler Steven J Karpowicz Steven G Clarke Joseph A Loo	The Plant Cell
Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle.	2012-10-10	Subhash J Jakhesara Chaitanya G. Joshi Ajai K. Tripathi	Amrutlal K Patel Vaibhav D Bhatt Manisha R Sajnani Prakash G Koringa	Genomics
New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain.	2012-10-11	Julien Rougeot Anne Coléno-Costes Jean-Michel Gibert Frédérique Peronnet Stéphane Le Crom	Suk Min Jang Augustin de Vanssay Tahar Bouceba Neel B Randsholt Emmanuèle Mouchel-Vielh Sébastien Bloyer	PLOS Genetics
Faster-X evolution of gene expression in Drosophila	2012-10-11	Richard P Meisel	John H Malone Andrew G Clark	PLOS Genetics
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.	2012-10-11	Wei Li	Tao Jiang	Bioinformatics
Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.	2012-10-12	Naoto Imamachi Hidenori Tani	Kazi Abdus Salam Rena Mizutani Kenichi Ijiri Takuma Irie Tetsushi Yada Yutaka Suzuki Nobuyoshi Akimitsu	RNA Biology
The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii.	2012-10-13	Eugen Urzica David Casero Matteo Pellegrini Sabeeha Merchant	Scott I Hsieh Madeli Castruita Davin Malasarn Jonathan Erde M Dudley Page Hiroaki Yamasaki Joseph A Loo	Molecular & Cellular Proteomics
High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.	2012-10-15	Hans Ellegren	Benoit Nabholz Jochen B W Wolf	Molecular Biology and Evolution
The biology of nematode- and IL4Rα-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics.	2012-10-16	Graham D Thomas Dominik Ruckerl Phillip D. Whitfield Mark Blaxter Judith Allen	Benjamin H Maskrey	Blood
A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites.	2012-10-17	David R. Colquhoun Jürgen Hartler Gerhard G Thallinger Jesus Martinez-Barnetche Antonis Rokas Rhoel Dinglasan	Ceereena Ubaida Mohien Derrick K Mathias John G Gibbons Jennifer S Armistead Maria C Rodriguez Mario Henry Rodriguez Nathan J Edwards David R Graham	Molecular & Cellular Proteomics
Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.	2012-10-23	Matteo Benelli Marco Severgnini Alberto Magi	Chiara Pescucci Giuseppina Marseglia Francesca Torricelli	Bioinformatics
Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period.	2012-10-23	Paul A McGettigan Jane A Irwin Alan Baird Brendan Loftus	Katarzyna Pluta Colm J Reid John A Browne Tharmala Tharmalingam Anthony Corfield Alexander C O Evans Stephen D Carrington	Physiological Genomics
Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus	2012-10-24	Daniel Gautheret Philippe Bouloc Annick Jacq	Claire Toffano-Nioche An N Nguyen Claire Kuchly Alban Ott	RNA
STAR: ultrafast universal RNA-seq aligner	2012-10-25	Philippe Batut Thomas R. Gingeras	Alexander Dobin Carrie A Davis Felix Schlesinger Jorg Drenkow Chris Zaleski Sonali Jha Mark Chaisson	Bioinformatics
Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola	2012-10-25	Igor V Grigoriev	Yangrae Cho Akhil Srivastava Robin A Ohm Christopher B Lawrence Koon-Hui Wang Sharadchandra P Marahatta	PLOS Pathogens
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.	2012-10-25	Matthew Berriman	Jonathan D Stoltzfus Samuel Minot Thomas J Nolan James B Lok	PLOS Neglected Tropical Diseases
The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq.	2012-10-25	Nolan Kane Brook T Moyers Sébastien Renaut Loren H. Rieseberg	Christopher J Grassa	Biology
Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq.	2012-10-27	Richard D Newcomb Thomas R. Buckley Duckchul Park Brent J Sinclair Alice B Dennis Luke T Dunning		Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Identification of PADI2 as a potential breast cancer biomarker and therapeutic target.	2012-10-30	Obi Griffith Venkataraman Subramanian John L. McElwee Brian D Cherrington Louise R Howe	Sunish Mohanan Heike C Breuer Lynne J Anguish Ashley M Palmer Corey P Causey Paul R Thompson Joe W Gray Scott A Coonrod	BMC Cancer
Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II	2012-11	Jerry F. Tien Malachi Griffith Gregg B Morin	S-W Grace Cheng Michael A Kuzyk Annie Moradian Taka-Aki Ichu Vicky C-D Chang Sarah E Vollett Marco A Marra	Molecular and Cellular Biology
Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas.	2012-11-01	Dean Palejev Flora M. Vaccarino	Oksana Yu Naumova Natalia V Vlasova Maria Lee Sergei Yu Rychkov Olga N Babich Elena L Grigorenko	Development and Psychopathology
Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses	2012-11-05	Andrew M Carroll Caroline Meharg David J Vandenbergh	Arimantas Lionikas Jonathan Mj Derry Aivaras Ratkevicius David A Blizard	BMC Genomics
Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote	2012-11-05	Shikai Liu Eric Peatman Geoff Waldbieser Huseyin Kucuktas	Yu Zhang Zunchun Zhou Geoff Waldbieser Fanyue Sun Jianguo Lu Jiaren Zhang Yanliang Jiang Hao Zhang Xiuli Wang K V Rajendran Lester Khoo Zhanjiang Liu	BMC Genomics
Novel BRD4-NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma.	2012-11-05	Adrian K. Charles Alex H. Beesley	K Thompson-Wicking R W Francis A Stirnweiss E Ferrari M D Welch E Baker A R Murch A M Gout K W Carter M B Phillips U R Kees	Oncogene
Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region	2012-11-06	Marie-Laure Endale Ahanda Dario Beraldi Jordi Estellé Claire Rogel-Gaillard James M Reecy	Eric R Fritz Zhi-Liang Hu Ole Madsen Martien A M Groenen Ronan Kapetanovic David A Hume Robert R R Rowland Joan K Lunney Elisabetta Giuffra	PLOS ONE
Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.	2012-11-06	Takeshi Itoh	Yoshihiro Kawahara Youko Oono Hiroyuki Kanamori Takashi Matsumoto Eiichi Minami	PLOS ONE
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.	2012-11-15	D. Neil Hayes	Yin Hu Yan Huang Ying Du Christian F Orellana Darshan Singh Amy R Johnson Anaïs Monroy Pei-Fen Kuan Scott M Hammond Liza Makowski Scott H Randell Derek Y Chiang Corbin Jones Yufeng Liu Jan F Prins Jinze Liu	Nucleic Acids Research
Methods, Challenges and Potentials of Single Cell RNA-seq.	2012-11-16	Daniel Hebenstreit		Biology
The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.	2012-11-20	Aurelien L Carlier Christian H Ahrens Ulrich Omasits Gabriella Pessi	Nadine Schmid Yinyue Deng Claudio Aguilar Alexander Grunau Lian-Hui Zhang Leo Eberl	PLOS ONE
Intron-centric estimation of alternative splicing from RNA-seq data.	2012-11-21	Roderic Guigó i Serra	Dmitri D Pervouchine David G Knowles	Bioinformatics
High-throughput sequencing of the melanoma genome.	2012-11-22	Janet Kelso	Manfred Kunz Michael Dannemann	Experimental Dermatology
A comprehensive analysis of the Manduca sexta immunotranscriptome.	2012-11-23	Haobo Jiang	Ramesh T Gunaratna	Developmental and Comparative Immunology
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.	2012-11-24	Charles Plessy Piero Carninci	Dave T P Tang Md Salimullah Ana Maria Suzuki Raffaella Calligaris Stefano Gustincich	Nucleic Acids Research
iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data	2012-11-29	Derek Y Chiang Michael Brudno	Aziz M Mezlini Eric J M Smith Marc Fiume Orion Buske Gleb L Savich Sohrab Shah Sam Aparicio Anna Goldenberg	Genome Research
Nuclear RNA sequencing of the mouse erythroid cell transcriptome	2012-11-29	Chih-Yu Chen Jennifer A. Mitchell Ieuan Clay Peter Fraser	David Umlauf Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano	PLOS ONE
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus.	2012-12-01	Xiaofan Zhou Antonis Rokas	John G Gibbons Anne Beauvais Jean-Paul Latgé	Annals of the New York Academy of Sciences
An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells.	2012-12-04	Songnian Hu	Lina Ma Linghu Nie Jing Liu Bing Zhang Shuhui Song Min Sun Jin Yang Yadong Yang Xiangdong Fang Yongliang Zhao Jun Yu	Genomics Proteomics and Bioinformatics
A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.	2012-12-06	Alexander Stark Denes Hnisz Karl Kuchler	Anaïs F Bardet Clarissa J Nobile Andriy Petryshyn Walter Glaser Ulrike Schöck	PLOS Genetics

Article

publication date

author

author name string

published in

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.

2023-05-18

Jürg Bähler
Ian Goodhead
Valerie Wood

Brian T Wilhelm
Samuel Marguerat
Stephen Watt
Falk Schubert
Christopher J Penkett
Jane Rogers
Jürg Bähler

Nature

The transcriptional landscape of the yeast genome defined by RNA sequencing

2023-06-06

Mark Bender Gerstein

Ugrappa Nagalakshmi
Zhong Wang
Karl Waern
Chong Shou
Debasish Raha
Michael Snyder

Science

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

2023-07-03

Stefan Haas

Marc Sultan
Marcel H Schulz
Hugues Richard
Alon Magen
Andreas Klingenhoff
Matthias Scherf
Martin Seifert
Tatjana Borodina
Aleksey Soldatov
Dmitri Parkhomchuk
Dominic Schmidt
Sean O'Keeffe
Martin Vingron
Hans Lehrach
Marie-Laure Yaspo

Science

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

2008-09

Yoav Gilad
John C Marioni

Christopher E Mason
Shrikant M Mane
Matthew Stephens

Genome Research

Transcript length bias in RNA-seq data confounds systems biology

2009

Alicia Oshlack
Matthew Wakefield

Biology Direct

RNA-Seq: a revolutionary tool for transcriptomics

2009-01

Mark Bender Gerstein

Zhong Wang
Michael Snyder

Nature Reviews Genetics

Estimating accuracy of RNA-Seq and microarrays with proteomics

2009-04-16

Wei Chen

Xing Fu
Ning Fu
Song Guo
Zheng Yan
Ying Xu
Hao Hu
Corinna Menzel
Yixue Li
Rong Zeng
Philipp Khaitovich

BMC Genomics

TopHat: discovering splice junctions with RNA-Seq

2009-05-01

Steven Salzberg
Lior Pachter

Cole Trapnell

Bioinformatics

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

2009-07-17

Julian Parkhill
Paul P. Gardner
Jyoti Choudhary
Nicholas Thomson

Timothy T Perkins
Robert A Kingsley
Maria C Fookes
Keith D James
Lu Yu
Samuel A Assefa
Miao He
Nicholas J Croucher
Derek J Pickard
Duncan J Maskell
Gordon Dougan

PLOS Genetics

A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.

2009-09-01

Simon J van Heeringen
Gert Jan C Veenstra

Robert C Akkers
Ulrike G Jacobi
Eva M Janssen-Megens
Kees-Jan Françoijs
Hendrik G Stunnenberg

Developmental Cell

Identifiability of isoform deconvolution from junction arrays and RNA-Seq.

2009-09-16

Hui Jiang

David Hiller
Weihong Xu
Wing Hung Wong

Bioinformatics

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

2009-10-16

Chad Nusbaum

Joshua Z Levin
Michael F Berger
Xian Adiconis
Peter Rogov
Alexandre Melnikov
Timothy Fennell
Levi A Garraway
Andreas Gnirke

Genome Biology

Transcript quantification with RNA-Seq data.

2009-10-19

Gunnar Rätsch

Regina Bohnert
Jonas Behr

BMC Bioinformatics

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

2009-10-24

Likun Wang
Xi Wang

Zhixing Feng
Xiaowo Wang
Xuegong Zhang

Bioinformatics

RNA-seq: from technology to biology.

2009-10-27
2010-02-01

Jürg Bähler

Samuel Marguerat
Jürg Bähler

Cellular and Molecular Life Sciences

GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.

2009-11-12

M Boutros

Moritz Gilsdorf
Thomas Horn
Zeynep Arziman
Oliver Pelz
Evgeny Kiner

Nucleic Acids Research

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.

2009-11-18

Cynthia Sharma
Jörg Vogel
Richard Reinhardt

Marco Albrecht
Thomas Rudel

Nucleic Acids Research

H-DBAS: human-transcriptome database for alternative splicing: update 2010

2009-12-07

Takashi Gojobori
Tadashi Imanishi

Jun-ichi Takeda
Yutaka Suzuki
Ryuichi Sakate
Yoshiharu Sato
Sumio Sugano

Nucleic Acids Research

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data

2009-12-11

Daniel Ramsköld
Rickard Sandberg

Eric T Wang
Christopher B Burge

PLOS Computational Biology

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.

2009-12-30

Kathryn J Boor
Martin Wiedmann
Uri Keich

Haley F Oliver
Renato H Orsi
Lalit Ponnala
Wei Wang
Qi Sun
Samuel W Cartinhour
Melanie J Filiatrault

BMC Genomics

Differential expression analysis for sequence count data

2010

Simon Anders
Wolfgang Huber

Genome Biology

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

2010

Sandro Banfi
Elia Stupka
Vincenzo Alessandro Gennarino
Remo Sanges

Danilo Licastro
Francesca Petrera

BMC Genomics

From RNA-seq reads to differential expression results

2010
2010-12-22

Alicia Oshlack
Mark D. Robinson

Matthew D Young

Genome Biology

A scaling normalization method for differential expression analysis of RNA-seq data

2010

Alicia Oshlack
Mark D. Robinson

Genome Biology

Global and unbiased detection of splice junctions from RNA-seq data

2010

Ulf Gyllensten
Adam Ameur

Anna Wetterbom
Lars Feuk

Genome Biology

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.

2010-01-01

Vincent Plagnol
Graham Heap
Charles Mein
David A van Heel
Richard Dobson
Lude Franke

Jennie H M Yang
Kate Downes
Barry C Healy
Karen A Hunt
Nicholas Bockett
Patrick C Dubois
Thomas J Albert
Matthew J Rodesch
David G Clayton
John A Todd

Human Molecular Genetics

Next-generation sequencing

2010-01-01

Jonathan Arnold

Momiao Xiong
Zhongming Zhao
Fuli Yu

Journal of Biomedicine and Biotechnology

Defining transcribed regions using RNA-seq.

2010-01-21

Jürg Bähler

Brian T Wilhelm
Samuel Marguerat
Ian Goodhead
Jürg Bähler

Nature Protocols

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

2010-01-26

Mark Johnston
Antonis Rokas

Chris Todd Hittinger
John T Tossberg

Proceedings of the National Academy of Sciences of the United States of America

Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq.

2010-01-29

Luciano Xumerle
Giovanni Malerba
Diana Bellin

Sara Zenoni
Alberto Ferrarini
Enrico Giacomelli
Marianna Fasoli
Mario Pezzotti
Massimo Delledonne

Plant Physiology

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

2010-02-04

Thomas D Otto
Arnab Pain
Chris Newbold
Matthew Berriman
Ulrike Böhme

Daniel Wilinski
Sammy Assefa
Thomas M Keane
Louis R Sarry
Jacob Lemieux
Bart Barrell
Manuel Llinás

Molecular Microbiology

Gene ontology analysis for RNA-seq: accounting for selection bias.

2010-02-04

Alicia Oshlack
Matthew Wakefield
Gordon K Smyth

Matthew D Young

Genome Biology

Close association of RNA polymerase II and many transcription factors with Pol III genes

2010-02-05

Mark Bender Gerstein

Debasish Raha
Zhong Wang
Zarmik Moqtaderi
Linfeng Wu
Guoneng Zhong
Kevin Struhl
Michael Snyder

Proceedings of the National Academy of Sciences of the United States of America

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

2010-02-11

Marie-Laure Yaspo
Stefan Haas
Hans Lehrach
Martin Vingron

Hugues Richard
Marcel H Schulz
Marc Sultan
Asja Nürnberger
Sabine Schrinner
Daniela Balzereit
Emilie Dagand
Axel Rasche
Marie-Laure Yaspo

Nucleic Acids Research

RNA-Seq analysis to capture the transcriptome landscape of a single cell.

2010-02-25

Azim Surani

Fuchou Tang
Catalin Barbacioru
Ellen Nordman
Bin Li
Nanlan Xu
Vladimir I Bashkirov
Kaiqin Lao

Nature Protocols

The primary transcriptome of the major human pathogen Helicobacter pylori

2010-03-11

Peter F. Stadler
Jörg Vogel
Kristin Reiche
Fabien Darfeuille
Cynthia Sharma
Jörg Hackermüller
Richard Reinhardt

Steve Hoffmann
Jérémy Reignier
Sven Findeiss
Alexandra Sittka
Sandrine Chabas

Nature

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.

2010-03-19

Qiye Li
Guojie Zhang
Jun Wang
Karsten Kristiansen
Huanming Yang
Jian Wang
Xiuqing Zhang

Guangwu Guo
Xueda Hu
Yong Zhang
Ruiqiang Li
Ruhong Zhuang
Zhike Lu
Zengquan He
Xiaodong Fang
Li Chen
Wei Tian
Yong Tao
Songgang Li

Genome Research

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines

2010-03-25

Daniel Klevebring

Magnus Bjursell
Olof Emanuelsson
Joakim Lundeberg

PLOS ONE

Integrative analysis of the melanoma transcriptome

2010-04

Eric Lander
Chad Nusbaum
Carrie Sougnez
Andreas Gnirke
Gad Getz
Kristian Cibulskis
Wendy Winckler
Reinhard Dummer
Liuda Ziaugra
Jordi Barretina
Matthew Meyerson
Stacey Gabriel

Michael F Berger
Joshua Z Levin
Krishna Vijayendran
Andrey Sivachenko
Xian Adiconis
Jared Maguire
Laura A Johnson
James Robinson
Roel G Verhaak
Robert C Onofrio
Elisabeth Laine
David E Fisher
David B Jaffe
Levi A Garraway

Genome Research

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus

2010-04-01

Stéphane Audic
Chantal Abergel
Jean-Michel Claverie
Julie Poulain
Pascal Hingamp

Matthieu Legendre
Olivier Poirot
Virginie Seltzer
Deborah Byrne
Audrey Lartigue
Magali Lescot
Alain Bernadac

Genome Research

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

2010-04-05

Hui Jiang

Kin Fai Au
Lan Lin
Yi Xing
Wing Hung Wong

Nucleic Acids Research

Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites

2010-04-12

Tim Nicolai Siegel

Doeke R Hekstra
Xuning Wang
Scott Dewell
George A M Cross

Nucleic Acids Research

Supersplat--spliced RNA-seq alignment.

2010-04-21

Weng-Keen Wong

Douglas W Bryant
Rongkun Shen
Henry D Priest
Todd C Mockler

Bioinformatics

Bacillus anthracis genome organization in light of whole transcriptome sequencing

2010-04-29

Karla D Passalacqua

Jeffrey Martin
Wenhan Zhu
Nicholas Bergman
Mark Borodovsky

BMC Bioinformatics

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

2010-05

Steven Salzberg
Lior Pachter

Cole Trapnell
Brian A Williams
Geo Pertea
Ali Mortazavi
Gordon Kwan
Marijke J van Baren
Barbara J Wold

Nature Biotechnology

Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.

2010-05-01

Azim Surani

Fuchou Tang
Catalin Barbacioru
Siqin Bao
Caroline Lee
Ellen Nordman
Xiaohui Wang
Kaiqin Lao

Cell Stem Cell

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

2010-05-02

J Z Levin
Magdalena J Koziol
John L. Rinn

Mitchell Guttman
Manuel Garber
Julie Donaghey
James Robinson
Xian Adiconis
Lin Fan
Andreas Gnirke
Chad Nusbaum
Eric S Lander
Aviv Regev

Nature Biotechnology

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

2010-05-05

James R. Bradford
Crispin J. Miller

Yvonne Hey
Tim Yates
Yaoyong Li
Stuart D Pepper

BMC Genomics

Modeling non-uniformity in short-read rates in RNA-Seq data

2010-05-11

Jun Li

Hui Jiang
Wing Hung Wong

Genome Biology

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.

2010-05-28

Elizabeth T Cirulli

Abanish Singh
Kevin V Shianna
Dongliang Ge
Jason P Smith
Jessica M Maia
Erin L Heinzen
James J Goedert
David B Goldstein
Center for HIV/AIDS Vaccine Immunology (CHAVI)

Genome Biology

rQuant.web: a tool for RNA-Seq-based transcript quantitation

2010-06-15

Gunnar Rätsch

Regina Bohnert

Nucleic Acids Research

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.

2010-06-17

Andrea Sboner
Joel Rozowsky
Mark Bender Gerstein
Valerie Reinke

Ashish Agarwal
David Koppstein
Lukas Habegger
Ladeana W Hillier
Rajkumar Sasidharan
Robert H Waterston

BMC Genomics

A probabilistic framework for aligning paired-end RNA-seq data

2010-06-23

Derek Y Chiang

Yin Hu
Kai Wang
Xiaping He
Jan F Prins
Jinze Liu

Bioinformatics

Uncovering the complexity of transcriptomes with RNA-Seq.

2010-06-27

Valerio Costa
Claudia Angelini
Italia DeFeis

Alfredo Ciccodicola

Journal of Biomedicine and Biotechnology

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

2010-06-28

Dale Hedges
Erik K Flemington

Guorong Xu
Claire Fewell
Christopher Taylor
Nan Deng
Dale Hedges
Xia Wang
Kun Zhang
Michelle Lacey
Haitao Zhang
Qinyan Yin
Jennifer Cameron
Zhen Lin
Dongxiao Zhu

RNA

RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.

2010-06-29

David Casero
Sabeeha Merchant
Matteo Pellegrini

David González-Ballester
Shawn Cokus
Arthur R Grossman

The Plant Cell

Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

2010-07-01

Mehmet Somel
Wei Chen
Augix Guohua Xu
Svante Pääbo

Liu He
Zhongshan Li
Ying Xu
Mingfeng Li
Xing Fu
Zheng Yan
Yuan Yuan
Corinna Menzel
Na Li
Hao Hu
Philipp Khaitovich

PLOS Computational Biology

Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice.

2010-07-01

Timofey Skvortsov

D V Ignatov
K B Majorov
A S Apt
T L Azhikina

Acta naturae

Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.

2010-07-02

Minou Nowrousian

Eukaryotic Cell

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.

2010-07-13

Guojun Lu
Bin Han

Tingting Lu
Danlin Fan
Chuanrang Zhu
Wei Li
Qiang Zhao
Qi Feng
Yan Zhao
Yunli Guo
Wenjun Li
Xuehui Huang

Genome Research

An integrative approach to genomic introgression mapping.

2010-07-23

David L. Hyten

Andrew J Severin
Gregory A Peiffer
Wayne W Xu
Bruna Bucciarelli
Jamie A O'Rourke
Yung-Tsi Bolon
David Grant
Andrew D Farmer
Gregory D May
Carroll P Vance
Randy C Shoemaker
Robert M Stupar

Plant Physiology

Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro.

2010-08-01

Paul Klenerman

Stephen D Woodhouse
Ramamurthy Narayan
Sally Latham
Sheena Lee
Robin Antrobus
Bevin Gangadharan
Shujun Luo
Gary P Schroth
Nicole Zitzmann

Hepatology

RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome

2010-08-05

Michelle Graham
Gary J Muehlbauer

Andrew J Severin
Jenna L Woody
Yung-Tsi Bolon
Bindu Joseph
Brian W Diers
Andrew D Farmer
Rex T Nelson
David Grant
James E Specht
Steven B Cannon
Gregory D May
Carroll P Vance
Randy C Shoemaker

BMC Plant Biology

Recent advances in RNA sequence analysis

2010-08-19

Steven Salzberg

F1000 biology reports

Transcribed dark matter: meaning or myth?

2010-08-25

Chris Ponting

T Grant Belgard

Human Molecular Genetics

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

2010-08-27

Charles M. Perou
Piotr A Mieczkowski
Derek Y Chiang

Kai Wang
Darshan Singh
Zheng Zeng
Stephen J Coleman
Yan Huang
Gleb L Savich
Xiaping He
Sara A Grimm
James N MacLeod
Jan F Prins
Jinze Liu

Nucleic Acids Research

Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.

2010-09-01

Lauren McIntyre

Alison M Morse
Valentina Carballo
Donald A Baldwin
Christopher G Taylor

Journal of Biomolecular Techniques

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.

2010-09-01

Gavin Sherlock
Sadie L Marjani

Vincent M Bruno
Zhong Wang
Ghia M Euskirchen
Jeffrey Martin
Michael Snyder

Genome Research

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.

2010-09-16

Nicholas J Loman
Mark Pallen

Charles W Penn

Current Opinion in Microbiology

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

2010-09-19

Christoph Bock
Peggy Farnham
David Haussler
Junchen Gu
Mattia Pelizzola
Ryan Lister
Alexander Meissner

R Alan Harris
Ting Wang
Cristian Coarfa
Raman P Nagarajan
Chibo Hong
Sara L Downey
Brett E Johnson
Shaun D Fouse
Allen Delaney
Yongjun Zhao
Adam Olshen
Tracy Ballinger
Xin Zhou
Kevin J Forsberg
Lorigail Echipare
Henriette O'Geen
Yuanxin Xi
Charles B Epstein
Bradley E Bernstein
R David Hawkins
Bing Ren
Wen-Yu Chung
Hongcang Gu
Andreas Gnirke
Michael Q Zhang
Joseph R Ecker
Wei Li
Robert A Waterland
Marco A Marra
Martin Hirst
Aleksandar Milosavljevic
Joseph F Costello

Nature Biotechnology

Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data.

2010-09-27

Zhaohui Steve Qin

Debashis Ghosh

Genes

Studying bacterial transcriptomes using RNA-seq.

2010-09-29
2010-10-01

Nicholas Thomson

Nicholas J Croucher

Current Opinion in Microbiology

Single molecule sequencing with a HeliScope genetic analysis system

2010-10-01

John F Thompson

Kathleen E Steinmann

Current protocols in molecular biology

De novo assembly and analysis of RNA-seq data.

2010-10-10

Shaun Jackman
Malachi Griffith
Timothee Cezard
Steven Jones
Pamela A. Hoodless
Inanc Birol

Gordon Robertson
Jacqueline Schein
Readman Chiu
Richard Corbett
Matthew Field
Karen Mungall
Sam Lee
Hisanaga Mark Okada
Jenny Q Qian
Anthony Raymond
Nina Thiessen
Yaron S Butterfield
Richard Newsome
Simon K Chan
Rong She
Richard Varhol
Baljit Kamoh
Anna-Liisa Prabhu
Angela Tam
YongJun Zhao
Richard A Moore
Martin Hirst
Marco A Marra

Nature Methods

Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells.

2010-10-13

Erik K Flemington

Zhen Lin
Guorong Xu
Nan Deng
Christopher Taylor
Dongxiao Zhu

Journal of Virology

Analysis of next-generation genomic data in cancer: accomplishments and challenges

2010-10-15

Elaine Mardis

Li Ding
Michael C Wendl
Daniel C Koboldt

Human Molecular Genetics

The RNA-Seq approach to studying the expression of mosquito mitochondrial genes.

2010-10-19

Gareth J Lycett

M Neira-Oviedo
A Tsyganov-Bodounov
V Kokoza
A S Raikhel
J Krzywinski

Insect Molecular Biology

RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity.

2010-10-27

Geneviève Boucher

Brian T Wilhelm
Mathieu Briau
Pamela Austin
Amélie Faubert
Pierre Chagnon
Kristin Hope
Simon Girard
Nadine Mayotte
Josette-Renee Landry
Josée Hébert
Guy Sauvageau

Blood

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.

2010-10-29

Andrea Sboner
Stéphane Terry
Francesca Demichelis
Mark Rubin
Mark Bender Gerstein

Dorothee Pflueger
Lukas Habegger
Raquel Esgueva
Pei-Chun Lin
Maria A Svensson
Naoki Kitabayashi
Benjamin J Moss
Theresa Y MacDonald
Xuhong Cao
Terrence Barrette
Ashutosh K Tewari
Mark S Chee
Arul M Chinnaiyan
David S Rickman

Genome Research

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

2010-11-06

Alma Islas-Trejo

Angela Cánovas
Gonzalo Rincon
Saumya Wickramasinghe
Juan F Medrano

Mammalian Genome

Analysis and design of RNA sequencing experiments for identifying isoform regulation

2010-11-07

Edoardo M Airoldi

Yarden Katz
Eric T Wang
Christopher B Burge

Nature Methods

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

2010-11-24

Gavin Sherlock
Matthew Blow

Jeffrey Martin
Vincent M Bruno
Zhide Fang
Xiandong Meng
Tao Zhang
Michael Snyder
Zhong Wang

BMC Genomics

Scaffolding a Caenorhabditis nematode genome with RNA-seq

2010-12

Erich M Schwarz
Paul W. Sternberg

Ali Mortazavi
Brian Williams
Lorian Schaeffer
Igor Antoshechkin
Barbara J Wold

Genome Research

RNA-Seq Read Alignments with PALMapper

2010-12

Gunnar Rätsch

Géraldine Jean
André Kahles
Vipin T. Sreedharan
Fabio De Bona

Defining the transcriptome and proteome in three functionally different human cell lines.

2010-12-01

Cajsa Algenäs
Daniel Klevebring
Linn Fagerberg
Ivan Matic
Mathias Uhlén

Emma Lundberg
Tamar Geiger
Juergen Cox
Cajsa Algenäs
Joakim Lundeberg
Matthias Mann

Molecular Systems Biology

A high-resolution comparative map of porcine chromosome 4 (SSC4).

2010-12-01

Lawrence B. Schook
Craig W. Beattie

J-G Ma
T-C Chang
H Yasue
A D Farmer
J A Crow
K Eyer
H Hiraiwa
T Shimogiri
S N Meyers
J E Beever
E F Retzel
W-S Liu

Animal Genetics

Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.

2010-12-01

Xi Wang

Zhengpeng Wu
Xuegong Zhang

Journal of Bioinformatics and Computational Biology

De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology

2010-12-02

Jacob E. Crawford

Wamdaogo M Guelbeogo
Antoine Sanou
Alphonse Traoré
Kenneth D Vernick
N'Fale Sagnon
Brian P Lazzaro

PLOS ONE

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

2010-12-02

Mathias Uhlén
Daniel Klevebring
Linn Fagerberg

Emma Lundberg
Olof Emanuelsson
Joakim Lundeberg

BMC Genomics

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

2010-12-05

Andrea Sboner
Joel Rozowsky
Mark Bender Gerstein

Lukas Habegger
Tara A Gianoulis
Ashish Agarwal
Michael Snyder

Bioinformatics

The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment.

2010-12-14

Alexey I Nesvizhskii

Kang Ning

BMC Bioinformatics

A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology

2010-12-14

Aziz A. Aboobaker

Martin J Blythe
Damian Kao
Sunir Malla
Joanna Rowsell
Ray Wilson
Deborah Evans
Jamie Jowett
Amy Hall
Virginie Lemay
Sabrina Lam

PLOS ONE

H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3

2010-12-16

Richard Bartfai
Arne H Smits
Moritz Treeck

Wieteke A M Hoeijmakers
Adriana M Salcedo-Amaya
Eva Janssen-Megens
Anita Kaan
Tim-Wolf Gilberger
Kees-Jan Françoijs
Hendrik G Stunnenberg

PLOS Pathogens

Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq

2010-12-17

Wen Huang

Hasan Khatib

BMC Genomics

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.

2010-12-17

Xi Wang

Zhengpeng Wu
Xuegong Zhang

Bioinformatics

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

2010-12-22

Ayelet T. Lamm

Michael R Stadler
Huibin Zhang
Jonathan I Gent
Andrew Z Fire

Genome Research

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

2010-12-22

Moritz Gerstung

Daniel Enderle
Christian Beisel
Michael B Stadler
Prashanth Athri
Renato Paro

Genome Research

miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1.

2010-12-31

Johan Flygare
Harvey Lodish

Lingbo Zhang
Piu Wong
Bing Lim

Genes & Development

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

2011

Celina Sanchez Rivers
Zora Modrusan
Brock A Peters

Serban Nacu
Wenlin Yuan
Zhengyan Kan
Deepali Bhatt
Jeremy Stinson
Kenneth Jung
Somasekar Seshagiri
Thomas D Wu

BMC Medical Genomics

Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing

2011

Songnian Hu

Wanfei Liu
Yuhui Zhao
Peng Cui
Qiang Lin
Feng Ding
Chengqi Xin
Xinyu Tan
Shuhui Song
Jun Yu

Frontiers in Genetics

RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti

2011

Mariangela Bonnizoni
Osvaldo Marinotti

W Augustine Dunn
Corey L Campbell
Ken E Olson
Michelle T Dimon
Anthony A James

BMC Genomics

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

2011

Matthew Berriman
Karen Mungall
Gary Saunders
Anna V Protasio
Martin Hunt
Roz Laing
Michael Andrew Quail

Steven Laing
Frank Jackson
Robin Beech
John S Gilleard

PLOS ONE

The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair

2011

Benjamin Yu

Gloria K Lefkowitz
Anandaroop Mukhopadhyay
Christopher Cowing-Zitron

PLOS ONE

A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq

2011

Thomas Brutnell

Lin Wang
Yaqing Si
Lauren K Dedow
Ying Shao
Peng Liu

PLOS ONE

ENCODE whole-genome data in the UCSC genome browser (2011 update)

2011-01

David Haussler
Venkat S Malladi
Angie S. Hinrichs
Donna Karolchik
Hiram Clawson
Ann S Zweig

Brian J Raney
Melissa S Cline
Kate R Rosenbloom
Timothy R Dreszer
Katrina Learned
Galt P Barber
Laurence R Meyer
Cricket A Sloan
Krishna M Roskin
Bernard B Suh
Vanessa Kirkup
Pauline A Fujita
Brooke Rhead
Kayla E Smith
Andy Pohl
Robert M Kuhn
W James Kent

Nucleic Acids Research

Insights into global mechanisms and disease by gene expression profiling.

2011-01-01

Hubert Hackl
Johannes Rainer
Ana Dopazo

Fátima Sánchez-Cabo
Zlatko Trajanoski

Methods in Molecular Biology

Identifying mRNA editing deaminase targets by RNA-Seq.

2011-01-01

Nina Papavasiliou

Brad R Rosenberg
Scott Dewell
F Nina Papavasiliou

Methods in Molecular Biology

The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq

2011-01-12

Jeff H. Chang

Yanming Di
Daniel W Schafer
Jason S Cumbie

Statistical Applications in Genetics and Molecular Biology

A pipeline for RNA-seq data processing and quality assessment

2011-01-13

Alvis Brazma
Angela Goncalves

Andrew Tikhonov
Misha Kapushesky

Bioinformatics

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

2011-01-17

Katherine Lontok

Michelle T Dimon
Joseph L DeRisi

Nucleic Acids Research

Length bias correction for RNA-seq data in gene set analyses

2011-01-19

Xiangqin Cui

Liyan Gao
Zhide Fang
Kui Zhang
Degui Zhi

Bioinformatics

Identification of fusion genes in breast cancer by paired-end RNA-sequencing.

2011-01-19

Olli-Pekka Kallioniemi
Anne-Lise Børresen-Dale
Sara Kangaspeska
Vesa Hongisto
Kristine Kleivi

Henrik Edgren
Astrid Murumagi
Sara Kangaspeska
Daniel Nicorici
Vesa Hongisto
Inga H Rye
Sandra Nyberg
Maija Wolf

Genome Biology

Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics?

2011-01-19

Greg T. Sutherland
Jillian J. Kril

Michal Janitz

Journal of Neurochemistry

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

2011-01-21

Shikai Liu
Eric Peatman
Huseyin Kucuktas
Ludmilla Kaltenboeck
Shaolin Wang
Zhanjiang Liu

Zunchun Zhou
Jianguo Lu
Fanyue Sun
Hong Liu
Yanliang Jiang

BMC Genomics

Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.

2011-01-26

Agnes Grallert
Valerie Wood
Iain M. Hagan
Crispin J. Miller

Danny A Bitton
Paul J Scutt
Tim Yates
Duncan L Smith

Genetics

In vitro culture and characterization of putative porcine embryonic germ cells derived from domestic breeds and Yucatan mini pig embryos at Days 20-24 of gestation.

2011-01-31

Hendrik Marks
Yu Gao
Poul Hyttel

Stoyan G Petkov
Tino Klein
Rodrigo S Garcia
Henk Stunnenberg

Stem Cell Research

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs

2011-02

Nina Papavasiliou

Brad R Rosenberg
Claire E Hamilton
Michael M Mwangi
Scott Dewell
F Nina Papavasiliou

Nature Structural & Molecular Biology

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

2011-02-01

Jochen Wolf
Jarosław Bryk

Jochen Bw Wolf

BMC Genomics

The next generation: using new sequencing technologies to analyse gene regulation.

2011-02-01

Olivia Alder
Pamela A. Hoodless

Rebecca Cullum

Respirology

Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.

2011-02-08

Michael Eisen
S E Lott

Jacqueline E Villalta
Gary P Schroth
Shujun Luo
Leath A Tonkin

PLOS Biology

Identification and optimization of small molecules that restore E-cadherin expression and reduce invasion in colorectal carcinoma cells.

2011-02-09

Robert Daniel Beauchamp
Craig W Lindsley

Sydney L Stoops
A Scott Pearson
Connie Weaver
Alex G Waterson
Emily Days
Chris Farmer
Suzanne Brady
C David Weaver

ACS Chemical Biology

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

2011-02-10

Ernest Turro
Angela Goncalves
Lachlan Coin
Sylvia Richardson
Alexandra M. Lewin

Shu-Yi Su

Genome Biology

Isoform-level microRNA-155 target prediction using RNA-seq

2011-02-11

Erik K Flemington

Nan Deng
Adriane Puetter
Kun Zhang
Kristen Johnson
Zhiyu Zhao
Christopher Taylor
Dongxiao Zhu

Nucleic Acids Research

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.

2011-02-15

Peggy Farnham

Kimberly R Blahnik
Lei Dou
Lorigail Echipare
Sushma Iyengar
Henriette O'Geen
Erica Sanchez
Yongjun Zhao
Marco A Marra
Martin Hirst
Joseph F Costello
Ian Korf

PLOS ONE

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

2011-02-16

Vineet Bafna
Olivier Harismendy

Marcus Kinsella
Masakazu Nakano
Kelly A Frazer

Bioinformatics

Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.

2011-02-17

Thomas D Otto
Arnab Pain
Anthony A Holder
Rita Tewari

Solabomi A Ogun
Steven A Howell
Ellen Knuepfer
Deirdre A Cunningham
Zhengyao Xu

PLOS Pathogens

RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture

2011-02-17

Avigdor Eldar

Adam Z Rosenthal
Eric G Matson
Jared R Leadbetter

The ISME Journal

ACT: aggregation and correlation toolbox for analyses of genome tracks.

2011-02-23

Joel Rozowsky
Kevin Y Yip
Lucas Lochovsky

Justin Jee
Robert Bjornson
Guoneng Zhong
Zhengdong Zhang
Yutao Fu
Jie Wang
Zhiping Weng
Mark Gerstein

Bioinformatics

Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.

2011-03-01

Traver Hart

Steven R Head
H Kiyomi Komori
John Shimashita
Lana Schaffer
Daniel R Salomon
Phillip T Ordoukhanian

BioTechniques

Accurate estimation of expression levels of homologous genes in RNA-seq experiments.

2011-03-01

Bogdan Pasaniuc
Noah Zaitlen

Eran Halperin

Journal of Computational Biology

The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles.

2011-03-02

Bratati Mukherjee

James V Moroney
Yunbing Ma
Wesley D Frey
Katelyn A Fusilier
Trang T Pham
Tiffany A Simms
Robert J DiMario
Jing Yang

Photosynthesis Research

Improving RNA-Seq expression estimates by correcting for fragment bias.

2011-03-16

Lior Pachter
John L. Rinn

Adam Roberts
Cole Trapnell
Julie Donaghey

Genome Biology

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers

2011-03-17

Louis M Staudt
Ujunwa C Okoye
Pedro Farinha
Anke van den Berg
Steven Jones

Christian Steidl
Sohrab P Shah
Bruce W Woolcock
Lixin Rui
Masahiro Kawahara
Nathalie A Johnson
Yongjun Zhao
Adele Telenius
Susana Ben Neriah
Andrew McPherson
Barbara Meissner
Arjan Diepstra
Mark Sun
Gillian Leung
Joseph M Connors
David G Huntsman
Kerry J Savage
Lisa M Rimsza
Douglas E Horsman
Ulrich Steidl
Marco A Marra
Randy D Gascoyne

Nature

A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii.

2011-03-21

Sabeeha Merchant
Matteo Pellegrini
David Casero

Janette Kropat
Anne Hong-Hermesdorf
Petr Ent
Madeli Castruita
Davin Malasarn

The Plant Journal

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.

2011-03-22

Graziano Pesole
Ernesto Picardi

Mattia D'Antonio
Danilo Carrabino
Tiziana Castrignanò

Bioinformatics

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

2011-03-24

Peter Robinson
Stefan Mundlos

Marten Jäger
Claus-Eric Ott
Johannes Grünhagen
Jochen Hecht
Hanna Schell
Stefan Mundlos
Georg N Duda
Jasmin Lienau

BMC Genomics

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

2011-03-24

Nicole A Walter
Jessica Ezzell Hunter
Michael A Mooney
Shannon K McWeeney

Daniel Bottomly
Priscila Darakjian
Sunita Kawane
Kari J Buck
Robert P Searles
Robert Hitzemann

PLOS ONE

Effects of nickel treatment on H3K4 trimethylation and gene expression.

2011-03-24

Stuart M. Brown
Phillip R Smith

Kam-Meng Tchou-Wong
Kathrin Kiok
Zuojian Tang
Thomas Kluz
Adriana Arita
Max Costa

PLOS ONE

Developmental changes in transcriptional profiles.

2011-03-30

Gad Shaulsky

William F Loomis

Development, Growth and Differentiation

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation.

2011-04-05

Vladimir Benes
Gunnar Rätsch

Tanja Dorothe Rösel
Lee-Hsueh Hung
Jan Medenbach
Katrin Donde
Stefan Starke
Albrecht Bindereif

The EMBO Journal

Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.

2011-04-08

Stylianos Antonarakis
Christian Iseli
Carlo Rivolta
Ioannis Xenarios
Jacques S. Beckmann
Armand Valsesia

Donata Rimoldi
Danielle Martinet
Mark Ibberson
Paola Benaglio
Manfredo Quadroni
Patrice Waridel
Muriel Gaillard
Mireille Pidoux
Blandine Rapin
Andrew J G Simpson
C Victor Jongeneel
Brian J Stevenson

PLOS ONE

Genome-wide analysis of the 5' and 3' ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts.

2011-04-13

Bernard Moss

Zhilong Yang
Daniel P Bruno
Craig A Martens
Stephen F Porcella

Journal of Virology

A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.

2011-04-15

Jeremy Davis-Turak
Yu Zhou

Kristi Fox-Walsh
Hairi Li
Xiang-Dong Fu

Genomics

Design and validation issues in RNA-seq experiments.

2011-04-15

Xiangqin Cui

Zhide Fang

Briefings in Bioinformatics

Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.

2011-04-15

David Casero
Sabeeha Merchant
Matteo Pellegrini
Astrid Vieler
Christoph Benning

Madeli Castruita
Steven J Karpowicz
Janette Kropat
Scott I Hsieh
Weihong Yan
Shawn Cokus
Joseph A Loo

The Plant Cell

Estimation of alternative splicing isoform frequencies from RNA-Seq data

2011-04-19

Ion I. Mandoiu
Alexander Zelikovsky

Marius Nicolae
Serghei Mangul

Algorithms for Molecular Biology

Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.

2011-04-20

Luciana D'Apice
Aldo Donizetti
Monica Rienzo
Paola Salvatore
Stefania Crispi
Valerio Costa
Piergiuseppe De Berardinis
Teresa Infante
Claudia Angelini
Marco Picardi
Berardo Sarubbi
Raffaele Calabrò
Claudio Napoli
Amelia Casamassimi

Margherita Mutarelli
Linda Sommese
Maria Assunta Gallo
Marianna Aprile
Roberta Esposito
Luigi Leone
Alfredo Ciccodicola

PLOS ONE

BM-map: Bayesian mapping of multireads for next-generation sequencing data.

2011-04-22

Yuan Yuan
Han Liang

Yuan Ji
Yanxun Xu
Qiong Zhang
Kam-Wah Tsui
Clift Norris
Shoudan Liang

Biometrics

Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.

2011-04-27

Cynthia Sharma
Jörg Vogel
Gabriele Klug

Bork A Berghoff
Jens Glaeser
Monica Zobawa
Friedrich Lottspeich

Molecular Microbiology

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.

2011-05-05

Jeremy Chien
Jian Ma

Yang Li
David I Smith

Bioinformatics

Protocol dependence of sequencing-based gene expression measurements

2011-05-06

John F Thompson

Tal Raz
Philipp Kapranov
Doron Lipson
Stan Letovsky
Patrice M Milos

PLOS ONE

Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.

2011-05-11

Antonella Bacchiocchi

Fabio Parisi
Stephan Ariyan
Deepak Narayan
Kathleen Hoyt
Elaine Cheng
Fang Xu
Peining Li
Ruth Halaban
Yuval Kluger

BMC Genomics

The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue

2011-05-13

Curtis A. Suttle
Julia A Gustavsen
Jan M Friedman
Robert A Holt

Richard A Moore
René L Warren
J Douglas Freeman
Caroline Chénard
Yongjun Zhao

PLOS ONE

NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.

2011-05-16

Zheng Xia

Jianguo Wen
Chung-Che Chang
Xiaobo Zhou

BMC Bioinformatics

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

2011-05-18

Wolfgang Hoeck

Huanying Ge
Kejun Liu
Todd Juan
Fang Fang
Matthew Newman

Bioinformatics

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

2011-05-19

Malachi Griffith
Gavin Ha

Andrew McPherson
Fereydoun Hormozdiari
Abdalnasser Zayed
Ryan Giuliany
Mark G F Sun
Alireza Heravi Moussavi
Janine Senz
Nataliya Melnyk
Marina Pacheco
Marco A Marra
Martin Hirst
Torsten O Nielsen
S Cenk Sahinalp
David Huntsman
Sohrab P Shah

PLOS Computational Biology

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.

2011-05-19

A S Weyrich

Jesse W Rowley
Andrew J Oler
Neal D Tolley
Benjamin N Hunter
Elizabeth N Low
David A Nix
Christian C Yost
Guy A Zimmerman

Blood

The zebrafish transcriptome during early development.

2011-05-24

Juha Kere
Outi Hovatta
Liselotte Vesterlund

Hong Jiao
Per Unneberg
Outi Hovatta

BMC Developmental Biology

Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding

2011-05-27

Antonis Rokas
Laurence J. Zwiebel

R Jason Pitts
David C Rinker
Patrick L Jones

BMC Genomics

Pyrosequencing-based expression profiling and identification of differentially regulated genes from Manduca sexta, a lepidopteran model insect.

2011-05-27

Haobo Jiang

Shuguang Zhang
Ramesh T Gunaratna
Xiufeng Zhang
Fares Najar
Yang Wang
Bruce Roe

Insect Biochemistry and Molecular Biology

Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events.

2011-05-31

Loredana Bury
A S Weyrich
Paolo Gresele

Luca Cecchetti
Neal D Tolley
Noemi Michetti

Blood

Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq

2011-06

Frank Schembri
Jennifer Beane
Yuriy O Alekseyev
Avrum Spira
Marc E Lenburg
Shawn Levy

Jessica Vick
Christina Anderlind
Adam Gower
Joshua Campbell
Lingqi Luo
Xiao Hui Zhang
Ji Xiao
Shenglong Wang
Pierre P Massion

Cancer Prevention Research

RNA-seq: technical variability and sampling.

2011-06-06

Lauren McIntyre

Kenneth K Lopiano
Alison M Morse
Victor Amin
Ann L Oberg
Linda J Young
Sergey V Nuzhdin

BMC Genomics

Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics.

2011-06-07

Tracy L Bergemann

Jason Wilson

BMC Bioinformatics

RNA sequencing reveals two major classes of gene expression levels in metazoan cells.

2011-06-07

Sarah Teichmann
Alexander van Oudenaarden
Muxin Gu
Varodom Charoensawan
Daniel Hebenstreit

Miaoqing Fang

Molecular Systems Biology

PR-domain-containing Mds1-Evi1 is critical for long-term hematopoietic stem cell function.

2011-06-10

Subhash Juneja

Yi Zhang
Sandra Stehling-Sun
Kimberly Lezon-Geyda
Lucie Coillard
Gouri Chatterjee
Charles A Wuertzer
Fernando Camargo
Archibald S Perkins

Blood

Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.

2011-06-22

Dirce Carraro
Emmanuel Dias-Neto
Helena Brentani
Renata Pasqualini

Elisa Napolitano Ferreira
Gustavo de Campos Molina
Renato David Puga
Eduardo Fernandes Abrantes
Adriana Priscila Trapé
Bedrich L Eckhardt
Diana Noronha Nunes
Maria Mitzi Brentani
Wadih Arap
Ricardo Renzo Brentani

PLOS ONE

Deterministic and stochastic allele specific gene expression in single mouse blastomeres

2011-06-23

Azim Surani

Fuchou Tang
Catalin Barbacioru
Ellen Nordman
Siqin Bao
Caroline Lee
Xiaohui Wang
Brian B Tuch
Edith Heard
Kaiqin Lao

PLOS ONE

Transcription factor TEAD4 regulates expression of myogenin and the unfolded protein response genes during C2C12 cell differentiation

2011-06-24

Gabrielle Mengus
Irwin Davidson

A Benhaddou
C Keime
T Ye
A Morlon
I Michel
B Jost

Cell Death & Differentiation

Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation.

2011-06-28

Filip Van Nieuwerburgh
James W Golden

Britt L Flaherty
Steven R Head

BMC Genomics

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

2011-07

Sten Linnarsson
Peter Lönnerberg

Saiful Islam
Una Kjällquist
Annalena Moliner
Pawel Zajac
Jian-Bing Fan

Genome Research

Full-length transcriptome assembly from RNA-Seq data without a reference genome

2011-07

Kerstin Lindblad-Toh
Aviv Regev
Chad Nusbaum
Andreas Gnirke
Evan Mauceli
Nir Friedman
Nicholas Rhind
Nir Hacohen
Raktima Raychowdhury

Manfred G Grabherr
Brian J Haas
Moran Yassour
Joshua Z Levin
Dawn A Thompson
Ido Amit
Xian Adiconis
Lin Fan
Raktima Raychowdhury
Qiandong Zeng
Zehua Chen
Federica di Palma
Bruce W Birren

Nature Biotechnology

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

2011-07-01

Paweł P Łabaj
Steven Wiley
D Kreil

Germán G Leparc
Bryan E Linggi
Lye Meng Markillie

Bioinformatics

Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus.

2011-07-01

Antonis Rokas

John G Gibbons
Anne Beauvais
Remi Beau
Kriston L McGary
Jean-Paul Latgé

Eukaryotic Cell

Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq.

2011-07-02

Ricardo DeMarco
Sergio Verjovski-Almeida

Giulliana Tessarin Almeida
Murilo Sena Amaral
Felipe Cesar Ferrarezi Beckedorff
João Paulo Kitajima

Experimental Parasitology

An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.

2011-07-05

Iain W Wilson

Qi Tang
Xiaojun Ma
Changming Mo
Cai Song
Huan Zhao
Yanfang Yang
Wei Fu
Deyou Qiu

BMC Genomics

A comparative analysis of DNA methylation across human embryonic stem cell lines.

2011-07-06

Matteo Pellegrini

Pao-Yang Chen
Suhua Feng
Jong Wha Joanne Joo
Steve E Jacobsen

Genome Biology

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

2011-07-07

Tak-Wah Lam

Songbo Huang
Jinbo Zhang
Ruiqiang Li
Wenqian Zhang
Zengquan He
Zhiyu Peng
Siu-Ming Yiu

Frontiers in Genetics

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.

2011-07-12

David Casero
Matteo Pellegrini
Sabeeha Merchant

David Lopez
Shawn J Cokus

BMC Bioinformatics

De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome.

2011-07-19

Ya-Ting Chao

Chun-lin Su
Yao-Chien Alex Chang
Wan-Chieh Chen
Chun-Yi Chen
Ann-Ying Lee
Kee Tuan Hwa
Ming-Che Shih

Plant and Cell Physiology

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

2011-07-19

Angel Pizarro
Gregory R Grant
Eric A Pierce

Michael H Farkas
Nicholas F Lahens
Jonathan Schug
Brian P Brunk
Christian J Stoeckert
John B Hogenesch

Bioinformatics

RseqFlow: workflows for RNA-Seq data analysis.

2011-07-27

Ewa Deelman

Ying Wang
Gaurang Mehta
Rajiv Mayani
Jingxi Lu
Tade Souaiaia
Yangho Chen
Andrew Clark
Hee Jae Yoon
Lin Wan
Oleg V Evgrafov
James A Knowles
Ting Chen

Bioinformatics

Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length

2011-07-27

Jing Woei Li
Stephen Kwok-Wing Tsui
T F Chan

Shao-Ke Lou
Hao Qin
Aldrin Kay-Yuen Yim
Leung-Yau Lo
Bing Ni
Kwong-Sak Leung

BMC Bioinformatics

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.

2011-07-28

Tom Maniatis
Brad Friedman

Genome Biology

Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.

2011-07-29

Mikhail Matz

E Meyer
G V Aglyamova

Molecular Ecology

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

2011-07-31

John R. Prensner
Qi Cao
Irfan Asangani
Nallasivam Palanisamy

Matthew K Iyer
O Alejandro Balbin
Saravana M Dhanasekaran
J Chad Brenner
Bharathi Laxman
Catherine S Grasso
Hal D Kominsky
Xuhong Cao
Xiaojun Jing
Xiaoju Wang
Javed Siddiqui
John T Wei
Daniel Robinson
Hari K Iyer
Christopher A Maher
Arul M Chinnaiyan

Nature Biotechnology

RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.

2011-08-01

Jennifer M Ritchie

Anjali Mandlik
Jonathan Livny
William P Robins
John J Mekalanos
Matthew K Waldor

Cell Host & Microbe

AlleleSeq: analysis of allele-specific expression and binding in a network framework.

2011-08-02

Yong Kong
Alexej Abyzov
Joel Rozowsky
Mark Rubin
Mark Bender Gerstein

Jing Wang
Pedro Alves
Debasish Raha
Arif Harmanci
Jing Leng
Robert Bjornson
Naoki Kitabayashi
Nitin Bhardwaj
Michael Snyder

Molecular Systems Biology

Synthetic spike-in standards for RNA-seq experiments.

2011-08-04

Thomas R. Gingeras

Lichun Jiang
Felix Schlesinger
Carrie A Davis
Yu Zhang
Renhua Li
Marc Salit
Brian Oliver

Genome Research

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

2011-08-04

Paul P. Gardner
Roy R Chaudhuri
Jyoti Choudhary

Lu Yu
Alpa Kanji
Timothy T Perkins
Duncan J Maskell
Andrew J Grant

Microbiology

RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes

2011-08-05

Eran Pichersky

Petra M Bleeker
Eleni A Spyropoulou
Paul J Diergaarde
Hanne Volpin
Michiel T J De Both
Philipp Zerbe
Joerg Bohlmann
Vasiliki Falara
Yuki Matsuba
Eran Pichersky
Michel A Haring
Robert C Schuurink

Plant Molecular Biology

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

2011-08-08

Derek Y Chiang

Darshan Singh
Christian F Orellana
Yin Hu
Corbin D Jones
Yufeng Liu
Jinze Liu
Jan F Prins

Bioinformatics

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

2011-08-11

Steven Salzberg

Daehwan Kim

Genome Biology

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.

2011-08-11

Jason Gertz
Katherine E Varley
Timothy E Reddy

Kevin M Bowling
Florencia Pauli
Stephanie L Parker
Katerina S Kucera
Huntington F Willard
Richard M Myers

PLOS Genetics

Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing

2011-08-12

Robert W. Williams

Hao Chen
Zhimin Liu
Suzhen Gong
Xingjun Wu
William L Taylor
Shannon G Matta
Burt M Sharp

Frontiers in Neuroscience

Local and global factors affecting RNA sequencing analysis.

2011-08-16

Graham D Johnson

Edward Sendler
Stephen A Krawetz

Analytical Biochemistry

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

2011-08-18

Martin Hirst
Yaron Butterfield
Angela Brooks-Wilson
Eric Y Zhao
Malachi Griffith
Andrew Mungall

Ryan D Morin
Maria Mendez-Lago
Rodrigo Goya
Karen L Mungall
Richard D Corbett
Nathalie A Johnson
Tesa M Severson
Readman Chiu
Matthew Field
Shaun Jackman
Martin Krzywinski
David W Scott
Diane L Trinh
Jessica Tamura-Wells
Sa Li
Marlo R Firme
Sanja Rogic
Susanna Chan
Oleksandr Yakovenko
Irmtraud M Meyer
Duane Smailus
Michelle Moksa
Suganthi Chittaranjan
Lisa Rimsza
John J Spinelli
Susana Ben-Neriah
Barbara Meissner
Bruce Woolcock
Merrill Boyle
Helen McDonald
Angela Tam
Yongjun Zhao
Allen Delaney
Thomas Zeng
Kane Tse
Inanç Birol
Rob Holt
Jacqueline Schein
Douglas E Horsman
Richard Moore
Steven J M Jones
Joseph M Connors
Randy D Gascoyne
Marco A Marra

Nature

An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype

2011-08-18

Michele Balsamo

Irina M Shapiro
Albert W Cheng
Nicholas C Flytzanis
John S Condeelis
Maja H Oktay
Christopher B Burge
Frank B Gertler

PLOS Genetics

Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes.

2011-08-18

Ali Jabbari

Mayte Suárez-Fariñas
Scott Dewell
James G Krueger

Journal of Investigative Dermatology

The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression

2011-08-19

Songnian Hu

Peng Cui
Qiang Lin
Lingfang Zhang
Feng Ding
Chengqi Xin
Daoyong Zhang
Fanglin Sun
Jun Yu

PLOS ONE

Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry.

2011-08-23

Daojun Yuan
Xianlong Zhang

Li Xu
Longfu Zhu
Lili Tu
Linlin Liu
Li Jin
Lu Long

Journal of Experimental Botany

Bioaccumulation and effects of CdTe/CdS quantum dots on Chlamydomonas reinhardtii - nanoparticles or the free ions?

2011-08-25

Rute F. Domingos
Kevin J Wilkinson

Dana F Simon
Charles Hauser

Environmental Science & Technology

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.

2011-08-26

Daniel A Skelly

Marnie Johansson
Jennifer Madeoy
Jon Wakefield
Joshua M Akey

Genome Research

Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system.

2011-09-01

Deborah Charlesworth

Roberta Bergero

Current Biology

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

2011-09-02

Loyal Goff
Magdalena J Koziol
John L. Rinn

Moran N Cabili
Cole Trapnell
Barbara Tazon-Vega
Aviv Regev

Genes & Development

Wnt gene loss in flatworms.

2011-09-03

Nick Riddiford

Peter D Olson

Development Genes and Evolution

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

2011-09-06

W. Richard McCombie
Adrian Robert Krainer

Jie Wu
Martin Akerman
Shuying Sun
Michael Q Zhang

Bioinformatics

Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation.

2011-09-06

Ross C Hardison
James C Mullikin

Andre M Pilon
Subramanian S Ajay
Swathi Ashok Kumar
Laurie A Steiner
Praveen F Cherukuri
Stephen Wincovitch
Stacie M Anderson
NISC Comparative Sequencing Center
Patrick G Gallagher
Elliott H Margulies
David M Bodine

Blood

wapRNA: a web-based application for the processing of RNA sequences.

2011-09-06

Songnian Hu

Wenming Zhao
Wanfei Liu
Dongmei Tian
Bixia Tang
Yanqing Wang
Caixia Yu
Rujiao Li
Yunchao Ling
Jiayan Wu
Shuhui Song

Bioinformatics

RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.

2011-09-07

Deyou Zheng

Mingyan Lin
Erika Pedrosa
Abhishek Shah
Anastasia Hrabovsky
Shahina Maqbool
Herbert M Lachman

PLOS ONE

Differential expression in RNA-seq: a matter of depth.

2011-09-08

Joaquín Dopazo
Ana Conesa
Sonia Tarazona
Alberto Ferrer

Fernando García-Alcalde

Genome Research

Proteomic and phosphoproteomic comparison of human ES and iPS cells.

2011-09-11

Justin Brumbaugh

Douglas H Phanstiel
Craig D Wenger
Shulan Tian
Mitchell D Probasco
Derek J Bailey
Danielle L Swaney
Mark A Tervo
Jennifer M Bolin
Victor Ruotti
Ron Stewart
James A Thomson
Joshua J Coon

Nature Methods

Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.

2011-09-12

Elia Stupka
Christiaan V. Henkel
Herman P Spaink

Yanju Zhang
Hans J Jansen
Fons J Verbeek

Journal of integrative bioinformatics

Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.

2011-09-13

Jurian Schuijers
Michal Mokry

Pantelis Hatzis
Nico Lansu
Frans-Paul Ruzius
Hans Clevers
Edwin Cuppen

Nucleic Acids Research

Integrative approach involving RNA-Seq, foliar traits and growth measurements revealed genotype-specific plasticity on Eucalyptus subjected to seasonal water shortage.

2011-09-13

Christophe Plomion

Emilie Villar
Jean-Marc Gion

BMC Proceedings

Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant.

2011-09-15

Daniel L Kiss

Sarah B Smith
Edward Turk
Alan M Tartakoff
Erik D Andrulis

Yeast

RNA-Seq methods for imperfect samples: development, evaluation and applications

2011-09-19
2011

Aviv Regev
Chad Nusbaum
Gad Getz

Xian Adiconis
Lin Fan
David DeLuca
Andrey Sivachenko
Nathalie Pochet
Aaron Berlin
Sarah Young
Andreas Gnirke
Joshua Z Levin

Genome Biology

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

2011-09-22

Davis J McCarthy
Alicia Oshlack
Gordon K Smyth

Matthew D. Young
Matthew J. Wakefield
Mark D. Robinson

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.

2011-09-25

Vincent Lynch
Gunter P Wagner

Robert D Leclerc
Gemma May

Nature Genetics

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).

2011-09-28

Thomas Schmutzer
Martin Mascher
Uwe Scholz
Nils Stein
Klaus Mayer
Eva Bauer

Grit Haseneyer
Michael Seidel
Ruonan Zhou
Chris-Carolin Schön
Stefan Taudien

BMC Plant Biology

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.

2011-09-29

Jae-Hyung Lee
Guangdun Peng
Xinshu Xiao

Jae Hoon Bahn
Gang Li
Christopher Greer

Genome Research

Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing.

2011-10-01

Ece D. Gamsiz
Eric M. Morrow

Qing Ouyang
Michael Schmidt
Shailender Nagpal

Genomics

RNA-Seq analysis in MeV.

2011-10-05

John Quackenbush

Eleanor A Howe
Raktim Sinha
Daniel Schlauch

Bioinformatics

RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs

2011-10-05

Tirza Doniger

Shulamit Michaeli
Sachin Kumar Gupta
Omri Wurtzel
Mali Romano
Damian Visnovezky
Rotem Sorek
Ron Unger
Elisabetta Ullu

Nucleic Acids Research

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

2011-10-06

Jeff H. Chang
Jeffrey A Kimbrel
James C. Carrington

Jason S Cumbie
Yanming Di
Daniel W Schafer
Larry J Wilhelm
Samuel E Fox
Christopher M Sullivan
Aron D Curzon
Todd C Mockler

PLOS ONE

S-MART, a software toolbox to aid RNA-Seq data analysis

2011-10-06

Hadi Quesneville

Matthias Zytnicki

PLOS ONE

Nonrandom gene loss from the Drosophila miranda neo-Y chromosome.

2011-10-10

Doris Bachtrog

Vera B Kaiser
Qi Zhou

Genome Biology and Evolution

The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction.

2011-10-13

Gaedigk R
Steven N. Hart

Dan Li
J Steven Leeder
Xiao-bo Zhong

Molecular Pharmacology

RNA-Seq for Plant Pathogenic Bacteria.

2011-10-13

Jeffrey A Kimbrel
Jeff H. Chang

Yanming Di
Jason S Cumbie

Genes

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.

2011-10-18

Charles D. Johnson
Ulisses Braga Neto

Ying Wang
Noushin Ghaffari
Hui Wang
Rui Chen
Huaijun Zhou

BMC Bioinformatics

The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity

2011-10-21

Paulo José Pereira Lima Teixeira
Joan Barau
Antonio Costa-filho

Gustavo Zaparoli
Mario Ramos de Oliveira Barsottini
Juliana Ferreira de Oliveira
Fabio Dyszy
Odalys Garcia
Andre Luis Berteli Ambrosio
Gonçalo Amarante Guimarães Pereira
Sandra Martha Gomes Dias

Biochemistry

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.

2011-10-23

Thomas R. Gingeras
Jay Shendure
David Sturgill

Xinxian Deng
Joseph B Hiatt
Di Kim Nguyen
Sevinc Ercan
LaDeana W Hillier
Felix Schlesinger
Carrie A Davis
Valerie J Reinke
Robert H Waterston
Brian Oliver
Jason D Lieb
Christine M Disteche

Nature Genetics

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines

2011-10-27

Anne Vincent-Salomon
William D Foulkes
Jorge Reis-Filho
Rachael Natrajan
Alan Ashworth

Kevin C H Ha
Emilie Lalonde
Lili Li
Luca Cavallone
Maryou B Lambros
Costas Mitsopoulos
Jarle Hakas
Iwanka Kozarewa
Kerry Fenwick
Chris J Lord
Mark Basik
Jacek Majewski

BMC Medical Genomics

RNA-Seq reveals an integrated immune response in nucleated erythrocytes.

2011-10-27

Nerea Roher
Laia Ribas
Joan C Balasch
Sebastian Boltana
Steven B. Roberts
Simon Mackenzie

Davinia Morera
Carmen Doñate
Agnes Callol
Giles Goetz
Frederick W Goetz

PLOS ONE

The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.

2011-10-28

Giovanni Giuliano
Kevin L. Childs

Alicia N Massa
Haining Lin
Glenn J Bryan
C Robin Buell

PLOS ONE

RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

2011-11-02

Christophe Plomion
Evandro Novaes

Emilie Villar
Christophe Klopp
Céline Noirot
Matias Kirst
Jean-Marc Gion

BMC Genomics

RNA-Seq improves annotation of protein-coding genes in the cucumber genome.

2011-11-02

Zhen Li
Sanwen Huang

Zhonghua Zhang
Pengcheng Yan
Zhangjun Fei
Kui Lin

BMC Genomics

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

2011-11-03

Peter F. Stadler
Jan Gorodkin
David Langenberger
Claus T. Ekstrøm
Sachin Pundhir

Steve Hoffmann

Bioinformatics

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.

2011-11-06

Adam Ameur
Ulf Gyllensten

Ammar Zaghlool
Jonatan Halvardson
Anna Wetterbom
Lucia Cavelier
Lars Feuk

Nature Structural & Molecular Biology

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

2011-11-08

Giovanni Bussotti
Robert Kofler
Cedric Notredame
Miguel Perez-Enciso
Anna Esteve-Codina

Nicola Palmieri

BMC Genomics

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.

2011-11-08

Ming Hu
Zhaohui Steve Qin

Yu Zhu
Jeremy M G Taylor
Jun S Liu

Bioinformatics

An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.

2011-11-10

Andreas Sommer
Irena Vlatkovic
Hendrik Marks
Robert Kralovics

Ru Huang
Markus Jaritz
Philipp Guenzl
Ido M Tamir
Thorsten Klampfl
Hendrik G Stunnenberg
Denise P Barlow
Florian M Pauler

PLOS ONE

Non-laser capture microscopy approach for the microdissection of discrete mouse brain regions for total RNA isolation and downstream next-generation sequencing and gene expression profiling.

2011-11-13

Norman Atkins

Charlie M Miller
Joseph R Owens
Fred W Turek

Journal of Visualized Experiments

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.

2011-11-16

Jeffrey T. Leek
Ben Langmead

Alyssa C Frazee

BMC Bioinformatics

Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq.

2011-11-16

Melody Baddoo
Dale Hedges
Erik K Flemington

Monica Concha
Xia Wang
Subing Cao
Melody Baddoo
Claire Fewell
Zhen Lin
William Hulme
Dale Hedges
Jane McBride

Journal of Virology

Genetic variation of pre-mRNA alternative splicing in human populations

2011-11-17

Zhi-xiang Lu

Peng Jiang
Yi Xing

Wiley interdisciplinary reviews. RNA

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.

2011-11-22

Aviv Regev
Eivind Valen
Albin Sandelin
John L. Rinn

Andrea Pauli
Michael F Lin
Manuel Garber
Nadine L Vastenhouw
Joshua Z Levin
Lin Fan
Alexander F Schier

Genome Research

RNA-Seq and find: entering the RNA deep field.

2011-11-22

Lior Pachter

Adam Roberts

Genome Medicine

Estimation of alternative splicing variability in human populations.

2011-11-23

Roderic Guigó i Serra
Michael Sammeth

Mar Gonzàlez-Porta
Miquel Calvo

Genome Research

RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.

2011-11-24

Blake Meyers

Sridhara G Kunjeti
Thomas A Evans
Adam G Marsh
Nancy F Gregory
Saritha Kunjeti
Venugopal S Kalavacharla
Nicole M Donofrio

Molecular Plant Pathology

Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.

2011-11-28

Robert Tibshirani

Jun Li

Statistical Methods in Medical Research

Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.

2011-11-28

Paola Tosi
J Paul Knox
Jackie Freeman

Till K Pellny
Alison Lovegrove
Christopher G Love
Peter R Shewry
Rowan A C Mitchell

Plant Physiology

Transposase mediated construction of RNA-seq libraries.

2011-11-29

Jason Gertz
Katherine E Varley

Nicholas S Davis
Bradley J Baas
Igor Y Goryshin
Ramesh Vaidyanathan
Scott Kuersten
Richard M Myers

Genome Research

Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.

2011-11-30

Jian Luo
Mingyao Liu

Geng Chen
Kangping Yin
Leming Shi
Yuanzhang Fang
Ya Qi
Peng Li
Bing He
Tieliu Shi

PLOS ONE

Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120

2011-11-30

Agustín Vioque
Fabian Haas
Wolfgang R Hess
Alicia María Muro-Pastor

Jan Mitschke

Proceedings of the National Academy of Sciences of the United States of America

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

2011-12-01

Jingyi Jessica Li

Ci-Ren Jiang
James B Brown
Haiyan Huang
Peter J Bickel

Proceedings of the National Academy of Sciences of the United States of America

EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.

2011-12-01

Jing Qin
Junwen Wang

Lily Yan Wang
Panwen Wang
Mulin Jun Li
Xiaowo Wang
Michael Q Zhang

Epigenetics

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).

2011-12-02

Jérôme Salse

Caroline Pont
Florent Murat
Carole Confolent
Sandrine Balzergue

Genome Biology

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription

2011-12-04

Ruslan I Sadreyev

Eda Yildirim
Stefan F Pinter
Jeannie T Lee

Nature Structural & Molecular Biology

Isoform diversity and its importance for axon regeneration.

2011-12-13

John L. Bixby
Vance P. Lemmon

Jessica K Lerch

Neuropathology

Protein identification using customized protein sequence databases derived from RNA-Seq data.

2011-12-14

David Tabb
Daniel C. Liebler

Xiaojing Wang
Robbert J C Slebos
Dong Wang
Patrick J Halvey
Bing Zhang

Journal of Proteome Research

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.

2011-12-14

Qiong-Yi Zhao

Yi Wang
Yi-Meng Kong
Da Luo
Xuan Li
Pei Hao

BMC Bioinformatics

GC-content normalization for RNA-Seq data

2011-12-17

Gavin Sherlock
Davide Risso

Katja Schwartz
Sandrine Dudoit

BMC Bioinformatics

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

2011-12-22

Desmond G. Higgins
Geraldine Butler
Sarah L Maguire
Matthew Berriman

Alessandro Guida
Claudia Lindstädt
Chen Ding
Nicola J Corton

BMC Genomics

Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses.

2011-12-22

Laurence Florens
Swaminathan Venkatesh
Michael P. Washburn

Joshua M Gilmore
Mihaela E Sardiu
Brent Stutzman
Allison Peak
Chris W Seidel
Jerry L Workman

Molecular & Cellular Proteomics

Statistical methods on detecting differentially expressed genes for RNA-seq data.

2011-12-23

Saralees Nadarajah

Zhongxue Chen
Jianzhong Liu
Hon Keung Tony Ng
Saralees Nadarajah
Howard L Kaufman
Jack Y Yang
Youping Deng

BMC Systems Biology

Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders

2011-12-27

Jordan L Meier
Peter Dervan

Jevgenij A Raskatov
James W Puckett
Fei Yang
Parameswaran Ramakrishnan

Proceedings of the National Academy of Sciences of the United States of America

Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.

2011-12-28

Fangqing Zhao

Qi Liu
Chong Chen
Enjian Shen
Zhongsheng Sun
Jinyu Wu

Genomics

Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection.

2011-12-28

Steven G Schroeder

Robert W Li

Functional and Integrative Genomics

Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

2011-12-29

Steven B. Roberts

Mackenzie R Gavery

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms

2012

Christina A Cuomo

Kelly L Robertson
Anahita Mostaghim
Carissa M Soto
Nikolai Lebedev
Robert F Bailey
Zheng Wang

PLOS ONE

Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq

2012

John L. Bixby
Vance P. Lemmon
Dario Motti

Jessica K Lerch
Frank Kuo
Richard Morris

PLOS ONE

Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers

2012

Jacqueline Salit

Guoqing Wang
Zhibo Xu
Rui Wang
Mohammed Al-Hijji
Yael Strulovici-Barel
Ann E Tilley
Jason G Mezey
Ronald G Crystal

BMC Medical Genomics

The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain

2012

Andrea Telatin
Stefano Campanaro
Giorgio Valle

Fabio De Pascale
Riccardo Schiavon
Douglas H Bartlett

BMC Genomics

Computational analysis of noncoding RNAs

2012

Manolis Kellis
Stefan Washietl
Bonnie Berger
John L. Rinn

Sebastian Will
David A. Hendrix
Loyal A. Goff

Wiley interdisciplinary reviews. RNA

Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea

2012

Brenton R. Graveley

Alissa M Resch
Dasaradhi Palakodeti
Yi-Chien Lu
Michael Horowitz

PLOS ONE

RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi

2012

Tae Sung Jung

Ho Bin Jang
Young Kyu Kim
Carmelo S Del Castillo
Seong Won Nho
In Seok Cha
Seong Bin Park
Mi Ae Ha
Jun-Ichi Hikima
Sung Jong Hong
Takashi Aoki

PLOS ONE

GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats

2012

David Goldman

Mary-Anne Enoch
Zhifeng Zhou
Mitsuru Kimura
Deborah C Mash
Qiaoping Yuan

PLOS ONE

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line

2012

Mark Bender Gerstein
Vincent Schulz

Jia Qian Wu
Montrell Seay
Manoj Hariharan
David Tuck
Jin Lian
Jiang Du
Minyi Shi
Zhijia Ye
Michael P Snyder
Sherman Weissman

PLOS Genetics

Gene expression profiling of liver cancer stem cells by RNA-sequencing

2012

Timothy Wan

David W Y Ho
Zhen Fan Yang
Kang Yi
Chi Tat Lam
Michael N P Ng
Wan Ching Yu
Joyce Lau
Xiaoqi Wang
Zhixiang Yan
Hang Liu
Yong Zhang
Sheung Tat Fan

PLOS ONE

Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene

2012

Feng Gao
Abdul B Abou-Samra

Ren Zhang
Fayi Yao

PLOS ONE

RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells

2012

Sten Linnarsson

Kersti Jääger
Saiful Islam
Pawel Zajac
Toomas Neuman

PLOS ONE

Stable gene targeting in human cells using single-strand oligonucleotides with modified bases

2012

George M. Church

Xavier Rios
Adrian W Briggs
Danos Christodoulou
Josh M Gorham
Jonathan G Seidman

PLOS ONE

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data

2012

Jean-Baptiste Veyrieras
Daniel J Gaffney

Jean-Baptiste Veyrieras
Joseph K Pickrell
Yoav Gilad
Matthew Stephens
Jonathan K Pritchard

PLOS ONE

Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment

2012

Honghuang Lin

N. Medina-Medina
A. Broka
S. Lacey
E. S. Klings
C. T. Baldwin
M. H. Steinberg
P. Sebastiani

Advances in Intelligent and Soft Computing

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

2012-01

Sumio Sugano

Riu Yamashita
Yutaka Suzuki
Kenta Nakai

Nucleic Acids Research

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

2012-01-01

Andreas Gnirke
Georgia Giannoukos
Ashlee Earl
Chad Nusbaum
Dirk Gevers

Dawn M Ciulla
Katherine Huang
Brian J Haas
Jacques Izard
Joshua Z Levin
Jonathan Livny
Doyle V Ward
Bruce W Birren

Genome Biology

How to analyze gene expression using RNA-sequencing data.

2012-01-01

Daniel Ramsköld
Rickard Sandberg

Ersen Kavak

Methods in Molecular Biology

Detection and quantification of alternative splicing variants using RNA-seq.

2012-01-01

Henry D Priest

Douglas W Bryant
Todd C Mockler

Methods in Molecular Biology

Retinal transcriptome profiling by directional next-generation sequencing using 100 ng of total RNA.

2012-01-01

Anand Swaroop

Matthew J Brooks
Harsha Karur Rajasimha

Methods in Molecular Biology

Sex-biased transcriptome evolution in Drosophila.

2012-01-01

Doris Bachtrog

Raquel Assis
Qi Zhou

Genome Biology and Evolution

Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach.

2012-01-01

Jordi Solana
Aziz A. Aboobaker

Damian Kao
Yuliana Mihaylova
Farah Jaber-Hijazi
Sunir Malla
Ray Wilson

Genome Biology

Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.

2012-01-01

Gangqing Hu

Gang Wei
Kairong Cui
Keji Zhao

Methods in Enzymology

Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells.

2012-01-01

Yasuyuki Ohkawa
Kazu Kobayakawa
Seiji Okada
Hideyuki Okano

Hiromi Kumamaru
Hirokazu Saiwai
Hisakata Yamada
Kensuke Kubota
Koichi Akashi
Yukihide Iwamoto

Nature Communications

Computational analysis of RNA-seq.

2012-01-01

Scott A. Givan

Christopher A Bottoms
William G Spollen

Methods in Molecular Biology

Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.

2012-01-03

Robert K. Bradley

Jason Merkin
Nicole J Lambert
Christopher B Burge

PLOS Biology

Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.

2012-01-03

Baojin Yao

Yu Zhao
Haishan Zhang
Mei Zhang
Meichen Liu
Hailong Liu
Juan Li

Biotechnology Letters

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

2012-01-04

Zemin Ning
Peter A.C. 't Hoen
Pieternella E Slagboom

Yanju Zhang
Eric-Wubbo Lameijer
Kai Ye

Bioinformatics

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.

2012-01-06

Andrea Sboner
Mark Bender Gerstein

Jiang Du
Jing Leng
Lukas Habegger
Drew McDermott

PLOS ONE

Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.

2012-01-11

Melody Baddoo
Erik K Flemington

Zhen Lin
Adriane Puetter
Joseph Coco
Guorong Xu
Michael J Strong
Xia Wang
Claire Fewell
Melody Baddoo
Christopher Taylor

Journal of Virology

Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.

2012-01-13

Andrew C. Allan
Xue-ren Yin

Chao Feng
Ming Chen
Chang-jie Xu
Lin Bai
Xian Li
Ian B Ferguson
Kun-song Chen

BMC Genomics

Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy

2012-01-14

Peadar Ó Gaora
Helen M Roche

Eoin P Brennan
Melissa J Morine
David W Walsh
Sarah A Roxburgh
Maja T Lindenmeyer
Derek P Brazil
Denise M Sadlier
Clemens D Cohen
GENIE Consortium
Catherine Godson
Finian Martin

Biochimica et Biophysica Acta

The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression.

2012-01-17

Cynthia Sharma

Vinoy K Ramachandran
Neil Shearer
Jobin J Jacob
Arthur Thompson

BMC Genomics

FX: an RNA-Seq analysis tool on the cloud.

2012-01-17

Young Seok Ju
Thomas Bleazard

Dongwan Hong
Arang Rhie
Sung-Soo Park
Jongkeun Lee
Sujung Kim
Saet-Byeol Yu
Hyun-Seok Park
Hwanseok Rhee
Hyonyong Chong
Kap-Seok Yang
Yeon-Su Lee
In-Hoo Kim
Jin Soo Lee
Jong-Il Kim
Jeong-Sun Seo

Bioinformatics

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.

2012-01-20

Zhi-xiang Lu
Jian Huang

Shihao Shen
Juw Won Park
Kimberly A Dittmar
Qing Zhou
Russ P Carstens
Yi Xing

Nucleic Acids Research

Application of RNA-Seq transcriptome analysis: CD151 is an Invasion/Migration target in all stages of epithelial ovarian cancer.

2012-01-24

Sergio Marchini
Robert Fruscio
Maurizio D'Incalci

Rebecca A Mosig
Li Lin
Emir Senturk
Hardik Shah
Fei Huang
Peter Schlosshauer
Samantha Cohen
Ravi Sachidanandam
Peter Dottino
John A Martignetti

Journal of Ovarian Research

A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.

2012-01-26

Philip Rosenstiel
Ueli Grossniklaus
Marc W Schmid

Anja Schmidt
Ulrich C Klostermeier
Matthias Barann

PLOS ONE

Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.

2012-01-26

Robert Ekblom
Jon Slate
Terry Burke

Gavin J Horsburgh
Tim Birkhead

Comparative and Functional Genomics

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.

2012-01-27

David Tabb

Surendra Dasari
Matthew C Chambers
Misti A Martinez
Kristin L Carpenter
Amy-Joan L Ham
Lorenzo J Vega-Montoto

Journal of Proteome Research

Removing technical variability in RNA-seq data using conditional quantile normalization.

2012-01-27

Kasper D. Hansen
Zhijin Wu

Rafael A Irizarry

Biostatistics

The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.

2012-01-27

Lars Kraemer
Philip Rosenstiel

E E R Philipp
D Mountfort
M Schilhabel
S Schreiber

Bioinformatics

A new approach to bias correction in RNA-Seq

2012-01-28

Walter L. Ruzzo

Daniel C Jones
Xinxia Peng
Michael G Katze

Bioinformatics

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.

2012-01-28

Davis J McCarthy
Gordon K Smyth

Yunshun Chen

Nucleic Acids Research

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.

2012-01-31

Asa Ben-Hur

Mark F Rogers
Julie Thomas
Anireddy Sn Reddy

Genome Biology

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).

2012-02-01

W. Richard McCombie
Norman J Wickett
Mark W. Chase

Michael R McKain
Yeting Zhang
Saravanaraj Ayyampalayam
J Chris Pires
Claude W dePamphilis
Jim Leebens-Mack

American Journal of Botany

Spt4 is selectively required for transcription of extended trinucleotide repeats.

2012-02-01

Yijuang Chern

Chia-Rung Liu
Chuang-Rung Chang
Tzu-Han Wang
Wen-Chieh Hsieh
Wen-Chuan Shen
Chi-Yuan Chang
I-Chieh Chu
Ning Deng
Stanley N Cohen
Tzu-Hao Cheng

Cell

The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.

2012-02-03

Andreas Dötsch
Denitsa Eckweiler
Susanne Häussler

Monika Schniederjans
Ariane Zimmermann
Vanessa Jensen
Maren Scharfe
Robert Geffers

PLOS ONE

Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.

2012-02-07

Miao Tian

Jie Xiong
Xingyi Lu
Zhemin Zhou
Yue Chang
Dongxia Yuan
Zhigang Zhou
Lei Wang
Chengjie Fu
Eduardo Orias
Wei Miao

PLOS ONE

Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae.

2012-02-09

Nick Talbot

Darren M Soanes
Apratim Chakrabarti
Konrad H Paszkiewicz
Angus L Dawe

PLOS Pathogens

Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation.

2012-02-09

Jie Huang
Yu Zhou
Changwei Shao
Yi Zhang

Rui Xiao
Peng Tang
Bo Yang
Hairi Li
Hui Sun
Xiang-Dong Fu

Molecular Cell

Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.

2012-02-09

Andrew Paul Hutchins
Stéphane Poulain

Diego Miranda-Saavedra

Blood

Specific and sensitive mRNA biomarkers for the identification of skin in 'touch DNA' evidence.

2012-02-09

Cordula Haas

E Hanson
R Jucker
J Ballantyne

Forensic Science International: Genetics

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.

2012-02-12

Jun Wang
Bertrand Chin-Ming Tan
Zhiyu Peng

Yanbing Cheng
Lin Kang
Zhijian Tian
Yuankun Zhu
Wenwei Zhang
Yu Liang
Xueda Hu
Xuemei Tan
Jing Guo
Zirui Dong
Yan Liang
Li Bao

Nature Biotechnology

Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms

2012-02-14

Dan L. Warren
Michael B Thompson
Gunter P Wagner

Matthew C Brandley
Rebecca L Young

Genome Biology and Evolution

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

2012-02-17

Jens U Marquardt
Ugur Sahin

Markus Krupp
Peter R Galle
John Castle
Andreas Teufel

Bioinformatics

RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus.

2012-02-17

Eric Peatman

Chao Li
Yu Zhang
Ruijia Wang
Jianguo Lu
Samiran Nandi
Sriprakash Mohanty
Jeffery Terhune
Zhanjiang Liu

Fish and Shellfish Immunology

RNA-seq analysis of the functional compartments within the rat placentation site.

2012-02-21

Kartik Shankar

Ying Zhong
Ping Kang
Michael L Blackburn
Michael J Soares
Thomas M Badger
Horacio Gomez-Acevedo

Endocrinology

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.

2012-02-21

Jian-Hua Mao
Jun Wang
Huanming Yang

Shancheng Ren
Zhiyu Peng
Yongwei Yu
Changjun Yin
Xin Gao
Zilian Cui
Jibin Zhang
Kang Yi
Weidong Xu
Chao Chen
Fubo Wang
Xinwu Guo
Ji Lu
Jun Yang
Min Wei
Zhijian Tian
Yinghui Guan
Liang Tang
Chuanliang Xu
Linhui Wang
Xu Gao
Wei Tian
Jian Wang
Yinghao Sun

Cell Research

Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.

2012-02-29

Alexey I Nesvizhskii

Kang Ning
Damian Fermin

Journal of Proteome Research

RNA-Seq quantification of the human small airway epithelium transcriptome

2012-02-29

Juan L Rodriguez-Flores

Neil R Hackett
Marcus W Butler
Renat Shaykhiev
Jacqueline Salit
Larsson Omberg
Jason G Mezey
Yael Strulovici-Barel
Guoqing Wang
Lukas Didon
Ronald G Crystal

BMC Genomics

FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.

2012-02-29

Angelo Valleriani

Gong Zhang
Ivan Fedyunin
Sebastian Kirchner
Chuanle Xiao
Zoya Ignatova

Nucleic Acids Research

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

2012-03

Loyal Goff
Steven Salzberg
Lior Pachter
Harold Pimentel
John L. Rinn

Cole Trapnell
Adam Roberts
Geo Pertea
Daehwan Kim
David R Kelley

Nature Protocols

Characterization and differential expression analysis of complete coding sequences of Vitis vinifera L. sirtuin genes.

2012-03-03

Giacomo Morreale
Matteo Busconi
Luigi Bavaresco

M Cucurachi
A Zanetti
C Fogher

Plant Physiology and Biochemistry

A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.

2012-03-04

Franck Tirode
Olivier Delattre

Gaëlle Pierron
Carlo Lucchesi
Stéphanie Reynaud
Stelly Ballet
Sarah Cohen-Gogo
Virginie Perrin
Jean-Michel Coindre

Nature Genetics

The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.

2012-03-08

Gerton Lunter
Izortze Santin
Michael Sammeth
Miriam Cnop
Lorella Marselli
Piero Marchetti
Fernanda Ortis
Mark McCarthy

Décio L Eizirik
Thomas Bouckenooghe
Guy Bottu
Giorgia Sisino
Mariana Igoillo-Esteve
Maikel L Colli
Jenny Barthson
Luc Bouwens
Linda Hughes
Lorna Gregory

PLOS Genetics

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.

2012-03-08

Vladimir Benes
Gunnar Rätsch
Hans-Martin Jäck

Marco Preussner
Silke Schreiner
Lee-Hsueh Hung
Martina Porstner
Albrecht Bindereif

Nucleic Acids Research

Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia.

2012-03-09

Annalisa Lonetti
Giovanni Malerba
Alberto Ferrarini
Luciano Xumerle
Anna Ferrari
Cristina Papayannidis
Simona Soverini

I Iacobucci
M Sazzini
E Giacomelli
D Luiselli
A Boattini
P Garagnani
A Vitale
F Pane
M Baccarani
M Delledonne
G Martinelli

Blood Cancer Journal

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells.

2012-03-12

Sascha Brunke
Karl Kuchler
Reinhard Guthke

Lanay Tierney
Jörg Linde
Sebastian Müller
Juan Camilo Molina
Bernhard Hube
Ulrike Schöck

Frontiers in Microbiology

A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.

2012-03-19

Effie Mutasa-Göttgens
Berthold Gottgens

Anagha Joshi
Helen F Holmes
Peter Hedden

BMC Genomics

Transcriptome landscape of the human placenta

2012-03-27

Zhi-xiang Lu
Jin-kai Wang

Jinsil Kim
Keyan Zhao
Peng Jiang
Jeffrey C Murray
Yi Xing

BMC Genomics

Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers.

2012-03-27

Jennifer Thomson
Cong-Jun Li

Ransom L Baldwin
Robert W Li
Brian J Bequette

Physiological Genomics

Alternative splicing networks regulated by signaling in human T cells.

2012-03-27

Nicole M Martinez

Qun Pan
Brian S Cole
Christopher A Yarosh
Grace A Babcock
Florian Heyd
William Zhu
Sandya Ajith
Benjamin J Blencowe
Kristen W Lynch

RNA

RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts

2012-03-28

Francisco Peñagaricano

Ashley M Driver
Wen Huang
Khawaja R Ahmad
Katie S Hackbart
Milo C Wiltbank
Hasan Khatib

BMC Genomics

A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis

2012-03-28

Paolo Miotto
Alessandro Ambrosi

Danilo Pellin
Daniela Maria Cirillo
Clelia Di Serio

PLOS ONE

Identification of allele-specific alternative mRNA processing via transcriptome sequencing.

2012-03-29

Jae-Hyung Lee
Guangdun Peng
Xinshu Xiao

Gang Li
Jae Hoon Bahn
Zugen Chen
Stanley F Nelson

Nucleic Acids Research

Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis.

2012-04-01

Songnian Hu

Peng Cui
Wanfei Liu
Yuhui Zhao
Qiang Lin
Daoyong Zhang
Feng Ding
Chengqi Xin
Zhang Zhang
Shuhui Song
Fanglin Sun
Jun Yu

Genomics Proteomics and Bioinformatics

Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.

2012-04-01

Ellen V. Rothenberg

Jingli A Zhang
Ali Mortazavi
Brian A Williams
Barbara J Wold

Cell

A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola.

2012-04-01

Igor V Grigoriev

Akhil Srivastava
Robin A Ohm
Lindsay Oxiles
Fred Brooks
Christopher B Lawrence
Yangrae Cho

Molecular Plant-Microbe Interactions

Identification of shortened 3' untranslated regions from expression arrays.

2012-04-01

Andrei Zinovyev
Loredana Martignetti
Emmanuel Barillot

Journal of Bioinformatics and Computational Biology

Improving RNA-Seq Precision with MapAl.

2012-04-02

D Kreil

Paweł P Labaj
Bryan E Linggi
H Steven Wiley

Frontiers in Genetics

RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis

2012-04-02

Alex Schultink
Jacob K Jensen
Markus Pauly

Kenneth Keegstra
Curtis G Wilkerson

Plant Physiology Journal

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

2012-04-03

Gregory R Grant

Michael E Hughes
Christina Paquin
Jack Qian
Michael N Nitabach

Genome Research

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

2012-04-04

Gavin Ha
D Yap
Daniel Lai
Inanc Birol
Malachi Griffith
Gregg B Morin
Suet-feung Chin
Christina Curtis
Mackey JR
Wyeth W Wasserman
Steven Jones

Sohrab P Shah
Andrew Roth
Rodrigo Goya
Arusha Oloumi
Yongjun Zhao
Gulisa Turashvili
Jiarui Ding
Kane Tse
Gholamreza Haffari
Ali Bashashati
Leah M Prentice
Jaswinder Khattra
Angela Burleigh
Virginie Bernard
Andrew McPherson
Karey Shumansky
Anamaria Crisan
Ryan Giuliany
Alireza Heravi-Moussavi
Jamie Rosner
Richard Varhol
Angela Tam
Noreen Dhalla
Thomas Zeng
Kevin Ma
Simon K Chan
Annie Moradian
S-W Grace Cheng
Peter Watson
Karen Gelmon
Stephen Chia
Oscar M Rueda
Paul D Pharoah
Sambasivarao Damaraju
Kelly Hoon
Timothy Harkins
Vasisht Tadigotla
Mahvash Sigaroudinia
Philippe Gascard
Thea Tlsty
Joseph F Costello
Irmtraud M Meyer
Connie J Eaves
David Huntsman
Martin Hirst
Carlos Caldas
Marco A Marra
Samuel Aparicio

Nature

Spatial proximity and similarity of the epigenetic state of genome domains.

2012-04-04

Ekaterina E Khrameeva
Gennady G Fedonin
Mikhail S Gelfand

Andrey A Mironov
Philipp Khaitovich

PLOS ONE

Computational inference of mRNA stability from histone modification and transcriptome profiles

2012-04-10

Yong Zhang

Chengyang Wang
Rui Tian
Qian Zhao
Han Xu
Clifford A Meyer
Cheng Li
X Shirley Liu

Nucleic Acids Research

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.

2012-04-12

J Duitama

Pramod K Srivastava
Ion I Măndoiu

BMC Genomics

Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes.

2012-04-17

Niklaus Zemp

Aline Muyle
Clothilde Deschamps
Sylvain Mousset
Alex Widmer
Gabriel A B Marais

PLOS Biology

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

2012-04-19

Pierre Peterlongo
Marie-France Sagot

Gustavo A T Sacomoto
Janice Kielbassa
Rayan Chikhi
Raluca Uricaru
Pavlos Antoniou
Vincent Lacroix

BMC Bioinformatics

A context-based approach to identify the most likely mapping for RNA-seq experiments.

2012-04-19

Ralf Zimmer

Thomas Bonfert
Gergely Csaba
Caroline C Friedel

BMC Bioinformatics

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

2012-04-24

Daniel S. Rokhsar
Kranthi Varala

Kankshita Swaminathan
Won Byoung Chae
Therese Mitros
Liang Xie
Adam Barling
Katarzyna Glowacka
Megan Hall
Stanislaw Jezowski
Ray Ming
Matthew Hudson
John A Juvik
Stephen P Moose

BMC Genomics

RNA-SeQC: RNA-seq metrics for quality control and process optimization

2012-04-25

Gad Getz
Wendy Winckler

David S DeLuca
Joshua Z Levin
Andrey Sivachenko
Timothy Fennell
Marc-Danie Nazaire
Chris Williams
Michael Reich

Bioinformatics

Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin

2012-04-25

Ana Conesa
Diana Huestis
Jeffrey A Fabrick
Juan Luis Jurat-Fuentes

Brenda Oppert
Scot E Dowd
Pascal Bouffard
Lewyn Li
Marcé D Lorenzen
Michelle Toutges
Jeremy Marshall
Cris Oppert

PLOS ONE

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.

2012-04-26

Ralf Zimmer

Lukas Windhager
Thomas Bonfert
Kaspar Burger
Zsolt Ruzsics
Stefan Krebs
Stefanie Kaufmann
Georg Malterer
Anne L'Hernault
Markus Schilhabel
Stefan Schreiber
Philip Rosenstiel
Dirk Eick
Caroline C Friedel
Lars Dölken

Genome Research

Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.

2012-04-27

Jingqin Wu
Xi Wang
Murray J Cairns

Natalie J Beveridge
Paul A Tooney
Rodney J Scott
Vaughan J Carr

PLOS ONE

Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq

2012-05

John Quackenbush
Naftali Kaminski

Rebecca L. Kusko
John Brothers II
Gang Liu
Lingqi Luo
Brenda J. Guardela
John R. Tedrow
Yuriy Aleksyev
Ivana V. Yang
Mick Correll
Mark Geraci
Frank C. Sciurba
Marc Lenburg
David A. Schwartz
Jennifer Beane
Avrum Spira

Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease

2012-05-01

Olivier Elemento

Seema Gollamudi
Ashu Johri
Noel Y Calingasan
Lichuan Yang
M Flint Beal

PLOS ONE

Utilizing RNA-Seq data for de novo coexpression network inference

2012-05-03

Shannon K McWeeney

Ovidiu D Iancu
Sunita Kawane
Daniel Bottomly
Robert Searles
Robert Hitzemann

Bioinformatics

Identifying differentially expressed transcripts from RNA-seq data with biological variation.

2012-05-03

Magnus Rattray
Antti Honkela

Peter Glaus
Antti Honkela

Bioinformatics

PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.

2012-05-04

Douwe Molenaar

Jumamurat R Bayjanov
Vesela Tzeneva
Roland J Siezen
Sacha A F T van Hijum

BMC Genomics

RNA-Seq identifies SNP markers for growth traits in rainbow trout

2012-05-04

Timothy D Leeds

Mohamed Salem
Roger L Vallejo
Yniv Palti
Sixin Liu
Annas Sabbagh
Caird E Rexroad
Jianbo Yao

PLOS ONE

Gene mapping via bulked segregant RNA-Seq (BSR-Seq).

2012-05-07

Cheng-Ting Yeh
Dan Nettleton
Patrick S Schnable

Sanzhen Liu
Ho Man Tang

PLOS ONE

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.

2012-05-15

Marie-Laure Yaspo
Hans Lehrach

Marc Sultan
Simon Dökel
Vyacheslav Amstislavskiy
Daniela Wuttig
Holger Sültmann
Marie-Laure Yaspo

Biochemical and Biophysical Research Communications

Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.

2012-05-15

Weizhong Li

Sitao Wu
Robert W Li
Cong-Jun Li

PLOS ONE

Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions

2012-05-18

Lars K. Nielsen
Robin William Palfreyman
Quan Nguyen

Leslie C L Chan
Steven Reid

PLOS ONE

RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance.

2012-05-20

David J. Lynn
Christopher J. Creevey
David A Kenny

Matthew McCabe
Sinéad Waters
Dermot Morris

BMC Genomics

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

2012-05-24

Anders Krogh
Jun Wang
Johannes Waage
Joachim Weischenfeldt
Bo Torben Porse
Janus Schou Jakobsen
Karsten Kristiansen

Geng Tian
Jing Zhao
Inge Damgaard

Genome Biology

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

2012-05-25

Gavin Ha
Daniel Lai
Suet-feung Chin

Andrew Roth
Ali Bashashati
Jiarui Ding
Rodrigo Goya
Ryan Giuliany
Jamie Rosner
Arusha Oloumi
Karey Shumansky
Gulisa Turashvili
Martin Hirst
Marco A Marra
Samuel Aparicio
Sohrab P Shah
Carlos Caldas

Genome Research

Dissect: detection and characterization of novel structural alterations in transcribed sequences

2012-06-01

Inanc Birol

Deniz Yorukoglu
Faraz Hach
Lucas Swanson
Colin C Collins
S Cenk Sahinalp

Bioinformatics

Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.

2012-06-01

Piero Carninci
Yukihiko Noro

Alka Saxena
Akiko Wagatsuma
Takenobu Kuji
Atsuko Asaka-Oba
Akira Watahiki
Cecile Gurnot
Michela Fagiolini
Takao K Hensch

BioTechniques

Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection.

2012-06-02

Eric Peatman
Shikai Liu

Fanyue Sun
Chao Li
Yanliang Jiang
Zunchun Zhou
Zhanjiang Liu

Developmental and Comparative Immunology

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

2012-06-08

John E. Lunn
Björn Usadel
Alisdair R Fernie
Mark Stitt

Marc Lohse
Anthony M Bolger
Axel Nagel

Nucleic Acids Research

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

2012-06-08

Gabriel Kreiman
Nicole Cloonan
Sean M. Grimmond

Martin Hemberg
Jesse M Gray
Scott Kuersten
Michael E Greenberg

Nucleic Acids Research

Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.

2012-06-10

Marek Żywicki
Marcel Scheideler
Mathieu Rederstorff

Konstantinia Skreka
Michael Karbiener
Alexander Hüttenhofer

Journal of Nucleic Acids

Modeling gene expression using chromatin features in various cellular contexts

2012-06-13

Roderic Guigó i Serra
Mark Bender Gerstein
Ewan Birney
Sarah Djebali
Xianjun Dong
Anshul Kundaje
Thomas R. Gingeras

Melissa C Greven
James B Brown
Chao Cheng
Zhiping Weng

Genome Biology

Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma.

2012-06-13

Stephanie Ma
Li Fu
Xin-Yuan Guan
Xin-Yuan Guan

Jessie Y J Bao
Pak Shing Kwan
Yuen Piu Chan
Carol M Tong
Na Zhang
Amy H Y Tong
Yan-Ru Qin
Sai Wah Tsao
Kwok Wah Chan
Si Lok

Gastroenterology

Alternative splicing regulated by butyrate in bovine epithelial cells.

2012-06-14

Wen Huang
Weizhong Li

Sitao Wu
Congjun Li
Robert W Li

PLOS ONE

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.

2012-06-17

Alberto Ferrarini
Elisa Ficarra
Simona Soverini
Giovanni Martinelli
Ilaria Iacobucci

Francesco Abate
Andrea Acquaviva
Giulia Paciello
Carmelo Foti
Massimo Delledonne
Enrico Macii

Bioinformatics

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.

2012-06-18

Sean Doyle
David J. Lynn
Bernadette Earley

Aran O'Loughlin
Mark McGee
Matthew McCabe

BMC Genomics

Detecting differential usage of exons from RNA-seq data

2012-06-21

Alejandro Reyes
Simon Anders
Wolfgang Huber

Genome Research

PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification

2012-06-21

Zhaohui Steve Qin

Han Wu
Yu Zhu

Statistics in biosciences

Expressed pseudogenes in the transcriptional landscape of human cancers

2012-06-22

John R. Prensner
Shanker Kalyana-Sundaram
Chandan Kumar-Sinha
Irfan Asangani
Nallasivam Palanisamy

Sunita Shankar
Dan R Robinson
Yi-Mi Wu
Xuhong Cao
Vishal Kothari
Robert J Lonigro
Matthew K Iyer
Terrence Barrette
Achiraman Shanmugam
Saravana M Dhanasekaran
Arul M Chinnaiyan

Cell

RNA-Seq and human complex diseases: recent accomplishments and future perspectives.

2012-06-27

Valerio Costa

Marianna Aprile
Roberta Esposito
Alfredo Ciccodicola

European Journal of Human Genetics

FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.

2012-06-27

Richard W Francis
Kim Carter
Denise Anderson
Alex H. Beesley

Katherine Thompson-Wicking
Ursula R Kees

PLOS ONE

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.

2012-06-29

Gregory J. Kato

Nalini Raghavachari
Jennifer Barb
Yanqin Yang
Poching Liu
Kimberly Woodhouse
Daniel Levy
Christopher J O'Donnell
Peter J Munson

BMC Medical Genomics

SAVoR: a server for sequencing annotation and visualization of RNA structures

2012-07

Otto Valladares
Fan Li

Paul Ryvkin
Daniel M Childress
Brian D Gregory
Li-San Wang

Nucleic Acids Research

Digging in the RNA-seq Garbage: Evaluating the Characteristics of Unmapped RNA-seq Reads in Normal Tissues

2012-07

Federica Cavallo

Matteo Carrara
Maddalena Arigoni
Raffaele A. Calogero

Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks

2012-07-01

Catherine L Peichel

Anna K Greenwood
Jennifer N Cech

Evolution & Development

Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions

2012-07-01

Iros Barozzi
Gioacchino Natoli

Dev M Bhatt
Amy Pandya-Jones
Ann-Jay Tong
Michelle M Lissner
Douglas L Black
Stephen T Smale

Cell

RNA-seq analysis of the C. briggsae transcriptome.

2012-07-06

Bora Uyar

Jeffrey S C Chu
Ismael A Vergara
Shu Yi Chua
Martin R Jones
Tammy Wong
David L Baillie
Nansheng Chen

Genome Research

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

2012-07-12

Simon White

John E Collins
Stephen M J Searle
Derek L Stemple

Genome Research

Paired-end sequencing of Fosmid libraries by Illumina.

2012-07-16

Gad Getz
Chad Nusbaum
Yotam Drier

Louise J S Williams
Diana G Tabbaa
Na Li
Aaron M Berlin
Terrance P Shea
Iain Maccallum
Michael S Lawrence
Sarah K Young
David B Jaffe
Andreas Gnirke

Genome Research

Inflammatory priming predisposes mice to age-related retinal degeneration.

2012-07-17

Krzysztof Palczewski

Debarshi Mustafi
Tadao Maeda
Hideo Kohno
Joseph H Nadeau

Journal of Clinical Investigation

RNA processing in the minimal organism Nanoarchaeum equitans

2012-07-18

L Randau

Lennart Randau

Genome Biology

Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

2012-07-20

Daojun Yuan

Xiyan Yang
Xianlong Zhang
Fangyan Jin
Yunchao Zhang
Jiao Xu

BMC Plant Biology

Genomic imprinting absent in Drosophila melanogaster adult females.

2012-07-20

C Joel McManus
Brenton R. Graveley

Joseph D Coolon
Kraig R Stevenson
Patricia J Wittkopp

Cell Reports

Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data

2012-07-23

Willard M. Freeman
Kent Vrana

Kathryn J Huber-Keener
Xiuping Liu
Zhong Wang
Yaqun Wang
Song Wu
Maricarmen D Planas-Silva
Xingcong Ren
Yan Cheng
Yi Zhang
Chang-Gong Liu
Jin-Ming Yang
Rongling Wu

PLOS ONE

Metabolic Regulation of "Ca. Methylacidiphilum Fumariolicum" SolV Cells Grown Under Different Nitrogen and Oxygen Limitations.

2012-07-25

Huub J.M. Op den Camp

Ahmad F Khadem
Arjan Pol
Adam S Wieczorek
Mike S M Jetten

Frontiers in Microbiology

Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq.

2012-07-26

Akshay Kakumanu
Andy Pereira

Madana M R Ambavaram
Curtis Klumas
Arjun Krishnan
Utlwang Batlang
Elijah Myers
Ruth Grene

Plant Physiology

Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells.

2012-07-27

Guoping Fan

Ganlu Hu
Kevin Huang
Juehua Yu
Sailesh Gopalakrishna-Pillai
Jun Kong
He Xu
Zhenshan Liu
Kunshan Zhang
Jun Xu
Yuping Luo
Siguang Li
Yi E Sun
Linda E Iverson
Zhigang Xue

PLOS ONE

Identification of novel transcripts deregulated in buccal cancer by RNA-seq.

2012-07-27

Ajai K. Tripathi
Subhash J Jakhesara
Chaitanya G. Joshi

Manisha R Sajnani
Amrutlal K Patel
Vaibhav D Bhatt
Viral B Ahir
Vangipuram Shankar
Siddharth Shah
Tejas M Shah
Prakash G Koringa

Gene

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis

2012-07-29

Anastassios Vourekas
Panagiotis Alexiou
Manolis Maragkakis
Yohei Kirino
Zissimos Mourelatos

Qi Zheng
Brian D Gregory

Nature Structural & Molecular Biology

A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin.

2012-07-30

Karla D Passalacqua

Sarah W Satola
Emily K Crispell
Timothy D Read

Antimicrobial Agents and Chemotherapy

easyRNASeq: a bioconductor package for processing RNA-Seq data

2012-07-30

Eileen E. M. Furlong
Lars M Steinmetz

Nicolas Delhomme
Ismaël Padioleau

Bioinformatics

RNASeq profiling of UTR expression during neuronal plasticity.

2012-07-31

Robert M. Flight
Jeffrey C. Petruska

Benjamin J Harrison
Abdallah Eteleeb
Eric C Rouchka

BMC Bioinformatics

Recurrent R-spondin fusions in colon cancer.

2012-08-01

Robert Gentleman

Somasekar Seshagiri
Eric W Stawiski
Steffen Durinck
Zora Modrusan
Elaine E Storm
Caitlin B Conboy
Subhra Chaudhuri
Yinghui Guan
Vasantharajan Janakiraman
Bijay S Jaiswal
Joseph Guillory
Connie Ha
Gerrit J P Dijkgraaf
Jeremy Stinson
Florian Gnad
Melanie A Huntley
Jeremiah D Degenhardt
Peter M Haverty
Richard Bourgon
Weiru Wang
Hartmut Koeppen
Timothy K Starr
Zemin Zhang
David A Largaespada
Thomas D Wu
Frederic J de Sauvage

Nature

Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.

2012-08-04

Stéphane Poulain
Andrew Paul Hutchins
Hodaka Fujii

Diego Miranda-Saavedra

Genomics

Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.

2012-08-05

Altus Viljoen

Chun-Yu Li
Gui-Ming Deng
Jing Yang
Yan Jin
Rui-Bin Kuang
Cun-Wu Zuo
Zhi-Cheng Lv
Qiao-Song Yang
Ou Sheng
Yue-Rong Wei
Chun-Hua Hu
Tao Dong
Gan-Jun Yi

BMC Genomics

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.

2012-08-08

Vincent Lynch

Günter P Wagner
Koryu Kin

Theory in Biosciences

RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.

2012-08-13

Stan Gaj
Hans Lehrach
Ralf Herwig
Jos Kleinjans

Joost van Delft
Stan Gaj
Matthias Lienhard
Marcus W Albrecht
Alexander Kirpiy
Karen Brauers
Sandra Claessen
Daneida Lizarraga

Toxicological Sciences

Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish.

2012-08-13

Ian A Johnston

Graham R Scott

Proceedings of the National Academy of Sciences of the United States of America

Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.

2012-08-16

Peter A. DiMaggio
Barry M Zee

Gary LeRoy
Iouri Chepelev
Mario A Blanco
Keji Zhao
Benjamin A Garcia

Genome Biology

Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.

2012-08-16

Marilyn Renfree
Anthony T. Papenfuss
Emily S Wong
Camilla M Whittington
Glenn F King

David Morgenstern
Ehtesham Mofiz
Sara Gombert
Katrina M Morris
Peter Temple-Smith
Wesley C Warren
Katherine Belov

Molecular & Cellular Proteomics

RNA-seq transcriptome analysis of male and female zebra finch cell lines

2012-08-21

Christopher N. Balakrishnan
Ya-Chi Lin
Sarah E London
David F. Clayton

Christopher N Balakrishnan
Ya-Chi Lin
Sarah E London
David F Clayton

Genomics

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data

2012-08-21

Shaojie Zhang

Peter Tonner
Vinodh Srinivasasainagendra
Degui Zhi

BMC Genomics

Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome.

2012-08-21

Michael McManus
Hail Kim

Gregory M Ku
Ian W Vaughn
Matthew J Hangauer
Chang Myung Oh
Michael S German

Molecular Endocrinology

shortran: a pipeline for small RNA-seq data analysis.

2012-08-22

Stig Uggerhøj Andersen
Jens Stougaard

Vikas Gupta
Katharina Markmann
Christian N S Pedersen

Bioinformatics

Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis

2012-08-22

Karla D Passalacqua

Anjana Varadarajan
Charlotte Weist
Brian D Ondov
Benjamin Byrd
Timothy D Read
Nicholas H Bergman

PLOS ONE

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

2012-08-24

Yong Zhang

Jianxing Feng
Clifford A Meyer
Qian Wang
Jun S Liu
X Shirley Liu

Bioinformatics

An injury-response mechanism conserved across kingdoms determines entry of the fungus Trichoderma atroviride into development.

2012-08-27

Miguel Hernández-Oñate
Alfredo Herrera-Estrella

Edgardo U Esquivel-Naranjo
Artemio Mendoza-Mendoza
Alison Stewart

Proceedings of the National Academy of Sciences of the United States of America

A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.

2012-08-28

Anna Terry
Niall G. Campbell
Charles Mein

Scott Brouilette
Scott Kuersten
Monika Bozek
Kerith-Rae Dias
Leena Bhaw-Rosun
Yasunori Shintani
Steven Coppen
Chiho Ikebe
Vinit Sawhney
Masahiro Kaneko
Nobuko Tano
Hidekazu Ishida
Ken Suzuki
Kenta Yashiro

Developmental Dynamics

A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq.

2012-08-30

Winfriede Weschke

Stefan Kohl
Julien Hollmann
Frank R Blattner
Volodymyr Radchuk
Franka Andersch
Burkhard Steuernagel
Thomas Schmutzer
Uwe Scholz
Karin Krupinska
Hans Weber

BMC Plant Biology

Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders

2012-08-30

Deyou Zheng

Mingyan Lin
Anastasia Hrabovsky
Erika Pedrosa
Tao Wang
Herbert M Lachman

PLOS ONE

RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter

2012-08-30

Nicolas Rouhier
Julie Poulain
Benjamin Petre
Sébastien Duplessis
Corinne Da Silva
Francis Martin
Emmanuelle Morin
Annegret Kohler

Emilie Tisserant
Stéphane Hacquard
Christine Delaruelle

PLOS ONE

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

2012-09

Roderic Guigó i Serra
Sarah Djebali
Rory Johnson
Thomas R. Gingeras

Hagen Tilgner
David G Knowles
Carrie A Davis
Sudipto Chakrabortty
João Curado
Michael Snyder

Genome Research

Dual RNA-seq of pathogen and host.

2012-09-01

Alexander Westermann
Jörg Vogel

Stanislaw A Gorski

Nature Reviews Microbiology

Long noncoding RNAs are rarely translated in two human cell lines

2012-09-01

Yanbao Yu
Anshul Kundaje
Brian D Strahl
Krzysztof Krajewski

Balázs Bánfai
Hui Jia
Jainab Khatun
Emily Wood
Brian Risk
William E Gundling
Harsha P Gunawardena
Ling Xie
Xian Chen
Peter Bickel
Morgan C Giddings
James B Brown
Leonard Lipovich

Genome Research

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

2012-09-01

Andrea Tanzer
Jose M Gonzalez
Bronwen Aken
Tim Hubbard
Jennifer Harrow
Felix Kokocinski
Roderic Guigó i Serra
Cédric Howald
Thibaut Hourlier
Thomas Derrien
Alexandre Reymond
Simon White
Adam Frankish

Jacqueline Chrast
Nathalie Walters
Jan-Hinnerk Vogel
Stephen Searle

Genome Research

Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes.

2012-09-03

Xiaohan Yang
Gerald A Tuskan
Sara S Jawdy
Lee Gunter
Stan D Wullschleger

Abhijit A Karve
Sara M Allen
David J Weston

New Phytologist

The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.

2012-09-04

Silvia Dal Santo
Giovanni Battista Tornielli
Vittorio Murino
Luca Venturini
Lorenzo Farina

Marianna Fasoli
Sara Zenoni
Anita Zamboni
Andrea Porceddu
Manuele Bicego
Alberto Ferrarini
Massimo Delledonne
Mario Pezzotti

The Plant Cell

A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue

2012-09-05

Graziano Pesole
Angela Gallo
Ernesto Picardi

Federica Galeano
Sara Tomaselli

PLOS ONE

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

2012-09-07

Roderic Guigó i Serra
Michael Sammeth

Thasso Griebel
Benedikt Zacher
Paolo Ribeca
Emanuele Raineri
Vincent Lacroix

Nucleic Acids Research

Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-Seq

2012-09-07

Mariangela Bonnizoni
Guiyun Yan

Yaw Afrane
William Augustine Dunn
Francis K Atieli
Goufa Zhou
Daibin Zhong
Jun Li
Andrew Githeko

PLOS ONE

Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.

2012-09-08

Taejoon Kwon
Rosa A Uribe
Jeffrey M Gross

Developmental Biology

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

2012-09-10

Jens Nielsen
Natapol Pornputtapong
Linn Fagerberg
Intawat Nookaew

Marta Papini
Gionata Scalcinati
Matthias Uhlén

Nucleic Acids Research

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.

2012-09-11

Todd P Michael

Chongyuan Luo
David J Sidote
Yi Zhang
Randall A Kerstetter
Eric Lam

The Plant Journal

The bench scientist's guide to statistical analysis of RNA-Seq data.

2012-09-14

Craig R Yendrek

Elizabeth A Ainsworth
Jyothi Thimmapuram

BMC Research Notes

Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.

2012-09-17

Georgi K Marinov
Peter Dervan

Jevgenij A Raskatov
Nicholas G Nickols
Amanda E Hargrove
Barbara Wold

Proceedings of the National Academy of Sciences of the United States of America

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

2012-09-18

Harri Lähdesmäki
Vivek Anantharaman
Lakshminarayanan Aravind
Tarmo Aijö
John Gagnon
Xing Chang

Micah J Benson
Tarmo Aijö
Utz J Pape
Juha-Pekka Pursiheimo
Shalini Oberdoerffer
X Shirley Liu
Riitta Lahesmaa
Anjana Rao

Proceedings of the National Academy of Sciences of the United States of America

Functional transcriptomics of a migrating cell in Caenorhabditis elegans.

2012-09-18

Erich M Schwarz
Paul W. Sternberg

Mihoko Kato

Proceedings of the National Academy of Sciences of the United States of America

Differential Expression Analysis for RNA-Seq Data.

2012-09-20

Alok Bhattacharya

Rashi Gupta
Isha Dewan
Richa Bharti

ISRN bioinformatics

A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters

2012-09-20

Yi Zheng

Yun-Ru Chen
Bao Liu
Silin Zhong
Jim Giovannoni
Zhangjun Fei

Plant Methods

High-resolution transcriptome of human macrophages.

2012-09-21

Joachim Schultze
Andrea Nino-Castro

Marc Beyer
Michael R Mallmann
Jia Xue
Andrea Staratschek-Jox
Daniela Vorholt
Wolfgang Krebs
Daniel Sommer
Jil Sander
Christina Mertens
Susanne V Schmidt

PLOS ONE

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.

2012-09-22

Hao Wu
Zhijin Wu

Chi Wang

Biostatistics

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.

2012-09-24

Axel Künstner

Nagarjun Vijay
Jelmer W Poelstra
Jochen B W Wolf

Molecular Ecology

RNA-Seq Assembly - Are We There Yet?

2012-09-25

Andrea Bräutigam

Simon Schliesky
Udo Gowik
Andreas P M Weber

Frontiers in Plant Science

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.

2012-09-26

Peggy Farnham

Seth Frietze
Rui Wang
Lijing Yao
Yu Gyoung Tak
Zhenqing Ye
Malaina Gaddis
Heather Witt
Victor X Jin

Genome Biology

A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level.

2012-10-01

Israel Barrantes
Jeremy Leipzig

Wolfgang Marwan

Gene Regulation and Systems Biology

The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation

2012-10-01

Sen-Lin Lai

Michael R Miller
Kristin J Robinson
Chris Q Doe

Developmental Cell

Dual lineage-specific expression of Sox17 during mouse embryogenesis.

2012-10-01

Momoko Yoshimoto
Mark A. Magnuson
Elisabetta Manduchi
Anne Grapin-Botton

Eunyoung Choi
Marine R C Kraus
Laurence A Lemaire
Sasidhar Vemula
Leah A Potter
Christian J Stoeckert

Stem Cells

Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq.

2012-10-01

Jennifer Beane
John Quackenbush
Naftali Kaminski

Rebecca L Kusko
John Brothers
Gang Liu
Lingqi Luo
Brenda Juan Guardela
John Tedrow
Yuriy Aleksyev
Ivana V Yang
Mick Correll
Mark Geraci
Frank Sciurba
Marc Lenburg
David A Schwartz
Avrum Spira

BMC Proceedings

SERE: single-parameter quality control and sample comparison for RNA-Seq.

2012-10-03

Rahul Kanwar

Stefan K Schulze
Meike Gölzenleuchter
Terry M Therneau
Andreas S Beutler

BMC Genomics

Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.

2012-10-03

Anton Suvorov

Nicola Palmieri
Viola Nolte
Carolin Kosiol
Christian Schlötterer

PLOS ONE

Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage.

2012-10-05

David Casero
Eugen Urzica
Crysten E Blaby-Haas
Matteo Pellegrini
Sabeeha Merchant

Hiroaki Yamasaki
Scott I Hsieh
Lital N Adler
Steven J Karpowicz
Steven G Clarke
Joseph A Loo

The Plant Cell

Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle.

2012-10-10

Subhash J Jakhesara
Chaitanya G. Joshi
Ajai K. Tripathi

Amrutlal K Patel
Vaibhav D Bhatt
Manisha R Sajnani
Prakash G Koringa

Genomics

New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain.

2012-10-11

Julien Rougeot
Anne Coléno-Costes
Jean-Michel Gibert
Frédérique Peronnet
Stéphane Le Crom

Suk Min Jang
Augustin de Vanssay
Tahar Bouceba
Neel B Randsholt
Emmanuèle Mouchel-Vielh
Sébastien Bloyer

PLOS Genetics

Faster-X evolution of gene expression in Drosophila

2012-10-11

Richard P Meisel

John H Malone
Andrew G Clark

PLOS Genetics

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.

2012-10-11

Wei Li

Tao Jiang

Bioinformatics

Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.

2012-10-12

Naoto Imamachi
Hidenori Tani

Kazi Abdus Salam
Rena Mizutani
Kenichi Ijiri
Takuma Irie
Tetsushi Yada
Yutaka Suzuki
Nobuyoshi Akimitsu

RNA Biology

The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii.

2012-10-13

Eugen Urzica
David Casero
Matteo Pellegrini
Sabeeha Merchant

Scott I Hsieh
Madeli Castruita
Davin Malasarn
Jonathan Erde
M Dudley Page
Hiroaki Yamasaki
Joseph A Loo

Molecular & Cellular Proteomics

High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.

2012-10-15

Hans Ellegren

Benoit Nabholz
Jochen B W Wolf

Molecular Biology and Evolution

The biology of nematode- and IL4Rα-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics.

2012-10-16

Graham D Thomas
Dominik Ruckerl
Phillip D. Whitfield
Mark Blaxter
Judith Allen

Benjamin H Maskrey

Blood

A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites.

2012-10-17

David R. Colquhoun
Jürgen Hartler
Gerhard G Thallinger
Jesus Martinez-Barnetche
Antonis Rokas
Rhoel Dinglasan

Ceereena Ubaida Mohien
Derrick K Mathias
John G Gibbons
Jennifer S Armistead
Maria C Rodriguez
Mario Henry Rodriguez
Nathan J Edwards
David R Graham

Molecular & Cellular Proteomics

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.

2012-10-23

Matteo Benelli
Marco Severgnini
Alberto Magi

Chiara Pescucci
Giuseppina Marseglia
Francesca Torricelli

Bioinformatics

Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period.

2012-10-23

Paul A McGettigan
Jane A Irwin
Alan Baird
Brendan Loftus

Katarzyna Pluta
Colm J Reid
John A Browne
Tharmala Tharmalingam
Anthony Corfield
Alexander C O Evans
Stephen D Carrington

Physiological Genomics

Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus

2012-10-24

Daniel Gautheret
Philippe Bouloc
Annick Jacq

Claire Toffano-Nioche
An N Nguyen
Claire Kuchly
Alban Ott

RNA

STAR: ultrafast universal RNA-seq aligner

2012-10-25

Philippe Batut
Thomas R. Gingeras

Alexander Dobin
Carrie A Davis
Felix Schlesinger
Jorg Drenkow
Chris Zaleski
Sonali Jha
Mark Chaisson

Bioinformatics

Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola

2012-10-25

Igor V Grigoriev

Yangrae Cho
Akhil Srivastava
Robin A Ohm
Christopher B Lawrence
Koon-Hui Wang
Sharadchandra P Marahatta

PLOS Pathogens

RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

2012-10-25

Matthew Berriman

Jonathan D Stoltzfus
Samuel Minot
Thomas J Nolan
James B Lok

PLOS Neglected Tropical Diseases

The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq.

2012-10-25

Nolan Kane
Brook T Moyers
Sébastien Renaut
Loren H. Rieseberg

Christopher J Grassa

Biology

Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq.

2012-10-27

Richard D Newcomb
Thomas R. Buckley
Duckchul Park
Brent J Sinclair
Alice B Dennis
Luke T Dunning

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Identification of PADI2 as a potential breast cancer biomarker and therapeutic target.

2012-10-30

Obi Griffith
Venkataraman Subramanian
John L. McElwee
Brian D Cherrington
Louise R Howe

Sunish Mohanan
Heike C Breuer
Lynne J Anguish
Ashley M Palmer
Corey P Causey
Paul R Thompson
Joe W Gray
Scott A Coonrod

BMC Cancer

Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II

2012-11

Jerry F. Tien
Malachi Griffith
Gregg B Morin

S-W Grace Cheng
Michael A Kuzyk
Annie Moradian
Taka-Aki Ichu
Vicky C-D Chang
Sarah E Vollett
Marco A Marra

Molecular and Cellular Biology

2012-11-01

Dean Palejev
Flora M. Vaccarino

Oksana Yu Naumova
Natalia V Vlasova
Maria Lee
Sergei Yu Rychkov
Olga N Babich
Elena L Grigorenko

Development and Psychopathology

Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

2012-11-05

Andrew M Carroll
Caroline Meharg
David J Vandenbergh

Arimantas Lionikas
Jonathan Mj Derry
Aivaras Ratkevicius
David A Blizard

BMC Genomics

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

2012-11-05

Shikai Liu
Eric Peatman
Geoff Waldbieser
Huseyin Kucuktas

Yu Zhang
Zunchun Zhou
Geoff Waldbieser
Fanyue Sun
Jianguo Lu
Jiaren Zhang
Yanliang Jiang
Hao Zhang
Xiuli Wang
K V Rajendran
Lester Khoo
Zhanjiang Liu

BMC Genomics

Novel BRD4-NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma.

2012-11-05

Adrian K. Charles
Alex H. Beesley

K Thompson-Wicking
R W Francis
A Stirnweiss
E Ferrari
M D Welch
E Baker
A R Murch
A M Gout
K W Carter
M B Phillips
U R Kees

Oncogene

Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region

2012-11-06

Marie-Laure Endale Ahanda
Dario Beraldi
Jordi Estellé
Claire Rogel-Gaillard
James M Reecy

Eric R Fritz
Zhi-Liang Hu
Ole Madsen
Martien A M Groenen
Ronan Kapetanovic
David A Hume
Robert R R Rowland
Joan K Lunney
Elisabetta Giuffra

PLOS ONE

Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.

2012-11-06

Takeshi Itoh

Yoshihiro Kawahara
Youko Oono
Hiroyuki Kanamori
Takashi Matsumoto
Eiichi Minami

PLOS ONE

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

2012-11-15

D. Neil Hayes

Yin Hu
Yan Huang
Ying Du
Christian F Orellana
Darshan Singh
Amy R Johnson
Anaïs Monroy
Pei-Fen Kuan
Scott M Hammond
Liza Makowski
Scott H Randell
Derek Y Chiang
Corbin Jones
Yufeng Liu
Jan F Prins
Jinze Liu

Nucleic Acids Research

Methods, Challenges and Potentials of Single Cell RNA-seq.

2012-11-16

Daniel Hebenstreit

Biology

The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.

2012-11-20

Aurelien L Carlier
Christian H Ahrens
Ulrich Omasits
Gabriella Pessi

Nadine Schmid
Yinyue Deng
Claudio Aguilar
Alexander Grunau
Lian-Hui Zhang
Leo Eberl

PLOS ONE

Intron-centric estimation of alternative splicing from RNA-seq data.

2012-11-21

Roderic Guigó i Serra

Dmitri D Pervouchine
David G Knowles

Bioinformatics

High-throughput sequencing of the melanoma genome.

2012-11-22

Janet Kelso

Manfred Kunz
Michael Dannemann

Experimental Dermatology

A comprehensive analysis of the Manduca sexta immunotranscriptome.

2012-11-23

Haobo Jiang

Ramesh T Gunaratna

Developmental and Comparative Immunology

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.

2012-11-24

Charles Plessy
Piero Carninci

Dave T P Tang
Md Salimullah
Ana Maria Suzuki
Raffaella Calligaris
Stefano Gustincich

Nucleic Acids Research

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data

2012-11-29

Derek Y Chiang
Michael Brudno

Aziz M Mezlini
Eric J M Smith
Marc Fiume
Orion Buske
Gleb L Savich
Sohrab Shah
Sam Aparicio
Anna Goldenberg

Genome Research

Nuclear RNA sequencing of the mouse erythroid cell transcriptome

2012-11-29

Chih-Yu Chen
Jennifer A. Mitchell
Ieuan Clay
Peter Fraser

David Umlauf
Catherine A Moir
Christopher H Eskiw
Stefan Schoenfelder
Lyubomira Chakalova
Takashi Nagano

PLOS ONE

The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus.

2012-12-01

Xiaofan Zhou
Antonis Rokas

John G Gibbons
Anne Beauvais
Jean-Paul Latgé

Annals of the New York Academy of Sciences

An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells.

2012-12-04

Songnian Hu

Lina Ma
Linghu Nie
Jing Liu
Bing Zhang
Shuhui Song
Min Sun
Jin Yang
Yadong Yang
Xiangdong Fang
Yongliang Zhao
Jun Yu

Genomics Proteomics and Bioinformatics

A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.

2012-12-06

Alexander Stark
Denes Hnisz
Karl Kuchler

Anaïs F Bardet
Clarissa J Nobile
Andriy Petryshyn
Walter Glaser
Ulrike Schöck

PLOS Genetics

The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells.

2012-12-06

Wolf Reik
Felix Krueger
Bernard Thienpont
Julia Arand

Stefanie Seisenberger
Simon Andrews
Jörn Walter
Fátima Santos
Christian Popp
Wendy Dean

Molecular Cell

RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering

2012-12-10

Martin Crane

Alina Sîrbu
Gráinne Kerr
Heather J Ruskin

PLOS ONE

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.

2012-12-13

Andrew C Perkins
Timothy L. Bailey

Lei Sun
Zhihua Zhang
Michael R Tallack
Zhao Xu
Hui Liu

BMC Bioinformatics

Chromatin is an ancient innovation conserved between Archaea and Eukarya.

2012-12-13

Corey Nislow
Gary D. Bader

Ron Ammar
Dax Torti
Kyle Tsui
Marinella Gebbia
Tanja Durbic
Guri Giaever

eLife

RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia

2012-12-17

Xiangning Chen

Junzhe Xu
Jingchun Sun
Jingchun Chen
Lily Wang
Anna Li
Matthew Helm
Steven L Dubovsky
Silviu-Alin Bacanu
Zhongming Zhao

BMC Genomics

A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees.

2012-12-17

Jörg Bohlmann

Ye Wang
Lynette Lim
Scott DiGuistini
Gordon Robertson
Colette Breuil

New Phytologist

Circular RNAs are abundant, conserved, and associated with ALU repeats.

2012-12-18

Norman Sharpless

William R Jeck
Jessica A Sorrentino
Kai Wang
Michael K Slevin
Christin E Burd
Jinze Liu
William F Marzluff

RNA

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency.

2012-12-20

Jeremy Luban

Federico A Santoni
Jessica Guerra

Retrovirology

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.

2012-12-22

Guojun Lu

Tingting Lu
Chuanrang Zhu
Yunli Guo
Yan Zhou
Zhiyong Zhang
Yan Zhao
Wenjun Li
Ying Lu
Weihua Tang
Qi Feng
Bin Han

BMC Genomics

A comprehensive evaluation of alignment algorithms in the context of RNA-seq

2012-12-26

Caroline C Friedel

Robert Lindner

PLOS ONE

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

2012-12-27

Chad Nusbaum

Brian J Haas
Melissa Chin
Bruce W Birren
Jonathan Livny

BMC Genomics

Correlates of relative resistance against low-dose rectal simian immunodeficiency virus challenges in peripheral blood mononuclear cells of vaccinated rhesus macaques.

2012-12-27

Sarah J. Ratcliffe

Raj Kurupati
Steve Tuyishime
Andrew V Kossenkov
Marina Sazanovich
Larissa H Haut
Marcio O Lasaro
Steven E Bosinger
Diane G Carnathan
Mark Lewis
Louise C Showe
Guido Silvestri
Hildegund C J Ertl

Journal of Leukocyte Biology

Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data

2013

Matthias Kretzler
Gil Omenn

Ridvan Eksi
Hong-Dong Li
Rajasree Menon
Yuchen Wen
Yuanfang Guan

PLOS Computational Biology

Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement

2013

Cecilia Kim
Hakon Hakonarson

Kai Wang
Jonathan Bradfield
Yunfei Guo
Elina Toskala
Frederick G Otieno
Cuiping Hou
Kelly Thomas
Christopher Cardinale
Gholson J Lyon
Ryan Golhar

Genome Medicine

Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation

2013

Hong-Ye Li

Zhi-Kai Yang
Ying-Fang Niu
Yu-Han Ma
Jiao Xue
Meng-Han Zhang
Wei-Dong Yang
Jie-Sheng Liu
Song-Hui Lu
Yuanfang Guan

Biotechnology for Biofuels

"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids"

2013

Jennifer Ann Harikrishna

Mark W Davey
Ranganath Gudimella
Lee Wan Sin
Norzulaani Khalid
Johan Keulemans

BMC Genomics

RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib

2013

James R. Bradford

Matthew Farren
Steve J Powell
Sarah Runswick
Susie L Weston
Helen Brown
Oona Delpuech
Mark Wappett
Neil R Smith
T Hedley Carr
Jonathan R Dry
Neil J Gibson
Simon T Barry

PLOS ONE

RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse

2013

Arthur L. Horwich
Justin Cotney

Urmi Bandyopadhyay
Maria Nagy
Sunghee Oh
Jing Leng
Milind Mahajan
Shrikant Mane
Wayne A Fenton
James P Noonan

PLOS ONE

Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer

2013

Olivier Harismendy

Christian L Barrett
Richard B Schwab
HyunChul Jung
Brian Crain
Daniel J Goff
Catriona H M Jamieson
Patricia A Thistlethwaite
Dennis A Carson
Kelly A Frazer

PLOS ONE

RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches

2013

Yaodong Yang
Annaliese S Mason

Haikuo Fan
Yong Xiao
Wei Xia
Zhihui Xia
Fei Qiao
Songlin Zhao
Haoru Tang

PLOS ONE

Integrative approach reveals composition of endoparasitoid wasp venoms

2013

Todd A Schlenke
Nathan T Mortimer
James Taylor

Jeremy Goecks
James A Mobley
Gregory J Bowersock

PLOS ONE

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing

2013

Yinglong Chen

Yan Wang
Liang Xu
Hong Shen
Yiqin Gong
Cecilia Limera
Liwang Liu

PLOS ONE

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data

2013

Philip D Dunne
Darragh G McArt
Shu-Dong Zhang

Jaine K Blayney
Manuel Salto-Tellez
Sandra Van Schaeybroeck
Peter W Hamilton

PLOS ONE

Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe

2013

Michael Janitz
Glenda Halliday

James D Mills
Tomas Kavanagh
Woojin S Kim
Bei Jun Chen
Yoshihiro Kawahara

PLOS ONE

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy

2013

Majid Kazemian

Qiong Cheng
Hannah Pham
Charles Blatti
Susan E Celniker
Scot A Wolfe
Michael H Brodsky
Saurabh Sinha

PLOS Genetics

Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands

2013

Wilhelm Boland
René R Bodemann
Marco Groth

Magdalena Stock
Simone Eiserloh
Antje Burse

PLOS ONE

MicroRNA discovery by similarity search to a database of RNA-seq profiles

2013

Jan Gorodkin
Sachin Pundhir

Frontiers in Genetics

Differential analysis of gene regulation at transcript resolution with RNA-seq

2013-01

John L. Rinn

Trapnell C
Hendrickson DG
Sauvageau M
Goff L
Pachter L

Nature Biotechnology

Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data

2013-01-01

Yves A. Lussier

Alan Perez-Rathke
Haiquan Li

Pacific Symposium on Biocomputing

Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.

2013-01-01

Stephane Rombauts
Alain Goossens

Jacob Pollier

Methods in Molecular Biology

High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences

2013-01-01

Rod A. Wing

Chengjun Zhang
Jun Wang
Nicholas C Marowsky
Manyuan Long
Chuanzhu Fan

Genome Biology and Evolution

RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations.

2013-01-01

Loren H. Rieseberg

Graeme D M Bell
Nolan C Kane
Keith L Adams

Genome Biology and Evolution

Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.

2013-01-01

Hans Ellegren

Severin Uebbing
Axel Künstner
Hannu Mäkinen

Genome Biology and Evolution

Genomic, RNAseq, and molecular modeling evidence suggests that the major allergen domain in insects evolved from a homodimeric origin

2013-01-01

Thomas A Randall
Geoffrey A Mueller
Lalith Perera

Robert E London

Genome Biology and Evolution

Transcriptome sequencing of neonatal thymic epithelial cells.

2013-01-01

Claude Perreault

Charles St-Pierre
Sylvie Brochu
Juan Ruiz Vanegas
Maude Dumont-Lagacé
Sébastien Lemieux

Scientific Reports

In vitro expansion of fetal neural progenitors as adherent cell lines.

2013-01-01

Steven M Pollard

Methods in Molecular Biology

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

2013-01-07

Ching-Chia Yang
Tsuyoshi Tanaka
Takeshi Itoh

Hiroaki Sakai
Sung Shin Lee
Hisataka Numa
Jungsok Kim
Yoshihiro Kawahara
Hironobu Wakimoto
Masao Iwamoto
Takashi Abe
Yuko Yamada
Akira Muto
Hachiro Inokuchi
Toshimichi Ikemura
Takashi Matsumoto
Takuji Sasaki

Plant and Cell Physiology

RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism.

2013-01-07

Pingzhao Hu
Michael Janitz

James D Mills
Thomas Nalpathamkalam
Heidi I L Jacobs
Caroline Janitz
Daniele Merico

Neuroscience Letters

Dual functions of TAF7L in adipocyte differentiation.

2013-01-08

Michael Eisen
Ivan Grubisic
Tommy Kaplan
Haiying Zhou
Yan Li
Zhengjian Zhang
P Jeremy Wang
Robert Tjian

eLife

MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.

2013-01-08

Jonathon T Hill

Bradley L Demarest
Brent W Bisgrove
Bushra Gorsi
Yi-Chu Su
H Joseph Yost

Genome Research

SIBER: systematic identification of bimodally expressed genes using RNAseq data

2013-01-09

Kevin R. Coombes

Pan Tong
Yong Chen
Xiao Su

Bioinformatics

Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls.

2013-01-11

Frank Baas

Ching Yong Yick
Aeilko H Zwinderman
Peter W Kunst
Katrien Grünberg
Thais Mauad
Annemiek Dijkhuis
Elisabeth H Bel
René Lutter
Peter J Sterk

European Respiratory Journal

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.

2013-01-12

Raymond Wan

Jing-Woei Li
Chi-Shing Yu
Ngai Na Co
Nathalie Wong
Ting-Fung Chan

Bioinformatics

Comparative RNA-seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.

2013-01-14

Joël F. Pothier
A Patocchi

Didier Socquet-Juglard
Tim Kamber
Danilo Christen
Cesare Gessler
Brion Duffy

PLOS ONE

Dynamic DNA methylation across diverse human cell lines and tissues

2013-01-16

Gregory E Crawford
John A Stamatoyannopoulos

Katherine E Varley
Jason Gertz
Kevin M Bowling
Stephanie L Parker
Timothy E Reddy
Florencia Pauli-Behn
Marie K Cross
Brian A Williams
Devin M Absher
Barbara J Wold
Richard M Myers

Genome Research

RNA-Seq data: a goldmine for organelle research.

2013-01-18

David Roy Smith

Briefings in functional genomics

Efficient and comprehensive representation of uniqueness for next-generation sequencing by minimum unique length analyses.

2013-01-18

Daniel Ramsköld
Rickard Sandberg

Helena Storvall

PLOS ONE

Analysis of RNA-Seq data reveals involvement of JAK/STAT signalling during leg regeneration in the cricket Gryllus bimaculatus.

2013-01-23

Taro Nakamura

Tetsuya Bando
Yoshiyasu Ishimaru
Takuro Kida
Yoshimasa Hamada
Yuji Matsuoka
Hideyo Ohuchi
Sumihare Noji
Taro Mito

Development

Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor.

2013-01-25

Gernot Glöckner

Anika Schmith
Marco Groth
Josephine Ratka
Sara Gatz
Thomas Spaller
Oliver Siol
Thomas Winckler

Eukaryotic Cell

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

2013-01-28

John C Marioni
Jong Kyoung Kim

Genome Biology

Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.

2013-01-31

Jozef Gécz
Lam S Nguyen
James F. Gusella

Hyung-Goo Kim
Jill A Rosenfeld
Yiping Shen
Yves Lacassie
Lawrence C Layman
Lisa G Shaffer

Human Molecular Genetics

The evolutionary causes and consequences of sex-biased gene expression.

2013-02-01

Hans Ellegren

John Parsch

Nature Reviews Genetics

Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.

2013-02-01

Cristian Del Fabbro

Federico M Giorgi
Francesco Licausi

Bioinformatics

puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.

2013-02-05

Magnus Rattray

Xuejun Liu
Zhenzhu Gao
Li Zhang

BMC Bioinformatics

Genetic screens: RNA-seq into the toolkit.

2013-02-05

Darren J. Burgess

Nature Reviews Genetics

Expression profile of ectopic olfactory receptors determined by deep sequencing.

2013-02-06

Hanns Hatt
Günter Gisselmann

Caroline Flegel
Stavros Manteniotis
Sandra Osthold
Günter Gisselmann

PLOS ONE

A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers

2013-02-06

Wan Kyu Kim
Namshin Kim

Sang Cheol Kim
Yeonjoo Jung
Jinah Park
Sooyoung Cho
Chaehwa Seo
Jaesang Kim
Pora Kim
Jehwan Park
Jihae Seo
Jiwoong Kim
Seongjin Park
Insu Jang
Jin Ok Yang
Byungwook Lee
Kyoohyoung Rho
Yeonhwa Jung
Juhee Keum
Jinseon Lee
Jungho Han
Sangeun Kang
Sujin Bae
So-Jung Choi
Sujin Kim
Jong-Eun Lee
Jhingook Kim
Sanghyuk Lee

PLOS ONE

FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns.

2013-02-06

Zissimos Mourelatos
Manolis Maragkakis
Panagiotis Alexiou

Tadashi Nakaya
Alexandra Chang

RNA

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.

2013-02-14

Jun Wang
Wenlong Jia

Kunlong Qiu
Minghui He
Pengfei Song
Quan Zhou
Feng Zhou
Yuan Yu
Dandan Zhu
Michael L Nickerson
Shengqing Wan
Xiangke Liao
Xiaoqian Zhu
Shaoliang Peng
Yingrui Li
Guangwu Guo

Genome Biology

The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle

2013-02-14

Paul W. Sternberg

Jagan Srinivasan
Adler R Dillman
Marissa G Macchietto
Liisa Heikkinen
Merja Lakso
Kelley M Fracchia
Igor Antoshechkin
Ali Mortazavi
Garry Wong

Genetics

mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex.

2013-02-17

Dagmar Galter
David N Hauser
Mark R Cookson

Allissa A Dillman
J Raphael Gibbs
Michael A Nalls
Melissa K McCoy
Iakov N Rudenko

Nature Neuroscience

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.

2013-02-21

Christina Kendziorski

Ning Leng
John A Dawson
James A Thomson
Victor Ruotti
Anna I Rissman
Bart M G Smits
Jill D Haag
Michael N Gould
Ron M Stewart

Bioinformatics

Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii.

2013-02-25

Sabeeha Merchant
Matteo Pellegrini
David Casero

Davin Malasarn
Janette Kropat
Scott I Hsieh
Giovanni Finazzi
Joseph A Loo
Francis-André Wollman

Journal of Biological Chemistry

Activity of a Py-Im polyamide targeted to the estrogen response element.

2013-02-26

Jerzy O Szablowski
Peter Dervan

Nicholas G Nickols
Amanda E Hargrove
Benjamin C Li
Jevgenij A Raskatov

Molecular Cancer Therapeutics

Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility.

2013-02-27

Scott E. Lindner
Sebastian A. Mikolajczak

Ashley M Vaughan
Wonjong Moon
Brad R Joyce
William J Sullivan
Stefan H I Kappe

Cellular Microbiology

SplicingCompass: differential splicing detection using RNA-seq data.

2013-02-28

Roland Eils

Moritz Aschoff
Agnes Hotz-Wagenblatt
Karl-Heinz Glatting
Matthias Fischer
Rainer König

Bioinformatics

Epstein - Barr virus transforming protein LMP-1 alters B cells gene expression by promoting accumulation of the oncoprotein ΔNp73α

2013-03

Florence Le Calvez-Kelm
Birke Bartosch
Evelyne Manet
Hector Hernandez-Vargas

Rosita Accardi
Ikbal Fathallah
Henri Gruffat
Giuseppe Mariggiò
Catherine Voegele
James McKay
Bakary S Sylla
Massimo Tommasino

PLOS Pathogens

WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.

2013-03-06

David K. Crossman

Wen Jiang
Elizabeth H Mitchell
Philip Sohn
Michael R Crowley
Rosa Serra

PLOS ONE

RNA-seq reveals activation of both common and cytokine-specific pathways following neutrophil priming.

2013-03-06

Huw B Thomas
Helen L Wright

Robert J Moots
Steven W Edwards

PLOS ONE

Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA.

2013-03-06

Cyprian Rossetto
Subhash Verma
Gregory S. Pari

Margaret Tarrant-Elorza
Pravinkumar Purushothaman

Journal of Virology

RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula.

2013-03-06

Anca Macovei
Daniela Carbonera
Alma Balestrazzi

Mattia Donà
Massimo Confalonieri
Andrea Minio
Marco Biggiogera
Armando Buttafava
Elena Raimondi
Massimo Delledonne
Lorenzo Ventura
Maria Elisa Sabatini
Giorgio Giraffa

Journal of Experimental Botany

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

2013-03-07

Bianca Habermann
Elly M Tanaka

Ron Stewart
Cynthia Alexander Rascón
Shulan Tian
Jeff Nie
Chris Barry
Li-Fang Chu
Hamisha Ardalani
Ryan J Wagner
Mitchell D Probasco
Jennifer M Bolin
Ning Leng
Srikumar Sengupta
Michael Volkmer
James A Thomson
Colin N Dewey

PLOS Computational Biology

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR).

2013-03-08

Jasmine Jacob-Hirsch

Oz Solomon
Shirley Oren
Michal Safran
Naamit Deshet-Unger
Pinchas Akiva
Jasmine Jacob-Hirsch
Karen Cesarkas
Reut Kabesa
Ninette Amariglio
Ron Unger
Gideon Rechavi
Eran Eyal

RNA

A comparison of methods for differential expression analysis of RNA-seq data

2013-03-09

Charlotte Soneson

Mauro Delorenzi

BMC Bioinformatics

Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.

2013-03-13

Susan Fanayan
Ling Yen Lee

Joshua T Smith
Fangfei Yan
Michael Snyder
William S Hancock
Edouard Nice

Journal of Proteome Research

CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data.

2013-03-14

Stephane Rombauts
Kirsi-Marja Oksman-Caldentey
Michele Fabris
Alex Van Moerkercke
Jacob Pollier
Johan Memelink
Alain Goossens

Gino J E Baart
Ghulam Hasnain
Heiko Rischer

Plant and Cell Physiology

Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling

2013-03-14

Christina A Cuomo

Amber J Marty
Marcel Wüthrich
John C Carmen
Thomas D Sullivan
Bruce S Klein
Gregory M Gauthier

Fungal Genetics and Biology

TDP-43 high throughput screening analyses in neurodegeneration: advantages and pitfalls.

2013-03-14

Emanuele Buratti
Maurizio Romano

Francisco E Baralle

Molecular and Cellular Neuroscience

Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.

2013-03-14

Peter K. Rogan
Paul I Costea

Ben C Shirley
Eliseos J Mucaki
Tyson Whitehead
Pelin Akan

Genomics Proteomics and Bioinformatics

Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus.

2013-03-14

Subhash J Jakhesara
Chaitanya G. Joshi

Prakash G Koringa

Journal of Biotechnology

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels.

2013-03-16

Matthias Platzer

Andreas Petzold
Kathrin Reichwald
Marco Groth
Stefan Taudien
Nils Hartmann
Steffen Priebe
Dmitry Shagin
Christoph Englert

BMC Genomics

A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19.

2013-03-19

Rob Lavigne

Elke Lecoutere
Jeroen Wagemans
William Cenens
Abram Aertsen
Liliane Schoofs
Bart Landuyt
Jan Paeshuyse
Maurice Scheer
Max Schobert
Pieter-Jan Ceyssens

mBio

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.

2013-03-21

Maxime Wery
Daniel Gautheret

Marc Descrimes
Claude Thermes
Antonin Morillon

Methods

Investigation of radiation-induced transcriptome profile of radioresistant non-small cell lung cancer A549 cells using RNA-seq

2013-03-22

Namshin Kim

Hee Jung Yang
Ki Moon Seong
HyeSook Youn
BuHyun Youn

PLOS ONE

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

2013-03-24

Jun Wang
Junyi Wang
Klaus Mayer
Thomas Wicker
Huanming Yang

Jizeng Jia
Shancen Zhao
Xiuying Kong
Yingrui Li
Guangyao Zhao
Weiming He
Rudi Appels
Matthias Pfeifer
Yong Tao
Xueyong Zhang
Ruilian Jing
Chi Zhang
Youzhi Ma
Lifeng Gao
Chuan Gao
Manuel Spannagl
Dong Li
Shengkai Pan
Fengya Zheng
Qun Hu
Xianchun Xia
Jianwen Li
Qinsi Liang
Jie Chen
Caiyun Gou
Hanhui Kuang
Genyun He
Yadan Luo
Beat Keller
Qiuju Xia
Peng Lu
Hongfeng Zou
Rongzhi Zhang
Junyang Xu
Jinlong Gao
Christopher Middleton
Zhiwu Quan
Guangming Liu
Jian Wang
Xu Liu
Zhonghu He
Long Mao

Nature

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome

2013-03-25

Brigitte Galliot

Yvan Wenger

BMC Genomics

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome.

2013-03-25

Alicia Oshlack
Nadia M Davidson
Craig A. Smith

Katie L Ayers
Diana Demiyah
Kelly N Roeszler
Frank Grützner
Andrew H Sinclair

Genome Biology

Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data

2013-03-26

Michael Gill
Elaine M Kenny
Richard Anney
Derek W. Morris
Aiden Corvin

Emma M Quinn
Paul Cormican
Matthew Hill

PLOS ONE

Differential expression analysis for paired RNA-Seq data

2013-03-27

Ruth R Montgomery

Lisa M Chung
John P Ferguson
Wei Zheng
Feng Qian
Vincent Bruno
Hongyu Zhao

BMC Bioinformatics

Predicting long non-coding RNAs using RNA sequencing.

2013-03-27

Chris Ponting
Nicholas E Ilott

Methods

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

2013-03-28

Jon Jerlström-Hultqvist
Staffan G Svärd

Oscar Franzén
Elin Einarsson
Johan Ankarklev
Marcela Ferella
Björn Andersson

PLOS Computational Biology

Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans

2013-03-28

Adam C. Siepel
Robert A Burne

Lin Zeng
Sang Chul Choi
Charles G Danko
Michael J Stanhope

PLOS ONE

Comprehensive molecular screening: from the RT-PCR to the RNA-seq.

2013-04-01

Rafael Rosell

Carlota Costa
Ana Giménez-Capitán
Niki Karachaliou

Translational lung cancer research

Spatial transcriptional profile of the chick and mouse endocardial cushions identify novel regulators of endocardial EMT in vitro.

2013-04-01

Daniel M DeLaughter

Daniel M DeLaughter
Danos C Christodoulou
Jamille Y Robinson
Christine E Seidman
H Scott Baldwin
J G Seidman
Joey V Barnett

Journal of Molecular and Cellular Cardiology

Frogs and estivation: transcriptional insights into metabolism and cell survival in a natural model of extended muscle disuse.

2013-04-02

Craig E. Franklin
David I Schlipalius
Paul R Ebert
Rebecca L. Cramp

Beau D Reilly

Physiological Genomics

New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics.

2013-04-03

Patrick May
Alexander Goesmann

Jörg Toepel
Maike Illmer-Kephalides
Sebastian Jaenicke
Jasmin Straube
Olaf Kruse

Plant Biotechnology Journal

Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.

2013-04-04

Noel Monks

Marie Mooney
Jeffrey Bond
Emily Eugster
David Cherba
Pamela Berlinski
Steve Kamerling
Keith Marotti
Heather Simpson
Tony Rusk
Waibhav Tembe
Christophe Legendre
Hollie Benson
Winnie Liang
Craig Paul Webb

PLOS ONE

The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq.

2013-04-04

A Rastrojo
Rosa M. Reguera

Fernando Carrasco-Ramiro
Diana Martín
Antonio Crespillo
Begoña Aguado
Jose M Requena

BMC Genomics

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro.

2013-04-08

Amanda J Lohan
Kévin Rue-Albrecht
Karsten Hokamp
Brendan Loftus
Eamonn Gormley
David E. MacHugh
Stephen V. Gordon
Kate Killick

Nicolas C Nalpas
Stephen D E Park
David A Magee
Maria Taraktsoglou
John A Browne
Kevin M Conlon

BMC Genomics

Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq.

2013-04-08

Marka van Blitterswijk
Brad Friedman
Leonard H van den Berg
Jan H Veldink

Eric T Wang
Pamela J Keagle
Patrick Lowe
Ashley Lyn Leclerc
David E Housman
John E Landers

PLOS ONE

Functional genomics based understanding of rice endosperm development.

2013-04-10

Shi-Rong Zhou

Lin-Lin Yin
Hong-Wei Xue

Current Opinion in Plant Biology

Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.

2013-04-11

Abhinav Nellore

Alexander D Ramos
Aaron Diaz
Ryan N Delgado
Ki-Youb Park
Gabriel Gonzales-Roybal
Michael C Oldham
Jun S Song
Daniel A Lim

Cell Stem Cell

Accurate detection of differential RNA processing.

2013-04-12

Oliver Stegle
Gunnar Rätsch
Karsten M Borgwardt

Philipp Drewe
Lisa Hartmann
André Kahles
Regina Bohnert
Andreas Wachter

Nucleic Acids Research

Exome-based analysis for RNA epigenome sequencing data.

2013-04-14

Jia Meng

Xiaodong Cui
Manjeet K Rao
Yidong Chen
Yufei Huang

Bioinformatics

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.

2013-04-14

Keiichi Mochida
Tetsuya Sakurai
Carsten O Daub
Toshiya Muranaka
Kazuki Saito

Jordan A Ramilowski
Satoru Sawai
Hikaru Seki
Takuhiro Yoshida

Plant and Cell Physiology

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.

2013-04-14

Wolfgang Huber

Danni Yu
Olga Vitek

Bioinformatics

Faculty of 1000 evaluation for Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq

2013-04-16

Christen Rune Stensvold

C Graham Clark

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

2013-04-17

Yohei Sasagawa
Tetsutaro Hayashi
Itoshi Nikaido
Takeshi Imai
Hiroki R Ueda

Hiroki Danno
Kenichiro D Uno

Genome Biology

Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases.

2013-04-17

Arne Klungland

Guanqun Zheng
John Arne Dahl
Yamei Niu
Ye Fu
Yun-Gui Yang
Chuan He

RNA Biology

Characterization of differential transcript abundance through time during Nematostella vectensis development.

2013-04-19

Sarah Tulin
Joel Smith
Casey W. Dunn

Rebecca Rae Helm
Stefan Siebert

BMC Genomics

Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish

2013-04-23

Ingo Braasch

Fanwei Meng
Jennifer B Phillips
Xiwen Lin
Tom Titus
Chunguang Zhang
John H Postlethwait

Molecular Biology and Evolution

Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.

2013-04-23

Elaine Ostrander
Agata Smogorzewska
Arleen D. Auerbach
NISC Comparative Sequencing Program

Settara C Chandrasekharappa
Francis P Lach
Danielle C Kimble
Aparna Kamat
Jamie K Teer
Frank X Donovan
Elizabeth Flynn
Shurjo K Sen
Supawat Thongthip
Erica Sanborn

Blood

A model based criterion for gene expression calls using RNA-seq data.

2013-04-25

Vincent Lynch

Günter P Wagner
Koryu Kin

Theory in Biosciences

Transcriptome analysis of Japanese pear (Pyrus pyrifolia Nakai) flower buds transitioning through endodormancy.

2013-04-26

Songling Bai

Takanori Saito
Daisuke Sakamoto
Akiko Ito
Hiroshi Fujii
Takaya Moriguchi

Plant and Cell Physiology

RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea.

2013-04-26

Barbara De Coninck

Kaat De Cremer
Janick Mathys
Christine Vos
Lutz Froenicke
Richard W Michelmore
Bruno P A Cammue

Plant, Cell and Environment

Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data.

2013-04-29

Johannes Grillari
Alexandra B Graf
Matthias Hackl
Nicole Borth

Matthias Peter Gerstl

Journal of Biotechnology

RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish.

2013-04-30

Shikai Liu
Eric Peatman
Huseyin Kucuktas
Ludmilla Kaltenboeck
Luyang Sun
Yu Zhang

Xiuli Wang
Fanyue Sun
Jiaren Zhang
Jianbin Feng
Hong Liu
K V Rajendran
Yanliang Jiang
Zhanjiang Liu

Physiological Genomics

Erratum: RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

2013-05

Jun Wang
Huanming Yang

Shancheng Ren
Zhiyu Peng
Jian-Hua Mao
Yongwei Yu
Changjun Yin
Xin Gao
Zilian Cui
Jibin Zhang
Kang Yi
Weidong Xu
Chao Chen
Fubo Wang
Xinwu Guo
Ji Lu
Jun Yang
Min Wei
Zhijian Tian
Yinghui Guan
Liang Tang
Chuanliang Xu
Linhui Wang
Xu Gao
Wei Tian
Jian Wang
Yinghao Sun

Cell Research

Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma.

2013-05-01

Frank Baas
Kees Fluiter

Ching Yong Yick
Aeilko H Zwinderman
Peter W Kunst
Katrien Grünberg
Thais Mauad
Elisabeth H Bel
René Lutter
Peter J Sterk

American Journal of Respiratory and Critical Care Medicine

Transcription factors that convert adult cell identity are differentially polycomb repressed

2013-05-01

Sean Eddy
Davis FP

PLOS ONE

Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans

2013-05-04

Stuart J Macdonald

Joel V Tamayo
Mahekta Gujar
Erik A Lundquist

BMC Genomics

Research resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes.

2013-05-09

Agne Velthut
Madis Metsis
Andres Salumets

Jaak Simm
Timo Tuuri
Juha S Tapanainen

Molecular Endocrinology

Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.

2013-05-09

Melody Baddoo
Michelle Lacey
Erik K Flemington

Michael J Strong
Guorong Xu
Joseph Coco
Carl Baribault
Dass S Vinay
Amy L Strong
Teresa A Lehman
Michael B Seddon
Zhen Lin
Monica Concha
Melody Baddoo
Marybeth Ferris
Kenneth F Swan
Deborah E Sullivan
Matthew E Burow
Christopher M Taylor

PLOS Pathogens

In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue

2013-05-10

Thomas G Beach

Brooke E Hjelm
Bodour Salhia
Ahmet Kurdoglu
Szabolcs Szelinger
Rebecca A Reiman
Lucia I Sue
Matthew J Huentelman
David W Craig

Human Molecular Genetics

Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm.

2013-05-12

Zhixiang Zuo

Yi Lv
Xiao Xu

Genomics

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.

2013-05-13

Peter F. Stadler
David Langenberger

Gero Doose
Maria Alexis
Rebecca Kirsch
Sven Findeiß
Rainer Machné
Mario Mörl
Steve Hoffmann

RNA Biology

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.

2013-05-14

Stephen A. Smith

Ya Yang

BMC Genomics

OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis.

2013-05-15

Tesfaye Wubet
Martin Schädler
Mika T Tarkka
Stefan Scheu
François Buscot

Sylvie Herrmann
Lasse Feldhahn
Sabine Recht
Florence Kurth
Sarah Mailänder
Markus Bönn
Maren Neef
Oguzhan Angay
Michael Bacht
Marcel Graf
Hazel Maboreke
Frank Fleischmann
Thorsten E E Grams
Liliane Ruess
Roland Brandl
Silvia D Schrey
Ivo Grosse

New Phytologist

Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq.

2013-05-16

Laurie T. Krug

Current opinion in virology

Comparative analysis of RNA sequencing methods for degraded or low-input samples.

2013-05-19

Aviv Regev
Rahul Satija
Nathalie Pochet

Xian Adiconis
Diego Borges-Rivera
David S DeLuca
Michele A Busby
Aaron M Berlin
Andrey Sivachenko
Dawn Anne Thompson
Alec Wysoker
Timothy Fennell
Andreas Gnirke
Joshua Z Levin

Nature Methods

Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1

2013-05-21

Guillaume Blanc

Janet M Rowe
David D Dunigan
James R Gurnon
Yuannan Xia
James L Van Etten

Virology

Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.

2013-05-22

Gil Omenn
Susan Fanayan

Emma Yue Zhang
Massimo Cristofanilli
Fredika Robertson
James M Reuben
Zhaomei Mu
Ronald C Beavis
Hogune Im
Michael Snyder
Matan Hofree
Trey Ideker
Seul-Ki Jeong
Young-Ki Paik
Anna Fan Zhang
Shiaw-Lin Wu
William S Hancock

Journal of Proteome Research

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing

2013-05-22

Ryan D Morin
Andrew Mungall
Steven Jones

Karen Mungall
Erin Pleasance
Rodrigo Goya
Ryan D Huff
David W Scott
Jiarui Ding
Andrew Roth
Readman Chiu
Richard D Corbett
Fong Chun Chan
Maria Mendez-Lago
Diane L Trinh
Madison Bolger-Munro
Greg Taylor
Alireza Hadj Khodabakhshi
Susana Ben-Neriah
Julia Pon
Barbara Meissner
Bruce Woolcock
Noushin Farnoud
Sanja Rogic
Emilia L Lim
Nathalie A Johnson
Sohrab Shah
Christian Steidl
Robert Holt
Inanc Birol
Richard Moore
Joseph M Connors
Randy D Gascoyne
Marco A Marra

Blood

A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells.

2013-05-26

Nina Papavasiliou
Thomas Tuschl

Eric L Fritz
Brad R Rosenberg
Kenneth Lay
Aleksandra Mihailović
F Nina Papavasiliou

Nature Immunology

Identification of the zebrafish maternal and paternal transcriptomes

2013-05-29

James Cuthbert Smith

Steven A Harvey
Ian Sealy
Ross Kettleborough
Fruzsina Fenyes
Richard White
Derek Stemple

Development

Transcriptome sequencing (RNA-seq) analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii.

2013-05-31

Rute F. Domingos
William Zerges
Kevin J Wilkinson

Dana F Simon
Charles Hauser
Colin M Hutchins

Applied and Environmental Microbiology

Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs

2013-06

Michael McManus

Matthew J Hangauer
Ian W Vaughn

PLOS Genetics

The gene desert mammary carcinoma susceptibility locus Mcs1a regulates Nr2f1 modifying mammary epithelial cell differentiation and proliferation

2013-06

Christina Kendziorski

Bart M G Smits
Jill D Haag
Anna I Rissman
Deepak Sharma
Ann Tran
Alexi A Schoenborn
Rachael C Baird
Dan S Peiffer
David Q Leinweber
Matthew J Muelbl
Amanda L Meilahn
Mark R Eichelberg
Ning Leng
Manorama C John
Patricia A Powers
Caroline M Alexander
Michael N Gould

PLOS Genetics

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica

2013-06

Chad Nusbaum
Carsten Russ
Berend Snel
Stephan Wawra
Sucheta Tripathy
Irene de Bruijn
Michael F. Seidl
Guido Van den Ackerveken
Pieter van West
Francine Govers
Stan Oome
Neil Horner
Bernard Dumas
Marcia Saraiva
Julio C Vega-Arreguín
Paul F Morris

Rays H Y Jiang
Brian J Haas
Rodrigo Belmonte
Lars Löbach
James Christie
Arnaud Bottin
Vincent Bulone
Sara M Díaz-Moreno
Lin Fan
Elodie Gaulin
Laura J Grenville-Briggs
Joshua Z Levin
Marco Mammella
Harold J G Meijer
Stan Oome
Andrew J Phillips
David van Rooyen
Elzbieta Rzeszutek
Chris J Secombes
Joost H M Stassen
Sean Sykes
Herbert van den Berg
Sarah K Young
Qiandong Zeng
Javier Dieguez-Uribeondo
Brett M Tyler

PLOS Genetics

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species.

2013-06-05

Steve Smith
Luciano B. Beheregaray

Louis Bernatchez

BMC Genomics

Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq

2013-06-05

Michelle D Williams
Funda Meric-Bernstam

Joseph D Khoury
Nizar M Tannir
Yunxin Chen
Hui Yao
Jianping Zhang
Erika J Thompson
TCGA Network
L Jeffrey Medeiros
John N Weinstein
Xiaoping Su

Journal of Virology

A meta-analysis of the genomic and transcriptomic composition of complex life.

2013-06-06

John Mattick

Ganqiang Liu
Ryan J Taft

Cell Cycle

Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue.

2013-06-07

Jacob K Jensen

Nathan Johnson
Curtis G Wilkerson

Frontiers in Plant Science

A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples

2013-06-10

Paolo Piazza
Elizabeth M Batty
Tanya Golubchik
Kate E Dingle
Paul Klenerman
Daniel Wilson
Eleanor Barnes

T H Nicholas Wong
Amy Trebes
Karène Argoud
Moustafa Attar
David Buck
Camilla L C Ip
Madeleine Cule
Rory Bowden
Charis Manganis
A Sarah Walker
David H Wyllie
Tim E A Peto
Derrick W Crook

PLOS ONE

Assessment of gene expression in peripheral blood using RNAseq before and after weight restoration in anorexia nervosa

2013-06-15

Cynthia M. Bulik

Yunjung Kim
Sara E Trace
James J Crowley
Kimberly A Brownley
Robert M Hamer
David S Pisetsky
Patrick F Sullivan

Psychiatry Research

Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing

2013-06-20

Stéphane Bentolila
Maureen R. Hanson

Julyun Oh
Robert Bukowski

PLOS Genetics

RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism

2013-06-20

Erin Osborne

Nirav M Amin
Panna Tandon
Frank L Conlon

Methods

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.

2013-06-20

Anamaria Necsulea

Magali Soumillon
Manuela Weier
David Brawand
Xiaolan Zhang
Hongcang Gu
Pauline Barthès
Maria Kokkinaki
Serge Nef
Andreas Gnirke
Martin Dym
Bernard de Massy
Tarjei S Mikkelsen
Henrik Kaessmann

Cell Reports

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

2013-06-21

Avi Ma'ayan
Caroline Baroukh

Huilei Xu
Ruth Dannenfelser
Edward Y Chen
Christopher M Tan
Yan Kou
Yujin E Kim
Ihor R Lemischka

Database

Global transcriptome profiles of Camellia sinensis during cold acclimation

2013-06-22

Qiong-Yi Zhao

Xin-Chao Wang
Chun-Lei Ma
Zong-Hong Zhang
Hong-Li Cao
Yi-Meng Kong
Chuan Yue
Xin-Yuan Hao
Liang Chen
Jian-Qiang Ma
Ji-Qiang Jin
Xuan Li
Ya-Jun Yang

BMC Genomics

Evaluating the impact of sequencing depth on transcriptome profiling in human adipose

2013-06-24

Jane Ferguson
Muredach P. Reilly

Yichuan Liu
Chenyi Xue
Ian M Silverman
Brian Gregory
Mingyao Li

PLOS ONE

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

2013-06-28

W. Richard McCombie

Xiao Xu
Yuanhao Zhang
Jennie Williams
Eric Antoniou
Song Wu
Wei Zhu
Nicholas O Davidson
Paula Denoya
Ellen Li

BMC Bioinformatics

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.

2013-07-01

Sayan Mukherjee
Uwe Ohler

Dina Hafez
Ting Ni
Jun Zhu

Bioinformatics

Classification of topological domains based on gene expression and regulation.

2013-07-01

Nadav Ahituv

Jingjing Zhao
Hongbo Shi

Genome

RNA-Seq-based analysis of the physiologic cold shock-induced changes in Moraxella catarrhalis gene expression.

2013-07-02

Stefan Wyder
Christoph Aebi

Violeta Spaniol

PLOS ONE

Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA

2013-07-03

Andrzej Dziembowski
Rafał Tomecki
Torben Heick Jensen
Dominik Cysewski

Michal Lubas
Christian K Damgaard

The EMBO Journal

RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction

2013-07-04

Claus O. Wilke

Changhoon Lee
R Adron Harris
Jason K Wall
R Dayne Mayfield

Biology Direct

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

2013-07-05

Mark Bender Gerstein

Gang Fang
Karla D Passalacqua
Jason Hocking
Paula Montero Llopis
Nicholas H Bergman
Christine Jacobs-Wagner

BMC Genomics

Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases

2013-07-07

Carlo Gambacorti-Passerini
Vera Magistroni

Roberta Spinelli
Alessandra Pirola
Sara Redaelli
Nitesh Sharma
Hima Raman
Simona Valletta
Rocco Piazza

Molecular genetics & genomic medicine

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.

2013-07-08

Sebastian Kurscheid
Ruth R Montgomery
Erol Fikrig
Mark Bender Gerstein

Feng Qian
Lisa Chung
Wei Zheng
Vincent Bruno
Roger P Alexander
Zhong Wang
Xiaomei Wang
Hongyu Zhao
Michael Snyder

Viruses

Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis.

2013-07-10

Wenying Yan

Jiajia Chen
Daqing Zhang
Wenyu Zhang
Yifei Tang
Lingchuan Guo
Bairong Shen

Journal of Translational Medicine

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

2013-07-12

Geir Kjetil Sandve
Gavin Giovannoni

Adam E Handel
Giulio Disanto
Antonio J Berlanga-Taylor
Giuseppe Gallone
Heather Hanwell
Finn Drabløs
George C Ebers
Sreeram V Ramagopalan

BMC Medicine

Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome.

2013-07-12

Shikai Liu
Ludmilla Kaltenboeck
Luyang Sun
Rex Dunham

Fanyue Sun
Xiaoyu Gao
Yanliang Jiang
Dayan Perera
Xiuli Wang
Chao Li
Jiaren Zhang
Zhanjiang Liu

PLOS ONE

Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.

2013-07-14

Kevin G. Becker
Myriam Gorospe
Kotb Abdelmohsen

Amaresh Panda
Min-Ju Kang
Jason Xu
Roza Selimyan
Je-Hyun Yoon
Jennifer L Martindale
Supriyo De
William H Wood

Aging Cell

Transcriptome analysis of mouse brain infected with Toxoplasma gondii.

2013-07-15

Yoshifumi Nishikawa

Sachi Tanaka
Maki Nishimura
Fumiaki Ihara
Junya Yamagishi
Yutaka Suzuki

Infection and Immunity

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.

2013-07-16

Hirokazu Handa
Takeshi Itoh

Youko Oono
Yoshihiro Kawahara
Takayuki Yazawa
Hiroyuki Kanamori
Masato Kuramata
Harumi Yamagata
Satomi Hosokawa
Hiroshi Minami
Satoru Ishikawa
Jianzhong Wu
Baltazar Antonio
Takashi Matsumoto

Plant Molecular Biology

Proteogenomic database construction driven from large scale RNA-seq data.

2013-07-17

Vineet Bafna

Sunghee Woo
Seong Won Cha
Gennifer Merrihew
Yupeng He
Natalie Castellana
Clark Guest
Michael MacCoss

Journal of Proteome Research

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes

2013-07-18

Jennifer Doudna
Lei S Qi
Jonathan Weissman
Noam Stern-Ginossar

Luke A Gilbert
Matthew H Larson
Leonardo Morsut
Zairan Liu
Gloria A Brar
Sandra E Torres
Onn Brandman
Evan H Whitehead
Wendell A Lim

Cell

Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans

2013-07-18

Natalia Vanduyn

Martina Rudgalvyte
Vuokko Aarnio
Liisa Heikkinen
Juhani Peltonen
Merja Lakso
Richard Nass
Garry Wong

Toxicology Letters

Using a periclinal chimera to unravel layer-specific gene expression in plants.

2013-07-19

James Abbott

Ioannis Filippis
Rosa Lopez-Cobollo
Sarah Butcher
Gerard J Bishop

The Plant Journal

Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.

2013-07-19

Lakshminarayan M. Iyer

Sabarinath Sundaram
Sunee Kertbundit
Eugene V Shakirov
Lakshminarayan M Iyer
Miloslav Jurícek
Timothy C Hall

The Plant Cell

Enhanced expression of codon optimized interferon gamma in CHO cells.

2013-07-19

Dong-Yup Lee

Bevan Kai-Sheng Chung
Faraaz N K Yusufi
Mariati
Yuansheng Yang

Journal of Biotechnology

GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.

2013-07-22

Zhi-xiang Lu

Keyan Zhao
Juw Won Park
Qing Zhou
Yi Xing

Genome Biology

Replication protein A subunit 3 and the iron efficiency response in soybean.

2013-07-22

Dianne Cook

Sarah E Atwood
Jamie A O'Rourke
Gregory A Peiffer
Tengfei Yin
Mahbubul Majumder
Chunquan Zhang
Silvia R Cianzio
John H Hill
Steven A Whitham
Randy C Shoemaker
Michelle A Graham

Plant, Cell and Environment

Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos

2013-07-22

Francisco Peñagaricano
Wen Huang

Ashley M Driver
Jenna Kropp
Hasan Khatib

PLOS ONE

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.

2013-07-22

Ulrich Omasits
Christian H Ahrens
Mark D. Robinson
Christoph Dehio

Maxime Quebatte
Daniel J Stekhoven
Claudia Fortes
Bernd Roschitzki

Genome Research

Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level.

2013-07-27

Christian Bendixen

Leila Farajzadeh
Henrik Hornshøj
Jamal Momeni
Bo Thomsen
Knud Larsen
Jakob Hedegaard
Lone Bruhn Madsen

Biochemical and Biophysical Research Communications

Basal polarization of the mucosal compartment in Flavobacterium columnare susceptible and resistant channel catfish (Ictalurus punctatus).

2013-07-27

Eric Peatman

Chao Li
Brian C Peterson
David L Straus
Bradley D Farmer
Benjamin H Beck

Molecular Immunology

Differential programming of B cells in AID deficient mice

2013-07-29

Bas van Steensel

Marc A Hogenbirk
Marinus R Heideman
Arno Velds
Paul C M van den Berk
Ron M Kerkhoven
Heinz Jacobs

PLOS ONE

DNA methylation, genotype and gene expression: who is driving and who is along for the ride?

2013-07-29

Meaghan J Jones
Michael S Kobor

Anthony P Fejes

Genome Biology

Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology

2013-08

Nathaniel Rothman

Reuben Thomas
Cliona M McHale
Qing Lan
Alan E Hubbard
Luoping Zhang
Roel Vermeulen
Guilan Li
Stephen M Rappaport
Songnian Yin
Martyn T Smith

Environmental and Molecular Mutagenesis

Computational analysis of bacterial RNA-Seq data

2013-08

Paul Sumby

Ryan McClure
Divya Balasubramanian
Yan Sun
Maksym Bobrovskyy
Caroline A Genco
Carin K Vanderpool
Brian Tjaden

Nucleic Acids Research

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

2013-08-01

Jay Shendure
Joshua N Burton

Andrew Adey
Jacob O Kitzman
Joseph B Hiatt
Alexandra P Lewis
Beth K Martin
Ruolan Qiu
Choli Lee

Nature

Increased BCAR1 predicts poor outcomes of non-small cell lung cancer in multiple-center patients.

2013-08-01

Zhifu Sun

Bo Deng
Wampfler Jason
Ping Yang

Annals of Surgical Oncology

RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus

2013-08-02

Christine G Elsik
Monica F Poelchau

Julie A Reynolds
David L Denlinger
Peter A Armbruster

The Journal of Experimental Biology

Photoreceptor phagocytosis is mediated by phosphoinositide signaling.

2013-08-02

Krzysztof Palczewski

Debarshi Mustafi
Brian M Kevany
Christel Genoud
Xiaodong Bai

FASEB Journal

Simultaneous profiling of 194 distinct receptor transcripts in human cells

2013-08-06

Kevin A. Janes

Byong H Kang
Karin J Jensen
Jaime A Hatch

Science Signaling

Masculinization of the x chromosome in the pea aphid.

2013-08-08

Solenn Stoeckel
Fabrice Legeai
Gaël Le Trionnaire
Julie Jaquiéry
Nathalie Prunier-Leterme
Béatrice Ségurens
Julie Poulain
Denis Tagu
Corinne Da Silva
Claude Rispe

Denis Roze
Lucie Mieuzet
Béatrice Ségurens
Jean-Christophe Simon

PLOS Genetics

BlackOPs: increasing confidence in variant detection through mappability filtering.

2013-08-08

Charles M. Perou

Christopher R Cabanski
Matthew D Wilkerson
Matthew Soloway
Joel S Parker
Jinze Liu
Jan F Prins
J S Marron
D Neil Hayes

Nucleic Acids Research

Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger

2013-08-09

Stéphane Delmas
Steven T. Pullan

Laure Ries
Sunir Malla
Martin J Blythe
David B Archer

BMC Genomics

Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.

2013-08-12

Cameron Brennan
David Haussler
Lynda Chin

J Zachary Sanborn
Sofie R Salama
Mia Grifford
Tom Mikkelsen
Suresh Jhanwar
Sol Katzman

Cancer Research

Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach.

2013-08-13

Emmanuel J. P. Douzery

Jeanne Tonnabel
Isabelle Olivieri
Agnès Mignot
Anthony Rebelo
Fabienne Justy
Sylvain Santoni
Stéfanie Caroli
Laure Sauné
Olivier Bouchez

Molecular Phylogenetics and Evolution

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.

2013-08-14

Joao Carlos Setubal
Maxuel O Andrade

Neha Jalan
Dibyendu Kumar
Fahong Yu
Jeffrey B Jones
James H Graham
Frank F White
Nian Wang

BMC Genomics

Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.

2013-08-14

Owen J Sansom
Chris Ponting
Andreas Heger
Ian Sudbery
Imran Ahmad
Joanne Edwards
Hing Y Leung
Prabhakar Rajan

M Eugenia M Villasevil
Ernest Mui
Janis Fleming
Mark Davis
David Sims
Rhona M McMenemin
Ian D Pedley

European Urology

Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis.

2013-08-17

Petrus Tang

Kuo-Yang Huang
Yi-Ywan Margaret Chen
Yi-Kai Fang
Wei-Hung Cheng
Chih-Chieh Cheng
Yu-Chuen Chen
Tiffany E Wu
Fu-Man Ku
Shih-Chieh Chen
Rose Lin

Biochimica et Biophysica Acta

Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish.

2013-08-19

Helen M Gunter
Paolo Franchini
Axel Meyer
Carmelo Fruciano

Shaohua Fan
Fan Xiong

Molecular Ecology

Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq.

2013-08-19

Niklas Janz
Sören Nylin
Maria de la Paz Celorio-Mancera

Christopher W Wheat
Heiko Vogel
Lina Söderlind

Molecular Ecology

Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.

2013-08-20

Quanhu Sheng
David C Samuels

Yan Guo
Jiang Li
Fei Ye
Yu Shyr

PLOS ONE

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.

2013-08-21

Pedro Puig

Mikel Esnaola
David Gonzalez
Robert Castelo
Juan R Gonzalez

BMC Bioinformatics

Whole transcriptome RNA-Seq allelic expression in human brain

2013-08-22

Wolfgang Sadee

Ryan M Smith
Amy Webb
Audrey C Papp
Leslie C Newman
Samuel K Handelman
Adam Suhy
Roshan Mascarenhas
John Oberdick

BMC Genomics

Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach.

2013-08-23

Knud A. Jønsson
Emmanuel J. P. Douzery

Pierre-Henri Fabre

Gene

Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.

2013-08-24

Daniel G. Bradley
Peter Vegh
David J. Lynn
David E. MacHugh
Stephen V. Gordon

Amir B K Foroushani
David A Magee
Matthew S McCabe
John A Browne
Nicolas C Nalpas
Kevin M Conlon

Veterinary Immunology and Immunopathology

Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle.

2013-08-24

Subhash J Jakhesara
Chaitanya G. Joshi

Prakash G Koringa
Vaibhav D Bhatt
Anand B Patel
Debabrata Dash

Gene

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

2013-08-25

Gunnar Rätsch

Jonas Behr
André Kahles
Yi Zhong
Vipin T Sreedharan
Philipp Drewe

Bioinformatics

Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum

2013-08-26

Jianhui Zhang

Jianqin Li
Haimei Chen
Xiangdong Chen
Jin Lan
Chang Liu

PLOS ONE

Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.

2013-08-26

Isabelle Janoueix-Lerosey
Valérie Combaret
Valentina Boeva
Emmanuel Barillot
Olivier Delattre

Stéphanie Jouannet
Romain Daveau
Cécile Pierre-Eugène
Alex Cazes
Caroline Louis-Brennetot
Gudrun Schleiermacher
Sandrine Ferrand
Gaëlle Pierron
Alban Lermine
Thomas Rio Frio
Virginie Raynal
Gilles Vassal

PLOS ONE

Remodeling of membrane lipids in iron-starved Chlamydomonas.

2013-08-27

David Casero
Sabeeha Merchant
Matteo Pellegrini
Eugen Urzica
Sean D Gallaher
Astrid Vieler
Christoph Benning

Anne Hong-Hermesdorf
M Dudley Page
Janette Kropat

Journal of Biological Chemistry

Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.

2013-08-30

Jianmin Wang

Chunlan Zhang
Guizhi Wang
Zhibin Ji
Zhaohuan Liu
Xiushuang Pi
Cunxian Chen

PLOS ONE

SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

2013-08-31

Enrique Macpherson

C Schunter
J C Garza
M Pascual

Molecular Ecology Resources

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

2013-08-31

Shintaro Katayama
Juha Kere
Sten Linnarsson

Virpi Töhönen

Bioinformatics

Editorial for “Diversity of the non-coding transcriptomes revealed by RNA-seq technologies”

2013-09

Jean-Christophe Andrau

Antonin Morillon

Methods

Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.

2013-09-01

Nuria Cerdá-Esteban
Nancy Mah
Francesca Spagnoli

Elisa Rodríguez-Seguel
Heike Naumann
Igor M Pongrac
Jean-Fred Fontaine
Yongbo Wang
Wei Chen
Miguel A Andrade-Navarro

Genes & Development

Mining RNA-seq data for infections and contaminations.

2013-09-03

Caroline C Friedel
Ralf Zimmer

Thomas Bonfert
Gergely Csaba

PLOS ONE

RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici.

2013-09-03

Xiao-Ren Chen

Yu-Ping Xing
Yan-Peng Li
Yun-Hui Tong
Jing-You Xu

PLOS ONE

Trametes versicolor protein YZP activates regulatory B lymphocytes - gene identification through de novo assembly and function analysis in a murine acute colitis model.

2013-09-03

Fuu Sheu

Yen-Chou Kuan
Ying-Jou Wu
Chih-Liang Hung

PLOS ONE

Short-term feed deprivation alters immune status of surface mucosa in channel catfish (Ictalurus punctatus).

2013-09-04

Eric Peatman
Lisa Liu

Chao Li
Baofeng Su
Benjamin H Beck

PLOS ONE

Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia.

2013-09-06

David Casero
Thomas Happe
Sabeeha Merchant
Matteo Pellegrini
Anja Hemschemeier
Christoph Benning

Bensheng Liu

The Plant Cell

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.

2013-09-08

Yiqi Seow
Shahrouz Amini
Ali Miserez

Paul A Guerette
Shawn Hoon
Manfred Raida
Admir Masic
Fong T Wong
Vincent H B Ho
Kiat Whye Kong
Melik C Demirel
Abdon Pena-Francesch
Gavin Z Tay
Dawei Ding

Nature Biotechnology

Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.

2013-09-09

Jeanette Baran-Gale

Emily E Fannin
C Lisa Kurtz
Praveen Sethupathy

PLOS ONE

U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.

2013-09-10

Yuxin Li
Drew R Jones
Hao Wu
Eric B Dammer
David A Bennett

Bing Bai
Chadwick M Hales
Ping-Chung Chen
Yair Gozal
Jason J Fritz
Xusheng Wang
Qiangwei Xia
Duc M Duong
Craig Street
Gloria Cantero
Dongmei Cheng
Zhiping Wu
Ian Diner
Craig J Heilman
Howard D Rees
Li Lin
Keith E Szulwach
Marla Gearing
Elliott J Mufson
Thomas J Montine
Nicholas T Seyfried
Thomas S Wingo
Yi E Sun
Peng Jin
John Hanfelt
Donna M Willcock
Allan Levey
James J Lah
Junmin Peng

Proceedings of the National Academy of Sciences of the United States of America

Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.

2013-09-11

Aldons Jake Lusis
Eleazar Eskin
Pierre-François Roux
Sandrine Lagarrigue

Lisa Martin
Farhad Hormozdiari
Calvin Pan
Atila van Nas
Olivier Demeure
Rita Cantor
Anatole Ghazalpour

Genetics

Androgen receptor signaling regulates DNA repair in prostate cancers.

2013-09-11

Deyou Zheng
Daniel E. Spratt
Michael J Zelefsky

William R Polkinghorn
Joel S Parker
Man X Lee
Elizabeth M Kass
Phillip J Iaquinta
Vivek K Arora
Wei-Feng Yen
Ling Cai
Brett S Carver
Yu Chen
Philip A Watson
Neel P Shah
Sho Fujisawa
Alexander G Goglia
Anuradha Gopalan
Haley Hieronymus
John Wongvipat
Peter T Scardino
Maria Jasin
Jayanta Chaudhuri
Simon N Powell
Charles L Sawyers

Cancer Discovery

A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease

2013-09-14

Kenneth J McDowall

Yu-fei Lin
David Romero A
Shuang Guan
Lira Mamanova

BMC Genomics

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

2013-09-15

Ann-Christine Syvänen
Michael Sammeth
Tuuli Lappalainen
Xavier Estivill i Pallejà
Peter A.C. 't Hoen
Marc Friedlander
Jeroen Laros

Jonas Almlöf
Irina Pulyakhina
Seyed Yahya Anvar
Henk P J Buermans
Olof Karlberg
Mathias Brännvall
GEUVADIS Consortium
Johan T den Dunnen
Gert-Jan B van Ommen
Ivo G Gut
Roderic Guigó
Emmanouil T Dermitzakis

Nature Biotechnology

Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy

2013-09-16

Niles A. Pierce
Xinning Zhang
Vikas Trivedi

Adam Z Rosenthal
Kaitlyn S Lucey
Elizabeth A Ottesen
Harry M T Choi
Niles A Pierce
Jared R Leadbetter

Proceedings of the National Academy of Sciences of the United States of America

RNA-Seq analysis of Mycobacterium avium non-coding transcriptome

2013-09-16

Dmitriy Ignatov
Timofey Skvortsov
Alexander S Apt

Sofia Malakho
Konstantin Majorov
Tatyana Azhikina

PLOS ONE

DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions

2013-09-17

Sepp Hochreiter
Günter Klambauer
Thomas Unterthiner

Nucleic Acids Research

Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice.

2013-09-18

Fan Li

Ruth Elliott
Isabelle Dragomir
Ming Ming W Chua
Brian D Gregory
Susan R Weiss

PLOS ONE

Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.

2013-09-18

John Quackenbush

Xuanhui Sharron Lin
Lan Hu
Kirley Sandy
Mick Correll
Chin-Lee Wu
William Scott McDougal

Urologic Oncology

Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.

2013-09-18

Melody Baddoo
Tina O'Grady
Erik K Flemington

Michael J Strong
Zhen Lin
Guorong Xu
Melody Baddoo
Chris Parsons
Kun Zhang
Christopher M Taylor

Journal of Virology

Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.

2013-09-20

Jens Nielsen
Mathias Uhlén
Elton P. Hudson

Josefine Anfelt
Björn Hallström

Applied and Environmental Microbiology

Accounting for technical noise in single-cell RNA-seq experiments.

2013-09-22

Simon Anders
Vladimir Benes
Sarah Teichmann
John C Marioni
Valentina Proserpio
Marcus Heisler
Jong Kyoung Kim

Philip Brennecke
Aleksandra A Kołodziejczyk
Xiuwei Zhang
Bianka Baying

Nature Methods

Cryptic FUS-ERG fusion identified by RNA-sequencing in childhood acute myeloid leukemia.

2013-09-25

Sverre Heim
Ioannis Panagopoulos

Ludmila Gorunova
Bernward Zeller
Anne Tierens

Oncology Reports

Next-generation sequence analysis of cancer xenograft models.

2013-09-26

Fernando J Rossello
Kara L. Britt
Richard W. Tothill
Luciano G. Martelotto
Jason Li
Luigi Marchionni

Kieren D Marini
Jeanette Falzon
David M Thomas
Craig D Peacock
Samara Bennett
Erwin Tantoso
Tracey Brown
Philip Chan
D Neil Watkins

PLOS ONE

Taf7l cooperates with Trf2 to regulate spermiogenesis.

2013-09-30

Ke Zheng
Ivan Grubisic
Tommy Kaplan
Robert Tjian

Haiying Zhou
Ying He
P Jeremy Wang

Proceedings of the National Academy of Sciences of the United States of America

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.

2013-09-30

Margaret F Romine
Ronald Taylor

Bobbie-Jo M Webb Robertson
Lye Meng Markillie
Margrethe H Serres
Bryan E Linggi
Joshua T Aldrich
Eric A Hill
Mary S Lipton
H Steven Wiley

Integrative Biology

Human housekeeping genes, revisited

2013-10

Eli Eisenberg

Erez Y. Levanon

Trends in Genetics

Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling

2013-10

Russ Hauser
Zhen Chen

Shihong Mao
Robert J Goodrich
Steven M Schrader
Stephen A Krawetz

Systems Biology in Reproductive Medicine

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

2013-10-01

Heiko Liesegang
Sandra Wiegand
Rolf Daniel

Sascha Dietrich
Robert Hertel
Johannes Bongaerts
Stefan Evers
Sonja Volland

BMC Genomics

RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response.

2013-10-03

Luciano T. Kishi

Carolina M Rodrigues
Alessandra A de Souza
Marco A Takita
Marcos A Machado

BMC Genomics

Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts

2013-10-03

Deyou Zheng
John J. Foxe

Jian Chen
Mingyan Lin
Erika Pedrosa
Anastasia Hrabovsky
Reed Carroll
Herbert M Lachman

PLOS ONE

Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes

2013-10-03

Bradley I. Hillman

Sandra M Mathioni
Nrupali Patel
Bianca Riddick
James A Sweigard
Kirk J Czymmek
Jeffrey L Caplan
Sridhara G Kunjeti
Saritha Kunjeti
Vidhyavathi Raman
Donald Y Kobayashi
Nicole M Donofrio

PLOS ONE

Function of lncRNAs and approaches to lncRNA-protein interactions.

2013-10-05

Hanjiang Fu

Juanjuan Zhu
Yongge Wu
Xiaofei Zheng

Science in China. Series C: Life Sciences

In vitro grown pollen tubes of Nicotiana alata actively synthesise a fucosylated xyloglucan.

2013-10-08

Edwin R. Lampugnani
Ed Newbigin
Antony Bacic

Isabel E Moller
Andrew Cassin
Daniel F Jones
Poh Ling Koh
Sunil Ratnayake
Cherie T Beahan
Sarah M Wilson

PLOS ONE

Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study

2013-10-09

Gregory Poland

Brooke L Fridley
Gregory D Jenkins
Diane E Grill
Richard B Kennedy
Ann L Oberg

Scientific Reports

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.

2013-10-09

Mikhail G Dozmorov

Cory B Giles
Reshmi Girija-Devi
Jonathan D Wren

BMC Bioinformatics

Towards the integration, annotation and association of historical microarray experiments with RNA-seq

2013-10-09

Michael A Bauer

Shweta S Chavan
Erich A Peterson
Christoph J Heuck
Donald J Johann

BMC Bioinformatics

Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection.

2013-10-10

Srinand Sreevatsan

Elise A Lamont
Wayne W Xu

BMC Genomics

Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles.

2013-10-10

Chad Rappleye

Jessica A Edwards
Chenxi Chen
Megan M Kemski
Jinnan Hu
Thomas K Mitchell

BMC Genomics

Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation.

2013-10-10

Hongkui Wei

Shuzhong Jiang
Tongxing Song
Yang Yang
Jian Peng
Siwen Jiang

PLOS ONE

Modeling the next generation sequencing sample processing pipeline for the purposes of classification.

2013-10-11

Charles D. Johnson
Edward R. Dougherty

Noushin Ghaffari
Mohammadmahdi R Yousefi
Ivan Ivanov

BMC Bioinformatics

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.

2013-10-11

W. Richard McCombie
Elena A Vidal
Gabriel Krouk
Milos Tanurdzic
Rodrigo A Gutiérrez

Tomás C Moyano
Manpreet S Katari
Gloria M Coruzzi

BMC Genomics

GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.

2013-10-11

Bernhard Y Renard

Franziska Zickmann
Martin S Lindner

Bioinformatics

F11R is a novel monocyte prognostic biomarker for malignant glioma

2013-10-11

Xi Feng
Winnie W Pong
Jaebok Choi
Malachi Griffith
Obi Griffith
Greg N. Fuller
David H Gutmann

Jason Walker
Todd Wylie
Vincent Magrini
Jingqin Luo
Ryan J Emnett
Matthew L Cooper
Joshua B Rubin
David Piwnica-Worms
Dolores Hambardzumyan
John F DiPersio
Elaine R Mardis

PLOS ONE

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.

2013-10-11

Tak-Wah Lam
Jun Wang
Jikun Wu
Zhiyu Peng

Wenqian Zhang
Songbo Huang
Zengquan He
Yanbing Cheng
Siu-Ming Yiu

Bioinformatics

Profiling the molecular mechanism of fullerene cytotoxicity on tumor cells by RNA-seq.

2013-10-12

Marco Gerdol
Alberto Pallavicini
Marianna Lucafò
Gianni Sava
Sabrina Pacor
Maurizio Prato

Sonia Zorzet
Tatiana Da Ros

Toxicology

Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

2013-10-14

David M Brazel

Zachary W Bent
Mary B Tran-Gyamfi
Rachelle Y Hamblin
Victoria A VanderNoot
Steven S Branda

PLOS ONE

Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season.

2013-10-14

Peter M. Visscher
Mark Slee
Joseph E. Powell
Grant W. Montgomery
Fiona C McKay

Grant P Parnell
Prudence N Gatt
Stephen Schibeci
Malgorzata Krupa
Jeannette Lechner-Scott
Simon Broadley
Christopher Liddle
Steve Vucic
Graeme J Stewart
David R Booth

Multiple Sclerosis Journal

An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process.

2013-10-16

Lim Chee Liew
Mohan B. Singh
Prem L. Bhalla

PLOS ONE

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

2013-10-16

Marcel E. Dinger
John Mattick
Animesh Ray
Shaojie Zhang

Jian-Liang Li
Joseph Mazar
Cuncong Zhong
Geoffrey J Faulkner
Subramaniam S Govindarajan
Zhan Zhang
Gavin Meredith
Christopher Adams
Ranjan J Perera

Scientific Reports

A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression.

2013-10-17

Ekaterina E Khrameeva

Tanja Dorothe Rösel-Hillgärtner
Lee-Hsueh Hung
Patrick Le Querrec
Mikhail S Gelfand
Albrecht Bindereif

PLOS Genetics

A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.

2013-10-17

Liming Xiong
Shoudong Zhang

Tao Chen
Peng Cui
Hao Chen
Shahjahan Ali

PLOS Genetics

Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032

2013-10-19

Alfred Pühler
Jörn Kalinowski

Almut Mentz
Armin Neshat
Katharina Pfeifer-Sancar
Christian Rückert

BMC Genomics

Quantitative assessment of single-cell RNA-sequencing methods.

2013-10-20

Barbara Treutlein
Piero Dalerba

Angela R Wu
Norma F Neff
Tomer Kalisky
Michael E Rothenberg
Francis M Mburu
Gary L Mantalas
Sopheak Sim
Michael F Clarke
Stephen R Quake

Nature Methods

HAMR: high-throughput annotation of modified ribonucleotides.

2013-10-22

Otto Valladares

Paul Ryvkin
Yuk Yee Leung
Ian M Silverman
Micah Childress
Isabelle Dragomir
Brian D Gregory
Li-San Wang

RNA

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.

2013-10-23

Monika Gullerova
Jürg Bähler
Nicholas Jarvis Proudfoot

Margarita Schlackow
Samuel Marguerat
Jürg Bähler
Radek Erban

RNA

Parallel deep transcriptome and proteome analysis of zebrafish larvae

2013-10-24

Christiaan V. Henkel
Magnus Palmblad
Herman P Spaink

Ron P Dirks
Annemarie H Meijer
André M Deelder

BMC Research Notes

Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress.

2013-10-24

Alistair C. Darby
Dong Xia

A Christina Gill
Stuart D Armstrong
Catherine S Hartley
Jonathan M Wastling
Benjamin L Makepeace

The ISME Journal

IMG 4 version of the integrated microbial genomes comparative analysis system.

2013-10-27

Natalia N. Ivanova
Nikos C. Kyrpides
Tanja Woyke
Neha Varghese
Konstantinos Billis
Amrita Pati
Marcel Huntemann
Iain J. Anderson
Konstantinos Mavromatis
Krishna Palaniappan

Victor M Markowitz
I-Min A Chen
Ken Chu
Ernest Szeto
Manoj Pillay
Anna Ratner
Jinghua Huang

Nucleic Acids Research

Differential expression of olfactory genes in the southern house mosquito and insights into unique odorant receptor gene isoforms.

2013-10-28

Walter S Leal

Young-Moo Choo
Pingxi Xu
Cherre S B da Silva
Carlos Ueira-Vieira

Proceedings of the National Academy of Sciences of the United States of America

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

2013-10-29

Ross C Hardison
Manolis Kellis

Ali Mortazavi
Shirley Pepke
Camden Jansen
Georgi K Marinov
Jason Ernst
Richard M Myers
Barbara J Wold

Genome Research

A unified model for yeast transcript definition.

2013-10-29

Harm van Bakel
Corey Nislow
Carl G de Boer
Quaid D Morris

Kyle Tsui
Joyce Li
Jack F Greenblatt
Timothy R Hughes

Genome Research

Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets.

2013-10-30

Erik K Flemington

Wensheng Zhang
Andrea Edwards
Kun Zhang

PLOS ONE

Probing bacterial metabolism during infection using high-resolution transcriptomics

2013-11

Marvin Whiteley

Peter Jorth
Urvish Trivedi
Kendra Rumbaugh

Journal of Bacteriology

An integrated model of the transcriptome of HER2-positive breast cancer.

2013-11-01

Kevin J Thompson
Xiaojia Tang
Krishna R Kalari
Richard W. Joseph
Zhifu Sun

Brian M Necela
Melissa Lau
Jeanette E Eckel-Passow
Jennifer M Kachergus
S Keith Anderson
Saurabh Baheti
Jennifer M Carr
Tiffany R Baker
Poulami Barman
Derek C Radisky
Sarah A McLaughlin
High-seng Chai
Stephan Camille
David Rossell
Yan W Asmann
E Aubrey Thompson
Edith A Perez

PLOS ONE

Identification of molecular tumor markers in renal cell carcinomas with TFE3 protein expression by RNA sequencing.

2013-11-01

Mark Rubin

Dorothee Pflueger
Andrea Sboner
Martina Storz
Jasmine Roth
Eva Compérat
Elisabeth Bruder
Peter Schraml
Holger Moch

Neoplasia

RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically.

2013-11-01

Fuli Li

Yang Tan
Juanjuan Liu
Xiaohua Chen
Huajun Zheng

Molecular BioSystems

Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis.

2013-11-01

Michael Thon
Serenella Sukno

Noam Alkan
Xiangchun Meng
Gilgi Friedlander
Eli Reuveni
Amir Sherman
Robert Fluhr
Dov Prusky

Molecular Plant-Microbe Interactions

Systematic evaluation of spliced alignment programs for RNA-seq data

2013-11-03

Jennifer Harrow
Roderic Guigó i Serra
Tamara Steijger
Pär G Engström
Gregory R Grant
Gunnar Rätsch
Nick Goldman
Paul Bertone

Botond Sipos
André Kahles
Tim J Hubbard
RGASP Consortium

Nature Methods

Assessment of transcript reconstruction methods for RNA-seq.

2013-11-03

Tim Hubbard
Jennifer Harrow
Felix Kokocinski
Roderic Guigó i Serra
Tamara Steijger
Pär G Engström
Josep F. Abril
Paul Bertone

RGASP Consortium

Nature Methods

Model-based clustering for RNA-seq data.

2013-11-04

Thomas Brutnell

Yaqing Si
Peng Liu
Pinghua Li

Bioinformatics

The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

2013-11-04

Gavin Sherlock
Jennifer R Wortman
Diane Inglis

Gustavo C Cerqueira
Martha B Arnaud
Marek S Skrzypek
Gail Binkley
Matt Simison
Stuart R Miyasato
Jonathan Binkley
Joshua Orvis
Prachi Shah
Farrell Wymore

Nucleic Acids Research

Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy.

2013-11-04

Anna Maria Pinto
Christopher Dengler

Zhenxi Zhang
Lili Wan
Wei Wang
Michael G Berg
Isabela Oliva
Larry N Singh
Zhi Wei
Gideon Dreyfuss

Proceedings of the National Academy of Sciences of the United States of America

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.

2013-11-05

Russell S. Thomas
Michael B Black

Bethany B Parks
Linda Pluta
Tzu-Ming Chu
Bruce C Allen
Russell D Wolfinger

Toxicological Sciences

Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.

2013-11-05

Tamas Bartfai

Jennifer M Spaethling
David Piel
Hannah Dueck
Peter T Buckley
Jacqueline F Morris
Stephen A Fisher
Jaehee Lee
Jai-Yoon Sul
Junhyong Kim
Sheryl G Beck
James H Eberwine

FASEB Journal

Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.

2013-11-05

Miguel Marcilla
Cristina Ruiz-Romero
Joan J Bech-Serra
Oscar Gallardo
Gorka Prieto
Concha Gil
Joaquín Abian
Marta Mendes
Irene Orera
Noelia Dasilva
Kerman Aloria
María I Mora
Manuel Fuentes
José M Mato

Víctor Segura
Juan Alberto Medina-Aunon
Salvador Martínez-Bartolomé
Oreto Antúnez
Jesús M Arizmendi
Mikel Azkargorta
Silvia Barceló-Batllori
Jabier Beaskoetxea
Francisco Blanco
Mariana B Monteiro
David Cáceres
Francesc Canals
Monserrat Carrascal
José Ignacio Casal
Felipe Clemente
Nuria Colomé
Paula Díaz
Félix Elortza
Patricia Fernández-Puente
Severine I Gharbi
Carmen González-Tejedo
María Luisa Hernáez
Manuel Lombardía
Maria Lopez-Lucendo
Eliandre Oliveira
Alberto Pascual-Montano
Manuel M Sánchez del Pino
Daniel Tabas-Madrid
Maria L Valero
Vital Vialas
Joan Villanueva
Juan Pablo Albar
Fernando J Corrales

Journal of Proteome Research

Modeling alternative splicing variants from RNA-Seq data with isoform graphs.

2013-11-07

Gianluca Della Vedova

Stefano Beretta
Paola Bonizzoni
Yuri Pirola
Raffaella Rizzi

Journal of Computational Biology

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation.

2013-11-07

Alexander van Oudenaarden
Wenqian Hu
Jiahai Shi
Harvey Lodish

Juan R Alvarez-Dominguez
Bingbing Yuan
Staphany S Park
Austin A Gromatzky

Blood

Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes

2013-11-07

Gil Omenn

Rajasree Menon
Hogune Im
Emma Yue Zhang
Shiaw-Lin Wu
Rui Chen
Michael Snyder
William S Hancock

Journal of Proteome Research

Comprehensive RNA-Seq expression analysis of sensory ganglia with a focus on ion channels and GPCRs in Trigeminal ganglia

2013-11-08

Hanns Hatt
Günter Gisselmann

Stavros Manteniotis
Ramona Lehmann
Caroline Flegel
Felix Vogel
Adrian Hofreuter
Benjamin S P Schreiner
Janine Altmüller
Christian Becker
Nicole Schöbel
Günter Gisselmann

PLOS ONE

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)

2013-11-09

David Sturgill

John H Malone
Xia Sun
Harold E Smith
Leonard Rabinow
Marie-Laure Samson
Brian Oliver

BMC Bioinformatics

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo

2013-11-11

Jinfeng Liu
Xinyang Zhao
Eunhee Kim
Omar Abdel-Wahab

Jie Gao
Mazhar Adli
Anwesha Dey
Thomas Trimarchi
Young Rock Chung
Cem Kuscu
Todd Hricik
Delphine Ndiaye-Lobry
Lindsay M Lafave
Richard Koche
Alan H Shih
Olga A Guryanova
Sheng Li
Suveg Pandey
Joseph Y Shin
Leon Telis
Parva K Bhatt
Sebastien Monette
Christopher E Mason
Christopher Y Park
Bradley E Bernstein
Iannis Aifantis
Ross L Levine

Journal of Experimental Medicine

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.

2013-11-13

Adam Ameur

Ammar Zaghlool
Linnea Nyberg
Jonatan Halvardson
Manfred Grabherr
Lucia Cavelier
Lars Feuk

BMC Biotechnology

Mapping genetic modifiers of survival in a mouse model of Dravet syndrome.

2013-11-14

Jennifer A Kearney

A R Miller
N A Hawkins
C E McCollom

Genes, Brain and Behavior

Early T helper cell programming of gene expression in human

2013-11-15

Riitta Lahesmaa

Soile Tuomela

Seminars in Immunology

Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration.

2013-11-15

Yizhi Cui
Qing-Yu He
Gong Zhang
Tong Wang

Jiayong Zhong
Jiahui Guo
Zhipeng Chen
Lijuan Yang

Journal of Proteome Research

Accuracy of allele frequency estimation using pooled RNA-Seq.

2013-11-16

Mateusz Konczal
Wieslaw Babik
Jacek Radwan
Paweł Koteja

M T Stuglik

Molecular Ecology Resources

Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

2013-11-18

Daniel C. Liebler

Patrick J Halvey
Xiaojing Wang
Jing Wang
Ajaz A Bhat
Punita Dhawan
Ming Li
Bing Zhang
Robbert J C Slebos

Cancer Research

Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis.

2013-11-19

Ann Progulske-Fox

Priscilla Phillips
Scott Grieshaber
Nicole Grieshaber

FEMS Microbiology Letters

Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens

2013-11-20

Dongwen Lv

Xiaohong Zhou
Ke Wang
Chengjun Wu
Jiarui Li
Pei Zhao
Zhishan Lin
Lipu Du
Yueming Yan
Xingguo Ye

PLOS ONE

Phenotypic and transcriptional fidelity of patient-derived colon cancer xenografts in immune-deficient mice

2013-11-20

Edus H Warren

Jeffrey Chou
Matthew P Fitzgibbon
Christie-Lynn L Mortales
Andrea M H Towlerton
Melissa P Upton
Raymond S Yeung
Martin W McIntosh

PLOS ONE

Global bidirectional transcription of the Epstein-Barr virus genome during reactivation.

2013-11-20

Melody Baddoo
Tina O'Grady
Erik K Flemington

Subing Cao
Michael J Strong
Monica Concha
Xia Wang
Sandra Splinter Bondurant
Marie Adams
Melody Baddoo
Sudesh K Srivastav
Zhen Lin
Claire Fewell
Qinyan Yin

Journal of Virology

Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.

2013-11-21

Graham Rose
Teresa Cortes
Olga T Schubert
Kristine B Arnvig
Iñaki Comas
Ruedi Aebersold

Douglas B Young

Cell Reports

DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.

2013-11-21

Zizhen Yao
Silvère M van der Maarel

Janet M Young
Jennifer L Whiddon
Bhavatharini Kasinathan
Lauren Snider
Linda N Geng
Judit Balog
Rabi Tawil
Stephen J Tapscott

PLOS Genetics

RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease

2013-11-21

Silvia Libro

Stefan T Kaluziak
Steven V Vollmer

PLOS ONE

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.

2013-11-21

Víctor Quesada
Núria López-Bigas
Alfonso Valencia
Carlos López Otín
Roderic Guigó i Serra
Jean Monlong
Panagiotis Papasaikas
Simone Ecker
Guillem Clot
Sarah Djebali
Pedro G Ferreira
Rory Johnson
Daniel Rico
Gonzalo Gómez-López
Xose S. Puente
David G. Pisano
María Rozman
José I Martín-Subero
Dolors Colomer
Elias Campo

Pedro Jares
Alejandra Martínez-Trillos
Neus Villamor
Abel González-Pérez
David G Knowles
Mónica López-Guerra
Cristina Royo
Maite Cazorla
Magda Pinyol
Marta Aymerich
Marta Kulis
David Tamborero
Anaïs Gouin
Julie Blanc
Marta Gut
Ivo Gut
Armando López-Guillermo

Genome Research

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

2013-11-22

Adam J Reid
Joshua P Ramsay
Laurent Gatto
Lars Barquist

Nabil M Wilf
Neil R Williamson
Nicholas J Croucher
Svenja S Hester
David Goulding
Kathryn S Lilley
Robert A Kingsley
Gordon Dougan
George Pc Salmond

BMC Genomics

Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq.

2013-11-22

Jonathan D. Moore
Andrew M Blanks
Siobhan Quenby

Yi-Wah Chan
Hugo A van den Berg

Experimental Physiology

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets

2013-11-24

Thomas Clouaire
Adrian Peter Bird

Gabriele Schweikert
Botond Cseke
Guido Sanguinetti

BMC Genomics

Flexible analysis of RNA-seq data using mixed effects models.

2013-11-26

Ernest Turro

William J Astle
Simon Tavaré

Bioinformatics

Characterization of the human ESC transcriptome by hybrid sequencing.

2013-11-26

Harm van Bakel
Renee Reijo Pera

Kin Fai Au
Vittorio Sebastiano
Pegah Tootoonchi Afshar
Jens Durruthy Durruthy
Lawrence Lee
Brian A Williams
Eric E Schadt
Jason G Underwood
Wing Hung Wong

Proceedings of the National Academy of Sciences of the United States of America

Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese black cattle during peri-implantation period.

2013-11-27

So Nakagawa

Toshihiro Sakurai
Min-Su Kim
Hanako Bai
Rulan Bai
Junyou Li
Kwan-Sik Min
Atsushi Ideta
Yoshito Aoyagi
Kazuhiko Imakawa

PLOS ONE

RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns.

2013-12-01

Judith Zoephel
L Randau

Judith Zoephel

Biochemical Society Transactions

An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.

2013-12-01

Carsten Kröger
Shabarinath Srikumar
Kristian Händler
Karsten Hokamp

Aoife Colgan
Sathesh K Sivasankaran
Disa L Hammarlöf
Rocío Canals
Joe E Grissom
Tyrrell Conway
Jay C D Hinton

Cell Host & Microbe

The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression.

2013-12-02

Anand Swaroop
Matthew Brooks

Sharda P Yadav
Hong Hao
Hyun-Jin Yang
Marie-Audrey I Kautzmann
Jacob Nellissery
Bernward Klocke
Martin Seifert

Human Molecular Genetics

Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines.

2013-12-02

Morten Thaysen-Andersen
Susan Fanayan
Mark Baker

Manveen K Sethi
Joshua T Smith
Nicolle H Packer
William S Hancock

Journal of Proteome Research

Comparison of software packages for detecting differential expression in RNA-seq studies.

2013-12-02

Laura L. Elo

Fatemeh Seyednasrollah
Asta Laiho

Briefings in Bioinformatics

Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.

2013-12-03

György Marko-Varga

Cheryl F Lichti
Huiling Liu
Alexander S Shavkunov
Ekaterina Mostovenko
Erik P Sulman
Ravesanker Ezhilarasan
Qianghu Wang
Roger A Kroes
Joseph C Moskal
David Fenyö
Betül Akgöl Oksuz
Charles A Conrad
Frederick F Lang
Frode S Berven
Akos Végvári
Melinda Rezeli
Sophia Hober
Carol L Nilsson

Journal of Proteome Research

Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.

2013-12-03

Stefano Calza

Chen Suo
Agus Salim
Yudi Pawitan

Bioinformatics

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

2013-12-04

Blake Meyers

Keerthi P Venkataramanan
Shawn W Jones
Kevin P McCormick
Sridhara G Kunjeti
Matthew T Ralston
Eleftherios T Papoutsakis

BMC Genomics

Simultaneous transcriptional profiling of bacteria and their host cells

2013-12-04

Claire M. Fraser
Naomi Sengamalay
Marcus C. Chibucos
Amol C Shetty
Todd Creasy

Michael S Humphrys
Yezhou Sun
Elliott F Drabek
Umar Farooq
Naomi Sengamalay
Sandy Ott
Huizhong Shou
Patrik M Bavoil
Anup Mahurkar
Garry S A Myers

PLOS ONE

Vespucci: a system for building annotated databases of nascent transcripts.

2013-12-04

Terry Gaasterland
Minna U Kaikkonen
Christopher K Glass

Karmel A Allison

Nucleic Acids Research

A platform independent RNA-Seq protocol for the detection of transcriptome complexity.

2013-12-05

Graziano Pesole
Flaviana Marzano
Mariano Francesco Caratozzolo
Ivana Kurelac
D D'Elia
Anna Maria D'Erchia
Flavio Licciulli
Ernesto Picardi

Claudia Calabrese
Marina Mangiulli
Caterina Manzari
Anna Maria Paluscio
Sabino Liuni
Marcella Attimonelli
Giuseppe Gasparre
Anna Maria Porcelli
Elisabetta Sbisà
Apollonia Tullo

BMC Genomics

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.

2013-12-05

Jens Nielsen
Mathias Uhlén
Jenny Ottosson Takanen
Cristina Al-Khalili Szigyarto
Kalle von Feilitzen
Linn Fagerberg
Jan Mulder
Mikael Huss
Jochen Schwenk
Jacob Odeberg
Peter Nilsson
Per Oksvold

Björn M Hallström
Caroline Kampf
Dijana Djureinovic
Masato Habuka
Simin Tahmasebpoor
Angelika Danielsson
Karolina Edlund
Anna Asplund
Evelina Sjöstedt
Emma Lundberg
Marie Skogs
Jenny Ottosson Takanen
Holger Berling
Hanna Tegel
Cecilia Lindskog
Frida Danielsson
Adil Mardinoglu
Asa Sivertsson
Kalle von Feilitzen
Mattias Forsberg
Martin Zwahlen
IngMarie Olsson
Sanjay Navani
Fredrik Ponten

Molecular & Cellular Proteomics

Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production.

2013-12-06

Sandra Wiegand
Heiko Liesegang
Rolf Daniel

Birgit Voigt
Dirk Albrecht
Johannes Bongaerts
Stefan Evers
Michael Hecker

Microbial Cell Factories

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

2013-12-06

Brian Scheffler
Megan J Bowman
Philip J Bauer

Wonkeun Park
Joshua A Udall
Justin T Page
Joshua Raney
Don C Jones
B Todd Campbell

PLOS ONE

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer

2013-12-09

John K. Field

Akshata R Udyavar
Megan D Hoeksema
Jonathan E Clark
Yong Zou
Zuojian Tang
Zhiguo Li
Ming Li
Heidi Chen
Alexander Statnikov
Yu Shyr
Daniel C Liebler
Rosana Eisenberg
Lourdes Estrada
Pierre P Massion
Vito Quaranta

BMC Systems Biology

ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer.

2013-12-10

Tetiana Bogdanova
Mark P Little

Rebecca J Leeman-Neill
Lindsey M Kelly
Pengyuan Liu
Alina V Brenner
Viktoria N Evdokimova
Maureen Hatch
Liudmyla Y Zurnadzy
Marina N Nikiforova
Ning J Yue
Miao Zhang
Kiyohiko Mabuchi
Mykola D Tronko
Yuri E Nikiforov

Cancer

Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.

2013-12-11

Abdimajid Osman

Antheia Kissopoulou
Jon Jonasson
Tomas L Lindahl

PLOS ONE

Transcriptome changes in the porcine endometrium during the preattachment phase.

2013-12-12

Susanne E. Ulbrich

Anastazia Samborski
Alexander Graf
Stefan Krebs
Barbara Kessler
Myriam Reichenbach
Horst-Dieter Reichenbach
Stefan Bauersachs

Biology of Reproduction

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.

2013-12-13

Michiel Van Bel
Klaas Vandepoele
Yves Van de Peer

Sebastian Proost
Christophe Van Neste
Dieter Deforce
Yves Van de Peer

Genome Biology

Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data

2013-12-13

Ariel Orellana

Mauricio González-Agüero
Miguel García-Rojas
Alex Di Genova
José Correa
Alejandro Maass
Patricio Hinrichsen

BMC Genomics

Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola.

2013-12-16

Jun-Jun Liu

Rona N Sturrock
Ross Benton

BMC Genomics

Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique

2013-12-17

Jörn Kalinowski

Katharina Pfeifer-Sancar
Almut Mentz
Christian Rückert

BMC Genomics

RNA-Seq optimization with eQTL gold standards.

2013-12-17

Andrew B. West

Shannon E Ellis
Simone Gupta
Foram N Ashar
Joel S Bader
Dan E Arking

BMC Genomics

Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.

2013-12-17
2014-03-01

Daniel Lawson
Paul J Kersey

Dana Nayduch
Lee W Cohnstaedt
Christopher Saski
Mark Fife
Simon Carpenter

Virus Research

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

2013-12-18

Eric Rivals

Nicolas Philippe
Elias Bou Samra
Anthony Boureux
Alban Mancheron
Florence Rufflé
Qiang Bai
John De Vos
Thérèse Commes

Nucleic Acids Research

Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia

2013-12-19

Iwona Wlodarska
Gert Hulselmans
Zeynep Kalender Atak
Kim De Keersmaecker
Peter Vandenberghe
Jan Cools
Stein Aerts
Robin Foà

Valentina Gianfelici
Arun George Devasia
Ellen Geerdens
Nicole Mentens
Sabina Chiaretti
Kaat Durinck
Anne Uyttebroeck
Jacqueline Cloos
Frank Speleman

PLOS Genetics

An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog.

2013-12-19

Sylvain Foissac

Agnes Bonnet
Cedric Cabau
Olivier Bouchez
Julien Sarry
Nathalie Marsaud
Florent Woloszyn
Philippe Mulsant
Beatrice Mandon-Pepin

BMC Genomics

Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua

2013-12-20

Alain Goossens

Sandra S A Soetaert
Christophe M F Van Neste
Mado L Vandewoestyne
Steven R Head
Filip C W Van Nieuwerburgh
Dieter L D Deforce

BMC Plant Biology

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

2013-12-20

Xianyun Mao
Jane Ferguson
Muredach P. Reilly

Yu Hu
Yichuan Liu
Cheng Jia
Chenyi Xue
Hongzhe Li
Mingyao Li

Nucleic Acids Research

Correction: RNA-Seq-Based Analysis of the Physiologic Cold Shock-Induced Changes in Moraxella catarrhalis Gene Expression.

2013-12-20

Stefan Wyder

Violeta Spaniol
Christoph Aebi

PLOS ONE

Quantitative single-cell RNA-seq with unique molecular identifiers.

2013-12-22

Sten Linnarsson
Peter Lönnerberg

Saiful Islam
Amit Zeisel
Simon Joost
Gioele La Manno
Pawel Zajac
Maria Kasper

Nature Methods

Divergent transcription is associated with promoters of transcriptional regulators.

2013-12-23

Marc Garibal
Jean-Christophe Andrau
Jean Imbert
Salvatore Spicuglia

Cyrille Lepoivre
Mohamed Belhocine
Aurélie Bergon
Aurélien Griffon
Miriam Yammine
Laurent Vanhille
Joaquin Zacarias-Cabeza
Frederic Koch
Muhammad Ahmad Maqbool
Romain Fenouil
Beatrice Loriod
Hélène Holota
Marta Gut
Ivo Gut
Denis Puthier

BMC Genomics

Lsh regulates LTR retrotransposon repression independently of Dnmt3b function.

2013-12-24

Colin A. Semple
Tracey Davey
Ian R. Adams
John Greally

Donncha S Dunican
Hazel A Cruickshanks
Masako Suzuki
Robert J Arceci
Richard R Meehan

Genome Biology

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

2013-12-24

Lennart Opitz

Hubert Rehrauer
Ge Tan
Lina Sieverling
Ralph Schlapbach

BMC Bioinformatics

Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.

2013-12-24

Laura Elnitski
Zhong Chen

Zhenqing Ye
Xun Lan
Stephen Hara
Benjamin Sunkel
Tim H-M Huang
Qianben Wang
Victor X Jin

Nucleic Acids Research

Mycorrhizal phosphate uptake pathway in maize: vital for growth and cob development on nutrient poor agricultural and greenhouse soils.

2013-12-26

Jan Jansa

Martin Willmann
Nina Gerlach
Benjamin Buer
Aleksandra Polatajko
Réka Nagy
Eva Koebke
René Flisch
Marcel Bucher

Frontiers in Plant Science

Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus).

2013-12-28

Eric Peatman

Chao Li
Benjamin H Beck

Developmental and Comparative Immunology

Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish.

2013-12-30

Luyang Sun
Shikai Liu

Ruijia Wang
Lisui Bao
Jiaren Zhang
Yanliang Jiang
Jun Yao
Lin Song
Jianbin Feng
Zhanjiang Liu

BMC Genomics

Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.

2013-12-30

Jean-Jack M Riethoven

Yong Ding
Ning Liu
Laetitia Virlouvet
Michael Fromm
Zoya Avramova

BMC Plant Biology

Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure

2014

Christian Tamburini

Amira Amrani
Aurélie Bergon
Hélène Holota
Marc Garel
Bernard Ollivier
Jean Imbert
Alain Dolla
Nathalie Pradel

PLOS ONE

Melanocytes in the skin--comparative whole transcriptome analysis of main skin cell types

2014

Viljar Jaks
Ene Reimann
Q24546281
Eero Vasar
Sulev Kõks

Paula Reemann
Sten Ilmjärv
Orm Porosaar
Helgi Silm

PLOS ONE

Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1

2014

Jean-Jack M Riethoven
Guillaume Blanc
David D. Dunigan

Michael Mozar
Irina V Agarkova
James R Gurnon
Giane Yanai-Balser
Janet M Rowe
Yuannan Xia
James L Van Etten

PLOS ONE

De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis

2014

Lisa Campbell

Darcie E Ryan
Alan E Pepper

BMC Genomics

Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains

2014

Helmut Denk
Hans Lehrach
Marie-Laure Yaspo
Christina Grimm
Kurt Zatloukal

Vikash Pandey
Marc Sultan
Karl Kashofer
Meryem Ralser
Vyacheslav Amstislavskiy
Julia Starmann
Ingrid Osprian
Hendrik Hache
Holger Sültmann
Michael Trauner
Christoph Wierling

PLOS ONE

Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation

2014

Darya Peregudova
Alexey A. Dmitriev
Sergey V Mylnikov
Peter O Fedichev
Nataliya Melnikova
Anna V Kudryavtseva
Mikhail V Shaposhnikov
Alexey A Moskalev

Anastasia Snezhkina
Valeria Kogan
Ekaterina Plyusnina
Leonid Uroshlev
Sergey Plusnin

PLOS ONE

The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs

2014

Angela M Yu
Patrícia Costa Reis
Michelle A. Petri

Lihua Shi
Zhe Zhang
Wei Wang
Zhi Wei
Ehtisham Akhter
Kelly Maurer
Li Song
Kathleen E Sullivan

PLOS ONE

Establishment of highly tumorigenic human colorectal cancer cell line (CR4) with properties of putative cancer stem cells

2014

Iwao Ojima

Rebecca A Rowehl
Stephanie Burke
Agnieszka B Bialkowska
Donald W Pettet
Leahana Rowehl
Ellen Li
Eric Antoniou
Yuanhao Zhang
Roberto Bergamaschi
Kenneth R Shroyer
Galina I Botchkina

PLOS ONE

RNA-sequencing analysis of HepG2 cells treated with atorvastatin

2014

Daniel Sachse
Jens P. Berg

Camilla Stormo
Marianne K Kringen
Robert Lyle
Ole Kristoffer Olstad
Armin P Piehler

PLOS ONE

The oncogenic MicroRNA Hsa-miR-155-5p targets the transcription factor ELK3 and links it to the hypoxia response

2014

Alain C Jung
Bohdan Wasylyk

E Douglas Robertson
Christine Wasylyk
Tao Ye

PLOS ONE

Genetics of gene expression in CNS

2014

Robert W. Williams

Ashutosh K Pandey

International Review of Neurobiology

Towards a computational model of a methane producing archaeum

2014

Piyush Labhsetwar
Zaida Luthey-Schulten

Joseph R Peterson
Jeremy R Ellermeier
Petra R A Kohler
Ankur Jain
Taekjip Ha
William W Metcalf

Archaea

Comparison between karyotyping-FISH-reverse transcription PCR and RNA-sequencing-fusion gene identification programs in the detection of KAT6A-CREBBP in acute myeloid leukemia

2014

Sverre Heim
Ioannis Panagopoulos

Synne Torkildsen
Ludmila Gorunova
Anne Tierens
Geir E Tjønnfjord

PLOS ONE

RNA families in Epstein-Barr virus

2014

Joan A. Steitz

Walter N Moss
Nara Lee
Genaro Pimienta

RNA Biology

Characterization of human pseudogene-derived non-coding RNAs for functional potential

2014

Deyou Zheng

Xingyi Guo
Mingyan Lin
Shira Rockowitz
Herbert M Lachman

PLOS ONE

Oqtans: a multifunctional workbench for RNA-seq data analysis

2014

Gunnar Rätsch

Vipin T Sreedharan
Sebastian J Schultheiss
Géraldine Jean
André Kahles
Regina Bohnert
Philipp Drewe
Pramod Mudrakarta
Nico Görnitz
Georg Zeller

BMC Bioinformatics

Blood biomarkers of the late phase asthmatic response using RNA-Seq

2014

Louis-Philippe Boulet

Amrit Singh
Casey P Shannon
Gail M Gauvreau
Paul M O'Byrne
J FitzGerald
Scott J Tebbutt

Allergy, Asthma & Clinical Immunology

Emerging RNA-Seq Applications in Food Science

2014

Alberto Valdés
Virginia García-Cañas
Carolina Simó

Clara Ibáñez

Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution

2014-01

Sarah L Maguire
Geraldine Butler
Theodore C White
Kenneth H. Wolfe
Jean-Marc Nicaud
Cécile Neuvéglise

Can Wang
Linda M Holland
François Brunel
Martin Zavrel

PLOS Genetics

CellFinder: a cell data repository

2014-01

Stefanie Seltmann
Fritz Lekschas
Mariana Lara Neves
Harald Stachelscheid
Nancy Mah
Andreas Kurtz

Jean-Fred Fontaine
Miguel A Andrade-Navarro
Ulf Leser

Nucleic Acids Research

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

2014-01-01

Michael Stratton

Tony Ly
Yasmeen Ahmad
Adam Shlien
Dominique Soroka
Allie Mills
Michael J Emanuele
Angus I Lamond

eLife

Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells

2014-01-01

Xiuqian Mu

Renzhong Li
Fuguo Wu
Raili Ruonala
Darshan Sapkota
Zihua Hu

PLOS ONE

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

2014-01-01

Danielle Thierry-Mieg
Lee Lancashire
Heng Luo
Nan Mei
Jean Thierry-Mieg

Ying Yu
James C Fuscoe
Chen Zhao
Chao Guo
Meiwen Jia
Tao Qing
Desmond I Bannon
Wenjun Bao
Tingting Du
Zhenqiang Su
Wendell D Jones
Carrie L Moland
William S Branham
Feng Qian
Baitang Ning
Yan Li
Huixiao Hong
Lei Guo
Tieliu Shi
Kevin Y Wang
Russell D Wolfinger
Yuri Nikolsky
Stephen J Walker
Penelope Duerksen-Hughes
Christopher E Mason
Weida Tong
Leming Shi
Charles Wang

Nature Communications

Correlating histone modification patterns with gene expression data during hematopoiesis.

2014-01-01

Gangqing Hu

Keji Zhao

Methods in Molecular Biology

Domestic dogs and cancer research: a breed-based genomics approach.

2014-01-01

Elaine Ostrander

Brian W Davis

ILAR Journal

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq.

2014-01-01

Sten Linnarsson
Peter Lönnerberg
Sabrina Zechel

Pawel Zajac
Carlos F Ibáñez

Genome Biology

RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain.

2014-01-01

Sean P Farris

R Dayne Mayfield

International Review of Neurobiology

Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets

2014-01-01

Liang-Hu Qu

Jun-Hao Li
Shun Liu
Ling-Ling Zheng
Jie Wu
Wen-Ju Sun
Ze-Lin Wang
Hui Zhou
Jian-Hua Yang

Frontiers in Bioengineering and Biotechnology

Next-generation sequencing applied to flower development: RNA-seq.

2014-01-01

Yuling Jiao

Jun He

Methods in Molecular Biology

Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites.

2014-01-01

Isabelle Rosinski-Chupin

Olga Soutourina
Isabelle Martin-Verstraete

Methods in Enzymology

Plant and fungal gene expression in mycorrhizal protocorms of the orchid Serapias vomeracea colonized by Tulasnella calospora.

2014-01-01

Fabiano Sillo
Silvia Perotto
Raffaella Balestrini

Luca Nerva
Mariangela Girlanda

Plant Signaling and Behavior

Shared transcription factors contribute to distinct cell fates

2014-01-01

Berthold Göttgens

Felicia S L Ng
Fernando J Calero-Nieto

Transcription

Transcriptomic changes in brain development.

2014-01-01

Mark R Cookson

Allissa A Dillman

International Review of Neurobiology

RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines.

2014-01-01

Youping Deng

Yan Li
Omid Rouhi
Hankui Chen
Rolando Ramirez
Jeffrey A Borgia

Cancer Informatics

Developmental analysis of spliceosomal snRNA isoform expression.

2014-01-01

Zhipeng Lu

A Gregory Matera

Deep sequencing of small chromatin-associated RNA: bioinformatic analysis.

2014-01-01

Sarah Diermeier
Gernot Längst

Methods in Molecular Biology

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.

2014-01-01

Daniel Ramsköld
Rickard Sandberg
Qiaolin Deng
Björn Reinius

Science

edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology.

2014-01-01

Mark D. Robinson

Olga Nikolayeva

Methods in Molecular Biology

Quantitative transcriptome analysis using RNA-seq.

2014-01-01

Andrea Bräutigam

Canan Külahoglu

Methods in Molecular Biology

Full-length RNA-seq from single cells using Smart-seq2.

2014-01-02

Omid R Faridani
Rickard Sandberg

Simone Picelli
Asa K Björklund
Gösta Winberg
Sven Sagasser

Nature Protocols

Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny.

2014-01-02

Marc T Nishimura
Jeff H. Chang
David A. Baltrus

Tatiana S Mucyn
Scott Yourstone
Abigail L Lind
Surojit Biswas
Jason S Cumbie
Corbin D Jones
Jeffery L Dangl
Sarah R Grant

PLOS Pathogens

RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium.

2014-01-04

Philippe Moncuquet

Sharon E Hook
Hannah L Osborn
Francesca Gissi
Natalie A Twine
Marc R Wilkins
Merrin S Adams

Marine Genomics

Differential expression analysis of RNA-seq data at single-base resolution

2014-01-06

Kasper D. Hansen
Jeffrey T. Leek

Alyssa C Frazee
Sarven Sabunciyan
Rafael A Irizarry

Biostatistics

A unique missense allele of BAF155, a core BAF chromatin remodeling complex protein, causes neural tube closure defects in mice.

2014-01-09

Dawn E Watkins-Chow
William J Pavan
Lee Niswander

Laura Harmacek
Jianfu Chen
Kenneth L Jones
J Michael Salbaum

Developmental Neurobiology

The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.

2014-01-09

Brian D Strahl
Scott B Rothbart

Brianna J Klein
Lianhua Piao
Yuanxin Xi
Hector Rincon-Arano
Danni Peng
Hong Wen
Connie Larson
Xi Zhang
Xia Zheng
Michael A Cortazar
Pedro V Peña
Anthony Mangan
David L Bentley
Mark Groudine
Wei Li
Xiaobing Shi
Tatiana G Kutateladze

Cell Reports

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

2014-01-11

Georg Zeller
Gunnar Rätsch

Vipin T Sreedharan
Sebastian J Schultheiss
Géraldine Jean
André Kahles
Regina Bohnert
Philipp Drewe
Pramod Mudrakarta
Nico Görnitz

Bioinformatics

Differential protein occupancy profiling of the mRNA transcriptome.

2014-01-13

Markus Landthaler

Markus Schueler
Mathias Munschauer
Lea Haarup Gregersen
Ana Finzel
Alexander Loewer
Wei Chen
Christoph Dieterich

Genome Biology

Production of RNA for transcriptomic analysis from mouse spinal cord motor neuron cell bodies by laser capture microdissection.

2014-01-13

Arthur L. Horwich

Urmi Bandyopadhyay
Wayne A Fenton
Maria Nagy

Journal of Visualized Experiments

GuavaH: a compendium of host genomic data in HIV biology and disease.

2014-01-15

Paul J. McLaren
Angela Ciuffi
Jacques Fellay

István Bartha
Amalio Telenti

Retrovirology

Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq.

2014-01-16

Shikai Liu

Jun Cui
Bing Zhang
Hongdi Wang
Hongjuan Sun
Shuhui Song
Xuemei Qiu
Yang Liu
Xiuli Wang
Zhiqiang Jiang
Zhanjiang Liu

PLOS ONE

Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms

2014-01-17

A Johnston
Lam C. Tsoi

Bingshan Li
William R Swindell
Johann E Gudjonsson
Trilokraj Tejasvi
Jun Ding
Philip E Stuart
Xianying Xing
James J Kochkodan
John J Voorhees
Hyun M Kang
Rajan P Nair
Goncalo R Abecasis
James T Elder

Journal of Investigative Dermatology

The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs.

2014-01-17

Matthew Baranski
Nicholas A. Robinson

Gopalapillay Gopikrishna
Vinaya Kumar Katneni
Mudagandur S Shekhar
Jayakani Shanmugakarthik
Sarangapani Jothivel
Chavali Gopal
Pitchaiyappan Ravichandran
Matthew Kent
Mariann Arnyasi
Alphis G Ponniah

PLOS ONE

Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.

2014-01-17

Wenwu Wu
James L. Manley

Xuexia Zhou
Huang Li
Yuanming Cheng
Ning Wei
Jie Zong
Xiaoyan Feng
Zhiqin Xie
Dai Chen
Hui Wang
Ying Feng

Nucleic Acids Research

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis

2014-01-17

Lior Pachter
Harold Pimentel
Narla Mohandas
Xiuli An

Marilyn Parra
Sherry Gee
Dana Ghanem
Jie Li
John G Conboy

Nucleic Acids Research

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.

2014-01-17

Sean R Collins
Devin A King
Ashby Morrison
Or Gozani

Glòria Mas Martín
Erin M Green
Pablo E Garcia-Nieto
Richard Alexander
Nevan J Krogan

Epigenetics

ALEA: a toolbox for allele-specific epigenomics analysis.

2014-01-21

Mohammad M Karimi
Torsten Möller
Matthew C. Lorincz

Hamid Younesy
Alireza Heravi-Moussavi
Jeffrey B Cheng
Joseph F Costello
Steven J M Jones

Bioinformatics

RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp.

2014-01-22

Kumar Sudesh

Nyok-Sean Lau
Choon Pin Foong
Yukio Kurihara
Kumar Sudesh
Minami Matsui

PLOS ONE

RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction.

2014-01-23

Wenqin Wang
Joachim Messing

Yongrui Wu

BMC Genomics

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.

2014-01-24

Andrew Paul Hutchins

Ralf Jauch
Mateusz Dyla
Diego Miranda-Saavedra

Cell regeneration (London, England)

A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.

2014-01-28

Christine Orengo
James R Perkins
Matthias Kohl
Stephen B McMahon

Ana Antunes-Martins
Margarita Calvo
John Grist
Werner Rust
Ramona Schmid
Tobias Hildebrandt
David L H Bennett

Molecular Pain

The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA.

2014-01-29

Anselm Enders

Vicky Cho
Yan Mei
Arleen Sanny
Stephanie Chan
Edward M Bertram
Andy Tan
Christopher C Goodnow
T Daniel Andrews

Genome Biology

RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation.

2014-01-30

Judith Breuer
Paul Kellam

Meleri Jones
Inga R Dry
Dan Frampton
Manuraj Singh
Ravinder K Kanda
Michael B Yee
Michael Hollinshead
Paul R Kinchington
Edel A O'Toole

PLOS Pathogens

bwtool: a tool for bigWig files.

2014-01-30

Miguel Beato del Rosal

Andy Pohl

Bioinformatics

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

2014-01-31

Matthew Meyerson
Mara Rosenberg
Marcin Imielinski
Juliann Chmielecki
Gad Getz
Gordon Saksena

Angela N Brooks
Peter S Choi
Luc de Waal
Tanaz Sharifnia
Chandra Sekhar Pedamallu
Andrey Sivachenko
Michael S Lawrence
David S DeLuca

PLOS ONE

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.

2014-02-01

Naama Elefant
Hadas Keren-Shaul
Franziska Paul
Alexander Mildner
Steffen Jung

Diego Adhemar Jaitin
Ephraim Kenigsberg
Hadas Keren-Shaul
Naama Elefant
Irina Zaretsky
Nadav Cohen
Amos Tanay
Ido Amit

Science

SOX9: a stem cell transcriptional regulator of secreted niche signaling factors.

2014-02-01

Deyou Zheng
Elaine Fuchs
Maria Genander

Meelis Kadaja
Brice E Keyes
Mingyan Lin
H Amalia Pasolli
Lisa Polak
Nicole Stokes

Genes & Development

Faculty of 1000 evaluation for Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells

2014-02-02

Marc S. Williams

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.

2014-02-03

Gordon K Smyth

Charity W Law
Yunshun Chen
Wei Shi

Genome Biology

Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs.

2014-02-03

Ramakanth Madhugiri
Stefanie Widder
Thomas Rattei

Sebastian Behrens
Gopala Krishna Mannala
Xiaoxing Qing
Nathalie Kefer
Mobarak Abu Mraheil
Torsten Hain

PLOS ONE

The Cryptococcus neoformans transcriptome at the site of human meningitis.

2014-02-04

Yuan Chen
David R. Boulware

Dena L Toffaletti
Jennifer L Tenor
Anastasia P Litvintseva
Charles Fang
Thomas G Mitchell
Tami R McDonald
Kirsten Nielsen
Tihana Bicanic
John R Perfect

mBio

Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases.

2014-02-06

Rachel L Ballantyne
Muredach P. Reilly

Yichuan Liu
Jane F Ferguson
Chenyi Xue
Ian M Silverman
Sager J Gosai
Jacquelyn Serfecz
Michael P Morley
Brian D Gregory
Mingyao Li

Arteriosclerosis, Thrombosis, and Vascular Biology

RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species.

2014-02-06

Sébastien Renaut
Louis Bernatchez

Anne-Marie Dion-Côté
Eric Normandeau

Molecular Biology and Evolution

Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems.

2014-02-07

Keywan Hassani-Pak
Angela Karp
Huw Dylan Jones

Yongfang Wan
Cristina Gritsch
Theodora Tryfona
Mike J Ray
Ambrose Andongabo
Paul Dupree
Peter R Shewry
Rowan A C Mitchell

Planta

Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq.

2014-02-07

Rui Vitorino
Gerald B Pier
Manuel Vilanova

Virginia Carvalhais
Angela França
Filipe Cerca
Nuno Cerca

Applied Microbiology and Biotechnology

Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections.

2014-02-07

Luyang Sun
Shikai Liu
Yu Zhang

Ruijia Wang
Chao Li
Lisui Bao
Jianbin Feng
Zhanjiang Liu

Developmental and Comparative Immunology

ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects.

2014-02-10

Erik D. Roberson
James Shorter
Eric J Huang

Haiyan Qiu
Sebum Lee
Yulei Shang
Wen-Yuan Wang
Kin Fai Au
Sherry Kamiya
Sami J Barmada
Steven Finkbeiner
Hansen Lui
Caitlin E Carlton
Amy A Tang
Michael C Oldham
Hejia Wang
Anthony J Filiano
Warren G Tourtellotte
Bin Chen
Li-Huei Tsai

Journal of Clinical Investigation

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

2014-02-13

Gane Ka-Shu Wong
Ruibang Luo
Tak-Wah Lam
Jun Wang

Yinlong Xie
Gengxiong Wu
Jingbo Tang
Jordan Patterson
Shanlin Liu
Weihua Huang
Guangzhu He
Shengchang Gu
Shengkang Li
Xin Zhou
Yingrui Li
Xun Xu

Bioinformatics

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.

2014-02-13

Ana Conesa
Corey Nislow
Eduardo Larriba
José Martín-Nieto
Luis V Lopez-Llorca

María D L A Jaime
José Carbonell-Caballero
Joaquín Dopazo

Fungal Genetics and Biology

Condition-specific target prediction from motifs and expression.

2014-02-14

Martin Vingron

Guofeng Meng

Bioinformatics

Dynamic recruitment of amino acid transporters to the insect/symbiont interface.

2014-02-16

John P. McCutcheon
Rebecca P. Duncan
Filip Husník

James T Van Leuven
Donald G Gilbert
Liliana M Dávalos
Alex C C Wilson

Molecular Ecology

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.

2014-02-17

Xi Wang
Murray J Cairns

Bioinformatics

Interaction of vitamin D with membrane-based signaling pathways

2014-02-18

María Jesús Larriba

José Manuel González-Sancho
Félix Bonilla
Alberto Muñoz

Frontiers in Physiology

Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2.

2014-02-18

Werner Liesack

Bomba Dam
Somasri Dam
Yongkyu Kim

Environmental Microbiology

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle.

2014-02-19

Songnian Hu

YuanYuan Zhou
Wei Gong
JingFa Xiao
JiaYan Wu
LinLin Pan
XiaoNuan Li
XuMin Wang
WeiWei Wang
Jun Yu

Science in China. Series C: Life Sciences

Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of Drosophila

2014-02-20

Luis A Milla
Wenxiu Ma
Maria L Spletter

Jian Cao
Julie Ni
Vanessa Shiu
Sangbin Park
Sheng Tang
Jun Zhang
Xing Wei
Seung K Kim
Matthew P Scott

Genetics

Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq.

2014-02-24

Jeremy A Miller
Vilas Menon
Jeff Goldy
Ajamete Kaykas
Chang-Kyu Lee
Kimberly A Smith
Elaine H Shen
John W Phillips
Ed S Lein
Mike J Hawrylycz

BMC Genomics

Context-selective death of acute myeloid leukemia cells triggered by the novel hybrid retinoid-HDAC inhibitor MC2392.

2014-02-24

Dante Rotili
Yves Collette
Angela Nebbioso
Antonello Mai
Hugues de Thé
Mariarosaria Conte
Sergio Valente
Lucia Altucci
Julien Ablain
Vincenzo Carafa

Floriana De Bellis
Francesca Petraglia
Filomena Matarese
Kees-Jan Françoijs
Rèmy Castellano
Armelle Goubard
Amit Mandoli
Joost H A Martens
Hendrik G Stunnenberg

Cancer Research

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets

2014-02-25

Erik K Flemington

Guorong Xu
Michael J Strong
Michelle R Lacey
Carl Baribault
Christopher M Taylor

PLOS ONE

Transcriptomic profiling of differential responses to drought in two freshwater mussel species, the giant floater Pyganodon grandis and the pondhorn Uniomerus tetralasmus.

2014-02-25

Eric Peatman

Yupeng Luo
Chao Li
Andrew Gascho Landis
Guiling Wang
James Stoeckel

PLOS ONE

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.

2014-02-25

Carlos Torroja
Francesco Mazzarotto
Enrique Lara-Pezzi
Alberto Gatto

Stuart A Cook
Paul J R Barton
Fátima Sánchez-Cabo

Nucleic Acids Research

AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.

2014-02-25

Claudia Angelini
Valerio Costa
Maria Rosaria Ambrosio

Margherita Scarpato
Roberta Esposito
Daniela Evangelista
Marianna Aprile
Alfredo Ciccodicola

Database

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample

2014-02-26

Nimrod Miller
Sarah A Boswell
Yong-Chao Ma
Nicole Cloonan
Sean M. Grimmond

Jesse M Gray
David A Harmin
Thomas E Mullen
Joseph J Ling
Scott Kuersten
Steven A McCarroll
Michael Springer

PLOS ONE

Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA.

2014-02-27

Deyou Zheng

Robert D Bell
Xiaochun Long
Mingyan Lin
Jan H Bergmann
Vivek Nanda
Sarah L Cowan
Qian Zhou
Yu Han
David L Spector
Joseph M Miano

Arteriosclerosis, Thrombosis, and Vascular Biology

Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani

2014-02-27

Jessica L Martin
Vladislav A Petyuk
Kristin E Burnum
Richard D. Smith

Phillip A Yates
Radika Soysa
Joshua F Alfaro
Feng Yang
Karl K Weitz
David G Camp
Phillip A Wilmarth
Larry L David
Gowthaman Ramasamy
Peter J Myler
Nicola S Carter

PLOS Pathogens

The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.

2014-02-28

Sean D Gallaher
Taylor L Weiss
David Casero
Shannon L Johnson
Matteo Pellegrini
Sabeeha Merchant
Ursula Goodenough

Ian Blaby
Carrie Goodson
Jae-Hyeok Lee
Robyn Roth
Jannette Rusch
Manmilan Singh
James G Umen
Tuya Wulan

Eukaryotic Cell

Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility

2014-02-28

Stephan Schmitz-Esser
Edward M Fox
Aidan Coffey

Aidan Casey
Edward M Fox
Aidan Coffey
Olivia McAuliffe
Kieran Jordan

Frontiers in Microbiology

ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa

2014-03-01

Yasuhiko Irie
Peter White

Christopher J. Jones
David Newsom
Benjamin Kelly
Laura K. Jennings
Binjie Xu
Dominique H. Limoli
Joe J. Harrison
Matthew R. Parsek
Daniel J. Wozniak

PLOS Pathogens

The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer.

2014-03-01

Elai Davicioni

John R Prensner
Anirban Sahu
Matthew K Iyer
Rohit Malik
Benjamin Chandler
Irfan A Asangani
Anton Poliakov
Ismael A Vergara
Mohammed Alshalalfa
Robert B Jenkins
Felix Y Feng
Arul M Chinnaiyan

Oncotarget

Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness

2014-03-04

Eric Haugen

R Kohen
A Dobra
J H Tracy

Translational Psychiatry

Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves.

2014-03-04

Juan C Begara-Morales
Francisco J. Corpas

Beatriz Sánchez-Calvo
Francisco Luque
María O Leyva-Pérez
Marina Leterrier
Juan B Barroso

Plant and Cell Physiology

Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents.

2014-03-05

Jeremy Searle
Petr Kotlík

S Marková

Heredity

The human testis-specific proteome defined by transcriptomics and antibody-based profiling.

2014-03-05

Linn Fagerberg
Mathias Uhlén

D Djureinovic
B Hallström
A Danielsson
C Lindskog
F Pontén

Molecular Human Reproduction

Overexpression of molecular chaperone genes in nucleomorph genomes.

2014-03-06

Patrick J. Keeling

Yoshihisa Hirakawa
Shigekatsu Suzuki
John M Archibald
Ken-ichiro Ishida

Molecular Biology and Evolution

Faculty of 1000 evaluation for SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

2014-03-06

Steven Salzberg

Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.

2014-03-07

Casey P. Shannon
Robert Balshaw

Heesun Shin
Nick Fishbane
Jian Ruan
Mi Zhou
Janet E Wilson-McManus
Raymond T Ng
Bruce M McManus
Scott J Tebbutt
PROOF Centre of Excellence Team

PLOS ONE

Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.

2014-03-12

Zhipeng Lu

A Gregory Matera

Nucleic Acids Research

RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.

2014-03-12

Linn Fagerberg
Mathias Uhlén
Per Oksvold

Charlotte Stadler
Åsa Sivertsson
Martin Zwahlen
Björn M Hallström
Emma Lundberg

Journal of Proteome Research

Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.

2014-03-13

Hans-Ulrich Schildhaus
Sabine Merkelbach-Bruse

Evgeny A Moskalev
Judith Frohnauer
Arno Dimmler
Thomas Schubert
Carsten Boltze
Helmut König
Florian Fuchs
Horia Sirbu
Ralf J Rieker
Abbas Agaimy
Arndt Hartmann
Florian Haller

Lung Cancer

Lacking alignments? The next-generation sequencing mapper segemehl revisited.

2014-03-13

Peter F. Stadler

Christian Otto
Steve Hoffmann

Bioinformatics

Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases.

2014-03-13

Carlo Gambacorti-Passerini

Roberta Spinelli
Alessandra Pirola
Sara Redaelli
Nitesh Sharma
Hima Raman
Simona Valletta
Vera Magistroni
Rocco Piazza

Molecular genetics & genomic medicine

Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines.

2014-03-14

NISC Comparative Sequencing Program
Leslie G Biesecker
Eric D. Green
James C Mullikin

Shurjo K Sen
Jennifer J Barb
Praveen F Cherukuri
David S Accame
Abdel G Elkahloun
Larry N Singh
Shih-Queen Lee-Lin
Frank D Kolodgie
Qi Cheng
XiaoQing Zhao
Marcus Y Chen
Andrew E Arai
Peter J Munson

BMC Genomics

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

2014-03-18

Hans J Nauwynck

Bouabid Badaoui
Teresa Rutigliano
Anna Anselmo
Merijn Vanhee
Elisabetta Giuffra
Sara Botti

PLOS ONE

The human liver-specific proteome defined by transcriptomics and antibody-based profiling.

2014-03-19

Jens Nielsen
Linn Fagerberg
Mathias Uhlén

Caroline Kampf
Adil Mardinoglu
Björn M Hallström
Karolina Edlund
Emma Lundberg
Fredrik Pontén

FASEB Journal

SNP discovery from transcriptome of the swimbladder of Takifugu rubripes

2014-03-20

Shikai Liu

Jun Cui
Hongdi Wang
Lifu Zhu
Xuemei Qiu
Zhiqiang Jiang
Xiuli Wang
Zhanjiang Liu

PLOS ONE

The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli.

2014-03-21

Jesus M Eraso
Ronald Taylor

Lye M Markillie
Hugh D Mitchell
Galya Orr
William Margolin

Journal of Bacteriology

Genomics of CpG methylation in developing and developed zebrafish

2014-03-21

David M McGaughey

Hatice Ozel Abaan
Ryan M Miller
Peter A Kropp
Lawrence C Brody

The characteristic direction: a geometrical approach to identify differentially expressed genes.

2014-03-21

Avi Ma'ayan

Neil R Clark
Kevin S Hu
Axel S Feldmann
Yan Kou
Edward Y Chen
Qiaonan Duan

BMC Bioinformatics

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism

2014-03-21

Matteo Chialva
Paola Bonfante

Inès Zouari
Alessandra Salvioli
Mara Novero
Laura Miozzi
Gian Carlo Tenore
Paolo Bagnaresi

BMC Genomics

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

2014-03-23

Albin Sandelin
Kristoffer Vitting-Seerup
Johannes Waage
Bo Torben Porse

BMC Bioinformatics

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

2014-03-23

John L. Rinn

Cole Trapnell
Davide Cacchiarelli
Jonna Grimsby
Prapti Pokharel
Shuqiang Li
Michael Morse
Niall J Lennon
Kenneth J Livak
Tarjei S Mikkelsen

Nature Biotechnology

RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin

2014-03-25

Oliver Berkowitz
James Whelan

David Secco
Huixia Shou

BMC Genomics

RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma

2014-03-25

Jianfeng Xu

Zuquan Xiong
Hongjie Yu
Yan Ding
Chenchen Feng
Hanming Wei
Sha Tao
Dan Huang
Siqun Lilly Zheng
Jielin Sun
Zujun Fang

BioMed Research International

De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers

2014-03-26

Luiz Gonzaga Paula de Almeida
Dominique Garcia
Daniel Guariz Pinheiro
Antonio Figueira
Luiz L Coutinho

Leonardo Rippel Salgado
Daniela Martins Koop
Ronan Rivallan
Vincent Le Guen
Marisa Fabiana Nicolás
Viviani Ribeiro Rocha
Milena Magalhães
Alexandra Lehmkuhl Gerber
Júlio Cézar de Mattos Cascardo
AnaTereza Ribeiro de Vasconcelos
Wilson Araújo Silva

BMC Genomics

De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.

2014-03-27

Doris Bachtrog

Vera B Kaiser

BMC Genomics

RNA-Seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini.

2014-03-27

Thewarach Laha
Smarn Tesana

Sattrachai Prasopdee
Javier Sotillo
Jutharat Kulsantiwong
Matthew J Nolan
Alex Loukas
Cinzia Cantacessi

PLOS Neglected Tropical Diseases

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.

2014-03-27

Hideya Kawaji
Masayoshi Itoh
Piero Carninci
Yoshihide Hayashizaki

Marina Lizio
Mutsumi Kanamori-Katayama
Ai Kaiho
Hiromi Nishiyori-Sueki
Jay W Shin
Miki Kojima-Ishiyama
Mitsuoki Kawano
Mitsuyoshi Murata
Noriko Ninomiya-Fukuda
Sachi Ishikawa-Kato
Sayaka Nagao-Sato
Shohei Noma
Alistair R R Forrest
FANTOM Consortium

Genome Research

Transcriptome analysis of the gill of Takifugu rubripes using Illumina sequencing for discovery of SNPs.

2014-03-27

Shikai Liu

Jun Cui
Hongdi Wang
Xuemei Qiu
Zhiqiang Jiang
Xiuli Wang

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.

2014-03-27

Kenneth B. Storey

Ye Zhao
Hongsheng Yang
Muyan Chen

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles.

2014-03-28

Janet Rossant
Gianmaria Frigè
Lorenzo Giordani
Alberto Termanini
Chiara Mozzetta
Giovanna Borsellino

Valentina Saccone
Silvia Consalvi
Iros Barozzi
Martina Sandoná
Tammy Ryan
Agustin Rojas-Muñoz
Luca Madaro
Pasquale Fasanaro
Marco De Bardi
Xin Sun
Benoit G Bruneau
Mark Mercola
Saverio Minucci
Pier Lorenzo Puri

Genes & Development

Differential meta-analysis of RNA-seq data from multiple studies

2014-03-29

Florence Jaffrézic

Andrea Rau
Guillemette Marot
Florence Jaffrézic

BMC Bioinformatics

The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.

2014-03-31

Amy E Pasquinelli
Priscilla M Van Wynsberghe

Emily F Finnegan
Thomas Stark
Evan P Angelus
Kathryn E Homan
Gene W Yeo

Developmental Biology

Small regulatory RNAs in Archaea.

2014-03-31

L Randau
Jörg Soppa

Julia Babski
Lisa-Katharina Maier
Ruth Heyer
Katharina Jaschinski
Daniela Prasse
Dominik Jäger
Ruth A Schmitz
Anita Marchfelder

RNA Biology

RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib.

2014-04

Henrik Lilljebjörn
Hans Ehrencrona
Thoas Fioretos

H Ågerstam
C Orsmark-Pietras
M Rissler
L Nilsson
J Richter

Leukemia

Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans

2014-04

Daniel K. Masiga
Paul O. Mireji
Alan Christoffels

George F O Obiero
Steven R G Nyanjom
Hugh M Robertson

PLOS Neglected Tropical Diseases

PRADA: pipeline for RNA sequencing data analysis

2014-04-01

Gad Getz

Wandaliz Torres-García
Siyuan Zheng
Andrey Sivachenko
Rahulsimham Vegesna
Qianghu Wang
Rong Yao
Michael F Berger
John N Weinstein
Roel G W Verhaak

Bioinformatics

RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.

2014-04-01

Arjan de Groot
Laurence Blanchard
David Vallenet
David Pignol
Jean Armengaud

David Roche
Bernard Fernandez
Monika Ludanyi
Stéphane Cruveiller

Genome Biology and Evolution

Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types.

2014-04-03

Erich Bornberg-Bauer
Susanne U Franssen

Jenny Gu
Gidon Winters
Ann-Kathrin Huylmans
Isabell Wienpahl
Maximiliane Sparwel
James A Coyer
Jeanine L Olsen
Thorsten B H Reusch

Marine Genomics

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

2014-04-07

Daniel C. Jeffares
Graeme C Smith
Charalampos Rallis
Jürg Bähler

Danny A Bitton
Charalampos Rallis
Graeme C Smith
Yuan Y C Chen
Sandra Codlin
Samuel Marguerat
Jürg Bähler

Genome Research

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells

2014-04-08

Lin Jiang
Ola Wallerman
Göran Andersson
Leif Andersson

Shady Younis
Carl-Johan Rubin
Elizabeth R Gilbert
Elisabeth Sundström
Awaisa Ghazal
Xiaolan Zhang
Li Wang
Tarjei S Mikkelsen

PLOS ONE

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

2014-04-10

Gordon G Simpson
Nicholas Schurch
Christian Cole
Sara J Brown
Geoffrey J. Barton

Alexander Sherstnev
Junfang Song
Céline Duc
Kate G Storey
W H Irwin McLean

PLOS ONE

Post-translational decrease in respiratory chain proteins in the Polg mutator mouse brain.

2014-04-10

David N Hauser
Mark R Cookson

Allissa A Dillman
Jinhui Ding
Yan Li

PLOS ONE

Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae

2014-04-10

Matteo Pellegrini

Tadashi Kawashima
Stephen Douglass
Jason Gabunilas
Guillaume F Chanfreau

PLOS Genetics

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS.

2014-04-11

Juan Pablo Tosar
Alfonso Cayota

Carlos Rovira
Hugo Naya

RNA

Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.

2014-04-11

Michael E Himmel

Hui Wei
Yan Fu
Lauren Magnusson
John O Baker
Pin-Ching Maness
Qi Xu
Shihui Yang
Andrew Bowersox
Igor Bogorad
Wei Wang
Melvin P Tucker
Shi-You Ding

Frontiers in Microbiology

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

2014-04-13

Doug Brownfield
Barbara Treutlein

Angela R Wu
Norma F Neff
Gary L Mantalas
F Hernan Espinoza
Tushar J Desai
Mark A Krasnow
Stephen R Quake

Nature

VDR primary targets by genome-wide transcriptional profiling.

2014-04-13

Graziano Pesole
Matteo Pallocca

Frauke Goeman
Francesca De Nicola
Paolo D'Onorio De Meo
Berardino Elmi
Tiziana Castrignanò
Sabrina Strano
Giovanni Blandino
Maurizio Fanciulli
Paola Muti

The Journal of Steroid Biochemistry and Molecular Biology

Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans.

2014-04-14

Gavin Sherlock
Jonathan Weissman

Dale Muzzey

Genome Research

Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon

2014-04-15

Deyou Zheng

Mingyan Lin
Dejian Zhao
Anastasia Hrabovsky
Erika Pedrosa
Herbert M Lachman

PLOS ONE

Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen

2014-04-16

Christina A Cuomo

Zehua Chen
Diego A Martinez
Sharvari Gujja
Sean M Sykes
Qiandong Zeng
Paul J Szaniszlo
Zheng Wang

Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree.

2014-04-16

Zhiyuan Yin

Xiwang Ke
Na Song
Qingqing Dai
Ralf T Voegele
Yangyang Liu
Haiying Wang
Xiaoning Gao
Zhensheng Kang
Lili Huang

Fungal Genetics and Biology

Structure and Function of Steroid Receptor RNA Activator Protein, the Proposed Partner of SRA Noncoding RNA

2014-04-17

Thomas Cech

David B McKay
Linghe Xi
Kristen K B Barthel

Journal of Molecular Biology

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

2014-04-17

Alexander Idnurm
Jason E. Stajich
Christina A Cuomo
Yuan Chen
Gautam Chatterjee
Kate L Ormerod
Yen-Ping Hsueh
James Fraser
Tristan Rossignol
Kaustuv Sanyal
Guilhem Janbon
Yong-Sun Bahn
Steven Jones
Piotr A Mieczkowski
Caroline Proux
Vikas Yadav
Cécile Neuvéglise
Joseph Heitman

Damien Paulet
Edmond J Byrnes
Nandita Mullapudi
Chung-Chau Hon
R Blake Billmyre
François Brunel
Weidong Chen
Eve W L Chow
Jean-Yves Coppée
Anna Floyd-Averette
Claude Gaillardin
Kimberly J Gerik
Jonathan Goldberg
Sara Gonzalez-Hilarion
Sharvari Gujja
Joyce L Hamlin
Giuseppe Ianiri
Chinnappa D Kodira
Lukasz Kozubowski
Woei Lam
Marco Marra
Larry D Mesner
Frédérique Moyrand
Kirsten Nielsen
Jacqueline E Schein
Sheng Sun
Carolin Wollschlaeger
Ian A Wood
Qiandong Zeng
Carol S Newlon
John R Perfect
Jennifer K Lodge
James W Kronstad
Fred S Dietrich

PLOS Genetics

IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation.

2014-04-17

Eric W-F Lam

Min Yan
Yan Zhang
Bin He
Jin Xiang
Zi-feng Wang
Fei-meng Zheng
Jie Xu
Ming-yuan Chen
Yu-liang Zhu
Hai-jun Wen
Xiang-bo Wan
Cai-feng Yue
Na Yang
Wei Zhang
Jia-liang Zhang
Jing Wang
Yang Wang
Lian-hong Li
Yi-xin Zeng
Mien-Chie Hung
Quentin Liu

Nature Communications

Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer.

2014-04-22

Diego Arango
Walter Bodmer
Oliver Sieber
Robert N Jorissen
Daniel D Buchanan
John M Mariadason

Dmitri Mouradov
Clare Sloggett
Christopher G Love
Shan Li
Antony W Burgess
Robert L Strausberg
Samuel Wormald
Liam O'Connor
Jennifer L Wilding
David Bicknell
Ian P M Tomlinson

Cancer Research

RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea: a pilot case-control study.

2014-04-24

Michael Camilleri

Paula Carlson
Andres Acosta
Irene Busciglio
Asha A Nair
Simon J Gibbons
Gianrico Farrugia
Eric W Klee

American Journal of Physiology - Gastrointestinal and Liver Physiology

Insights into the trypanosome-host interactions revealed through transcriptomic analysis of parasitized tsetse fly salivary glands.

2014-04-24

Michelle B O'Neill
Thiago Luiz Alves e Silva
Erich L Telleria
Serap Aksoy

Joshua B Benoit
Xin Zhao
Amy F Savage
Sandesh Regmi

PLOS Neglected Tropical Diseases

A novel highly divergent protein family identified from a viviparous insect by RNA-seq analysis: a potential target for tsetse fly-specific abortifacients.

2014-04-24

Geoffrey Attardo
Aaron A Baumann
Qirui Zhang
Paul O. Mireji
Serap Aksoy
José M. Ribeiro

Joshua B Benoit
Veronika Michalkova
Tyler B Krause
Jana Bohova
Peter Takáč
David L Denlinger

PLOS Genetics

A gene expression atlas of early craniofacial development

2014-04-26

Phillip Dexheimer

Eric W Brunskill
Andrew S Potter
Andrew Distasio
Andrew Plassard
Bruce J Aronow
S Steven Potter

Developmental Biology

The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets.

2014-04-27

David Robert Nelson
Geoff Waldbieser
Luyang Sun
Shikai Liu
Yu Zhang

Jiaren Zhang
Jun Yao
Ruijia Wang
Yanliang Jiang
Jianbin Feng
Nannan Liu
Geoff Waldbieser
Zhanjiang Liu

Biochimica et Biophysica Acta

An improved genome release (version Mt4.0) for the model legume Medicago truncatula.

2014-04-27

Haibao Tang
Vivek Krishnakumar
Laurent Gentzbittel
Kevin L. Childs

Shelby Bidwell
Benjamin Rosen
Agnes Chan
Shiguo Zhou
Mark Yandell
Heidrun Gundlach
Klaus F X Mayer
David C Schwartz
Christopher D Town

BMC Genomics

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.

2014-04-29

Spencer D. Martin
Brad H Nelson
Robert A Holt

Scott D Brown
Rene L Warren
Ewan A Gibb
John J Spinelli

Genome Research

Microfluidic single-cell whole-transcriptome sequencing.

2014-04-29

Liang Zhao
Yanyi Huang

Aaron M Streets
Xiannian Zhang
Chen Cao
Yuhong Pang
Xinglong Wu
Liang Xiong
Lu Yang
Yusi Fu
Fuchou Tang

Proceedings of the National Academy of Sciences of the United States of America

Longer Reads Do Not Significantly Improve RNA-seq Results.

2014-05-01

Sagar Chhangawala

Gabe Rudy
Po-Yen Wu
Scott Tighe
May D. Wang
Don A. Baldwin
George Grills
Christopher E. Mason
Jeffrey Rosenfeld

Journal of Biomolecular Techniques

From genome to function by studying eQTLs.

2014-05-04

Lude Franke

Harm-Jan Westra

Biochimica et Biophysica Acta

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.

2014-05-05

Gregory B. Gloor

Andrew D Fernandes
Jennifer Ns Reid
Jean M Macklaim
Thomas A McMurrough
David R Edgell

Microbiome

A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines

2014-05-05

Gil Omenn

Yuanfang Guan
Rajasree Menon

Journal of Proteomics

Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers.

2014-05-06

Matteo Carrara
Dario Livio Longo
Elena Quaglino
Manuela Iezzi
Silvio Bicciato
Raffaele A. Calogero
Federica Cavallo
Lorena Landuzzi

Federica Riccardo
Maddalena Arigoni
Genny Buson
Elisa Zago
Alessandra Fiore
Simona Nuzzo
Patrizia Nanni

BMC Genomics

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.

2014-05-08

Jana Sperschneider
James K Hane
Jonathan P Anderson
Karam B. Singh

Angela H Williams

PLOS Genetics

lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs.

2014-05-09

Wan Kyu Kim

Charny Park
Namhee Yu
Ikjung Choi
Sanghyuk Lee

Bioinformatics

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.

2014-05-12

Paul J Kersey
Arnaud Kerhornou
Sushma Naithani
Dan Bolser
Gerard Lazo

Samuel E Fox
Matthew Geniza
Mamatha Hanumappa
Chris Sullivan
Justin Preece
Vijay K Tiwari
Justin Elser
Jeffrey M Leonard
Abigail Sage
Cathy Gresham
Fiona McCarthy
Pankaj Jaiswal

PLOS ONE

Facile functional analysis of insect odorant receptors expressed in the fruit fly: validation with receptors from taxonomically distant and closely related species.

2014-05-13

Walter S Leal

Carlos Ueira-Vieira
Deborah A Kimbrell
Washington J de Carvalho

Cellular and Molecular Life Sciences

Identification of a radiation sensitivity gene expression profile in primary fibroblasts derived from patients who developed radiotherapy-induced fibrosis.

2014-05-13

Jason Li

Helen B Forrester
Trevor Leong
Michael J McKay
Carl N Sprung

Radiotherapy and Oncology

Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs

2014-05-14

Tiffany Hsu
Ronny Kellner
Eva H Stukenbrock

Amitava Bhattacharyya
Stephan Poppe
Rachel B Brem

Genome Biology and Evolution

Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling

2014-05-16

Roland Eils
Rosario M. Piro

Stefan Wiesberg
Gunnar Schramm
Nico Rebel
Marcus Oswald
Gerhard Reinelt
Rainer König

BMC Systems Biology

Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes.

2014-05-16

Glaucio Valdameri
Helisson Faoro
Lucélia Donatti
Leda S Chubatsu

Doumit Camilios-Neto
Paloma Bonato
Roseli Wassem
Michelle Z Tadra-Sfeir
Liziane C C Brusamarello-Santos
Vinicius A Weiss
Fábio O Pedrosa
Emanuel M Souza

BMC Genomics

Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data.

2014-05-19

Francis M Jiggins

Andrew Quinn
Punita Juneja

Bioinformatics

RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha.

2014-05-19

Mohan B. Singh
Prem L. Bhalla

Niharika Sharma
Chol-Hee Jung

PLOS ONE

Production, gene structure and characterization of two orthologs of leptin and a leptin receptor in tilapia.

2014-05-20

Tomer Ventura
Berta Levavi-Sivan

Michal Shpilman
Lian Hollander-Cohen
Arieh Gertler

General and Comparative Endocrinology

A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin.

2014-05-21

Maria Ina Arnone

Rossella Annunziata

Development

Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions

2014-05-22

George F Mayhew
Matthew T Aliota

Young-Jun Choi
Sara M Erickson
Bruce M Christensen

PLOS Neglected Tropical Diseases

Transcriptome of Atoh7 retinal progenitor cells identifies new Atoh7-dependent regulatory genes for retinal ganglion cell formation.

2014-05-22

Xiuqian Mu

Zhiguang Gao
Chai-An Mao
Ping Pan
William H Klein

Developmental Neurobiology

A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.

2014-05-22

Laura Eme
Matthew W. Brown
Mark van der Giezen
Courtney W Stairs
Graham Dellaire

Cornelis Mutsaers
Edward Susko
Darren M Soanes
Andrew J Roger

Current Biology

Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling

2014-05-23

Bruno M Vieira
Octávio S. Paulo
Filipa Monteiro
Lisete Sousa
Mónica Sebastiana
Rui Manuel Tavares
Andreia Figueiredo

Teresa Lino-Neto
Maria Salomé Pais

PLOS ONE

Sequential combination of karyotyping and RNA-sequencing in the search for cancer-specific fusion genes.

2014-05-23

Sverre Heim
Ioannis Panagopoulos

Jim Thorsen
Ludmila Gorunova
Francesca Micci

International Journal of Biochemistry & Cell Biology

Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage.

2014-05-26

Thomas Preiss

Stuart K Archer
Nikolay E Shirokikh

BMC Genomics

DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle

2014-05-26

Silvère M van der Maarel

Zizhen Yao
Lauren Snider
Judit Balog
Richard J L F Lemmers
Rabi Tawil
Stephen J Tapscott

Human Molecular Genetics

Time-resolved gene expression profiling during reprogramming of C/EBPα-pulsed B cells into iPS cells

2014-05-27

Bruno Di Stefano

Samuel Collombet
Thomas Graf

Scientific Data

Transcription of nuclear organellar DNA in a model plant system.

2014-05-27

David L. Adelson

Dong Wang
Zhipeng Qu
Jian-Kang Zhu
Jeremy N Timmis

Genome Biology and Evolution

The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis.

2014-05-29

Luis Solans
Jesús Gonzalo-Asensio
Claudia Sala
Carlos Martín

Andrej Benjak
Swapna Uplekar
Jacques Rougemont
Christophe Guilhot
Wladimir Malaga
Stewart T Cole

PLOS Pathogens

SHP2 regulates chondrocyte terminal differentiation, growth plate architecture and skeletal cell fates

2014-05-29

Margot Bowen

Ugur M Ayturk
Kyle C Kurek
Wentian Yang
Matthew L Warman

PLOS Genetics

RNA-seq: impact of RNA degradation on transcript quantification.

2014-05-30

Irene Gallego Romero

Athma A Pai
Jenny Tung
Yoav Gilad

BMC Biology

Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato

2014-06

Jason Reed

Ning Liu
Shan Wu
Jason Van Houten
Ying Wang
Biao Ding
Zhangjun Fei
Thomas H Clarke
Esther van der Knaap

Journal of Experimental Botany

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.

2014-06-01

Harri Lähdesmäki
Zhi Chen
Vincent Butty
Tarmo Äijö

Verna Salo
Subhash Tripathi
Christopher B Burge
Riitta Lahesmaa

Bioinformatics

Differential RNA-seq: the approach behind and the biological insight gained.

2014-06-01

Cynthia Sharma
Jörg Vogel

Current Opinion in Microbiology

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

2014-06-02

Charles M. Perou

Wei Zhao
Xiaping He
Katherine A Hoadley
Joel S Parker
David Neil Hayes

BMC Genomics

Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs.

2014-06-02

David M. Irwin

Zhong-Yin Zhou
Ai-Min Li
Adeniyi C Adeola
Yan-Hu Liu
Hai-Bing Xie
Ya-Ping Zhang

Genome Biology and Evolution

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

2014-06-03

Ana Conesa
Sonia Tarazona
María José Nueda

Bioinformatics

The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance.

2014-06-03

Remo Sanges
David A van Heel
Elia Stupka
Raquel Marco-Ferreres
Ivan Conte
Dejan Lazarevic
Paola Bovolenta
Sandro Banfi

Stefania Merella
Jose Manuel Garcia-Manteiga
Chiara Migliore
Sabrina Carrella
Raffaella Avellino
Nathan Paul Davidson
Warren Emmett
Nicholas Bockett
Germana Meroni

Nucleic Acids Research

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri.

2014-06-06

Nicholas Thomson

Marta Vergara-Irigaray
Maria C Fookes
Christoph M Tang

BMC Genomics

Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.

2014-06-06

Jörn Kalinowski

Armin Neshat
Almut Mentz
Christian Rückert

Journal of Biotechnology

Comparative transcriptional analysis of asexual and sexual morphs reveals possible mechanisms in reproductive polyphenism of the cotton aphid.

2014-06-10

Wei Guo

Li-Jun Liu
Hong-Yuan Zheng
Feng Jiang
Shu-Tang Zhou

PLOS ONE

Variable escape from X-chromosome inactivation: identifying factors that tip the scales towards expression

2014-06-10
2014-08-01

Allison M Cotton
Carolyn J. Brown

Samantha B Peeters

BioEssays

An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7.

2014-06-10

Robert W Jackson
Nicola Holden

Ashleigh Holmes
Louise Birse

Frontiers in Microbiology

ARH-seq: identification of differential splicing in RNA-seq data

2014-06-11

Marie-Laure Yaspo
Hans Lehrach
Ralf Herwig

Axel Rasche
Matthias Lienhard
Marie-Laure Yaspo

Nucleic Acids Research

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

2014-06-11

Nir Friedman
Aviv Regev
Rahul Satija
Nir Hacohen
Schraga Schwartz
Raktima Raychowdhury
Alex K. Shalek

Joe Shuga
John J Trombetta
Dave Gennert
Diana Lu
Peilin Chen
Rona S Gertner
Jellert T Gaublomme
Nir Yosef
Brian Fowler
Suzanne Weaver
Jing Wang
Xiaohui Wang
Ruihua Ding
Raktima Raychowdhury
Hongkun Park
Andrew P May

Nature

Comparison of REST cistromes across human cell types reveals common and context-specific functions

2014-06-12

Elaine Fuchs
Deyou Zheng

Shira Rockowitz
Wen-Hui Lien
Erika Pedrosa
Gang Wei
Mingyan Lin
Keji Zhao
Herbert M Lachman

PLOS Computational Biology

A novel functional role for MMSET in RNA processing based on the link between the REIIBP isoform and its interaction with the SMN complex

2014-06-12

Fabio Mirabella
Andrew Thompson
C Pawlyn
Christopher P Wardell
Brian A. Walker

Alexander Murison
Lauren I Aronson
Sarah J Hanrahan
Jacqueline H L Fok
Martin F Kaiser
Faith E Davies
Gareth J Morgan

PLOS ONE

Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts

2014-06-12

Ralph S Baric
Yoshihiro Kawaoka

Laurence Josset
Nicolas Tchitchek
Lisa E Gralinski
Martin T Ferris
Amie J Eisfeld
Richard R Green
Matthew J Thomas
Jennifer Tisoncik-Go
Gary P Schroth
Fernando Pardo Manuel de Villena
Mark T Heise
Xinxia Peng
Michael G Katze

RNA Biology

A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord.

2014-06-12

Diogo S. Castro

Mark D Borromeo
David M Meredith
Joshua C Chang
Kuang-Chi Tung
Francois Guillemot
Jane E Johnson

Development

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

2014-06-13

Jessica Lasky-Su

Blanca E Himes
Xiaofeng Jiang
Peter Wagner
Ruoxi Hu
Qiyu Wang
Barbara Klanderman
Reid M Whitaker
Qingling Duan
Christina Nikolos
William Jester
Martin Johnson
Reynold A Panettieri
Kelan G Tantisira
Scott T Weiss
Quan Lu

PLOS ONE

The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.

2014-06-13

Nina Opitz
Frank Hochholdinger
Cheng-Ting Yeh

Yanxiang Zhang
Anja Paschold
Caroline Marcon
Sanzhen Liu
Huanhuan Tai
Josefine Nestler
Christa Lanz
Patrick S Schnable

Journal of Experimental Botany

miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.

2014-06-14

Jikai Lei

Yanni Sun

Bioinformatics

An integrative method to normalize RNA-Seq data.

2014-06-14

Klopp Christophe

Cyril Filloux
Meersseman Cédric
Philippe Romain
Forestier Lionel
Rocha Dominique
Maftah Abderrahman
Petit Daniel

BMC Bioinformatics

Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression.

2014-06-14

Michael Poidinger

Jinmiao Chen
Yuezhen Xue
Thimothy Lim
Sung Hock Chew
Chai Ling Pang
Jean-Pierre Abastado
Françoise Thierry

Virology

A chemical potentiator of copper-accumulation used to investigate the iron-regulons of Saccharomyces cerevisiae.

2014-06-15

Ehmke Pohl
Nigel Robinson

Andrew W Foster
Samantha J Dainty
Carl J Patterson
Hannah Blackburn
Clare Wilson
Corinna R Hess
Julian C Rutherford
Laura Quaranta
Andy Corran

Molecular Microbiology

Transcriptomic landscape of prophase I sunflower male meiocytes.

2014-06-16

Octavio Martínez

Nathalia M V Flórez-Zapata
M H Reyes-Valdés
Fernando Hernandez-Godínez

Frontiers in Plant Science

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum

2014-06-17

W. Richard McCombie
Clícia Grativol
Felipe Rodrigues da Silva

Michael Regulski
Marcelo Bertalan
Adhemar Zerlotini Neto
Renato Vicentini
Laurent Farinelli
Adriana Silva Hemerly
Robert A Martienssen
Paulo Cavalcanti Gomes Ferreira

The Plant Journal

RNA-Seq analysis implicates detoxification pathways in ovine mycotoxin resistance

2014-06-17

Jinbi Zhang

Zengxiang Pan
Stephanie Moloney
Allan Sheppard

PLOS ONE

The Chlamydomonas genome project: a decade on.

2014-06-17

David Goodstein
Jane Grimwood
Crysten E Blaby-Haas
Sabeeha Merchant

Ian K Blaby
Nicolas Tourasse
Erik F Y Hom
David Lopez
Munevver Aksoy
Arthur Grossman
James Umen
Susan Dutcher
Mary Porter
Stephen King
George B Witman
Mario Stanke
Elizabeth H Harris
Jane Grimwood
Jeremy Schmutz
Olivier Vallon
Simon Prochnik

Trends in Plant Science

Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development

2014-06-18

Songnian Hu

Wei Xu
Chengqi Xin
Qiang Lin
Feng Ding
Wei Gong
Yuanyuan Zhou
Jun Yu
Peng Cui

Genomics Proteomics and Bioinformatics

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.

2014-06-19

Dominique Rocha
Daniel Gautheret

Coline Billerey
Mekki Boussaha
Diane Esquerré
Emmanuelle Rebours
Anis Djari
Cédric Meersseman
Christophe Klopp

BMC Genomics

RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells.

2014-06-19

Valerio Costa
Concetta Schiano
Claudio Napoli
Monica Rienzo
Amelia Casamassimi

Margherita Scarpato
Vincenzo Grimaldi
Alfredo Ciccodicola

Gene

Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche

2014-06-20

Richard Sandstrom
Eric Haugen

Michael R Foret
Douglas A Grow
Christopher T Rhodes
Astrid E Cardona
Clyde F Phelix
Yufeng Wang
Mitchel S Berger
Chin-Hsing Annie Lin

Scientific Reports

A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells.

2014-06-20

Elena Shklovskaya
Barbara Fazekas De St Groth

David G Hancock
Thomas V Guy
Reza Falsafi
Chris D Fjell
William Ritchie
Robert E W Hancock

PLOS ONE

Genomic characterization of acute leukemias.

2014-06-20

Robin Foà

Sabina Chiaretti
Valentina Gianfelici
Giulia Ceglie

Medical Principles and Practice

RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing.

2014-06-24

Markus Landthaler
Nikolaus Rajewsky
Marvin Jens
Martin Liss
Michael H Radke
Matthias Heinig
Michael Gotthardt
Eleonora Adami

Henrike Maatz
Sebastian Schafer
Marieluise Kirchner
Carola Rintisch
Vita Dauksaite
Matthias Selbach
Paul J R Barton
Stuart A Cook
Norbert Hubner

Journal of Clinical Investigation

Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method.

2014-06-24

Artur Gurgul
Maria Oczkowicz
Katarzyna Ropka-Molik
Katarzyna Piórkowska

Kacper Zukowski
Robert Eckert

Animal Genetics

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

2014-06-25

Richard Emes
Joanna Moreton
Stephen Dunham

Frontiers in Genetics

A comparison of transcriptional patterns and mycological phenotypes following infection of Fusarium graminearum by four mycoviruses

2014-06-25

Kyunghun Min

Kyung-Mi Lee
Won Kyong Cho
Jisuk Yu
Moonil Son
Hoseong Choi
Yin-Won Lee
Kook-Hyung Kim

PLOS ONE

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.

2014-06-27

Jia Meng

Zhiliang Lu
Hui Liu
Lin Zhang
Shaowu Zhang
Yidong Chen
Manjeet K Rao
Yufei Huang

Methods

Profile of whole blood gene expression following immune stimulation in a wild passerine

2014-06-27

Peeter Hõrak
Reidar Andreson

Richard Meitern
Peeter Hõrak

BMC Genomics

Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).

2014-06-30

Melissa S Monson

Robert E Settlage
Kevin W McMahon
Kristelle M Mendoza
Sumit Rawal
Hani S El-Nezami
Roger A Coulombe
Kent M Reed

PLOS ONE

Building the sugarcane genome for biotechnology and identifying evolutionary trends.

2014-06-30

Hélène Bergès
Monalisa Sampaio Carneiro
Claudio Benicio Cardoso-Silva
Carlos T Hotta
Cushla Jane Metcalfe
Glaucia Mendes Souza
Changsoo Kim
Alessandro Varani
Marie-Anne Van Sluys
Anete Pereira Souza

Nathalia de Setta
Cláudia Barros Monteiro-Vitorello
Guilherme Marcelo Queiroga Cruz
Luiz Eduardo Del Bem
Renato Vicentini
Fábio Tebaldi Silveira Nogueira
Roberta Alvares Campos
Sideny Lima Nunes
Paula Cristina Gasperazzo Turrini
Andreia Prata Vieira
Edgar Andrés Ochoa Cruz
Tatiana Caroline Silveira Corrêa
Sonia Vautrin
Adilson Silva da Trindade
Mariane de Mendonça Vilela
Carolina Gimiliani Lembke
Paloma Mieko Sato
Rodrigo Fandino de Andrade
Milton Yutaka Nishiyama
Katia Castanho Scortecci
Antônio Augusto Franco Garcia
Andrew H Paterson
Angélique D'Hont
Michel Vincentz
João Paulo Kitajima

BMC Genomics

Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection

2014-07

Marvin Whiteley

Keith H Turner
Jake Everett
Urvish Trivedi
Kendra P Rumbaugh

PLOS Genetics

The coding and noncoding architecture of the Caulobacter crescentus genome

2014-07

Bo Zhou
Jared M Schrader
Sean Crosson
Jonathan Weissman

Gene-Wei Li
Keren Lasker
W Seth Childers
Brandon Williams
Tao Long
Harley H McAdams
Lucy Shapiro

PLOS Genetics

Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing

2014-07-01

Aviv Regev
Rahul Satija
Alex K. Shalek

John J. Trombetta
David Gennert
Diana Lu

Current protocols in molecular biology

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.

2014-07-01

Jingyi Jessica Li
Steven E. Brenner

Haiyan Huang
Peter J Bickel

Genome Research

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.

2014-07-01

Christoph W. Sensen

Ian Reid
Nicholas O'Toole
Omar Zabaneh
Reza Nourzadeh
Mahmoud Dahdouli
Mostafa Abdellateef
Paul M K Gordon
Jung Soh
Gregory Butler
Adrian Tsang

BMC Bioinformatics

IMAGE GUIDED RNA-SEQ REVEALS SUBTYPE-SPECIFIC PATTERNS AT THE INFILTRATIVE MARGINS OF GLIOBLASTOMA.

2014-07-01

Michael B Sisti

Peter Canoll
Peter Sims
Brian Gil
David Pisapia
Hani Malone
Hannah Goldstein
Liang Lei
Adam Sonabend
Jonathan Yun
Jorge Samanamud
Jennifer Sims
Andrew Teich
Sameer Sheth
Guy McKhann
Jeffrey Bruce

Neuro-Oncology

Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.

2014-07-01

Kasper D. Hansen
Jeffrey T. Leek

Frazee AC
Sabunciyan S
Irizarry RA

Biostatistics

Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.

2014-07-02

Melody Baddoo
Asuka Nanbo

Michael J Strong
Melody Baddoo
Miao Xu
Adriane Puetter
Zhen Lin

Journal of Virology

Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.

2014-07-03

Gil Omenn

Yongsheng Bai
Justin Hassler
Ahdad Ziyar
Philip Li
Zachary Wright
Rajasree Menon
James D Cavalcoli
Randal J Kaufman
Maureen A Sartor

PLOS ONE

Status of duckweed genomics and transcriptomics.

2014-07-04

Wenqin Wang

J Messing

Plant Biology

Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets

2014-07-05

Jing Tu

Lei Wang
Dequan Zhou
Yan Wang
Zuhong Lu

Biology Direct

Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA.

2014-07-05

Suman B Pakala
Vinita S Joardar
Bridget M Barker
Nikhat Zafar

Liliana Losada
Suchitra Pakala
Stephanie Mounaud
Natalie Fedorova
William C Nierman
Robert A Cramer

Mycopathologia

Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.

2014-07-07

Gerhard G Thallinger
Richard Sparling
Bernard Henrissat

John J Schellenberg
Tobin J Verbeke
Peter McQueen
Oleg V Krokhin
Xiangli Zhang
Graham Alvare
Brian Fristensky
John A Wilkins
David B Levin

BMC Genomics

De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae).

2014-07-07

Liang Qiao

Bin Chen
Yu-Juan Zhang
Zhengbo He
Wanshun Li
Fengling Si
Yao Tang
Qiyi He
Zhentian Yan
Wenbo Fu
Yanfei Che

Parasites & Vectors

Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data

2014-07-09

Vivekanand Jha
Ahmad Firoz
Sanjay Kumar Singh

Adeel Malik
Amjad Ali

International Journal of Genomics

Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.

2014-07-09

Yuuri Yasuoka
Yoshikazu Haramoto
Makoto Asashima

Yutaka Suzuki
Shuji Takahashi
Haruka Someya
Norihiro Sudou
Ken W Cho
Sumio Sugano
Masanori Taira

Nature Communications

Analysis of the transcriptome and immune function of monocytes during IFNα-based therapy in chronic HCV revealed induction of TLR7 responsiveness.

2014-07-09

Andre Boonstra
Wilfred F J van IJcken

Jun Hou
Zwier M A Groothuismink
Ludi Koning
Robert Roomer
Kim Kreefft
Bi-Sheng Liu
Harry L A Janssen
Robert J de Knegt

Antiviral Research

Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation.

2014-07-10

Christian Sailer
Ueli Grossniklaus

Anja Schmidt
Marc W Schmid
Ulrich C Klostermeier
Weihong Qi
Daniela Guthörl
Manuel Waller
Philip Rosenstiel
Ueli Grossniklaus

PLOS Genetics

Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori.

2014-07-11

Moli Huang

Lei He
Guangli Cao
Renyu Xue
Xiaolong Hu
Chengliang Gong

Gene

A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data

2014-07-14

Aaron M. Tarone

Sing-Hoi Sze

BMC Genomics

Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data.

2014-07-15

Bruno Bastos

Daiane M Carvalho
Pablo H de Sá
Thiago L P Castro
Rodrigo D Carvalho
Anne Pinto
Danilo J P Gil
Priscilla Bagano
Lilia F M Costa
Roberto Meyer
Artur Silva
Vasco Azevedo
Rommel T J Ramos
Luis G C Pacheco

Antonie van Leeuwenhoek

Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase.

2014-07-15

Frank Hochholdinger

Josefine Nestler
Sanzhen Liu
Tsui-Jung Wen
Anja Paschold
Caroline Marcon
Ho Man Tang
Delin Li
Li Li
Robert B Meeley
Hajime Sakai
Wesley Bruce
Patrick S Schnable

The Plant Journal

Whole transcriptome RNA-seq analysis: tumorigenesis and metastasis of melanoma.

2014-07-15

Songnian Hu

Hua Zhao
Yongjun Li
Shaobin Wang
Yadong Yang
Junyun Wang
Xiuyan Ruan
Yaran Yang
Kan Cai
Bing Zhang
Peng Cui
Jiangwei Yan
Yongliang Zhao
Edward K Wakeland
Quanzhen Li
Xiangdong Fang

Gene

SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples

2014-07-16

Charles M. Perou
Liza Makowski
Patrick K Kimes

Christopher R Cabanski
Matthew D Wilkerson
Ni Zhao
Amy R Johnson
Christopher A Maher
Yufeng Liu
J S Marron
D Neil Hayes

Nucleic Acids Research

Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.

2014-07-16

Kenneth B. Storey

Ye Zhao
Hongsheng Yang
Muyan Chen

Marine Genomics

Polyphosphate accumulation is driven by transcriptome alterations that lead to near-synchronous and near-equivalent uptake of inorganic cations in an arbuscular mycorrhizal fungus.

2014-07-16

Katsuharu Saito
Tatsuhiro Ezawa

Yusuke Kikuchi
Nowaki Hijikata
Kaede Yokoyama
Ryo Ohtomo
Yoshihiro Handa
Masayoshi Kawaguchi

New Phytologist

Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes.

2014-07-17

Pasi K. Korhonen
Neil D. Young
Andreas Hofmann
Robin B. Gasser
Aaron R Jex
Paul W. Sternberg

Bert Breugelmans
Stefano Mangiola
Peter R Boag

International Journal for Parasitology

Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation.

2014-07-18

Kristy Red-Horse

Shah R Ali
Sara Ranjbarvaziri
Mahmood Talkhabi
Peng Zhao
Ali Subat
Armin Hojjat
Paniz Kamran
Antonia M S Müller
Katharina S Volz
Zhaoyi Tang
Kristy Red-Horse
Reza Ardehali

Circulation Research

Gene expression profiling of laser microdissected airway smooth muscle tissue in asthma and atopy.

2014-07-19

Frank Baas

C Y Yick
A H Zwinderman
P W Kunst
K Grünberg
T Mauad
S Chowdhury
E H Bel
R Lutter
P J Sterk

Allergy

Genome-wide characterization of light-regulated genes in Neurospora crassa.

2014-07-21

Jeremy Zucker
Erin Bredeweg
Matthew S. Sachs

Cheng Wu
Fei Yang
Kristina M Smith
Matthew Peterson
Rigzin Dekhang
Ying Zhang
Chandrashekara Mallappa
Xiaoying Zhou
Anna Lyubetskaya
Jeffrey P Townsend
James E Galagan
Michael Freitag
Jay C Dunlap
Deborah Bell-Pedersen

Sequence, structural and expression divergence of duplicate genes in the bovine genome.

2014-07-23

Graham Plastow
Paul Stothard

Xiaoping Liao
Hua Bao
Yan Meng
Stephen Moore

PLOS ONE

Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming

2014-07-24

Charles R Bradshaw
Richard P Halley-Stott
Vincent Pasque
Kei Miyamoto
John Gurdon

Jerome Jullien
George E Allen
Nigel J Garrett
Hiroshi Kimura
Keita Ohsumi

Molecular Cell

A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans.

2014-07-24

Marco A Ortiz
Judith Kimble

Daniel Noble
Elena P Sorokin

Transcriptome Analysis of the Human Striatum in Tourette Syndrome.

2014-07-24

Gianfilippo Coppola
Dean Palejev
Flora M. Vaccarino
Nenad Sestan

Jessica B Lennington
Yuko Kataoka-Sasaki
Thomas V Fernandez
Yifan Li
Anita Huttner
Mihovil Pletikos
Nenad Sestan
James F Leckman

Biological Psychiatry

iRegulon: from a gene list to a gene regulatory network using large motif and track collections.

2014-07-24

Zeynep Kalender Atak
Delphine Potier
Stein Aerts
Jean-Christophe Marine
Bram Van de Sande
Gert Hulselmans
Marina N Sanchez

Rekin's Janky
Annelien Verfaillie
Hana Imrichová
Laura Standaert
Valerie Christiaens
Koen Herten
Dmitry Svetlichnyy
Mark Fiers

PLOS Computational Biology

Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing.

2014-07-25

Olivier Cussenot

Gabriel G Malouf
Jianping Zhang
Ying Yuan
Eva Compérat
Morgan Rouprêt
Yunxin Chen
Erika J Thompson
Nizar M Tannir
John N Weinstein
Vicente Valero
David Khayat
Jean-Philippe Spano
Xiaoping Su

Molecular Oncology

RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis.

2014-07-25

Eva Terzibasi Tozzini
Francesco Spallotta
Mario Baumgart
Michela Ori
Marco Groth
Alessandro Cellerino
Carlo Gaetano
Matthias Platzer

Steffen Priebe
Aurora Savino
Giovanna Testa
Andreas Dix
Roberto Ripa
Reinhard Guthke

Aging Cell

Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS

2014-07-28

Alexey I Nesvizhskii

Avinash K Shanmugam
Anastasia K Yocum

Journal of Proteome Research

Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species.

2014-07-28

Jonathan Grandaubert
Angela P Van de Wouw
Barbara Jane Howlett

Rohan G T Lowe
Andrew Cassin
Bethany L Clark
Thierry Rouxel

PLOS ONE

Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.

2014-07-28

Joshua P. Der
Justin S Williams

Claude W dePamphilis
Teh-Hui Kao

The Plant Cell

Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster

2014-07-29

Vladimir N. Babenko

Igor F Zhimulev
Tatyana Yu Zykova
Fyodor P Goncharov
Varvara A Khoroshko
Olga V Demakova
Valeriy F Semeshin
Galina V Pokholkova
Lidiya V Boldyreva
Darya S Demidova
Sergey A Demakov
Elena S Belyaeva

PLOS ONE

Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.

2014-07-30

Richard Sandstrom

Michael R Foret
Christopher T Rhodes
Yufeng Wang
Mitchel S Berger
Chin-Hsing Annie Lin

Frontiers in Genetics

Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.

2014-07-31

Zheng Xia
Jernej Ule
Ravi K. Singh
Auinash Kalsotra

Christopher S Bland
Marissa A Scavuzzo
Tomaz Curk
Wei Li
Thomas A Cooper

Molecular Cell

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.

2014-07-31

Scott A. Givan

Antony M Chettoor
Rex A Cole
Clayton T Coker
Erica Unger-Wallace
Zuzana Vejlupkova
Erik Vollbrecht
John E Fowler
Matthew Ms Evans

Genome Biology

Single-cell RNA-seq: advances and future challenges

2014-08
2014-08-01

Jörg Vogel
Alexander Westermann

Antoine-Emmanuel Saliba
Stanislaw A. Gorski

Nucleic Acids Research

Temporally and spatially restricted gene expression profiling

2014-08-01

Alexandra Tallafuss

Philip Washbourne
John Postlethwait

Current Genomics

Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone

2014-08-01

Rene Olivares-Navarrete

Monica L Rojas-Peña
Sharon Hyzy
Dalia Arafat
Zvi Schwartz
Barbara D Boyan
Joseph Williams
Greg Gibson

Journal of genomics

c-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas

2014-08-01

Massimo Loda

Stefano Sioletic
Jeffrey Czaplinski
Lan Hu
Jonathan A Fletcher
Christopher D M Fletcher
Andrew J Wagner
George D Demetri
Ewa T Sicinska
Eric L Snyder

The Journal of Pathology

In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles

2014-08-05

Susanne Häussler
Sarah Pohl
Denitsa Eckweiler

Piotr Bielecki
Uthayakumar Muthukumarasamy
Agata Bielecka
Ansgar Schanz
Ute Niemeyer
Tonio Oumeraci
Nils von Neuhoff
Jean-Marc Ghigo

mBio

Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis.

2014-08-05

Changle Ma

Xiaoyan Shen
Zenglan Wang
Xiaofeng Song
Jiajia Xu
Chunyun Jiang
Yanxiu Zhao
Hui Zhang

Plant Molecular Biology

Reduction of systematic bias in transcriptome data from human peripheral blood mononuclear cells for transportation and biobanking.

2014-08-07

Hideki Ohmomo

Tsuyoshi Hachiya
Yu Shiwa
Ryohei Furukawa
Kanako Ono
Shigeki Ito
Yoji Ishida
Mamoru Satoh
Jiro Hitomi
Kenji Sobue
Atsushi Shimizu

PLOS ONE

MBASED: allele-specific expression detection in cancer tissues and cell lines.

2014-08-07

Jinfeng Liu

Oleg Mayba
Houston N Gilbert
Peter M Haverty
Suchit Jhunjhunwala
Zhaoshi Jiang
Colin Watanabe
Zemin Zhang

Genome Biology

Influence of RNA extraction methods and library selection schemes on RNA-seq data.

2014-08-11

Marie-Laure Yaspo
Hans Lehrach

Marc Sultan
Vyacheslav Amstislavskiy
Thomas Risch
Moritz Schuette
Simon Dökel
Meryem Ralser
Daniela Balzereit
Marie-Laure Yaspo

BMC Genomics

MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.

2014-08-11

Michael B Sisti

Brian J Gill
David J Pisapia
Hani R Malone
Hannah Goldstein
Liang Lei
Adam Sonabend
Jonathan Yun
Jorge Samanamud
Jennifer S Sims
Matei Banu
Athanassios Dovas
Andrew F Teich
Sameer A Sheth
Guy M McKhann
Jeffrey N Bruce
Peter A Sims
Peter Canoll

Proceedings of the National Academy of Sciences of the United States of America

SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis.

2014-08-11

Gurjit Khurana Hershey

Umasundari Sivaprasad
Kayla G Kinker
Mark B Ericksen
Mark Lindsey
Aaron M Gibson
Stacey A Bass
Nicolas S Hershey
Jingyuan Deng
Mario Medvedovic

Journal of Investigative Dermatology

A comparative study of techniques for differential expression analysis on RNA-Seq data.

2014-08-13

Naomi R. Wray
Zong Hong Zhang
Qiong-Yi Zhao
Janette Edson
Denis C Bauer

Dhanisha J Jhaveri
Vikki M Marshall
Ramesh K Narayanan
Gregory J Robinson
Andreas E Lundberg
Perry F Bartlett

PLOS ONE

Interferon gene expression signature in rheumatoid arthritis neutrophils correlates with a good response to TNFi therapy.

2014-08-13

Helen L Wright

Huw B Thomas
Robert J Moots
Steven W Edwards

Rheumatology

Functional expression of dental plaque microbiota.

2014-08-14

Andrew I. Su
Tobias Meißner

Scott N Peterson
Erik Snesrud
Ana C Ong
Nicholas J Schork
Walter A Bretz

Frontiers in cellular and infection microbiology

Discovering functional modules by topic modeling RNA-Seq based toxicogenomic data.

2014-08-14

Binsheng Gong

Ke Yu
Mikyung Lee
Zhichao Liu
Joshua Xu
Roger Perkins
Weida Tong

Chemical Research in Toxicology

Itch-associated peptides: RNA-Seq and bioinformatic analysis of natriuretic precursor peptide B and gastrin releasing peptide in dorsal root and trigeminal ganglia, and the spinal cord.

2014-08-14

Danielle Thierry-Mieg
Jean Thierry-Mieg

Samridhi C Goswami
Santosh Mishra
Mark A Hoon
Andrew J Mannes
Michael J Iadarola

Molecular Pain

De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.

2014-08-14

Arghavan Alisoltani

Sadegh Mousavi
Behrouz Shiran
Hossein Fallahi
Esameil Ebrahimie
Ali Imani
Saadollah Houshmand

PLOS ONE

RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research

2014-08-14

Leslie Birgit Vosshall
Michael McClelland
Cristina Aurrecoechea

Andrew S. Warren
Brian Brunk
Prerak Desai
Scott Emrich
Gloria I. Giraldo-Calderón
Omar Harb
Deborah Hix
Daniel Lawson
Dustin Machi
Chunhong Mao
Eric Nordberg
Maulik Shukla
Alice R. Wattam
Rebecca Will
Hyun Seung Yoo
Bruno Sobral

Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae

2014-08-15

Elena Gómez-Díaz
Fabrice Chandre

Ana Rivero
Victor G Corces

Frontiers in Genetics

Genetic and pharmacological reactivation of the mammalian inactive X chromosome.

2014-08-18

Sanchita Bhatnagar

Xiaochun Zhu
Jianhong Ou
Ling Lin
Lynn Chamberlain
Lihua J Zhu
Narendra Wajapeyee
Michael R Green

Proceedings of the National Academy of Sciences of the United States of America

H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.

2014-08-18

Karl Mechtler

Anna Sawicka
Dominik Hartl
Malgorzata Goiser
Oliver Pusch
Roman R Stocsits
Ido M Tamir
Christian Seiser

Genome Research

Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection.

2014-08-18

Yong Kong
Anders P. Hakansson

Melinda M Pettigrew
Laura R Marks
Janneane F Gent
Hazeline Roche-Hakansson

Infection and Immunity

Detecting translational regulation by change point analysis of ribosome profiling data sets

2014-08-21

Anze Zupanic
Daryl P Shanley
John C. Mathers

Catherine Meplan
Sushma N Grellscheid
Tom B L Kirkwood
John E Hesketh

RNA

A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development.

2014-08-21

Florian Freudenberg
Richard S. Nowakowski
Cynthia Vied
Alexandre A S F Raposo
David Feng

Yuting Wang

Frontiers in Neuroscience

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

2014-08-22

Pratik D. Jagtap

Gloria M Sheynkman
James E Johnson
Michael R Shortreed
Getiria Onsongo
Brian L Frey
Timothy J Griffin
Lloyd M Smith

BMC Genomics

MicroRNA and mRNA cargo of extracellular vesicles from porcine adipose tissue-derived mesenchymal stem cells.

2014-08-23

Lilach O. Lerman

Alfonso Eirin
Scott M Riester
Xiang-Yang Zhu
Hui Tang
Jared M Evans
Daniel O'Brien
Andre J van Wijnen

Gene

RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N₂ fixation before emerging P deficiency reaches the nodules.

2014-08-23

Gabriela Salinas-Riester
Claudia Pommerenke

Ricardo A Cabeza
Rebecca Liese
Annika Lingner
Ilsabe von Stieglitz
Janice Neumann
Klaus Dittert
Joachim Schulze

Journal of Experimental Botany

Normalization of RNA-seq data using factor analysis of control genes or samples

2014-08-24

Davide Risso

John Ngai
Terence P Speed
Sandrine Dudoit

Nature Biotechnology

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

2014-08-24

Danielle Thierry-Mieg
Michele Filosi
Roberto Visintainer
Florian Caiment
Samantha Riccadonna
Marco Chierici
Lee Lancashire
Binsheng Gong
Davide Albanese
Jean Thierry-Mieg
Giuseppe Jurman
Jos Kleinjans

Charles Wang
Pierre R Bushel
Joshua Xu
Hong Fang
Huixiao Hong
Jie Shen
Zhenqiang Su
Joe Meehan
Xiaojin Li
Lu Yang
Haiqing Li
Paweł P Łabaj
David P Kreil
Dalila Megherbi
Stan Gaj
Joost van Delft
Andreas Scherer
Viswanath Devanarayan
Jian Wang
Yong Yang
Hui-Rong Qian
Marina Bessarabova
Yuri Nikolsky
Cesare Furlanello
Ke K Zhang
Jianying Li
Jui-Hua Hsieh
Daniel L Svoboda
James C Fuscoe
Youping Deng
Leming Shi
Richard S Paules
Scott S Auerbach
Weida Tong

Nature Biotechnology

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.

2014-08-26

Kévin Rue-Albrecht
Karsten Hokamp
Eamonn Gormley
David E. MacHugh
Stephen V. Gordon
Kate Killick

Kirsten E McLoughlin
Nicolas C Nalpas
John A Browne
David A Magee
Stephen D E Park
Kieran G Meade
Cliona O'Farrelly

Frontiers in Immunology

Deletion of aryl hydrocarbon receptor AHR in mice leads to subretinal accumulation of microglia and RPE atrophy.

2014-08-26

Anand Swaroop
Soo-Young Kim
Wai T. Wong
Robert N. Fariss
Matthew Brooks
Emily Chew

Hyun-Jin Yang
Yi-Sheng Chang
Jung-Woong Kim
Rivka A Rachel
Tiziana Cogliati
Haohua Qian

Investigative Ophthalmology & Visual Science

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.

2014-08-26

Danielle Thierry-Mieg
Jean Thierry-Mieg

Binsheng Gong
Charles Wang
Zhenqiang Su
Huixiao Hong
Leming Shi
Scott S Auerbach
Weida Tong
Joshua Xu

Scientific Data

Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq.

2014-08-26

Danielle Thierry-Mieg
Jean Thierry-Mieg

Joshua Xu
Zhenqiang Su
Huixiao Hong
David P Kreil
Christopher E Mason
Weida Tong
Leming Shi

Scientific Data

RVboost: RNA-seq variants prioritization using a boosting method

2014-08-27

Andrew L Feldman

Chen Wang
Jaime I Davila
Saurabh Baheti
Aditya V Bhagwate
Xue Wang
Jean-Pierre A Kocher
Susan L Slager
Anne J Novak
James R Cerhan
E Aubrey Thompson
Yan W Asmann

Bioinformatics

RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor

2014-08-27

Joshua Shapiro
Nawar Naseer

Monica Chander

PLOS ONE

Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions.

2014-08-28

Ryan S McClure

Brian Tjaden
Caroline Genco

Frontiers in Microbiology

Ionotropic GABA and glycine receptor subunit composition in human pluripotent stem cell-derived excitatory cortical neurones.

2014-08-28

Owen Dando
Peter C Kind
David J Wyllie
Giles E. Hardingham
Siddharthan Chandran

Owain T James
Matthew R Livesey
Jing Qiu
Bilada Bilican
Ghazal Haghi
Rinku Rajan
Karen Burr

The Journal of Physiology

DNA copy number evolution in Drosophila cell lines

2014-08-28

Maurizio Gatti
Brenton R. Graveley
Teresa M Przytycka

Hangnoh Lee
C Joel McManus
Dong-Yeon Cho
Matthew Eaton
Fioranna Renda
Maria Patrizia Somma
Lucy Cherbas
Gemma May
Sara Powell
Dayu Zhang
Lijun Zhan
Alissa Resch
Justen Andrews
Susan E Celniker
Peter Cherbas
Brian Oliver
David MacAlpine

Genome Biology

Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing.

2014-08-28

Q85220273

Joshua T Gamse

Developmental Biology

Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis.

2014-08-28

Richard W. Joseph
Thai Huu Ho

Jeanette E Eckel-Passow
Daniel A Igel
Daniel J Serie
John C Cheville
Alexander S Parker

Urologic Oncology

RNA sequencing analysis of the broad-host-range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant

2014-09

Lei Li
Konrad Förstner
Wolfgang R Streit

Dagmar Krysciak
Jessica Grote
Mariita Rodriguez Orbegoso
Christian Utpatel
Christel Schmeisser
Hari B Krishnan

Applied and Environmental Microbiology

Using heterogeneity of the patient-derived xenograft model to identify the chemoresistant population in ovarian cancer

2014-09-01

Britt K. Erickson
David A Schneider

Zachary C Dobbin
Ashwini A Katre
Adam D Steg
Monjri M Shah
Ronald D Alvarez
Michael G Conner
Dongquan Chen
Charles N Landen

Oncotarget

miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling

2014-09-01

Melody Baddoo
Erik K Flemington

Elizabeth C Martin
Adrienne E Krebs
Hope E Burks
Steven Elliott
Melody Baddoo
Bridgette M Collins-Burow
Matthew E Burow

Genes & Cancer

Genome-wide interrogation of longitudinal FEV1 in children with asthma

2014-09-01

Hae Kyung Im
Nancy J Cox

Kehua Wu
Eric R Gamazon
Hae Kyung Im
Paul Geeleher
Steven R White
Julian Solway
George L Clemmer
Scott T Weiss
Kelan G Tantisira
Mark J Ratain
R Stephanie Huang

American Journal of Respiratory and Critical Care Medicine

Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.

2014-09-01

Gregory E Crawford

James A Browne
Rui Yang
Lingyun Song
Shih-Hsing Leir
Ann Harris

Molecular Human Reproduction

The devil in the details of RNA-seq

2014-09-01

Anton Kratz
Piero Carninci

Nature Biotechnology

Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.

2014-09-02

Ramon Y Birnbaum
Nadav Ahituv

N Oksenberg
G D E Haliburton
W L Eckalbar
I Oren
S Nishizaki
K Murphy
K S Pollard

Translational Psychiatry

RNA-seq reveals aurora kinase-driven mTOR pathway activation in patients with sarcomatoid metastatic renal cell carcinoma.

2014-09-02

Tommy Tong
Jeremy O Jones

Sumanta K Pal
Miaoling He
Huiqing Wu
Xueli Liu
Clayton Lau
Jin-Hui Wang
Charles Warden
Xiwei Wu
Sabina Signoretti
Toni K Choueiri
Jose A Karam

Molecular Cancer Research

Transcriptomic dissection of the rice-Burkholderia glumae interaction.

2014-09-03

Teresia J Buza
Peng Deng
Daniel G. Peterson

Zenaida V Magbanua
Mark Arick
Chuan-Yu Hsu
Kurt C Showmaker
Philippe Chouvarine
Shien Lu

BMC Genomics

Transcriptional profiles of bovine in vivo pre-implantation development.

2014-09-04

Junhong Luo

Zongliang Jiang
Jiangwen Sun
Hong Dong
Xinbao Zheng
Craig Obergfell
Yong Tang
Jinbo Bi
Rachel O'Neill
Yijun Ruan
Jingbo Chen
Xiuchun Cindy Tian

BMC Genomics

Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.

2014-09-04

Adam G Sowalsky

Zheng Xia
Liguo Wang
Hao Zhao
Shaoyong Chen
Glenn J Bubley
Steven P Balk
Wei Li

Molecular Cancer Research

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.

2014-09-04

Elisa Ficarra
Lasorella A
Iavarone A
Raul Rabadan

Francesco Abate
Sakellarios Zairis
Andrea Acquaviva
Chris H Wiggins
Veronique Frattini
Giorgio Inghirami

BMC Systems Biology

Caught in the act: RNA-Seq provides novel insights into mRNA degradation.

2014-09-04

Jörg Stülke

Jan Gerwig

Molecular Microbiology

Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells

2014-09-05

Matthew E R Butchbach

Miho Maeda
Ashlee W Harris
Brewster F Kingham
Casey J Lumpkin
Lynn M Opdenaker
Suzanne M McCahan
Wenlan Wang

PLOS ONE

Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming.

2014-09-05

Paweł Golik

Martin Picard
Jiangwen Zhang
Saege Hancock
Olga Derbeneva
Ryan Golhar
Sean O'Hearn
Shawn Levy
Prasanth Potluri
Maria Lvova
Antonio Davila
Chun Shi Lin
Juan Carlos Perin
Eric F Rappaport
Hakon Hakonarson
Ian A Trounce
Vincent Procaccio
Douglas C Wallace

Proceedings of the National Academy of Sciences of the United States of America

Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress.

2014-09-05

Weirong Xu

Ruimin Li
Ningbo Zhang
Fuli Ma
Yuntong Jiao
Zhenping Wang

Plant Molecular Biology

Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes.

2014-09-08

Yaping Fang

Le Zhan
Hui-Xin Liu
Bo Kong
Yuqi He
Xiao-Bo Zhong
Jianwen Fang
Yu-Jui Yvonne Wan
Grace L Guo

PLOS ONE

The sialotranscriptome of Amblyomma triste, Amblyomma parvum and Amblyomma cajennense ticks, uncovered by 454-based RNA-seq.

2014-09-08

Luiz Gustavo Gardinassi
José M. Ribeiro
Beatriz R Ferreira
C L Mafra
Matias Pablo Juan Szabó
Sandra Regina Maruyama

Gustavo Rocha Garcia
Elen Anatriello
Higo Nasser Santanna Moreira
Maria Marlene Martins
Isabel Kinney Ferreira de Miranda-Santos

Parasites & Vectors

RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.

2014-09-08

Q85275267
Santiago Castillo-Ramírez

Maria Luisa Tabche
Alfredo Mendoza-Vargas
Miguel A Ramírez-Romero
Guillermo Dávila

BMC Genomics

Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa.

2014-09-11

Søren Molin
Rasmus L Marvig

María Gómez-Lozano
Monica V L Tulstrup

BMC Genomics

Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies.

2014-09-11

Lucía Ramírez

Martha Lucía Meijueiro
Francisco Santoyo
Antonio G Pisabarro

Briefings in functional genomics

GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data

2014-09-12

Terrence S. Furey

Qing Xiong
Sayan Mukherjee

Scientific Reports

Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens

2014-09-12

Zeynep Madak-Erdogan

Ping Gong
Jilong Li
Jianlin Cheng
C Michael Greenlief
William Helferich
John A Katzenellenbogen
Benita S Katzenellenbogen

Nuclear Receptor Signaling

TELP, a sensitive and versatile library construction method for next-generation sequencing

2014-09-15

Feng Xu

Xu Peng
Jingyi Wu
Reinhard Brunmeir
Sun-Yee Kim
Qiongyi Zhang
Chunming Ding
Weiping Han
Wei Xie

Nucleic Acids Research

Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development.

2014-09-16

Xiuqian Mu

Darshan Sapkota
Hemabindu Chintala
Fuguo Wu
Steven J Fliesler
Zihua Hu

Proceedings of the National Academy of Sciences of the United States of America

Using normalization to resolve RNA-Seq biases caused by amplification from minimal input.

2014-09-16

Christiaan V. Henkel
Finn-Arne Weltzien

Eirill Ager-Wick
Trude M Haug

Physiological Genomics

Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems.

2014-09-17

Claudia Angelini
Valerio Costa

Frontiers in cell and developmental biology

Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing

2014-09-17

Bettina Haase
Benedikt Kirchner
Michael W Pfaffl

Melanie Spornraft
Vladimir Benes
Irmgard Riedmaier

PLOS ONE

SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters.

2014-09-17

Yue Lu

Chun-do Oh
Shoudan Liang
Yuko Mori-Akiyama
Di Chen
Benoit de Crombrugghe
Hideyo Yasuda

PLOS ONE

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.

2014-09-18

Francesca Finotello

Barbara Di Camillo

Briefings in functional genomics

Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model.

2014-09-18

Seppo Ylä-Herttuala
Minna Niittykoski

J J Ruotsalainen
M U Kaikkonen
M W Martikainen
C G Lemay
J Cox
N S De Silva
A Kus
T J Falls
J-S Diallo
F Le Boeuf
J C Bell
A E Hinkkanen
M J Vähä-Koskela

Gene Therapy

Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes.

2014-09-18

Bauke Ylstra
Michael Hackenberg
Nicoletta Zini
Jaap M Middeldorp

Danijela Koppers-Lalic
Irene V Bijnsdorp
Monique A J van Eijndhoven
Payman Sadek
Daud Sie
Renee X de Menezes
Thomas Würdinger
Gerrit A Meijer
D Michiel Pegtel

Cell Reports

Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.

2014-09-18

Kenneth J McDowall

Justin E Clarke
Louise Kime
David Romero A

Nucleic Acids Research

A comprehensive transcriptomic analysis of infant and adult mouse ovary.

2014-09-20

Songnian Hu

Linlin Pan
Wei Gong
Yuanyuan Zhou
Xiaonuan Li
Jun Yu

Genomics Proteomics and Bioinformatics

Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts.

2014-09-22

Avik Datta

Harshal Inamdar
Sunitha Manjari K
Rajendra Joshi

Journal of Bioinformatics and Computational Biology

Error estimates for the analysis of differential expression from RNA-seq count data.

2014-09-23

Conrad J Burden

Sumaira E Qureshi
Susan R Wilson

PeerJ

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

2014-09-23

Robert M. Waterhouse
Gareth L. Maslen
Daniel Lawson

Xiaofang Jiang
Ashley Peery
A Brantley Hall
Atashi Sharma
Xiao-Guang Chen
Aleksey Komissarov
Michelle M Riehle
Yogesh Shouche
Maria V Sharakhova
Nazzy Pakpour
Peter Arensburger
Victoria L M Davidson
Karin Eiglmeier
Scott Emrich
Phillip George
Ryan C Kennedy
Shrinivasrao P Mane
Chioma Oringanje
Yumin Qi
Robert Settlage
Marta Tojo
Jose M C Tubio
Maria F Unger
Bo Wang
Kenneth D Vernick
Jose M C Ribeiro
Anthony A James
Kristin Michel
Michael A Riehle
Shirley Luckhart
Igor V Sharakhov
Zhijian Tu

Genome Biology

Rare occurrence of EGFRvIII deletion in head and neck squamous cell carcinoma.

2014-09-23

Arun Khattri
Zhixiang Zuo
Everett E Vokes

Johannes Brägelmann
Michaela K Keck
Mohamed El Dinali
Christopher D Brown
Thomas Stricker
Anish Munagala
Ezra E W Cohen
Mark W Lingen
Kevin P White
Tanguy Y Seiwert

Oral Oncology

CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough.

2014-09-25

Matthew J. Marshall

Michael J Wilkins
David W Hoyt
Paul A Alderson
Andrew E Plymale
L Meng Markillie
Abby E Tucker
Eric D Walter
Bryan E Linggi
Alice C Dohnalkova
Ron C Taylor

Frontiers in Microbiology

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels.

2014-09-26

Louis Bernatchez
Hélène Budzinski

Lucie Baillon
Fabien Pierron
Raphaël Coudret
Eric Normendeau
Antoine Caron
Laurent Peluhet
Pierre Labadie
Gilles Durrieu
Jérôme Sarraco
Pierre Elie
Patrice Couture
Magalie Baudrimont

Ecotoxicology

Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.

2014-09-27

Chun-Ping Yu
Wen-Hsiung Li

Jinn-Jy Lin
Yao-Ming Chang
Sean Chun-Chang Chen

BMC Genomics

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.

2014-09-30

Valérie Montel

Waibhav D Tembe
Stephanie J K Pond
Christophe Legendre
Han-Yu Chuang
Winnie S Liang
Nancy E Kim
Shukmei Wong
Timothy K McDaniel
David W Craig
John D Carpten

BMC Genomics

Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.

2014-09-30

Tsuyoshi Tanaka

Pui Shan Wong
Michihiro Tanaka
Yoshihiko Sunaga
Masayoshi Tanaka
Takeaki Taniguchi
Tomoko Yoshino
Wataru Fujibuchi
Sachiyo Aburatani

PLOS ONE

Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.

2014-09-30

Martin Kampmann

Shuo Gu
Yue Zhang
Lan Jin
Yong Huang
Feijie Zhang
Michael C Bassik
Mark A Kay

Nucleic Acids Research

RNA-Seq gene profiling--a systematic empirical comparison.

2014-09-30

Nuno A. Fonseca
Alvis Brazma
John C Marioni

PLOS ONE

Global transcriptome analysis of Al-induced genes in an Al-accumulating species, common buckwheat (Fagopyrum esculentum Moench).

2014-09-30

Naoki Yamaji

Kengo Yokosho
Jian Feng Ma

Plant and Cell Physiology

A comparison of sperm RNA-seq methods

2014-10

Russ Hauser

Shihong Mao
Edward Sendler
Robert J Goodrich
Stephen A Krawetz

Systems Biology in Reproductive Medicine

Genome-wide discovery of drug-dependent human liver regulatory elements

2014-10

Marcelo Rizzatti Luizon
Nadav Ahituv

Robin P Smith
Walter L Eckalbar
Kari M Morrissey
Thomas J Hoffmann
Xuefeng Sun
Stacy L Jones
Shelley Force Aldred
Anuradha Ramamoorthy
Zeruesenay Desta
Yunlong Liu
Todd C Skaar
Nathan D Trinklein
Kathleen M Giacomini

PLOS Genetics

Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta.

2014-10-01

Reedik Mägi
Andres Metspalu
Ene Reimann
Kristiina Rull
Jaak Vilo
Lili Milani
Andres Salumets
Triin Viltrop
Maire Peters
Sulev Kõks

Tauno Metsalu
Airi Tiirats
Balaji Rajashekar
Ganesh Acharya
Purusotam Basnet
Kadri Haller-Kikkatalo

Epigenetics

How deep is enough in single-cell RNA-seq?

2014-10-01

Yanyi Huang

Aaron M Streets

Nature Biotechnology

RNA-seq analysis of the rat placentation site reveals maternal obesity-associated changes in placental and offspring thyroid hormone signaling.

2014-10-05

Kartik Shankar

J Saben
P Kang
Y Zhong
K M Thakali
H Gomez-Acevedo
S J Borengasser
A Andres
T M Badger

Placenta

Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology.

2014-10-06

Stefanie Wehner
Ramakanth Madhugiri

Gopala K Mannala
Xiaoxing Qing
Trinad Chakraborty
Mobarak A Mraheil
Torsten Hain
Manja Marz

PLOS ONE

Role for LSM genes in the regulation of circadian rhythms.

2014-10-06

Lauren J. Francey

Soledad Perez-Santángelo
Estefanía Mancini
Ruben Gustavo Schlaen
Ariel Chernomoretz
John B Hogenesch
Marcelo J Yanovsky

Proceedings of the National Academy of Sciences of the United States of America

Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome

2014-10-07

Vimal Rawat

Ranu Sharma
C G Suresh

PLOS ONE

Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study.

2014-10-08

Jessica C Kissinger
Jeremy Debarry
Karan Uppal

Kevin J Lee
Weiwei Yin
Dalia Arafat
Yan Tang
ViLinh Tran
Monica Cabrera-Mora
Stacey Lapp
Alberto Moreno
Esmeralda Meyer
Suman Pakala
Vishal Nayak
Dean P Jones
Mary Galinski
Mark P Styczynski
Greg Gibson

Frontiers in cell and developmental biology

Gene expression plasticity resulting from parental leaf damage in Mimulus guttatus.

2014-10-08

Lena Hileman

Jack M Colicchio
Patrick J Monnahan
John K Kelly

New Phytologist

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells.

2014-10-13

Eduardo Eyras
Eneritz Agirre
Matías Blaustein
Gwendal Dujardin
Federico Pelisch
Juan Valcárcel
Reinhard Georg Lührmann
Alberto Kornblihtt

Mariano Alló
Sergey Bessonov
Paola Bertucci
Luciana Gómez Acuña
Valeria Buggiano
Nicolás Bellora
Babita Singh
Ezequiel Petrillo
Belén Miñana
Berta Pozzi
Elías Bechara
Dmitry E Agafonov
Anabella Srebrow

Proceedings of the National Academy of Sciences of the United States of America

trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.

2014-10-13

Matthew C LaFave
Shawn M. Burgess

Gabriel Renaud
Jin Liang
Tyra G Wolfsberg

BMC Bioinformatics

Characterization of two regulators of the TNF-α signaling pathway in Apostichopus japonicus: LPS-induced TNF-α factor and baculoviral inhibitor of apoptosis repeat-containing 2.

2014-10-13

Chenghua Li

Xiumei Zhang
Pengjuan Zhang
Ye Li
Chunhua Jin
Weiwei Zhang

Developmental and Comparative Immunology

RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus

2014-10-14

David A Fitzpatrick
Gary W Jones
Thomas M Keane
Sean Doyle

Grainne O'Keeffe
Stephen Hammel
Rebecca A Owens

BMC Genomics

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.

2014-10-15

James S Blachly

Karl W Kroll
Nima E Mokaram
Alexander R Pelletier
David E Frankhouser
Maximillian S Westphal
Paige A Stump
Cameron L Stump
Ralf Bundschuh
Pearlly Yan

Cancer Informatics

Rcount: simple and flexible RNA-Seq read counting.

2014-10-15

Ueli Grossniklaus

Marc W Schmid
Ueli Grossniklaus

Bioinformatics

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.

2014-10-15

Ross C Hardison
Christapher S Morrissey
Mitchell J Weiss

Weisheng Wu
Cheryl A Keller
Tejaswini Mishra
Maxim Pimkin
Gerd A Blobel

Genome Research

Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis.

2014-10-18

Rafael Silva-Rocha

Amanda Cristina Campos Antoniêto
Lílian dos Santos Castro
Gabriela Felix Persinoti
Roberto Nascimento Silva

Fungal Genetics and Biology

Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta.

2014-10-19

Javier De Las Rivas
Fermin Sanchez-Guijo

Beatriz Roson-Burgo
Consuelo Del Cañizo

BMC Genomics

Comparative proteomic and transcriptomic profile of Staphylococcus epidermidis biofilms grown in glucose-enriched medium.

2014-10-19

Gerald B Pier
Manuel Vilanova
Nuno Cerca
Rui Vitorino

Virginia Carvalhais
Angela França

Talanta

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

2014-10-21

Nicholas Katsanis
Manolis Kellis
Stephen J Haggarty
Serkan Erdin
Michael E. Talkowski
Marta Biagioli
Christelle Golzio
James F. Gusella

Aarathi Sugathan
Ian Blumenthal
Poornima Manavalan
Ashok Ragavendran
Harrison Brand
Diane Lucente
Judith Miles
Steven D Sheridan
Alexei Stortchevoi

Proceedings of the National Academy of Sciences of the United States of America

Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut.

2014-10-21

Lynn Kimsey

Matan Shelomi
W Cameron Jasper
Joel Atallah
Brian R Johnson

BMC Genomics

Gene expression associated with intersterility in Heterobasidion.

2014-10-22

Mårten Lind
Malin Elfstrand
Magnus Karlsson
Jan Stenlid

M A Van der Nest
Å Olson
K Dalman
M Brandström-Durling
B D Wingfield

Fungal Genetics and Biology

Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins

2014-10-23

Aurélie Bonin
Stéphane Reynaud
Laurence Despres
Jean-Philippe David
Guillaume Tetreau

Renaud Stalinski
Margot Paris
Vincent Navratil

BMC Genomics

Expression profile of Caenorhabditis elegans mutant for the Werner syndrome gene ortholog reveals the impact of vitamin C on development to increase life span.

2014-10-27

Martin J. Simard

Alexandra Dallaire
Sophie Proulx
Michel Lebel

BMC Genomics

Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.

2014-10-28

Timothy A Linksvayer

William Cameron Jasper
Timothy A Linksvayer
Joel Atallah
Daniel Friedman
Joanna C Chiu
Brian R Johnson

Molecular Biology and Evolution

The multidrug resistance 1 gene Abcb1 in brain and placenta: comparative analysis in human and guinea pig

2014-10-29

Gustavo Turecki
Matthew Suderman

Jane J Pappas
Sophie Petropoulos
Majid Iqbal
Vasilis Moisiadis
Stephen G Matthews
Moshe Szyf

PLOS ONE

In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.

2014-10-29

Roberto Bonasio
Michiel Vermeulen

David B Beck
Varun Narendra
William J Drury
Ryan Casey
Pascal W T C Jansen
Zuo-Fei Yuan
Benjamin A Garcia

Journal of Proteome Research

Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient.

2014-10-29

Boyke Bunk
Barbara C. Kahl
Alexander Mellmann
Cathrin Spröer

Nadine Windmüller
Anika Witten
Desirée Block

International Journal of Medical Microbiology

Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

2014-10-31

Igor V Grigoriev

Jennifer M Hurley
Arko Dasgupta
Jillian M Emerson
Xiaoying Zhou
Carol S Ringelberg
Nicole Knabe
Anna M Lipzen
Erika A Lindquist
Christopher G Daum
Kerrie W Barry
Kristina M Smith
James E Galagan
Deborah Bell-Pedersen
Michael Freitag
Chao Cheng
Jennifer J Loros
Jay C Dunlap

Proceedings of the National Academy of Sciences of the United States of America

GeneFriends: a human RNA-seq-based gene and transcript co-expression database

2014-10-31

Thomas Craig

Sipko van Dam
João Pedro de Magalhães

Nucleic Acids Research

BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children.

2014-10-31

Stephen F Sarabia
Alexander J. Lazar

Tricia L Peters
Vijetha Kumar
Sumanth Polikepahad
Frank Y Lin
Yu Liang
Wei-Lien Wang
HarshaVardhan Doddapaneni
Hsu Chao
Donna M Muzny
David A Wheeler
M Fatih Okcu
Sharon E Plon
M John Hicks
Dolores López-Terrada
D Williams Parsons
Angshumoy Roy

Modern Pathology

Widespread intron retention in mammals functionally tunes transcriptomes

2014-11

Ulrich Braunschweig
Thomas Gonatopoulos-Pournatzis
Babak Alipanahi
Nuno L Barbosa-Morais
Manuel Irimia

Qun Pan
Emil N Nachman
Brendan Frey
Benjamin J Blencowe

Genome Research

Several fusion genes identified by whole transcriptome sequencing in a spindle cell sarcoma with rearrangements of chromosome arm 12q and MDM2 amplification

2014-11

Sverre Heim
Ioannis Panagopoulos

Bodil Bjerkehagen
Ludmila Gorunova
Jeanne-Marie Berner
Kjetil Boye

International Journal of Oncology

Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity.

2014-11-01

Carmela Gissi
Graziano Pesole
Matteo Chiara
Anna Maria D'Erchia
Ernesto Picardi
Anna Atlante

Gemma Gadaleta
Giulio Pavesi
Caterina De Virgilio
Caterina Manzari
Francesca Mastropasqua
Gian Marco Prazzoli
David Horner
Aurelio Reyes
Elisabetta Sbisà
Apollonia Tullo

Mitochondrion

Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells

2014-11-01

Gordon K Smyth

Wei Shi
Kevin Man
Stephen L Nutt
Axel Kallies

Genomics Data

Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples.

2014-11-04

Paul Stothard

Igseo Choi
Hua Bao
Arun Kommadath
Afshin Hosseini
Xu Sun
Yan Meng
Graham S Plastow
Christopher K Tuggle
James M Reecy
Eric Fritz-Waters
Samuel M Abrams
Joan K Lunney
Le Luo Guan

BMC Genomics

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.

2014-11-05

Shin Kawano

Ayako Suzuki
Hiroyuki Wakaguri
Riu Yamashita
Katsuya Tsuchihara
Sumio Sugano
Yutaka Suzuki
Kenta Nakai

Nucleic Acids Research

Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq

2014-11-05

Alex H Wagner
Adam P. DeLuca
Arlene Drack
Budd A. Tucker
Todd E. Scheetz
Robert F. Mullins
Edwin M. Stone

S Scott Whitmore
Shemin Zeng
Terry A Braun

Experimental Eye Research

The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.

2014-11-06

Xianzhi Lin
Feng Li
Xinshu Xiao

Jae Hoon Bahn
Qing Zhang
Tak-Ming Chan
Yong Kim
David T W Wong

Clinical Chemistry

Biochemical and molecular changes associated with heteroxylan biosynthesis in Neolamarckia cadamba (Rubiaceae) during xylogenesis

2014-11-07

Antony Bacic

Xianhai Zhao
Kunxi Ouyang
Siming Gan
Wei Zeng
Lili Song
Shuai Zhao
Juncheng Li
Monika S Doblin
Xiao-Yang Chen
Alan Marchant
Xiaomei Deng
Ai-Min Wu

Frontiers in Plant Science

Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state

2014-11-07

Christopher J. Lengner
Rudolf Jaenisch

Yarden Katz
Feifei Li
Nicole J Lambert
Ethan S Sokol
Wai-Leong Tam
Albert W Cheng
Edoardo M Airoldi
Piyush B Gupta
Zhengquan Yu
Christopher B Burge

eLife

Nasonia vitripennis venom causes targeted gene expression changes in its fly host.

2014-11-10

Aisha L Siebert

Ellen O Martinson
David Wheeler
Jeremy Wright
Mrinalini
John H Werren

Molecular Ecology

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

2014-11-11

Yasunobu Okamura
Shu Tadaka

Yuichi Aoki
Takeshi Obayashi
Satoshi Ito
Takafumi Narise
Kengo Kinoshita

Nucleic Acids Research

Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition

2014-11-12

Christopher Lowe
Michael V Gormally
Ajit Jadhav

Thomas S Dexheimer
Giovanni Marsico
Deborah A Sanders
Dijana Matak-Vinković
Sam Michael
Ganesha Rai
David J Maloney
Anton Simeonov
Shankar Balasubramanian

Nature Communications

The putative Leishmania telomerase RNA (LeishTER) undergoes trans-splicing and contains a conserved template sequence

2014-11-12

Marcelo Santos da Silva

Elton J R Vasconcelos
Vinícius S Nunes
Marcela Segatto
Peter J Myler
Maria Isabel N Cano

PLOS ONE

Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus.

2014-11-12

Shawn D Mansfield

Eshchar Mizrachi
Victoria J Maloney
Janine Silberbauer
Charles A Hefer
Dave K Berger
Alexander A Myburg

New Phytologist

Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

2014-11-13

Jean Weissenbach
Andrew C Tolonen
Adriana Alberti

Magali Boutard
Tristan Cerisy
Pierre-Yves Nogue
Marcel Salanoubat

PLOS Genetics

RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.

2014-11-13

Alessio Fini
Federico Sebastiani
Cecilia Brunetti
Massimiliano Tattini

Sara Torre
Silvia Fineschi
Francesco Ferrini

PLOS ONE

De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus.

2014-11-13

Stefan Bonn
Roman Stilling

Eva Benito
Michael Gertig
Jonas Barth
Vincenzo Capece
Susanne Burkhardt
Andre Fischer

Frontiers in Cellular Neuroscience

Transcriptomic and physiological insights into the robustness of long filamentous cells of Methanosaeta harundinacea, prevalent in upflow anaerobic sludge blanket granules.

2014-11-14

Songnian Hu

Liguang Zhou
Haiying Yu
Guomin Ai
Bo Zhang
Xiuzhu Dong

Applied and Environmental Microbiology

Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing.

2014-11-14

Gregory R Grant

Jonathan M Toung
Nicholas Lahens
John B Hogenesch

PLOS ONE

Construction and assessment of individualized proteogenomic databases for large-scale analysis of nonsynonymous single nucleotide variants.

2014-11-17

Boris Macek

Karsten Krug
Sasa Popic
Alejandro Carpy
Christoph Taumer

Proteomics

Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium

2014-11-18

Daniel Ilut

Olga P Yurchenko
Sunjung Park
Jay J Inmon
Jon C Millhollon
Zach Liechty
Justin T Page
Matthew A Jenks
Kent D Chapman
Joshua A Udall
Michael A Gore
John M Dyer

BMC Plant Biology

Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation.

2014-11-18

Vivian H. Pellizari
Adriano M C Pimenta

Hivana P M B Dall'Agnol
Rafael A Baraúna
Pablo H C G de Sá
Rommel T J Ramos
Felipe Nóbrega
Catarina I P Nunes
Diego A das Graças
Adriana R Carneiro
Daniel M Santos
Marta S P Carepo
Vasco Azevedo
Maria P C Schneider
Artur Silva

BMC Genomics

IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

2014-11-18

Pedro Miura
Piero Sanfilippo
Eric C Lai

Sol Shenker

RNA

Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling

2014-11-19

Mathias Uhlén
Linn Fagerberg

Per-Henrik D Edqvist
Björn M Hallström
Angelika Danielsson
Karolina Edlund
Fredrik Pontén

Journal of Histochemistry & Cytochemistry

Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance.

2014-11-19

Anne Yael Nossent
Kees Fluiter
A Sabers
Lisbeth Birk Møller
Asli Silahtaroglu
Rikke S Møller
Niels Tommerup
Eleonora Aronica

Sanne S Kaalund
Morten T Venø
Mads Bak
Henning Laursen
Flemming Madsen
Helle Broholm
Bjørn Quistorff
Peter Uldall
Sakari Kauppinen
Jørgen Kjems
Zeynep Tümer

Epilepsia

ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts

2014-11-20

Alfonso Valencia
Alessandro Gorohovski
Milana Frenkel-Morgenstern

Dunja Vucenovic
Lorena Maestre

Nucleic Acids Research

DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites.

2014-11-20

Tabea G Kischka
Marcin Jąkalski
Ikuo Igarashi
Xuenan Xuan
Yoshifumi Nishikawa

Hiroyuki Wakaguri
Shin-ichiro Kawazu
Makoto Matsubayashi
Fumiya Kawahara
Naotoshi Tsuji
Shinuo Cao
Fujiko Sunaga
Kazuhiro Okubo
Josef Tuda
Arthur E Mongan
Yuki Eshita
Ryuichiro Maeda
Wojciech Makałowski
Yutaka Suzuki
Junya Yamagishi

Nucleic Acids Research

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.

2014-11-20

Pierre Baldi

Nate P Hoverter
Michael D Zeller
Miriam M McQuade
Angela Garibaldi
Anke Busch
Elizabeth M Selwan
Klemens J Hertel
Marian L Waterman

Nucleic Acids Research

The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells

2014-11-20

Ralph A DeFronzo

Luke Norton
Xi Chen
Marcel Fourcaudot
Nikhil K Acharya
Sami Heikkinen

Nucleic Acids Research

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.

2014-11-24

Sten Linnarsson
Peter Lönnerberg
Jens Hjerling-Leffler
Patrik Ernfors

Dmitry Usoskin
Alessandro Furlan
Saiful Islam
Hind Abdo
Daohua Lou
Jesper Haeggström
Olga Kharchenko
Peter V Kharchenko

Nature Neuroscience

Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.

2014-11-25

Rhodri Ceredig

Peter Keane
Cathal Seoighe

Bioinformatics

Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR.

2014-11-26

Shu-Biao Wu

Zhen-Hua Dang
Qi Qi
Hui-Rong Zhang
Hao-Yu Li
Ying-Chun Wang

International Journal of Genomics

Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast

2014-11-28

Jürg Bähler
María Rodríguez-López
Francesc X. Marsellach
Christopher T. Workman

Mathieu Clément-Ziza
Sandra Codlin
Manos A Papadakis
Susanne Reinhardt
Stuart Martin
Samuel Marguerat
Alexander Schmidt
Eunhye Lee
Jürg Bähler
Andreas Beyer

Molecular Systems Biology

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

2014-12

Kerstin Lindblad-Toh
Jessica Alföldi
Federica Di Palma
Marcia Lara
Thibaut Hourlier
Adam C. Siepel
Christophe Dessimoz
Jason Turner-Maier
David Brawand
Kevin Gori
Bronwen Aken
John F Engelhardt
Yoshihiro Kawaoka

Xinxia Peng
Amie J Eisfeld
Scott R Tyler
Jennifer Tisoncik-Go
G Lynn Law
Nives Skunca
Masato Hatta
David J Gasper
Sara M Kelly
Jean Chang
Matthew J Thomas
Jeremy Johnson
Aaron M Berlin
Pamela Russell
Ross Swofford
Jason Turner-Maier
Sarah Young
Steve Searle
Xingshen Sun
Yaling Yi
M Suresh
Terrence M Tumpey
Samantha M Wisely
Bruce W Birren
Robert E Palermo
Michael G Katze

Nature Biotechnology

Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis

2014-12-01

Melinda K Duncan
Shawn W Polson

Abby L Manthey
Anne M Terrell
Salil A Lachke

Genomics Data

Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression.

2014-12-01

Devin A King
Ashby Morrison

Glòria Mas Martín
Pablo E Garcia-Nieto

Genomics Data

Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.

2014-12-01

Christoph Hafemeister

Bowen Yu
Harish Doraiswamy
Xi Chen
Emily Miraldi
Mario Luis Arrieta-Ortiz
Christoph Hafemeister
Aviv Madar
Richard Bonneau
Cláudio T Silva

IEEE Transactions on Visualization and Computer Graphics

Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement

2014-12-01

Taejoon Kwon

Mei-I Chung
Rakhi Gupta
Julie C Baker
John B Wallingford

Genomics Data

Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software.

2014-12-01

Laura Treu
Stefano Campanaro

Alessandro Sardu

BMC Genomics

Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.

2014-12-02

Nedeljka N. Rosic
Chon-Kit Kenneth Chan
Sophie Dove
David Edwards
Ove Hoegh-Guldberg

Paulina Kaniewska
Edmund Yew Siang Ling

BMC Genomics

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

2014-12-03

Lee Lancashire

Zhenqiang Su
Hong Fang
Huixiao Hong
Leming Shi
Wenqian Zhang
Wenwei Zhang
Yanyan Zhang
Zirui Dong
Marina Bessarabova
Xi Yang
Baitang Ning
Binsheng Gong
Joe Meehan
Joshua Xu
Weigong Ge
Roger Perkins
Matthias Fischer
Weida Tong

Genome Biology

Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress

2014-12-04

Marie-Laure Endale Ahanda

Tatiana Zerjal
Sophie Dhorne-Pollet
Andrea Rau
Amanda Cooksey
Elisabetta Giuffra

PLOS ONE

QuASAR: quantitative allele-specific analysis of reads.

2014-12-04

Xiaoquan Wen
Francesca Luca
Roger Pique-Regi

Chris T Harvey
Gregory A Moyerbrailean
Gordon O Davis

Bioinformatics

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

2014-12-05
2014-12-23

Zhi-xiang Lu
Michael D. Henry

Shihao Shen
Juw Won Park
Lan Lin
Ying Nian Wu
Qing Zhou
Yi Xing
Michael D. Henry

Proceedings of the National Academy of Sciences of the United States of America

RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

2014-12-05

Yaodong Yang
Annaliese S Mason

Xintao Lei
Yong Xiao
Wei Xia
Zilong Ma
Ming Peng

PLOS ONE

SNPlice: variants that modulate Intron retention from RNA-sequencing data.

2014-12-06

Kamran Kowsari

Prakriti Mudvari
Mercedeh Movassagh
Ali Seyfi
Maria Kokkinaki
Nathan J Edwards
Nady Golestaneh
Anelia Horvath

Bioinformatics

Direct and indirect consequences on gene expression of a thyroid hormone receptor alpha 1 mutation restricted to Sertoli cells.

2014-12-08

Gabriel Livera

Fabrice Chatonnet
Betty Fumel
Sophie FouchÉCourt
Frédéric Flamant

Molecular Reproduction and Development

Dynamic changes in the cardiac methylome during postnatal development.

2014-12-09

Mark Ziemann
James E Hudson
Enzo R Porrello
Assam El-osta

Choon Boon Sim
Antony Kaspi
K N Harikrishnan
Jenny Ooi
Ishant Khurana
Lisa Chang

FASEB Journal

MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.

2014-12-10

Edward R. Dougherty

Jason M Knight
Ivan Ivanov

BMC Bioinformatics

An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator.

2014-12-10

Thomas Bleazard
Thomas Preiss
Nicole Cloonan
Andras Nagy
Sean M. Grimmond

Dong-Sung Lee
Jong-Yeon Shin
Peter D Tonge
Mira C Puri
Seungbok Lee
Hansoo Park
Won-Chul Lee
Samer M I Hussein
Ji-Young Yun
Jihye Kim
Mira Li
David Wood
Jennifer L Clancy
Rowland Mosbergen
Jae-Hyuk Yi
Kap-Seok Yang
Hyungtae Kim
Hwanseok Rhee
Christine A Wells
Ian M Rogers
Jeong-Sun Seo

Nature Communications

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature.

2014-12-10

Carl J Schmidt

Derrick J Coble
Damarius Fleming
Michael E Persia
Chris M Ashwell
Max F Rothschild
Susan J Lamont

BMC Genomics

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

2014-12-11

Aviv Regev
Nir Hacohen
Raktima Raychowdhury
Nir Friedman

Michal Rabani
Raktima Raychowdhury
Marko Jovanovic
Michael Rooney
Deborah J Stumpo
Andrea Pauli
Alexander F Schier
Perry J Blackshear
Ido Amit

Cell

UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.

2014-12-11

Wei Yan
Shuiqiao Yuan
Jianqiang Bao
Bo Torben Porse

Chong Tang

Development

Whole exome sequencing of a single osteosarcoma case--integrative analysis with whole transcriptome RNA-seq data.

2014-12-11

Sulev Kõks

Ene Reimann
Xuan Dung Ho
Katre Maasalu
Aare Märtson

Human genomics

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data

2014-12-16

Richard Weinshilboum
Kevin J Thompson
Xiaojia Tang
Krishna R Kalari

Saurabh Baheti
Khader Shameer
Quin Wills
Nifang Niu
Ilona N Holcomb
Stephane C Boutet
Ramesh Ramakrishnan
Jennifer M Kachergus
Jean-Pierre A Kocher
Liewei Wang
E Aubrey Thompson

Nucleic Acids Research

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.

2014-12-16

Julie Dickerson

Ruolin Liu
Ann E Loraine

BMC Bioinformatics

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms

2014-12-16

Youping Deng

Jack Y Yang
A Dunker
Jun S Liu
Xiang Qin
Hamid R Arabnia
William Yang
Andrzej Niemierko
Zhongxue Chen
Zuojie Luo
Liangjiang Wang
Yunlong Liu
Dong Xu
Weida Tong
Mary Yang

BMC Bioinformatics

Identification of genes and pathways involved in kidney renal clear cell carcinoma

2014-12-16

Youping Deng

William Yang
Kenji Yoshigoe
Xiang Qin
Jun S Liu
Jack Y Yang
Andrzej Niemierko
Yunlong Liu
A Dunker
Zhongxue Chen
Liangjiang Wang
Dong Xu
Hamid R Arabnia
Weida Tong
Mary Yang

BMC Bioinformatics

Regulation of the KNOX-GA gene module induces heterophyllic alteration in North American lake cress.

2014-12-16

Hitoshi Sakakibara
Seisuke Kimura

Hokuto Nakayama
Naomi Nakayama
Sumer Seiki
Mikiko Kojima
Neelima Sinha

The Plant Cell

Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma.

2014-12-16

Fredrik Mertens

Jakob Hofvander
Johnbosco Tayebwa
Jenny Nilsson
Linda Magnusson
Otte Brosjö
Olle Larsson
Fredrik Vult von Steyern
Nils Mandahl
Christopher D M Fletcher

Clinical Cancer Research

Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells.

2014-12-17

Luca Roz
Giulia Bertolini
Louise Carter
Massimo Moro
Crispin J. Miller
Fiona Blackhall
Caroline Dive

Dominic G Rothwell
Yaoyong Li
Mahmood Ayub
Catriona Tate
Gillian Newton
Yvonne Hey
Suzanne Faulkner
Stuart Pepper
Ged Brady

BMC Genomics

Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer.

2014-12-18

Chris Ponting
Andreas Heger
Jacqueline Stockley
Ian Sudbery
Hing Y Leung
Prabhakar Rajan

Janis T Fleming
Ann Hedley
Gabriela Kalna
David Sims
Craig N Robson
Rhona M McMenemin
Ian D Pedley

BMC Cancer

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

2014-12-18

Delphine Potier
Kristofer Davie
Stein Aerts
Gert Hulselmans

Marina Naval Sanchez
Lotte Haagen
Vân Anh Huynh-Thu
Duygu Koldere
Arzu Celik
Pierre Geurts
Valerie Christiaens

Cell Reports

RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis.

2014-12-19

Paolo Ronza
Ana Paula Losada
Peter W Harrison
Belén G Pardo
Ariadna Sitjà-Bobadilla
Paulino Martínez

Diego Robledo
Roberto Bermúdez
María José Redondo
María Isabel Quiroga

BMC Genomics

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature.

2014-12-19

Maite Huarte
Alejandro Athie
Francesco P Marchese

Yolanda Sánchez
Victor Segura
Oskar Marín-Béjar
Jovanna González
Luis Bujanda
Shuling Guo
Ander Matheu

Nature Communications

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.

2014-12-23

Peter F. Stadler
David Langenberger

Deblina Patra
Mario Fasold
Gerhard Steger
Ivo Grosse

Frontiers in Plant Science

A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.

2014-12-26

Laura L. Elo

Asta Laiho

PLOS ONE

RNA-seq profiling of small numbers of Drosophila neurons.

2014-12-26

Michael Rosbash
E Nagoshi
Xiao Chen

Katharine Abruzzi
Abby Zadina

Methods in Enzymology

Considerations for RNA-seq analysis of circadian rhythms.

2014-12-26

Gregory R Grant

Jiajia Li
John B Hogenesch
Michael E Hughes

Methods in Enzymology

Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.

2014-12-29

Silvia Fustinoni
Giorgio Dieci
Davide Carnevali
Matteo Pellegrini
Anastasia Conti

Nucleic Acids Research

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.

2014-12-31

Ratan Chopra

Gloria Burow
Andrew Farmer
Joann Mudge
Charles E Simpson
Mark D Burow

PLOS ONE

Subgroup-elimination transcriptomics identifies signaling proteins that define subclasses of TRPV1-positive neurons and a novel paracrine circuit.

2014-12-31

Tim Hucho

Jörg Isensee
Carsten Wenzel
Rene Buschow
Robert Weissmann
Andreas W Kuss

PLOS ONE

Β-catenin-dependent control of positional information along the AP body axis in planarians involves a teashirt family member.

2014-12-31

Gilbert Weidinger

Hanna Reuter
Martin März
Matthias C Vogg
David Eccles
Laura Grífol-Boldú
Daniel Wehner
Suthira Owlarn
Teresa Adell
Kerstin Bartscherer

Cell Reports

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

2015

Eshita Mutt
Pritha Ghosh
Oommen K Mathew

Atul K Upadhyay
Anita R Chacko
A Gandhimathi
K Harini
Agnel P Joseph
Adwait G Joshi
Snehal D Karpe
Swati Kaushik
Nagesh Kuravadi
Chandana S Lingu
J Mahita
Ramya Malarini
Sony Malhotra
Manoharan Malini
Mahantesha Naika
Sathyanarayanan Nitish
Shaik Naseer Pasha
Upadhyayula S Raghavender
Anantharamanan Rajamani
S Shilpa
Prashant N Shingate
Heikham Russiachand Singh
Anshul Sukhwal
Margaret S Sunitha
Manojkumar Sumathi
S Ramaswamy
Malali Gowda
Ramanathan Sowdhamini

BMC Plant Biology

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

2015

Fabian Amman
Florian Eggenhofer

Michael T Wolfinger
Jörg Fallmann

F1000Research

Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis

2015

Margarita Villar
José de la Fuente
John Fazakerley
Mick Watson
Hana Tykalová
Lesley Bell-Sakyi

Sabine Weisheit
Marina Popara
Julia Loecherbach
Daniel Růžek
Libor Grubhoffer

Parasites & Vectors

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

2015

Daniel Spies
Constance Ciaudo

Computational and Structural Biotechnology Journal

Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications

2015

Valeri Zakhartchenko
Eckhard Wolf
Volker J Schmid

Jens Popken
Alexander Graf
Stefan Krebs
Helmut Blum
Axel Strauss
Tuna Guengoer
Thomas Cremer

PLOS ONE

Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum

2015

Andrew J McElrone
Grant Cramer

Stefan Czemmel
Erin R Galarneau
Renaud Travadon
Kendra Baumgartner

PLOS ONE

Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research

2015

Tetsuya Sakurai

Yoshikazu Mikami
Atsushi Fukushima
Takao Kuwada-Kusunose
Taiichi Kitano
Yusuke Komiyama
Takashi Iwase
Kazuo Komiyama

PLOS ONE

Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection

2015

Natalia Sevane

Javier Cañon
Ignacio Gil
Susana Dunner

PLOS ONE

Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle

2015

Fernando S Mesquita
Luiz L Coutinho

Angela María Gonella-Diaza
Sónia Cristina da Silva Andrade
Mariana Sponchiado
Guilherme Pugliesi
Veerle Van Hoeck
Ricardo de Francisco Strefezzi
Gustavo R Gasparin
Mario Binelli

PLOS ONE

Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism

2015

Rita Benítez
Ana Isabel Rey
Cristina Ovilo

Miriam Ayuso
Almudena Fernández
Yolanda Núñez
Beatriz Isabel
Carmen Barragán
Ana Isabel Fernández
Juan F Medrano
Ángela Cánovas
Antonio González-Bulnes
Clemente López-Bote

PLOS ONE

From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity

2015

Helge Bode
Nicholas J Tobias
Michael L. Beeton
Richard ffrench-Constant

Geraldine Mulley
Paul Wilkinson
Isabella Vlisidou
Nina Ockendon-Powell
Alexia Hapeshi
Friederike I Nollmann
Jean van den Elsen
Nicholas R Waterfield

PLOS ONE

Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma.

2015

Ruchira Ranaweera
Elana J. Fertig

Haixia Cheng
Hiroyuki Ozawa
Hiromitsu Hatakeyama
Jason D Howard
Jimena Perez
Michael Considine
Manjusha Thakar
Gabriel Krigsfeld
Christine H Chung

Cancer Biology and Therapy

A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination

2015

Nripesh Prasad
Parimal Samir
Sebastian Joyce
Shawn Levy
Q52577914

Kristen L Hoek
Leigh M Howard
Xinnan Niu
Allison Galassie
Qi Liu
Tara M Allos
Kyle A Floyd
Yan Guo
Yu Shyr
Andrew J Link

PLOS ONE

Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis

2015

Karl Stamm

Min-Su Kim
Audrey Horst
Steven Blinka
Donna Mahnke
James Schuman
Rebekah Gundry
Aoy Tomita-Mitchell
John Lough

PLOS ONE

mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer

2015

Manuel Nietert
Gabriela Salinas-Riester
Silvia von der Heyde

Steve Wagner
Alexander Czerny
Fabian Ludewig
Dorit Arlt
Tim Beißbarth

PLOS ONE

The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway

2015

Amber L. Mosley

Melanie J Fox
Hongyu Gao
Whitney R Smith-Kinnaman
Yunlong Liu

PLOS Genetics

A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family

2015

Diane Mather
Rachel A Burton
Brian Steffenson
Kanwarpal S Dhugga
Robbie Waugh

Kelly Houston
Beata Sznajder
Antoni J Rafalski
Jillian Taylor
Geoffrey B Fincher

PLOS ONE

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems

2015

Abdimajid Osman
Patrick Provost
Adam Ameur

Walter E Hitzler

PLOS ONE

Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development

2015

Kelsey L. Picard
Wei Zeng
Edwin R. Lampugnani
Antony Bacic

Lili Song
Aimin Wu
Roshan Cheetamun
Cherie Beahan
Andrew Cassin
Andrew Lonsdale
Monika S Doblin

PLOS ONE

Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax

2015

Matthew Berriman
Mandy Sanders
Sophie Goyard
Andrew P Jackson
Dong Xia
Paola Minoprio

Bernardo J Foth
Jonathan M Wastling

PLOS Neglected Tropical Diseases

Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages

2015

John Monahan

Anupama Reddy
Joseph D Growney
Nick S Wilson
Caroline M Emery
Jennifer A Johnson
Rebecca Ward
Kelli A Monaco
Joshua Korn
Mark D Stump
Felipa A Mapa
Christopher J Wilson
Janine Steiger
Jebediah Ledell
Richard J Rickles
Vic E Myer
Seth A Ettenberg
Robert Schlegel
William R Sellers
Heather A Huet
Joseph Lehár

PLOS ONE

RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors

2015

Janine Altmüller
Hanns Hatt
Günter Gisselmann

Caroline Flegel
Nicole Schöbel
Christian Becker
Andrea Tannapfel
Günter Gisselmann

PLOS ONE

Whole Body Melanoma Transcriptome Response in Medaka

2015

Manfred Schartl

Yingjia Shen
Katja Maurus
Ron Walter
Chad Tomlinson
Richard K Wilson
John Postlethwait
Wesley C Warren

PLOS ONE

OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes

2015

Sarath Chandra Janga

Kashish Chetal
Sarath Chandra Janga

BioMed Research International

Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009

2015

Annick Wilmotte

Magdalena Calusinska
Christopher Hamilton
Pieter Monsieurs
Gregory Mathy
Natalie Leys
Fabrice Franck
Bernard Joris
Philippe Thonart
Serge Hiligsmann

Biotechnology for Biofuels

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

2015

Detlef Weigel
Korbinian Schneeberger
Vimal Rawat

Ahmed Abdelsamad
Björn Pietzenuk
Danelle K Seymour
Daniel Koenig
Ales Pecinka

PLOS ONE

Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean

2015

Hon-Ming Lam

Aldrin Kay-Yuen Yim
Johanna Wing-Hang Wong
Yee-Shan Ku
Hao Qin
Ting-Fung Chan

PLOS ONE

274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB)

2015-01

Antonis Rokas

William Ackerman
Irina Buhimschi
Haley Eidem
David Rinker
Kara Rood
Guomao Zhao
Taryn Summerfield
Mark Landon
Catalin Buhimschi

American Journal of Obstetrics and Gynecology

Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli

2015-01-01

Thorsten Bischler
Alexander Herbig
Cynthia Sharma
Konrad Förstner

Maureen K Thomason
Sara K Eisenbart
Aixia Zhang
Kay Nieselt
Gisela Storz

Journal of Bacteriology

A pan-cancer analysis of prognostic genes.

2015-01-01

Stefan Bekiranov
Wei-Min Chen
Anindya Dutta

Jordan Anaya
Brian Reon
Stefan Bekiranov

PeerJ

The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells

2015-01-01

Anthony T. Papenfuss
Chen-Fang Weng
Louise Y. Cheng

Francesca Froldi
Milan Szuperak
Wei Shi

Genes & Development

Quantifying entire transcriptomes by aligned RNA-seq data.

2015-01-01

Raffaele A. Calogero

Francesca Zolezzi

Methods in Molecular Biology

Exploring the RNA editing potential of RNA-Seq data by ExpEdit.

2015-01-01

Graziano Pesole
Anna Maria D'Erchia
Ernesto Picardi

Mattia D'Antonio
Tiziana Castrignanò

Methods in Molecular Biology

Integrated whole transcriptome and DNA methylation analysis identifies gene networks specific to late-onset Alzheimer's disease.

2015-01-01

Margaret A. Pericak-Vance

Crystal E Humphries
Martin A Kohli
Lubov Nathanson
Patrice Whitehead
Gary Beecham
Eden Martin
Deborah C Mash
John Gilbert

Journal of Alzheimer's Disease

Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes.

2015-01-01

María Eugenia Zanetti

Mauricio A Reynoso
Piyada Juntawong
Marcos Lancia
Flavio A Blanco
Julia Bailey-Serres

Methods in Molecular Biology

Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming

2015-01-01

Piero Carninci

Alexandre Fort
Daisuke Yamada
Kosuke Hashimoto
Haruhiko Koseki

Cell Cycle

Plasticity of DNA methylation in a nerve injury model of pain.

2015-01-01

Julie M. Cunningham

Meike Gölzenleuchter
Rahul Kanwar
Manal Zaibak
Fadi Al Saiegh
Theresa Hartung
Jana Klukas
Regenia L Smalley
Maria E Figueroa
Gary P Schroth
Terry M Therneau
Michaela S Banck
Andreas S Beutler

Epigenetics

Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus.

2015-01-01

Michelle A. Petri

Yiu Tak Leung
Lihua Shi
Kelly Maurer
Li Song
Zhe Zhang
Kathleen E Sullivan

Epigenetics

Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate

2015-01-01

Kurunthachalam Kannan

Rebecca Lee Yean Wong
Quan Wang
Lindsey S Treviño
Maarten C Bosland
Jing Chen
Mario Medvedovic
Gail S Prins
Shuk-Mei Ho
Cheryl Lyn Walker

Epigenetics

Characterization of the Olfactory Receptors Expressed in Human Spermatozoa

2015-01-01

Hanns Hatt
Günter Gisselmann

Caroline Flegel
Felix Vogel
Adrian Hofreuter
Benjamin S P Schreiner
Sandra Osthold
Sophie Veitinger
Christian Becker
Norbert H Brockmeyer
Michael Muschol
Gunther Wennemuth
Janine Altmüller
Günter Gisselmann

Frontiers in molecular biosciences

MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.

2015-01-01

Kenneth Bryan
Daniel G. Bradley
David J. Lynn
David E. MacHugh
Stephen V. Gordon

Peter Vegh
David A Magee
Nicolas C Nalpas
Matthew S McCabe
John A Browne
Kevin M Conlon

Tuberculosis

Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.

2015-01-01

Michael C Washburn

Emily C Wheeler
Francois Major
Douglas B Rusch
Heather A Hundley

RNA Biology

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq.

2015-01-01

Jörg Vogel
Cynthia Sharma
Gaurav Dugar
Nadja Heidrich

Methods in Molecular Biology

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

2015-01-01

Oliver Stegle
Cyriac Kandoth
Nikolaus Schultz

Kjong-Van Lehmann
André Kahles
William Lee
Gunnar Rätsch

Pacific Symposium on Biocomputing

Analysis of alternative splicing events in custom gene datasets by AStalavista.

2015-01-01

Sylvain Foissac
Michael Sammeth

Methods in Molecular Biology

Computer-assisted annotation of small RNA transcriptomes.

2015-01-01

Grant W Hennig
Wei Yan

Nicole Ortogero
Dickson Luong

Methods in Molecular Biology

First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics.

2015-01-02

Bisong Yue

Lianming Du
Wujiao Li
Zhenxin Fan
Fujun Shen
Mingyu Yang
Zili Wang
Zuoyi Jian
Rong Hou
Xiuyue Zhang

Molecular Ecology Resources

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.

2015-01-05

Åslaug Helland
Lynnette Fernandez-Cuesta
Joachim H Clement
Martin Peifer
Stefan Haas
Gavin Wright
Peter Nürnberg
Steinar Solberg
Martin Vingron
Elisabeth Brambilla

Ruping Sun
Roopika Menon
Julie George
Susanne Lorenz
Leonardo A Meza-Zepeda
Dennis Plenker
Johannes M Heuckmann
Frauke Leenders
Thomas Zander
Ilona Dahmen
Mirjam Koker
Jakob Schöttle
Roland T Ullrich
Christian Becker
Henrik Seidel
Diana Böhm
Friederike Göke
Sascha Ansén
Prudence A Russell
Zoe Wainer
Benjamin Solomon
Iver Petersen
Jörg Sänger
Odd-Terje Brustugun
Marius Lund-Iversen
Reinhard Buettner
Jürgen Wolf
Sven Perner
Roman K Thomas

Genome Biology

Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing

2015-01-05

Laurence Florens
Michael P. Washburn

Kaiwei Liang
Xin Gao
Joshua M Gilmore
Edwin Smith
Ali Shilatifard

Molecular and Cellular Biology

rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.

2015-01-05

Wolfgang Kaisers

Wolfgang Kaisers
Heiner Schaal
Holger Schwender

Bioinformatics

iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data

2015-01-06

Susanne Mandrup
Bjørk Ditlev Larsen
Søren Fisker Schmidt

Jesper Grud Skat Madsen
Anne Loft
Ronni Nielsen

Nucleic Acids Research

Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients

2015-01-07

Vincent Plagnol
Divya Shah
Sofia Morfopoulou
Julianne R Brown
Judith Breuer
Waseem Qasim

Jonathan Hubb
Warren A Emmett
Winnie Ip
Tony Brooks
Simon M L Paine
Glenn Anderson
Alex Virasami
C Y William Tong
Duncan A Clark
Thomas S Jacques
Mike Hubank

Clinical Infectious Diseases

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

2015-01-07

Andrew Warren
Omar S. Harb
Daniel Lawson
Leslie Birgit Vosshall
Michael McClelland
Cristina Aurrecoechea

Brian Brunk
Prerak Desai
Scott Emrich
Gloria I Giraldo-Calderón
Deborah Hix
Dustin Machi
Chunhong Mao
Eric Nordberg
Maulik Shukla
Alice R Wattam
Rebecca Will
Hyun Seung Yoo
Bruno Sobral

Bioinformatics

Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat.

2015-01-08

Man Chun John Ma
Anne E Kwitek

Jinkai Wang
Amanda K Mennie
Janette M Pettus
Yang Xu
Lan Lin
Matthew G Traxler
Jessica Jakoubek
Santosh S Atanur
Timothy J Aitman
Yi Xing

Circulation: Cardiovascular Genetics

Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.

2015-01-12

Xiaoliang Sunney Xie

Huiyi Chen
Katsuyuki Shiroguchi
Hao Ge

Molecular Systems Biology

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.

2015-01-13

Oliver Kurzai
Reinhard Guthke

Jörg Linde
Seána Duggan
Michael Weber
Fabian Horn
Patricia Sieber
Daniela Hellwig
Konstantin Riege
Manja Marz
Ronny Martin

Nucleic Acids Research

Deep sequencing of the murine olfactory receptor neuron transcriptome.

2015-01-15

Hanns Hatt
Günter Gisselmann
Christian H. Wetzel
Eva M. Neuhaus

Ninthujah Kanageswaran
Marilen Demond
Maximilian Nagel
Benjamin S P Schreiner
Sabrina Baumgart
Paul Scholz
Janine Altmüller
Christian Becker
Julia F Doerner
Heike Conrad
Sonja Oberland
Günter Gisselmann

PLOS ONE

Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.

2015-01-15

Kemal Avican
Mikael Huss

Anna Fahlgren
Ann Kathrin Heroven
Michael Beckstette
Petra Dersch
Maria Fällman

PLOS Pathogens

Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness.

2015-01-16

Angel Barco

Anna Fiorenza
Jose P Lopez-Atalaya
Victor Rovira
Marilyn Scandaglia
Emilio Geijo-Barrientos

Cerebral Cortex

Partial dosage compensation in Strepsiptera, a sister group of beetles.

2015-01-18

Doris Bachtrog

Shivani Mahajan

Genome Biology and Evolution

Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect.

2015-01-20

Xiaolong Cao
Haobo Jiang

Insect Biochemistry and Molecular Biology

Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.

2015-01-20

Marco Mangone

Stephen M Blazie
Cody Babb
Henry Wilky
Alan Rawls
Jin G Park

BMC Biology

Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human.

2015-01-21

Bernard Jégou
Fatima Smagulova
Soazik P Jamin
Fabrice G Petit
Emmanuelle Becker
Frédéric Chalmel
Michael Primig

Christine Kervarrec
Chunxiang Hao
Bernard Jégou

Biology of Reproduction

Claudin multigene family in channel catfish and their expression profiles in response to bacterial infection and hypoxia as revealed by meta-analysis of RNA-Seq datasets.

2015-01-21

Luyang Sun
Shikai Liu

Lisui Bao
Yun Li
Jianbin Feng
Zhanjiang Liu

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Quantitative visualization of alternative exon expression from RNA-seq data.

2015-01-22

Schraga Schwartz
Jill P. Mesirov
Helga Thorvaldsdóttir

Yarden Katz
Eric T Wang
Jacob Silterra
Bang Wong
Helga Thorvaldsdóttir
James T Robinson
Edoardo M Airoldi
Christopher B Burge

Bioinformatics

RNA-Seq reveals a role for NFAT-signaling in human retinal microvascular endothelial cells treated with TNFα.

2015-01-24

Colin A Bretz

Sara R Savage
John S Penn

PLOS ONE

Blocking yersiniabactin import attenuates extraintestinal pathogenic Escherichia coli in cystitis and pyelonephritis and represents a novel target to prevent urinary tract infection.

2015-01-26

Harry L T Mobley

Ariel R Brumbaugh
Sara N Smith
Sargurunathan Subashchandrabose
Stephanie D Himpsl
Tracy H Hazen
David A Rasko

Infection and Immunity

The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4.

2015-01-26

Sergio Abrignani
Massimiliano Pagani

Valeria Ranzani
Grazisa Rossetti
Ilaria Panzeri
Alberto Arrigoni
Raoul Jp Bonnal
Serena Curti
Paola Gruarin
Elena Provasi
Elisa Sugliano
Maurizio Marconi
Raffaele De Francesco
Jens Geginat
Beatrice Bodega

Nature Immunology

Next-Generation Sequencing Reveals Low-Dose Effects of Cationic Dendrimers in Primary Human Bronchial Epithelial Cells

2015-01-27

Pekka Kohonen
Hanna L. Karlsson
Bengt Fadeel
Neus Feliu
Yuning Zhang

Neus Feliu
Jie Ji
Lena Palmberg
Andreas Nyström

ACS Nano

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome

2015-01-27

Stephanie McKay

Benjamin B Green
David E Kerr

BMC Genomics

Computational and analytical challenges in single-cell transcriptomics.

2015-01-28

Sarah Teichmann
John C Marioni
Oliver Stegle

Nature Reviews Genetics

The transcriptional stress response of Candida albicans to weak organic acids.

2015-01-29

Norman Pavelka
Michael Poidinger

Fabien Cottier
Alrina Shin Min Tan
Jinmiao Chen
Josephine Lum
Francesca Zolezzi

The avian transcriptome response to malaria infection

2015-01-29

Olof Hellgren
Gediminas Valkiūnas
Elin Videvall
Vaidas Palinauskas

Charlie K Cornwallis

Molecular Biology and Evolution

Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.

2015-01-30

Melline F Noronha
Luciana S Mofatto
Juan Lucas Argueso
Piotr A Mieczkowski

Osmar V Carvalho-Netto
Marcelo F Carazzolle
Paulo J P L Teixeira
Luige A L Calderón
Gonçalo A G Pereira

Microbial Cell Factories

RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery.

2015-01-30

Arghavan Alisoltani

Arghavan Alisoltani
Hossein Fallahi
Behrouz Shiran
Anousheh Alisoltani
Esmaeil Ebrahimie

Gene

RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance.

2015-01-31

Jérôme Gouzy

Arnaud Duhoux
Sébastien Carrère
Ludovic Bonin
Christophe Délye

Plant Molecular Biology

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.

2015-02-01

Federico Comoglio

Cem Sievers
Renato Paro

BMC Bioinformatics

Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.

2015-02-01

Trudee Fair
Niamh Forde
John R. Roche

P A McGettigan
J A Browne
S D Carrington
M A Crowe
B J Loftus
A Lohan
P Lonergan
K Pluta
S Mamo
A Murphy
S W Walsh
C J Creevey
B Earley
S Keady
D A Kenny
D Matthews
M McCabe
D Morris
A O'Loughlin
S Waters
M G Diskin
A C O Evans

Reproduction, Fertility and Development

The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA-mRNA interaction network.

2015-02-01

Teresa Colombo
Valerio Fulci

Jonathan Krell
Justin Stebbing
Adam Enver Frampton
Claudia Carissimi
Victoria Harding
Alexander De Giorgio
Giuseppe Macino
Leandro Castellano

The Lancet

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.

2015-02-02

Laura Clarke
Paul Flicek
Xabier Agirre
Michael I Robson
Marien Pascual
Avik Datta
Renée Beekman
David Richardson
Giancarlo Castellano
Juan R Rodriguez-Madoz
José I Martín-Subero
Norma C. Gutiérrez
José M García-Verdugo
Elias Campo
Simon Heath
Felipe Prosper
Eric C Schirmer
Reiner Siebert

Marta Kulis
Victor Segura
Anke Bergmann
Anna Esteve
Angelika Merkel
Emanuele Raineri
Lidia Agueda
Julie Blanc
Nuria Russiñol
Ana C Queirós
Edurne San José-Enériz
Fang Fang
Elisabeth Guruceaga
Joost H A Martens
Marta Gut
Maria J Calasanz
Jesús F San Miguel
Ari Melnick
Hendrik G Stunnenberg
Ivo G Gut

Genome Research

Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling.

2015-02-02

Jens Nielsen
Mathias Uhlén

Pouyan Ghaffari
Adil Mardinoglu
Anna Asplund
Saeed Shoaie
Caroline Kampf

Scientific Reports

The genomic landscape of phaeochromocytoma.

2015-02-02

Stephen B. Fox
Richard W. Tothill
Rodney J. Hicks
Aidan Flynn
Jason Li
Grant McArthur
Roderick J Clifton-Bligh

Diana Benn
Bruce Robinson
Alison H Trainer
Paul James
Annette Hogg
Kelly Waldeck
Joshy George
Anthony J Gill

The Journal of Pathology

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.

2015-02-04

Karsten Hokamp
David E. MacHugh
Kate Killick

Maura E Casey
Kieran G Meade
Nicolas C Nalpas
Maria Taraktsoglou
John A Browne
Stephen D E Park
Eamonn Gormley
David A Magee

Frontiers in Immunology

Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles

2015-02-04

Yanmei Huang

Fanny S Ng
F Rob Jackson

Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells.

2015-02-05

Chia-Lang Hsu
Hsuan-Cheng Huang
Hsueh-Fen Juan

Li-Ling Lin
Chieh-Ren Hsia

BMC Genomics

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.

2015-02-06

Reinhard Guthke

Sylvie Schulze
Sebastian G Henkel
Dominik Driesch
Jörg Linde

Frontiers in Microbiology

Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease

2015-02-07

Anand Swaroop
Rinki Ratnapriya

Hyun-Jin Yang
Tiziana Cogliati
Jung-Woong Kim

Progress in Retinal and Eye Research

Regulatory small RNAs from the 3' regions of bacterial mRNAs.

2015-02-09

Jörg Vogel
Masatoshi Miyakoshi
Yanjie Chao

Current Opinion in Microbiology

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

2015-02-10

Catherine Feuillet
Etienne Paux
Frédéric Choulet
Adriana Alberti

Lise Pingault
Natasha Glover
Patrick Wincker

Genome Biology

Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.

2015-02-10

David D. Pollock

Audra L Andrew
Daren C Card
Robert P Ruggiero
Drew R Schield
Richard H Adams
Stephen M Secor
Todd A Castoe

Physiological Genomics

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.

2015-02-11

Cody Ashby

Zheng Chang
Guojun Li
Juntao Liu
Yu Zhang
Deli Liu
Carole L Cramer
Xiuzhen Huang

Genome Biology

Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen.

2015-02-11

Daria Salyakina
Jean-Christophe Renauld

Eden Kleiman
Magali De Heusch
Kristen L Hoek
Joan M Llanes
Iris Castro
Jacqueline A Wright
Emily S Clark
Derek M Dykxhoorn
Enrico Capobianco
Akiko Takeda
Wasif N Khan

Frontiers in Immunology

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.

2015-02-12

Je Hyuk Lee
George M. Church

Evan R Daugharthy
Jonathan Scheiman
Reza Kalhor
Thomas C Ferrante
Richard Terry
Brian M Turczyk
Joyce L Yang
Ho Suk Lee
John Aach
Kun Zhang

Nature Protocols

The herbicide linuron inhibits cholesterol biosynthesis and induces cellular stress responses in brown trout.

2015-02-12

Eduarda M. Santos
Tamsyn M Uren Webster

Mandy H Perry

Environmental Science & Technology

The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species.

2015-02-13

Zhan Zhou

Libing Shen
Gangbiao Liu
Yangyun Zou
Zhixi Su
Xun Gu

PLOS ONE

Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.

2015-02-13

Peter Deplazes

Adrian B Hehl
Walter U Basso
Christoph Lippuner
Chandra Ramakrishnan
Michal Okoniewski
Robert A Walker
Michael E Grigg
Nicholas C Smith

BMC Genomics

SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

2015-02-14

Gaurav Sablok

Xiaoyong Sun
Fenghua Zuo
Yuanbin Ru
Jiqiang Guo
Xiaoyan Yan

Computer Methods and Programs in Biomedicine

Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape

2015-02-14

Jörn Kalinowski

Marta Irla
Armin Neshat
Trygve Brautaset
Christian Rückert
Volker F Wendisch

BMC Genomics

Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli.

2015-02-14

Vânia Pobre
Cecília Maria Arraiano

BMC Genomics

Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

2015-02-17

Cynthia Sharma
Kai Papenfort
Bonnie Bassler
Konrad Förstner

Jian-Ping Cong

Proceedings of the National Academy of Sciences of the United States of America

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.

2015-02-17

Ann-Christine Syvänen
Christofer L. Bäcklin
Ann Nordgren
Jonas Abrahamsson
Trond Flægstad
Kjeld Schmiegelow
Rolf Larsson

Jessica Nordlund
Vasilios Zachariadis
Lucia Cavelier
Johan Dahlberg
Ingegerd Öfverholm
Gisela Barbany
Elin Övernäs
Mats M Heyman
Ólafur G Jónsson
Jukka Kanerva
Josefine Palle
Mats G Gustafsson
Gudmar Lönnerholm
Erik Forestier

Clinical epigenetics

Aging-like changes in the transcriptome of irradiated microglia

2015-02-17

Matthew D Li
Steven A. Sloan

Terry C Burns
Sunny Kumar
Alexander A Morgan
Theo D Palmer

Glia

Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis).

2015-02-17

Barry J Pogson

Junxiang Zhang
Hui Yuan
Zhangjun Fei
Lugang Zhang
Li Li

Planta

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

2015-02-18

Steven Salzberg
Mihaela Pertea

Geo M Pertea
Corina M Antonescu
Tsung-Cheng Chang
Joshua T Mendell

Nature Biotechnology

RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis

2015-02-18

Peter Deplazes

Robert A Walker
Philippa A Sharman
Catherine M Miller
Christoph Lippuner
Michal Okoniewski
Ramon M Eichenberger
Chandra Ramakrishnan
Fabien Brossier
Adrian B Hehl
Nicholas C Smith

BMC Genomics

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.

2015-02-19

Sten Linnarsson
Peter Lönnerberg
Jens Hjerling-Leffler
Gioele La Manno
Hermany Munguba
Charlotte Rolny
Gonçalo Castelo-Branco
Christer Betsholtz

Amit Zeisel
Ana B Muñoz-Manchado
Simone Codeluppi
Anna Juréus
Sueli Marques
Liqun He

Science

Flexible expressed region analysis for RNA-seq with derfinder

2015-02-19

Michael I Love
Leonardo Collado-Torres
Jeffrey T. Leek
Ben Langmead
Abhinav Nellore

Alyssa C Frazee
Christopher Wilks
Rafael A Irizarry
Andrew E Jaffe

The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus.

2015-02-20

Anindya Dutta
Jordan Anaya

Kouhei Sakurai
Brian J Reon

Molecular Cancer Research

Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.

2015-02-21

Peter van Heusden
Uljana Hesse
Alan Christoffels

Stanley Kimbung Mbandi

BMC Bioinformatics

A phylogenetic backbone for Bivalvia: an RNA-seq approach

2015-02-22

Casey W. Dunn
Sónia C S Andrade
Rüdiger Bieler
Gonzalo Giribet
John D. Taylor

Vanessa L González
Timothy M Collins
Paula M Mikkelsen

Proceedings of the Royal Society B

A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis).

2015-02-23

Manfred Schartl
Shinichi Nakagawa

Dunja K Lamatsch
Sofia Adolfsson
Alistair M Senior
Guntram Christiansen
Maria Pichler
Yuichi Ozaki
Linnea Smeds

PLOS ONE

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.

2015-02-23

John Mattick
Peter M Clark
Aristeidis G Telonis
Yohei Kirino
Michelle Lally
Karen E Knudsen
Isidore Rigoutsos
George A. Calin
Michael J. Keating

Eric Londin
Phillipe Loher
Kevin Quann
Yi Jing
Eleftheria Hatzimichael
Shozo Honda
Bharat Ramratnam
Clay E S Comstock
Leonard Gomella
George L Spaeth
Lisa Hark
L Jay Katz
Agnieszka Witkiewicz
Abdolmohamad Rostami
Sergio A Jimenez
Michael A Hollingsworth
Jen Jen Yeh
Chad A Shaw
Steven E McKenzie
Paul Bray
Peter T Nelson
Simona Zupo
Katrien Van Roosbroeck
Charles Yeo
Masaya Jimbo
Joseph Cozzitorto
Jonathan R Brody
Kathleen Delgrosso
Paolo Fortina

Proceedings of the National Academy of Sciences of the United States of America

Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.

2015-02-23

Vivek Krishnakumar

Xingtan Zhang
Benjamin D Rosen
Haibao Tang
Christopher D Town

PLOS ONE

RNA-seq analysis of the response of the halophyte, Mesembryanthemum crystallinum (ice plant) to high salinity.

2015-02-23

Hironaka Tsukagoshi
Sumie Ishiguro

Takamasa Suzuki
Kouki Nishikawa
Sakae Agarie
Tetsuya Higashiyama

PLOS ONE

Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans toward pathogenic Bacillus thuringiensis.

2015-02-23

Andreas Tholey

Wentao Yang
Katja Dierking
Daniela Esser
Matthias Leippe
Philip Rosenstiel
Hinrich Schulenburg

Developmental and Comparative Immunology

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.

2015-02-24

Jesse Gillis

S Ballouz
W Verleyen

Bioinformatics

RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.

2015-02-25

Brian Scheffler
Ronald Pierik

David P Horvath
Stephanie A Hansen
Janet P Moriles-Miller
Changhui Yan
David E Clay
Sharon A Clay

New Phytologist

RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.

2015-02-26

Eric A Pierce

Michael H Farkas
Elizabeth D Au
Maria E Sousa

Cold Spring Harbor Perspectives in Medicine

Exon Skipping Is Correlated with Exon Circularization.

2015-02-26

Steven Kelly
Argyris Papantonis

Chris Greenman
Peter R Cook

Journal of Molecular Biology

The landscape of long noncoding RNAs in the human transcriptome

2015-03

John R. Prensner

Matthew K Iyer
Yashar S Niknafs
Rohit Malik
Udit Singhal
Anirban Sahu
Yasuyuki Hosono
Terrence R Barrette
Joseph R Evans
Shuang Zhao
Anton Poliakov
Xuhong Cao
Saravana M Dhanasekaran
Yi-Mi Wu
Dan R Robinson
David G Beer
Felix Y Feng
Hariharan K Iyer
Arul M Chinnaiyan

Nature Genetics

Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines

2015-03

James Taylor

Jeremy Goecks
Bassel F El-Rayes
Shishir K Maithel
H Jean Khoury
Michael R Rossi

Cancer Medicine

Simultaneous generation of many RNA-seq libraries in a single reaction

2015-03-02

Georgia Giannoukos
Jenny Chen
Alper Kucukural

Alexander A Shishkin
Dawn Ciulla
Michele Busby
Christine Surka
Roby P Bhattacharyya
Robert F Rudy
Milesh M Patel
Nathaniel Novod
Deborah T Hung
Andreas Gnirke
Manuel Garber
Mitchell Guttman
Jonathan Livny

Nature Methods

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.

2015-03-03

Steven A. Sloan

Qinghong Yan
Sebastien M Weyn-Vanhentenryck
Jie Wu
Ye Zhang
Kenian Chen
Jia Qian Wu
Ben A Barres
Chaolin Zhang

Proceedings of the National Academy of Sciences of the United States of America

Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits

2015-03-03

Shiri Freilich

Shery Lev
Itay Gonda
Eli Reuveni
Vitaly Portnoy
Elad Oren
Marc Lohse
Navot Galpaz
Einat Bar
Galil Tzuri
Guy Wissotsky
Ayala Meir
Joseph Burger
Yaakov Tadmor
Arthur Schaffer
Zhangjun Fei
James Giovannoni
Efraim Lewinsohn
Nurit Katzir

BMC Plant Biology

Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis.

2015-03-04

Jean Popovici
Jonathan M Keith

Megan Woolfit
Manjula Algama
Elizabeth A McGraw

PLOS ONE

Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.

2015-03-05

Gregg B Morin

Ewan A Gibb
René L Warren
Gavin W Wilson
Scott D Brown
Gordon A Robertson
Robert A Holt

Genome Medicine

PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function.

2015-03-09

Wilfried Ellmeier
Rengul Cetin-Atalay

Nazli Keskin
Emre Deniz
Jitka Eryilmaz
Manolya Un
Tugce Batur
Tulin Ersahin
Shinya Sakaguchi
Batu Erman

Molecular and Cellular Biology

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

2015-03-09

Lars K. Nielsen
Anton J. Enright
John Mattick
Marcel E. Dinger
Kim-Anh Lê Cao
Tommaso Leonardi
Giovanni Bussotti
Michael B. Clark
Joanna Crawford
Gethin Thomas

Tim R Mercer
Katelin R Haynes
Marion E Brunck
Kim-Anh Lê Cao
Wendy Y Chen
Ryan J Taft

Nature Methods

Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function

2015-03-10

Oliver Billker

A T Y Yeung
C Hale
J Xia
P H Tate
D Goulding
J A Keane
S Mukhopadhyay
L Forrester
W C Skarnes
R E W Hancock
G Dougan

Scientific Reports

DNA methylation dynamics at imprinted genes during bovine pre-implantation embryo development.

2015-03-10

Niamh Forde
Alan M O'Doherty
Trudee Fair

David A Magee
Lynee C O'Shea
Marijke E Beltman
Solomon Mamo

BMC Developmental Biology

Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation

2015-03-12

Andreas Hejnol
Gonzalo Giribet

Christopher E Laumer

eLife

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum

2015-03-12

Qin Ma

Wen-Chi Chou
Shihui Yang
Sha Cao
Dawn M Klingeman
Steven D Brown
Ying Xu

Nucleic Acids Research

RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.

2015-03-14

Jun Wang

Rama Rao
Ya Bing Zhu
Tahereh Alinejad
Suma Tiruvayipati
Kwai Lin Thong
Subha Bhassu

Gut Pathogens

Modifying effects of vitamin E on chlorpyrifos toxicity in atlantic salmon

2015-03-16

Pål A. Olsvik

Marc H G Berntssen
Liv Søfteland

PLOS ONE

Cyclic GMP balance is critical for malaria parasite transmission from the mosquito to the mammalian host

2015-03-17

Sebastian A. Mikolajczak

Viswanathan Lakshmanan
Matthew E Fishbaugher
Bob Morrison
Michael Baldwin
Michael Macarulay
Ashley M Vaughan
Stefan H I Kappe

mBio

Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis.

2015-03-17

Juan C Begara-Morales
Francisco J. Corpas

Capilla Mata-Pérez
Beatriz Sánchez-Calvo
Francisco Luque
Jaime Jiménez-Ruiz
María N Padilla
Jesús Fierro-Risco
Raquel Valderrama
Ana Fernández-Ocaña
Juan B Barroso

Frontiers in Plant Science

Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington's disease mice.

2015-03-17

Irwin Davidson
Christian Neri

Mayada Achour
Stéphanie Le Gras
Céline Keime
Frédéric Parmentier
François-Xavier Lejeune
Anne-Laurence Boutillier
Karine Merienne

Human Molecular Genetics

Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data

2015-03-18

Gu Mi

Yanming Di
Daniel W Schafer

PLOS ONE

Escape from X inactivation varies in mouse tissues.

2015-03-18

Jay Shendure

Joel B Berletch
Wenxiu Ma
Fan Yang
William S Noble
Christine M Disteche
Xinxian Deng

PLOS Genetics

Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.

2015-03-18

Albert de la Chapelle
John C Byrd

James S Blachly
Amy S Ruppert
Weiqiang Zhao
Susan Long
Joseph Flynn
Ian Flinn
Jeffrey Jones
Kami Maddocks
Leslie Andritsos
Emanuela M Ghia
Laura Z Rassenti
Thomas J Kipps

Proceedings of the National Academy of Sciences of the United States of America

A comparative study of RNA-seq analysis strategies.

2015-03-18

Ernest Turro
Alexandra M. Lewin

Jürgen Jänes
Fengyuan Hu

Briefings in Bioinformatics

Gene expression dosage regulation in an allopolyploid fish

2015-03-19

Maria Manuela Coelho
Manfred Schartl

I Matos
M P Machado

PLOS ONE

The transcriptome of equine peripheral blood mononuclear cells.

2015-03-19

Alicja Pacholewska

Michaela Drögemüller
Jolanta Klukowska-Rötzler
Simone Lanz
Eman Hamza
Emmanouil T Dermitzakis
Eliane Marti
Vincent Gerber
Tosso Leeb
Vidhya Jagannathan

PLOS ONE

Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma.

2015-03-19

Michelle Craig Barton

Melissa M Singh
Blake Johnson
Avinashnarayan Venkatarayan
Elsa R Flores
Jianping Zhang
Xiaoping Su
Frederick Lang
Joya Chandra

Neuro-Oncology

GLI2 inhibition abrogates human leukemia stem cell dormancy.

2015-03-21

John McPherson
Tannishtha Reya

Anil Sadarangani
Gabriel Pineda
Kathleen M Lennon
Hye-Jung Chun
Alice Shih
Annelie E Schairer
Angela C Court
Daniel J Goff
Sacha L Prashad
Ifat Geron
Russell Wall
Richard A Moore
Minya Pu
Lei Bao
Amy Jackson-Fisher
Michael Munchhof
Todd VanArsdale
Sheldon R Morris
Mark D Minden
Karen Messer
Hanna K A Mikkola
Marco A Marra
Thomas J Hudson
Catriona H M Jamieson

Journal of Translational Medicine

Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR.

2015-03-23

Ludwig Christian Hinske
Anamaria Aranha Camargo
Lucila Ohno-Machado

Pedro A F Galante
Elisabeth Limbeck
Patrick Möhnle
Raphael B Parmigiani
Simone Kreth

PLOS ONE

SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.

2015-03-23

Annemieke Aartsma-Rus
Peter A.C. 't Hoen
Jeroen Laros

Irina Pulyakhina
Isabella Gazzoli
Nisha Verwey
Johan T den Dunnen

Nucleic Acids Research

A cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.).

2015-03-24

Hideo Matsumura

Muluneh Tamiru
Jerwin R Undan
Hiroki Takagi
Akira Abe
Kakoto Yoshida
Jesusa Q Undan
Satoshi Natsume
Aiko Uemura
Hiromasa Saitoh
Naoya Urasaki
Takao Yokota
Ryohei Terauchi

Plant Molecular Biology

The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides.

2015-03-25

Victoriano Garre
Simon Moxon

Francisco E Nicolás
Ana Vila
María D Cascales
Santiago Torres-Martínez
Rosa M Ruiz-Vázquez

BMC Genomics

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

2015-03-25

Masahito Yoshihara
Hideya Kawaji
Masayoshi Itoh
Kohji Nishida
Yoshihide Hayashizaki

Hiroko Ohmiya
Susumu Hara
Satoshi Kawasaki
FANTOM consortium
Motokazu Tsujikawa

PLOS ONE

Correction: Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.

2015-03-25

PLOS Pathogens Staff

PLOS Pathogens

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.

2015-03-26

Michael Eisen
Peter A Combs

PeerJ

SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data

2015-03-26

Gunnar Rätsch

Andre Kahles
Cheng Soon Ong
Yi Zhong

Assessing allele-specific expression across multiple tissues from RNA-seq read data

2015-03-27

Tuuli Lappalainen
Matti Pirinen
Mark McCarthy
Peter Donnelly

Noah A Zaitlen
GTEx Consortium
Emmanouil T Dermitzakis
Manuel A Rivas

Bioinformatics

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels

2015-03-27

Cisca Wijmenga
Daria V. Zhernakova
Kristin Abbott
Patrick Deelen
Jingyuan Fu
Marc Jan Bonder
Morris A Swertz

Mark de Haan
Marijke van der Sijde
Juha Karjalainen
K Joeri van der Velde
Richard J Sinke
Lude Franke

Genome Medicine

Folate receptor-α (FOLR1) expression and function in triple negative tumors

2015-03-27

Krishna R Kalari
Karla V Ballman
Zhifu Sun

Brian M Necela
Jennifer A Crozier
Cathy A Andorfer
Laura Lewis-Tuffin
Jennifer M Kachergus
Xochiquetzal J Geiger
Daniel J Serie
Alvaro Moreno-Aspitia
Daniel J O'Shannessy
Julia D Maltzman
Ann E McCullough
Barbara A Pockaj
Heather E Cunliffe
E Aubrey Thompson
Edith A Perez

PLOS ONE

Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer

2015-03-27

Mark Rubin

Dorothee Pflueger
Christiane Mittmann
Silvia Dehler
Holger Moch
Peter Schraml

BMC Genomics

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.

2015-03-28

Yang Pan

Quan Wan
Hayley Dingerdissen
Yu Fan
Naila Gulzar
Tsung-Jung Wu
Cheng Yan
Haichen Zhang
Raja Mazumder

Database

The Listeria monocytogenes strain 10403S BioCyc database.

2015-03-28

Teresa M Bergholz
Kathryn J Boor
Martin Wiedmann

Renato H Orsi

Database

Linear mRNA amplification approach for RNAseq from limited amount of RNA.

2015-03-28

Maria A Nagai
Dirce Carraro
Helena Brentani
Renata Pasqualini

Elisa Napolitano Ferreira
Gustavo de Campos Molina
Renato David Puga
Antônio Hugo José Froes Marques Campos
Gustavo Cardoso Guimarães
Diana Noronha Nunes
Wadih Arap
Emmanuel Dias-Neto
Ricardo R Brentani

Gene

UV irradiation responses in Giardia intestinalis.

2015-03-28

Karin Troell
Staffan G Svärd

Elin Einarsson

Experimental Parasitology

Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter.

2015-03-29

Glenda Halliday
Eleonora Aronica

James D Mills
Jieqiong Chen
Woojin S Kim
Paul D Waters
Avanita S Prabowo
Michael Janitz

Neurogenetics

Assessing the consistency of public human tissue RNA-seq data sets.

2015-03-30

David Gomez-Cabrero
Mikael Huss

Frida Danielsson
Tojo James

Briefings in Bioinformatics

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

2015-04

Toni Gabaldón
Riccardo Aiese Cigliano
Walter Sanseverino
Salvador Capella-Gutierrez
Riccardo Aversano
James M Bradeen
Alessandra Dal Molin

Felice Contaldi
Maria Raffaella Ercolano
Valentina Grosso
Massimo Iorizzo
Filippo Tatino
Luciano Xumerle
Carla Avanzato
Alberto Ferrarini
Massimo Delledonne
Luigi Frusciante
Domenico Carputo

The Plant Cell

Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli.

2015-04-01

Jonathan Kipnis
Tajie H. Harris
Stephen D Turner
Steffen Jung
Igor Smirnov

James C Cronk
Noël C Derecki
Emily Ji
Yang Xu
Aaron E Lampano
Wendy Baker
Geoffrey T Norris
Ioana Marin
Nathan Coddington
Yochai Wolf
Alan Aderem
Alexander L Klibanov
Vladimir Litvak

Immunity

p53 Enables metabolic fitness and self-renewal of nephron progenitor cells

2015-04-01

Melody Baddoo
Yumei Feng

Yuwen Li
Jiao Liu
Wencheng Li
Aaron Brown
Melody Baddoo
Marilyn Li
Thomas Carroll
Leif Oxburgh
Zubaida Saifudeen

Development

A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.

2015-04-03

Ross A. Dickins
Matthew E Ritchie
Geoffrey J. Lindeman
Gordon K Smyth

Julie M Sheridan
Sarah A Best
Kun Jiang
Tamara J Beck
François Vaillant
Kevin Liu
Jane E Visvader

BMC Cancer

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.

2015-04-05

Christina Kendziorski

Ning Leng
Yuan Li
Brian E McIntosh
Bao Kim Nguyen
Bret Duffin
Shulan Tian
James A Thomson
Colin N Dewey
Ron Stewart

Bioinformatics

Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1.

2015-04-06

Stephen L. Nutt
Ellen V. Rothenberg

Ameya Champhekar
Sagar S Damle
George Freedman
Sebastian Carotta

Genes & Development

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

2015-04-06

Alexias Safi
Gregory E Crawford

Christopher L Frank
Fang Liu
Ranjula Wijayatunge
Lingyun Song
Matthew T Biegler
Marty G Yang
Christopher M Vockley
Charles A Gersbach
Anne E West

Nature Neuroscience

The level of residual dispersion variation and the power of differential expression tests for RNA-Seq data

2015-04-07

Gu Mi

Yanming Di

PLOS ONE

The immune signaling pathways of Manduca sexta

2015-04-07

Haobo Jiang

Xiaolong Cao
Yan He
Yingxia Hu
Yang Wang
Yun-Ru Chen
Bart Bryant
Rollie J Clem
Lawrence M Schwartz
Gary Blissard

Insect Biochemistry and Molecular Biology

Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor

2015-04-08

Andrew K. Groves
Huda Zoghbi

Tiantian Cai
Hsin-I Jen
Hyojin Kang
Tiemo J Klisch

Journal of Neuroscience

Genome-wide analysis of the family 1 glycosyltransferases in cotton.

2015-04-08

Juan Huang

Juan Huang
Chaoyou Pang
Shuli Fan
Meizhen Song
Jiwen Yu
Hengling Wei
Qifeng Ma
Libei Li
Chi Zhang
Shuxun Yu

Molecular Genetics and Genomics

Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells.

2015-04-08

Alicia Oshlack
Josephine Bowles
Kathryn S McClelland
Vincent R Harley
Peter Koopman

Katrina Bell
Christian Larney
Andrew H Sinclair

Biology of Reproduction

New basal cell carcinoma susceptibility loci.

2015-04-09

Laufey Tryggvadottir
Unnur Þorsteinsdóttir
Hrefna Johannsdottir
Anne Tjønneland
Gudmar Thorleifsson
Thorunn Rafnar
Y Gilaberte
Hreinn Stefansson
Eduardo Nagore
Rajiv Kumar
Ulla Vogel
Kim Overvad
Augustine Kong
Peter Rudnai
Patrick Sulem
Daniel F Gudbjartsson
Kári Stefánsson

Simon N Stacey
Hannes Helgason
Sigurjon A Gudjonsson
Florian Zink
Asgeir Sigurdsson
Birte Kehr
Julius Gudmundsson
Bardur Sigurgeirsson
Kristrun R Benediktsdottir
Kristin Thorisdottir
Rafn Ragnarsson
Victoria Fuentelsaz
Cristina Corredera
Matilde Grasa
Dolores Planelles
Onofre Sanmartin
Eugene Gurzau
Kvetoslava Koppova
Bjørn A Nexø
Jon G Jonasson
Anna M Kristinsdottir
Gisli Masson
Olafur T Magnusson
Bjarni V Halldorsson
José I Mayordomo
Jon H Olafsson

Nature Communications

New signaling pathways govern the host response to C. albicans infection in various niches.

2015-04-09

Jacques Ravel
Jennifer Schwartz
Amol C Shetty
Claire M. Fraser

Yaoping Liu
L Latey Bradford
Wenjie Xu
Qyunh T Phan
Priti Kumari
Anup Mahurkar
Aaron P Mitchell
Scott G Filler
Vincent M Bruno

Genome Research

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

2015-04-09

Bernhard Payer
David Colognori
Ruslan I Sadreyev

Stefan F Pinter
Brian J Beliveau
Eda Yildirim
Chao-Ting Wu
Jeannie T Lee

Genetics

Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.

2015-04-10

Reinhard Ertl
Fritz Sedlazeck
Regina Hofmann-Lehmann

Milica Krunic
Benedikt Hagen
Arndt von Haeseler
Dieter Klein

BMC Veterinary Research

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.

2015-04-13

Kaia Achim
Daria Gavriouchkina
Luis R. Saraiva
John C Marioni

Jean-Baptiste Pettit
Tomas Larsson
Detlev Arendt

Nature Biotechnology

Spatial reconstruction of single-cell gene expression data.

2015-04-13

Aviv Regev
Rahul Satija
Jeffrey A Farrell

David Gennert
Alexander F Schier

Nature Biotechnology

Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing

2015-04-13

Hodaka Fujii
Daisuke Okuzaki

Toshitsugu Fujita
Miyuki Yuno
Rieko Ohki

PLOS ONE

Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis.

2015-04-13

Erin Osborne
Bob Goldstein

Jay C Zhang
Adam D Werts
Jason D Lieb

PLOS Genetics

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

2015-04-13

Gad Shaulsky

Rafael David Rosengarten
Balaji Santhanam
Danny Fuller
Mariko Katoh-Kurasawa
William F Loomis
Blaz Zupan

BMC Genomics

ChIP-Seq and RNA-Seq analyses identify components of the Wnt and Fgf signaling pathways as Prep1 target genes in mouse embryonic stem cells.

2015-04-13

Miguel Torres
Hans-Jörg Warnatz
Marie-Laure Yaspo

Audrey Laurent
Manuela Calabrese
Marie-Laure Yaspo
Vsevolod Tkachuk
Francesco Blasi
Dmitry Penkov

PLOS ONE

A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii.

2015-04-13

Giel G van Dooren
Stuart A Ralph

Lee M Yeoh
Christopher D Goodman
Nathan E Hall
Geoffrey I McFadden

Nucleic Acids Research

RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress.

2015-04-13

Ahmed Bahieldin

Ahmed Atef
Jamal S M Sabir
Nour O Gadalla
Sherif Edris
Ahmed M Alzohairy
Nezar A Radhwan
Mohammed N Baeshen
Ahmed M Ramadan
Hala F Eissa
Sabah M Hassan
Nabih A Baeshen
Osama Abuzinadah
Magdy A Al-Kordy
Fotouh M El-Domyati
Robert K Jansen

Comptes Rendus Biologies

Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching

2015-04-14

Yonggui Fu
Jie Li

Rui Li
Leiming You
Anlong Xu
Shengfeng Huang

PLOS ONE

NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway.

2015-04-14

Paul Capewell
Isabel Roditi
Alasdair Ivens

Melanie Bühlmann
Pegine Walrad
Eva Rico
Arunasalam Naguleswaran
Keith R Matthews

Nucleic Acids Research

Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes

2015-04-15

Nadia Aubin-Horth
Mahesh Panchal
Iain Barber

Francois Olivier Hebert
Luke Phelps
Irene Samonte
Stephan Grambauer
Martin Kalbe
Christian R Landry

Parasites & Vectors

Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.

2015-04-16

Amanda J Ward
Jimena Giudice

Eric T Wang
Jennifer M Cherone
Thomas T Wang
Daniel J Treacy
Nicole J Lambert
Peter Freese
Tanvi Saxena
Thomas A Cooper
Christopher B Burge

Genome Research

Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast

2015-04-16

Jürg Bähler

Danny A Bitton
Sophie R Atkinson
Charalampos Rallis
Graeme C Smith
David A Ellis
Yuan Y C Chen
Michal Malecki
Sandra Codlin
Jean-François Lemay
Cristina Cotobal
François Bachand
Samuel Marguerat
Juan Mata
Jürg Bähler

Genome Research

SF3B1 association with chromatin determines splicing outcomes.

2015-04-16

Arnab Datta

Nir Kfir
Galit Lev-Maor
Ohad Glaich
Adi Alajem
Siu K Sze
Eran Meshorer
Gil Ast

Cell Reports

First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1.

2015-04-16

Ruth Schmitz-Streit
Dörte Becher

Daniela Prasse
Jens Thomsen
Rebecca De Santis
Jan Muntel

Biochimie

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.

2015-04-17

Sean M. Grimmond
Nicola J Waddell
Anil K Madugundu

Shivashankar H Nagaraj
Scott Wood
Alun Jones
Ramya A Mandyam
Katia Nones
John V Pearson

Journal of Proteome Research

ContextMap 2: fast and accurate context-based RNA-seq mapping

2015-04-17

Ralf Zimmer

Thomas Bonfert
Evelyn Kirner
Gergely Csaba
Caroline C Friedel

BMC Bioinformatics

High throughput profiling of the cotton bollworm Helicoverpa armigera immunotranscriptome during the fungal and bacterial infections

2015-04-18

Haobo Jiang

Guang-Hua Xiong
Long-Sheng Xing
Zhe Lin
Tusar T Saha
Chengshu Wang
Zhen Zou

BMC Genomics

Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection.

2015-04-18

Mark Ziemann

Naghmeh Nejat
David M Cahill
Ganesan Vadamalai
James Rookes
Neda Naderali

Molecular Genetics and Genomics

Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein

2015-04-19

Alain Kohl

Anne-Lie Blomström
Quan Gu
Gerald Barry
Gavin Wilkie
Jessica K Skelton
Margaret Baird
Melanie McFarlane
Esther Schnettler
Richard M Elliott
Massimo Palmarini

BMC Genomics

A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.

2015-04-21

David Murphy

Kory R Johnson
C C T Hindmarch
Yasmmyn D Salinas
YiJun Shi
Michael Greenwood
See Ziau Hoe
Harold Gainer

PLOS ONE

Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells.

2015-04-21

Robert Tjian
Claudia Cattoglio

Elisa T Zhang
Ivan Grubisic
Kunitoshi Chiba
Yick W Fong

Proceedings of the National Academy of Sciences of the United States of America

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.

2015-04-21

Winston Hide
Rory Kirchner

Emmanuel Dimont
Jiantao Shi

Bioinformatics

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.

2015-04-22

Thomas P Mawhinney

Jilong Li
Jie Hou
Lin Sun
Jordan Maximillian Wilkins
Yuan Lu
Chad E Niederhuth
Benjamin Ryan Merideth
Valeri V Mossine
C Michael Greenlief
John C Walker
William R Folk
Mark Hannink
Dennis B Lubahn
James A Birchler
Jianlin Cheng

PLOS ONE

Hepatitis D Virus Infection of Mice Expressing Human Sodium Taurocholate Co-transporting Polypeptide

2015-04-22

Wenhui Li
Jianhua Sui

Wenhui He
Bijie Ren
Fengfeng Mao
Zhiyi Jing
Yunfei Li
Yang Liu
Bo Peng
Huan Yan
Yonghe Qi
Yinyan Sun
Ju-Tao Guo
Fengchao Wang

PLOS Pathogens

Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).

2015-04-22

Chao Zheng

Lei Zhao
Yu Wang
Jiazhi Shen
Yinfei Zhang
Sisi Jia
Yusheng Li
Zhaotang Ding

PLOS ONE

Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease.

2015-04-22

Muredach P. Reilly

Hanrui Zhang
Chenyi Xue
Rhia Shah
Kate Bermingham
Christine C Hinkle
Wenjun Li
Amrith Rodrigues
Jennifer Tabita-Martinez
John S Millar
Marina Cuchel
Evanthia E Pashos
Ying Liu
Ruilan Yan
Wenli Yang
Sager J Gosai
Daniel VanDorn
Stella T Chou
Brian D Gregory
Edward E Morrisey
Mingyao Li
Daniel J Rader

Circulation Research

Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios.

2015-04-22

Ekaterina E Khrameeva
S Zhenilo

S Tsygankova
N Zhigalova
A Mazur
E Prokhortchouk

Gene

ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin

2015-04-23

Deyou Zheng

Jian Chen
Mingyan Lin
Anastasia Hrabovsky
Erika Pedrosa
Jason Dean
Swati Jain
Herbert M Lachman

PLOS ONE

De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development.

2015-04-23

Nikolai Slavov
Harvey Lodish

Juan R Alvarez-Dominguez
Zhiqiang Bai
Dan Xu
Bingbing Yuan
Kinyui Alice Lo
Myeong Jin Yoon
Yen Ching Lim
Marko Knoll
Shuai Chen
Chen Peng
Lei Sun

Cell Metabolism

Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern

2015-04-24

Christoph Bock
Sylvia Knapp
Josef M Penninger
Tomasz Kuliński
Paul Datlinger

M Rita T Casari
Philipp M Guenzl
Daniel Wenzel
Daniel Andergassen
Anastasiya Hladik
Matthias Farlik
H-Christian Theussl
Denise P Barlow
Quanah J Hudson

Developmental Biology

PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development.

2015-04-25

Wout Boerjan
Annegret Kohler

Fabien Baldacci-Cresp
Jihad Moussawi
Jean-Charles Leplé
Rebecca Van Acker
Julie Candiracci
Laure Twyffels
Antanas V Spokevicius
Gerd Bossinger
Françoise Laurans
Nicole Brunel
Marjorie Vermeersch
Mondher El Jaziri
Marie Baucher

The Plant Journal

Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair

2015-04-27

Guo-Li Ming
Hongjun Song
Daniel Geschwind

Huimei Yu
Yijing Su
Jaehoon Shin
Chun Zhong
Junjie U Guo
Yi-Lan Weng
Fuying Gao
Giovanni Coppola

Nature Neuroscience

High-performance probes for light and electron microscopy

2015-04-27

Gerald M. Rubin
Megan E Williams
Erik B. Bloss
Brian P. English

Sarada Viswanathan
Timothy J Stasevich
Colenso M Speer
Aljoscha Nern
Barret D Pfeiffer
Bryan M Hooks
Wei-Ping Li
Teresa Tian
Gilbert L Henry
John J Macklin
Ronak Patel
Charles R Gerfen
Xiaowei Zhuang
Yalin Wang
Loren L Looger

Nature Methods

Polyester: simulating RNA-seq datasets with differential transcript expression.

2015-04-28

Jeffrey T. Leek
Andrew E Jaffe
Ben Langmead

Alyssa C Frazee

Bioinformatics

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription.

2015-04-29

Melody Baddoo
Michael J Strong
Tina O'Grady
Erik K Flemington

Subing Cao
Walter Moss
Monica Concha
Xia Wang
Yi Yu
Melody Baddoo
Kun Zhang
Claire Fewell
Zhen Lin
Yan Dong

Journal of Virology

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.

2015-04-29

Gordon K Smyth

Ruijie Liu
Aliaksei Z Holik
Shian Su
Natasha Jansz
Kelan Chen
Huei San Leong
Marnie E Blewitt
Marie-Liesse Asselin-Labat
Matthew E Ritchie

Nucleic Acids Research

Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?

2015-04-29

Niamh Forde
Thomas E. Spencer
Alfonso Gutierrez-Adan
Gregory W Burns
V Maillo
Peadar Ó Gaora
D Rizos

Urban Besenfelder
Vitezslav Havlicek
Patrick Lonergan

Biology of Reproduction

Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap

2015-05

Thomas Quertermous
Sylvia T Nurnberg
Ivan Carcamo-Oribe
Michelle D Tallquist
Lars Maegdefessel
Ulf Hedin

Karen Cheng
Azad Raiesdana
Ramendra Kundu
Clint L Miller
Juyong B Kim
Komal Arora
Yiqin Xiong
Nikhil Tellakula
Vivek Nanda
Nikitha Murthy
William A Boisvert
Ljubica Perisic
Silvia Aldi
Milos Pjanic
Gary K Owens

PLOS Genetics

Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo.

2015-05-01

Sean D McGrath
Malachi Griffith
Timothy A. Graubert
Catrina Fronick

Cara Lunn Shirai
James N Ley
Brian S White
Sanghyun Kim
Justin Tibbitts
Jin Shao
Matthew Ndonwi
Brian Wadugu
Eric J Duncavage
Theresa Okeyo-Owuor
Tuoen Liu
Vincent Magrini
Robert S Fulton
Michelle O'Laughlin
Matthew J Walter

Cancer Cell

Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer.

2015-05-01

Saurabh Gupta

Pushpinder Bawa
Sajna Zackaria
Mohit Verma
R Srivatsan
Bibha Chaudhary
Subhashini Srinivasan

PLOS ONE

Perturbations of heart development and function in cardiomyocytes from human embryonic stem cells with trisomy 21.

2015-05-01

Stylianos Antonarakis
Outi Hovatta
Laura Sartiani
Marisa Jaconi
Biljana Dumevska

Alexis Bosman
Audrey Letourneau
Martina Del Lungo
Flavio Ronzoni
Rostyslav Kuziakiv
Virpi Tohonen
Marco Zucchelli
Federico Santoni
Michel Guipponi
Outi Hovatta

Stem Cells

Telomere dysfunction drives aberrant hematopoietic differentiation and myelodysplastic syndrome.

2015-05-01

Marianna D'Anca
Matteo Marchesini
Paola Storti
Simona Colla
Marcos Estecio
Nicola Giuliani
Lynda Chin
Hagop Kantarjian
Guillermo Garcia-Manero

Derrick Sek Tong Ong
Yamini Ogoti
Nipun A Mistry
Karen Clise-Dwyer
Sonny A Ang
Andrea Viale
Kathryn Ruisaard
Irene Ganan Gomez
Christopher A Bristow
David C Weksberg
Yan Wing Ho
Baoli Hu
Giannicola Genovese
Piergiorgio Pettazzoni
Asha S Multani
Shan Jiang
Sujun Hua
Michael C Ryan
Alessandro Carugo
Luigi Nezi
Yue Wei
Hui Yang
Li Zhang
Sarah Gaddis
Ting Gong
James W Horner
Timothy P Heffernan
Philip Jones
Laurence J N Cooper
Han Liang
Y Alan Wang
Carlos Bueso-Ramos
Ronald A DePinho

Cancer Cell

regionReport: Interactive reports for region-level and feature-level genomic analyses.

2015-05-01

Leonardo Collado-Torres
Andrew E Jaffe
Jeffrey T. Leek

F1000Research

A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.

2015-05-03

Tomoaki Sakamoto

Daisuke Ikeue
Christian Schudoma
Wenna Zhang
Yoshiyuki Ogata
Tetsuya Kurata
Takeshi Furuhashi
Friedrich Kragler
Koh Aoki

Plant Methods

Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study

2015-05-04

Yuna Blum
Karine Clément

Christine Poitou
Claire Perret
François Mathieu
Vinh Truong
Hervé Durand
Rohia Alili
Nadjim Chelghoum
Véronique Pelloux
Judith Aron-Wisnewsky
Adriana Torcivia
Jean-Luc Bouillot
Brian W Parks
Ewa Ninio
Laurence Tiret

PLOS ONE

The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa.

2015-05-05

Bernard Slippers

Caryn N Oates
Carsten Külheim
Alexander A Myburg
Sanushka Naidoo

Plant and Cell Physiology

Identification of genes involved in the phosphate metabolism in Cryptococcus neoformans.

2015-05-05

Yu Kanesaki

Akio Toh-e
Misako Ohkusu
Hao-Man Li
Kiminori Shimizu
Azusa Takahashi-Nakaguchi
Toru Gonoi
Susumu Kawamoto
Hirofumi Yoshikawa
Masafumi Nishizawa

Fungal Genetics and Biology

MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse

2015-05-07

Gil Omenn

Hong-Dong Li
Yuanfang Guan

Database

Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

2015-05-07

Igor Ulitsky

Hadas Hezroni
David Koppstein
Matthew G Schwartz
Alexandra Avrutin
David P Bartel

Cell Reports

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

2015-05-07

Jeffrey T. Leek
Ben Langmead
Abhinav Nellore

Leonardo Collado-Torres
Andrew E Jaffe
José Alquicira-Hernández
Jacob Pritt
James Morton

Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

2015-05-08

Gustavo Rodriguez-Esteban
Emili Salo
Josep F. Abril

Alejandro González-Sastre
José Ignacio Rojo-Laguna

BMC Genomics

Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep.

2015-05-08

Gwenola Tosser-Klopp
Julio Benavides
Gwenola Tosser-Klopp
Juan J Arranz
Valentín Pérez

Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
Christophe Klopp
Stephen J Keennel

PLOS ONE

Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus.

2015-05-09

Mikhail Matz

Rachel M Wright
Galina V Aglyamova
Eli Meyer

BMC Genomics

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.

2015-05-12

Angelika N Christ
Nicole Cloonan
Sean M. Grimmond

David L A Wood
Katia Nones
Anita Steptoe
Ivon Harliwong
Felicity Newell
Timothy J C Bruxner
David Miller

PLOS ONE

Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.

2015-05-12

Antti Honkela

Karolis Uziela
Antti Honkela

PLOS ONE

Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.

2015-05-13

Christina A Cuomo
Hiten D. Madhani
James J. Becnel

Christopher A Desjardins
Neil D Sanscrainte
Jonathan M Goldberg
David Heiman
Sarah Young
Qiandong Zeng

Nature Communications

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data.

2015-05-14

Frank Emmert-Streib

Ricardo de Matos Simoes
Sabine Dalleau
Kate E Williamson

BMC Systems Biology

GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development.

2015-05-17

Tin-Lap Lee

Alfred Chun-Shui Luk
Huayan Gao
Sizhe Xiao
Jinyue Liao
Daxi Wang
Jiajie Tu
Owen M Rennert
Wai-Yee Chan

Database

Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle.

2015-05-18

Steven G Schroeder
Weizhong Li
Cong-Jun Li

Robert W Li
Sitao Wu

Veterinary Parasitology

Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells

2015-05-18

Stephane Esnault

Keren B Turton
Douglas S Annis
Lixin Rui
Deane F Mosher

PLOS ONE

Genome-wide analysis links NFATC2 with asparaginase hypersensitivity.

2015-05-18

Seth Karol
Laura B Ramsey
Charles G. Mullighan
Ching-Hon Pui
Stephen P Hunger

Christian A Fernandez
Colton Smith
Wenjian Yang
Chunxu Qu
Eric Larsen
W Paul Bowman
Chengcheng Liu
Tamara Chang
Mignon L Loh
Elizabeth A Raetz
Naomi J Winick
William L Carroll
Sima Jeha
William E Evans
Meenakshi Devidas
Mary V Relling

Blood

Chlamydomonas reinhardtii cells adjust the metabolism to maintain viability in response to atrazine stress.

2015-05-19

Marta Esperanza
Marta Seoane
Concepción Herrero
Carmen Rioboo
Ángeles Cid

Aquatic Toxicology

Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis.

2015-05-20

Neil D. Young
Natali Krekeler

Christina D Marth
Lisa Y Glenton
Drew M Noden
Glenn F Browning

Reproduction, Fertility and Development

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

2015-05-21

Q85197310
Florian Buettner
Fabian J. Theis

Laleh Haghverdi

Bioinformatics

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

2015-05-21

Chris Ponting
Caroline Oedekoven
Fernando J Calero-Nieto
Florian Buettner
Iain C Macaulay
David Kent
Fabian J. Theis
Anthony R Green
Berthold Göttgens
Carlos Caldas

Nicola K Wilson
Mona Shehata
Manuel Sánchez Castillo
Evangelia Diamanti
Reiner Schulte
Thierry Voet
John Stingl

Cell Stem Cell

Effects of Tris(1,3-dichloro-2-propyl) Phosphate (TDCPP) in Tetrahymena Thermophila: Targeting the Ribosome.

2015-05-21

John P Giesy

Jing Li
Liqin Yu
Guangyu Li
Chunsheng Liu

Scientific Reports

Alzheimer disease (AD) specific transcription, DNA methylation and splicing in twenty AD associated loci

2015-05-21

Margaret A. Pericak-Vance

Crystal Humphries
Martin A Kohli
Patrice Whitehead
Deborah C Mash
John Gilbert

Molecular and Cellular Neuroscience

TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.

2015-05-24

Julio Rozas
Rafael Zardoya

Etienne Kornobis
Luis Cabellos
Fernando Aguilar
Cristina Frías-López
Jesús Marco

Evolutionary Bioinformatics

RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.

2015-05-25

Masayoshi Kawaguchi

Yoshihiro Handa
Hiroyo Nishide
Naoya Takeda
Yutaka Suzuki
Katsuharu Saito

Plant and Cell Physiology

A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data

2015-05-26

Shaokui Yi

Xiaoke Duan
Xianwu Guo
Weimin Wang

International Journal of Molecular Sciences

Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy

2015-05-26

Christopher DeBoever
Frazer KA

Christian L Barrett
Kristen Jepsen
Cheryl C Saenz
Dennis A Carson

Proceedings of the National Academy of Sciences of the United States of America

nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.

2015-05-27

Gaurav Sablok

Xiaoyan Yan
Gang Feng
Jiaxin Ma
Hongwei Zhao
Xiaoyong Sun

FEBS Letters

Cellular microRNA miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by activating innate antiviral immunity.

2015-05-27

Yuhai Bi

Xiaojuan Jia
Jing Li
Qing Xie
Hanchun Yang
Wenjun Liu

Scientific Reports

Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis

2015-05-28

Q85232174
Irini Pateraki
Fani Chatzopoulou
Albert Ferrer
Alain Tissier
Sotirios Kampranis
Angelos K Kanellis

Dimitra Papaefthimiou
Kathleen Brückner
Ric C H de Vos
Constantinos A Tsoleridis
Dimitra Katsarou
Antigoni Papanikolaou
Eleni Dimitriadou
Stefanos Kostas
David Manzano
Ulschan Scheler
Antonios M Makris

PLOS ONE

Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii

2015-05-28

Leslie M. Hicks

Mahmoud Gargouri
Jeong-Jin Park
F Omar Holguin
Min-Jeong Kim
Hongxia Wang
Rahul R Deshpande
Yair Shachar-Hill
David R Gang

Journal of Experimental Botany

Tracking global gene expression responses in T cell differentiation.

2015-05-28

Vincent Piras
Kumar Selvarajoo

Oriane Simeoni
Masaru Tomita

Gene

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

2015-05-29

Alexias Safi
Gregory E Crawford

Lauren R Polstein
Pablo Perez-Pinera
D Dewran Kocak
Christopher M Vockley
Peggy Bledsoe
Lingyun Song
Timothy E Reddy
Charles A Gersbach

Genome Research

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae

2015-05-30

Isabelle Rosinski-Chupin
Patrick Trieu-Cuot
Philippe Bouloc
Marie-Agnès Dillies
Marie-Frédérique Lartigue

Elisabeth Sauvage
Odile Sismeiro
Adrien Villain
Violette Da Cunha
Marie-Elise Caliot
Philippe Glaser

BMC Genomics

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma

2015-06

Wenchao Sun
Jacques Grill
Michelle Monje
Javad Nazarian
Maryam Fouladi
Cynthia Hawkins

Catherine S Grasso
Yujie Tang
Nathalene Truffaux
Noah E Berlow
Lining Liu
Marie-Anne Debily
Michael J Quist
Lara E Davis
Elaine C Huang
Pamelyn J Woo
Anitha Ponnuswami
Spenser Chen
Tessa B Johung
Mari Kogiso
Yuchen Du
Lin Qi
Yulun Huang
Marianne Hütt-Cabezas
Katherine E Warren
Ludivine Le Dret
Paul S Meltzer
Hua Mao
Martha Quezado
Dannis G van Vuurden
Jinu Abraham
Matthew N Svalina
Nicholas Wang
Marta M Alonso
Eric H Raabe
Esther Hulleman
Paul T Spellman
Xiao-Nan Li
Charles Keller
Ranadip Pal

Nature Medicine

3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments

2015-06-01

Anna Tramontano

Loredana Le Pera
Mariagiovanna Mazzapioda

Bioinformatics

FourCSeq: analysis of 4C sequencing data.

2015-06-01

Yad Ghavi-Helm
Wolfgang Huber
Simon Anders
Eileen E. M. Furlong

Felix A Klein
Tibor Pakozdi

Bioinformatics

FunPat: function-based pattern analysis on RNA-seq time series data.

2015-06-01

Francesca Finotello
Tiziana Sanavia

Barbara Di Camillo

BMC Genomics

Condensin-driven remodelling of X chromosome topology during dosage compensation.

2015-06-01

Rachel Patton McCord

Emily Crane
Qian Bian
Bryan R Lajoie
Bayly S Wheeler
Edward J Ralston
Satoru Uzawa
Job Dekker
Barbara J Meyer

Nature

Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system

2015-06-01

Ross C Hardison
Christapher S Morrissey
Mitchell J Weiss

Deepti Jain
Tejaswini Mishra
Belinda M Giardine
Cheryl A Keller
Susan Magargee
Christine M Dorman
Maria Long

Genomics Data

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

2015-06-01

Matteo Pallocca
Anna Maria D'Erchia
Ernesto Picardi
Raffaele A. Calogero

Mattia D'Antonio
Paolo D'Onorio De Meo
Tiziana Castrignanò
Graziano Pesole

BMC Genomics

Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.

2015-06-01

Gane Ka-Shu Wong
Megan M Augustin

Dan R Ruzicka
Ashutosh K Shukla
Jörg M Augustin
Courtney M Starks
Mark O'Neil-Johnson
Michael R McKain
Bradley S Evans
Matt D Barrett
Ann Smithson
Michael K Deyholos
Patrick P Edger
J Chris Pires
James H Leebens-Mack
David A Mann
Toni M Kutchan

The Plant Journal

Detecting disease genes of non-small lung cancer based on consistently differential interactions.

2015-06-01

Xiaoping Liu
Tao Zeng

Qianqian Shi
William Wang
Luonan Chen

Cancer and Metastasis Reviews

Immune cell profiling to guide therapeutic decisions in rheumatic diseases

2015-06-02

Deepak A Rao
Soumya Raychaudhuri

Joerg Ermann
Nikola C Teslovich
Michael B Brenner

Nature Reviews Rheumatology

RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.

2015-06-03

Carsten T Kuenne
Mario Looso
Thomas Braun

Stefan Guenther
Ting Zhang
Marcus Krueger
Yonggang Zhou
Johnny Kim

Genomics Data

CD24(+) cells fuel rapid tumor growth and display high metastatic capacity

2015-06-04

Derek LeRoith

Ran Rostoker
Sagi Abelson
Inna Genkin
Sarit Ben-Shmuel
Ravi Sachidanandam
Eyal J Scheinman
Keren Bitton-Worms
Zila Shen Orr
Avishay Caspi
Maty Tzukerman

Breast Cancer Research

Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton.

2015-06-05

Ling Min
Longfu Zhu
Daojun Yuan
Xianlong Zhang

Yuanlong Wu
Zancheng Wu
Li Yang
Xiyan Yang
Xiaoping Guo

Scientific Reports

The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.

2015-06-05

Najib El-sayed

Bryan D Fleming
Prabha Chandrasekaran
Laura A L Dillon
Elizabeth Dalby
Rahul Suresh
Arup Sarkar
David M Mosser

Journal of Leukocyte Biology

Scalable microfluidics for single-cell RNA printing and sequencing.

2015-06-06

Dana Pe'er
Peter A Sims

Sayantan Bose
Zhenmao Wan
Ambrose Carr
Abbas H Rizvi
Gregory Vieira
Dana Pe'er

Genome Biology

Flagellin Is Required for Host Cell Invasion and Normal Salmonella Pathogenicity Island 1 Expression by Salmonella enterica Serovar Paratyphi A

2015-06-08

Michael McClelland

Dana Elhadad
Prerak Desai
Galia Rahav
Ohad Gal-Mor

Infection and Immunity

Infiltration of chitin by protein coacervates defines the squid beak mechanical gradient.

2015-06-08

Ali Miserez

YerPeng Tan
Shawn Hoon
Paul A Guerette
Wei Wei
Ali Ghadban
Cai Hao
J Herbert Waite

Nature Chemical Biology

hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function

2015-06-09

Rhonda Bassel-Duby
Tom Maniatis
Junqiang Ye
Lindsey J. Macpherson

Nadine Beetz
Sean O'Keeffe
Juan Carlos Tapia
Weisheng V. Chen
Eric N. Olson

Proceedings of the National Academy of Sciences of the United States of America

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

2015-06-10

Barbara Blasi
Hakim Tafer

Donatella Tesei
Katja Sterflinger

PLOS ONE

Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus.

2015-06-10

Chenghua Li

Haihong Wang
Yina Shao
Weiwei Zhang
Zhimeng Lv
Chunhua Jin

Gene

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates

2015-06-12

Sean C Daugherty

Tracy H Hazen
Amol Shetty
Anup A Mahurkar
Owen White
James B Kaper
David A Rasko

Frontiers in Microbiology

The Impact of Normalization Methods on RNA-Seq Data Analysis.

2015-06-15

Marek Figlerowicz

J Zyprych-Walczak
A Szabelska
L Handschuh
K Górczak
K Klamecka
I Siatkowski

BioMed Research International

Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.

2015-06-15

Norman Sharpless
Nirali M Patel
Vonn Walter

Xiaobei Zhao
Anyou Wang
David A Eberhard
Michele C Hayward
Ashley H Salazar
Heejoon Jo
Matthew G Soloway
Matthew D Wilkerson
Joel S Parker
Xiaoying Yin
Guosheng Zhang
Marni B Siegel
Gary B Rosson
H Shelton Earp
Margaret L Gulley
Karen E Weck
D Neil Hayes
Stergios J Moschos

PLOS ONE

Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves.

2015-06-15

Yi Zheng
Abhaya Dandekar

Ting Wu
Yi Wang
Zhangjun Fei
Kenong Xu
Zhenhai Han
Lailiang Cheng

Plant and Cell Physiology

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.

2015-06-16

Cynthia Sharma

Thorsten Bischler
Hock Siew Tan
Kay Nieselt

Methods

RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.

2015-06-16

Lincoln Stein

Gavin W Wilson

Nucleic Acids Research

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.

2015-06-17

Abhaya Dandekar

Sandeep Chakraborty
Monica Britton
Jill Wegrzyn
Timothy Butterfield
Pedro José Martínez-García
Russell L Reagan
Basuthkar J Rao
Charles A Leslie
Mallikarjuna Aradhaya
David Neale
Keith Woeste

F1000Research

RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation

2015-06-18

Anna V Klepikova
Sergey E. Dmitriev

Maria D Logacheva
Aleksey A Penin

BMC Genomics

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.

2015-06-18

Gane Ka-Shu Wong
Udo Gowik

Ming-Ju Amy Lyu
Steve Kelly
Sarah Covshoff
Julia Mallmann
Peter Westhoff
Julian M Hibberd
Matt Stata
Rowan F Sage
Haorong Lu
Xiaofeng Wei
Xin-Guang Zhu

BMC Evolutionary Biology

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

2015-06-19

Dario Cantu

Abraham Morales-Cruz
Katherine C H Amrine
Barbara Blanco-Ulate
Daniel P Lawrence
Renaud Travadon
Philippe E Rolshausen
Kendra Baumgartner

BMC Genomics

PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome.

2015-06-19

Thomas Preiss
Traude H. Beilharz
David Powell
Ana Traven
Torsten Seemann

Paul F Harrison
Jennifer L Clancy
Peter R Boag

RNA

Benchmarking Transcriptome Quantification Methods for Duplicated Genes in Xenopus laevis.

2015-06-19

Taejoon Kwon

Cytogenetics and Genome Research

RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection.

2015-06-20

Jeff H. Chang

Aymeric Goyer
Launa Hamlin
James M Crosslin
Alex Buchanan

BMC Genomics

Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics.

2015-06-20

Alex K. Shalek

Marc H Wadsworth
Travis K Hughes

Genome Biology

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.

2015-06-22

Bonnie Berger

Sean Simmons
Jian Peng
Jadwiga Bienkowska

Journal of Computational Biology

ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli.

2015-06-22

Eve Syrkin Wurtele
Dan Nettleton

Fengwei Jiang
Chunxia An
Yinli Bao
Xuefeng Zhao
Robert L Jernigan
Andrew Lithio
Ling Li
Lisa K Nolan
Chengping Lu
Ganwu Li

Infection and Immunity

RNA Seq profiling reveals a novel expression pattern of TGF-β target genes in human blood eosinophils.

2015-06-22

Stephane Esnault

Zhong-Jian Shen
Jie Hu
Igor Dozmorov
James S Malter

Immunology Letters

RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.

2015-06-23

Yuan Chen
Liuyang Wang

Zhili Zhou
Huancheng Ma
Kevin Lin
Youjie Zhao
Zhi Xiong
Bin Tian

Evolutionary Bioinformatics

An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination.

2015-06-23

Songnian Hu

Ting Wei
Zilong He
XinYu Tan
Xue Liu
Xiao Yuan
Yingfeng Luo

Biochemical and Biophysical Research Communications

Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective.

2015-06-23

Alicia Poplawski
Federico Marini

Moritz Hess
Tanja Zeller
Johanna Mazur
Harald Binder

Briefings in Bioinformatics

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq.

2015-06-24

Luis Fernando García-Ortega
Octavio Martínez

PLOS ONE

Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.

2015-06-25

Juha Kere
Eeva-Mari Jouhilahti
Sten Linnarsson
Peter Lönnerberg
Tiina Skoog
Shintaro Katayama
Esko Kankuri

H Annika Siitonen
Kristo Nuutila
Mari H Tervaniemi
Jyrki Vuola
Anna Johnsson
Outi Elomaa

BMC Genomics

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

2015-06-25

Benedikt Brors
Danielle Thierry-Mieg
Falk Hertwig
Weihong Xu
Marco Chierici
Lee Lancashire
Richard G Grundy
Heng Luo
Davide Albanese
Martin Peifer
Jean Thierry-Mieg
Jun Wang
Zhiyu Peng
Jo Vandesompele

Wenqian Zhang
Ying Yu
Wenwei Zhang
Jian Wang
Cesare Furlanello
Viswanath Devanarayan
Jie Cheng
Youping Deng
Barbara Hero
Huixiao Hong
Meiwen Jia
Li Li
Simon M Lin
Yuri Nikolsky
André Oberthuer
Tao Qing
Zhenqiang Su
Ruth Volland
Charles Wang
May D Wang
Junmei Ai
Shahab Asgharzadeh
Smadar Avigad
Wenjun Bao
Marina Bessarabova
Murray H Brilliant
Tzu-Ming Chu
Jibin Zhang
Min Max He
Scott Hebbring
Howard L Kaufman
Samir Lababidi
Yan Li
Xin X Lu
Xiwen Ma
Baitang Ning
Rosa Noguera
John H Phan
Frederik Roels
Carolina Rosswog
Susan Shao
Jie Shen
Jessica Theissen
Gian Paolo Tonini
Po-Yen Wu
Wenzhong Xiao
Joshua Xu
Jiekun Xuan
Yong Yang
Zhan Ye
Zirui Dong
Ke K Zhang
Ye Yin
Chen Zhao
Yuanting Zheng
Russell D Wolfinger
Tieliu Shi
Linda H Malkas
Frank Berthold
Weida Tong
Leming Shi
Matthias Fischer

Genome Biology

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

2015-06-25

Eduardo Eyras
Allan B. James
Yamile Marquez
Maria Kalyna
Hugh G. Nimmo
Andrea Barta

Runxuan Zhang
Cristiane P G Calixto
Nikoleta A Tzioutziou
Craig G Simpson
Wenbin Guo
Rob Patro
John W S Brown

New Phytologist

Correction: A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.

2015-06-25

David Murphy

Kory R Johnson
C C T Hindmarch
Yasmmyn D Salinas
YiJun Shi
Michael Greenwood
See Ziau Hoe
Harold Gainer

PLOS ONE

Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy.

2015-06-26

Lalit Patel

Rajesh R Singh
Paari Murugan
Horatiu Voicu
Suk-Young Yoo
Tadeusz Majewski
Meenakshi Mehrotra
Khalida Wani
Nizar Tannir
Jose A Karam
Eric Jonasch
Christopher G Wood
Chad J Creighton
L Jeffrey Medeiros
Russell R Broaddus
Pheroze Tamboli
Keith A Baggerly
Kenneth D Aldape
Bogdan Czerniak
Rajyalakshmi Luthra
Kanishka Sircar

Modern Pathology

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

2015-06-27

Hideya Kawaji
Mathias Uhlén
Nancy Y Yu
Linn Fagerberg
Piero Carninci
Yoshihide Hayashizaki

Björn M Hallström
Fredrik Ponten
Alistair R R Forrest
Fantom Consortium
Carsten O Daub

Nucleic Acids Research

Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.

2015-06-29

Yohei Kirino

Shozo Honda
Phillipe Loher
Megumi Shigematsu
Juan P Palazzo
Ryusuke Suzuki
Issei Imoto
Isidore Rigoutsos

Proceedings of the National Academy of Sciences of the United States of America

Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.

2015-06-29

David Gisselsson
Fredrik Mertens

Charles Walther
Jakob Hofvander
Jenny Nilsson
Linda Magnusson
Henryk A Domanski
Johnbosco Tayebwa
Leona A Doyle
Christopher D M Fletcher

Laboratory Investigation

A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays.

2015-06-30

John D. Storey

David G Robinson
Jean Y Wang

Nucleic Acids Research

Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta

2015-07

Xiaolong Cao
Haobo Jiang

Xiufeng Zhang
Yan He
Ramesh T Gunaratna
Yun-ru Chen
Gary Blissard
Michael R Kanost

Insect Biochemistry and Molecular Biology

Isoform-level brain expression profiling of the spermidine/spermine N1-Acetyltransferase1 (SAT1) gene in major depression and suicide

2015-07

Victoria Arango
Peter L Nagy

Spiro P Pantazatos
Stuart J Andrews
Jane Dunning-Broadbent
Jiuhong Pang
Yung-Yu Huang
J John Mann

Neurobiology of Disease

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

2015-07

Giada Ferrari
Fergal M Waldron
Jewelna Osei-Poku
Elizabeth H Bayne
Ben Longdon
Amy H Buck
Darren J. Obbard

Claire L Webster
Shaun Robertson
Daisy Crowson
Juan F Quintana
Jean-Michel Brouqui
Brian P Lazzaro
Penelope R Haddrill

PLOS Biology

Computational assignment of cell-cycle stage from single-cell transcriptome data.

2015-07-01

Sarah Teichmann
Valentina Proserpio
Kedar N Natarajan
Antonio Scialdone
Florian Buettner
Luis R. Saraiva
Oliver Stegle
John C Marioni

Methods

The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs.

2015-07-01

Christopher Jones
Sandra Cristina Viegas
Cecília Maria Arraiano

Benjamin P Towler
Patricia Apura
Joseph A Waldron
Sarah K Smalley
Sarah F Newbury

RNA Biology

Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx.

2015-07-01

Prachi Jain

Jayalakshmi Nair
Udita Chandola
Vinayak Palve
N R Harsha Vardhan
Ram Bhupal Reddy
Vikram D Kekatpure
Amritha Suresh
Moni Abraham Kuriakose
Binay Panda

Genes & Cancer

Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits.

2015-07-03

Peter Ladurner
Eugene Berezikov

Roberto Arbore
Kiyono Sekii
Christian Beisel
Lukas Schärer

Frontiers in Zoology

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain.

2015-07-03

Catherine Dulac

Julio D Perez
Nimrod D Rubinstein
Daniel E Fernandez
Stephen W Santoro
Leigh A Needleman
Olivia Ho-Shing
John J Choi
Mariela Zirlinger
Shau-Kwaun Chen
Jun S Liu

eLife

"Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest.

2015-07-03

Florent Hube

Claire Francastel

Non-coding RNA

2015-07-06

Tobias Kollmann

Michelle M Lissner
Brandon J Thomas
Kathleen Wee
Ann-Jay Tong
Stephen T Smale

PLOS ONE

Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle.

2015-07-06

Cyriac Kandoth

Sarah W Keenan
Craig A Hill
Leslie T Buck
Daniel E Warren

PLOS ONE

Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans

2015-07-06

Denis Dupuy
Eric Cornes
J Cerón

Montserrat Porta-De-La-Riva
David Aristizábal-Corrales
Ana María Brokate-Llanos
Francisco Javier García-Rodríguez
Iris Ertl
Mònica Díaz
Laura Fontrodona
Kadri Reis
Robert Johnsen
David Baillie
Manuel J Muñoz
Mihail Sarov

RNA

Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.

2015-07-06

Najib El-sayed

Laura A L Dillon
Kwame Okrah
V Keith Hughitt
Rahul Suresh
Yuan Li
Maria Cecilia Fernandes
A Trey Belew
Hector Corrada Bravo
David M Mosser

Nucleic Acids Research

Biphasic components of sarcomatoid clear cell renal cell carcinomas are molecularly similar to each other, but distinct from, non-sarcomatoid renal carcinomas

2015-07-07

Lalit Patel

Kanishka Sircar
Suk-Young Yoo
Tadeusz Majewski
Khalida Wani
Horatiu Voicu
Wandaliz Torres-Garcia
Roel G W Verhaak
Nizar Tannir
Jose A Karam
Eric Jonasch
Christopher G Wood
Pheroze Tamboli
Keith A Baggerly
Kenneth D Aldape
Bogdan Czerniak

The journal of pathology. Clinical research

Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii.

2015-07-07

Sophie Shaw
Howard F. Jenkinson
Angela H Nobbs

L C Dutton
K H Paszkiewicz
R J Silverman
P R Splatt
R J Lamont
M Ramsdale

Molecular Oral Microbiology

Tungsten-induced carcinogenesis in human bronchial epithelial cells.

2015-07-08

Steven Shen
Maria Antonietta Zoroddu
Massimiliano Peana

Freda Laulicht
Jason Brocato
Laura Cartularo
Joshua Vaughan
Feng Wu
Thomas Kluz
Hong Sun
Betul Akgol Oksuz
Serenella Medici
Max Costa

Toxicology and Applied Pharmacology

Impact of feed additives on surface mucosal health and columnaris susceptibility in channel catfish fingerlings, Ictalurus punctatus.

2015-07-08

Eric Peatman
Wilawan Thongda

Honggang Zhao
Chao Li
Benjamin H Beck
Ran Zhang
Wilawan Thongda
D Allen Davis

Fish and Shellfish Immunology

Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics

2015-07-09

Parvathy Venugopal
Bergithe E Oftedal
Zhiqiang Hu
Chaochun Wei
David L. Adelson
Hamish S. Scott

Guangrong Qin
Guangyong Zheng
Xixia Chu
Lu Xie
Milena Babic
Christopher N Hahn
Bing Zhang
Xiaojing Wang
Nan Li

Scientific Reports

Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.

2015-07-10

Chet C. Sherwood

Amy L Bauernfeind
Erik J Soderblom
Meredith E Turner
M Arthur Moseley
John J Ely
Patrick R Hof
Gregory A Wray
Courtney C Babbitt

Genome Biology and Evolution

Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq

2015-07-11

Upasana Shokal
Julio Cesar Castillo
Todd Creasy

Priti Kumari
Amol Shetty
Luke J Tallon
Ioannis Eleftherianos

BMC Genomics

Differential and coherent processing patterns from small RNAs

2015-07-13

Jan Gorodkin
Sachin Pundhir

Scientific Reports

Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.

2015-07-13

Roman Stilling
Feargal J Ryan
Marcus J Claesson
Gerard Clarke
Timothy G. Dinan
John F. Cryan

Alan E Hoban
Fergus Shanahan

Brain, Behavior, and Immunity

Opposing roles of STAT1 and STAT3 in IL-21 function in CD4+ T cells

2015-07-13

Majid Kazemian

Chi-Keung Wan
Allison B Andraski
Rosanne Spolski
Peng Li
Jangsuk Oh
Leigh Samsel
Phillip A Swanson
Dorian B McGavern
Elizabeth P Sampaio
Alexandra F Freeman
Joshua D Milner
Steven M Holland
Warren J Leonard

Proceedings of the National Academy of Sciences of the United States of America

Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.)

2015-07-15

Eric Peatman

Miles Lange
Honggang Zhao
Benjamin H Beck

Tissue Barriers

Leveraging transcript quantification for fast computation of alternative splicing profiles.

2015-07-15

Eduardo Eyras

Gael P Alamancos
Amadís Pagès
Juan L Trincado
Nicolás Bellora

RNA

Correction: De novo Transcriptome Analysis of Portunus trituberculatus Ovary and Testis by RNA-Seq: Identification of Genes Involved in Gonadal Development.

2015-07-15

PLOS ONE staff

PLOS ONE

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

2015-07-16

María José Nueda
Antonio Di Pietro

Sonia Tarazona
Pedro Furió-Tarí
David Turrà
Alberto Ferrer
Ana Conesa

Nucleic Acids Research

Widespread Inducible Transcription Downstream of Human Genes.

2015-07-16

Joan A. Steitz

Anna Vilborg
Maria C Passarelli
Therese A Yario
Kazimierz T Tycowski

Molecular Cell

Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas

2015-07-17

Anne-Lise Børresen-Dale
Surendra Kumar
Vessela Kristensen
Bjørn Naume

Sunniva Stordal Bjørklund
Michael Seiler
Grethe I Grenaker Alnæs
Yao Ming
John Kerrigan
Ravi Sachidanandam
Gyan Bhanot
Shridar Ganesan

BMC Cancer

A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals.

2015-07-17

Emma C. Teeling
Sébastien J. Puechmaille
Michaël Bekaert

Zixia Huang
Aurore Gallot
Nga T Lao
Nicole M Foley
David Jebb

Molecular Ecology Resources

Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.

2015-07-17

Dragana Vuckovic
Sally J. Dawson
Giorgia Girotto
Anne Viljanen
Taina Rantanen
Marina Ciullo
Diego Vozzi
Teresa Nutile
Ginevra Biino
Anu Loukola

Deborah I Scheffer
Anna Morgan
Mariateresa Di Stazio
Maria P Concas
Lisa Nolan
Aileen Bahl
Adrian Davis
David P Corey
Mario Pirastu
Paolo Gasparini

Human Molecular Genetics

Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.

2015-07-17

David M. Irwin

Dong-Dong Wu
Ling-Qun Ye
Yan Li
Yan-Bo Sun
Yi Shao
Chunyan Chen
Zhu Zhu
Li Zhong
Lu Wang
Yong E Zhang
Ya-Ping Zhang

Journal of molecular cell biology

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

2015-07-19

James C Mullikin

Stephen W Hartley

BMC Bioinformatics

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

2015-07-21

Shane G. Poplawski
Lucia Peixoto
Davide Risso
Ted Abel

Mathieu E Wimmer
Terence P Speed
Marcelo A Wood

Nucleic Acids Research

Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.

2015-07-21

Tomasz Kuliński

Daniel Andergassen
Christoph P Dotter
Philipp M Guenzl
Philipp C Bammer
Denise P Barlow
Florian M Pauler
Quanah J Hudson

Nucleic Acids Research

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.

2015-07-23

Mihaela Zavolan
Andreas R Gruber
Foivos Gypas
Alexander Kanitz

Georges Martin

Genome Biology

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.

2015-07-23

Geoffrey J. Barton
Gordon G Simpson
Nicholas Schurch
Christian Cole
Tom Owen-Hughes
Karim Gharbi
Mark Blaxter

Marek Gierliński
Pietà Schofield
Alexander Sherstnev
Vijender Singh
Nicola Wrobel

Bioinformatics

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.

2015-07-23

Oliver H Tam

Ying Jin
Eric Paniagua
Molly Hammell

Bioinformatics

TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer.

2015-07-24

Lingxiang Liu
Jun Li
Leng Han

Paul Roebuck
Lixia Diao
Yuan Yuan
John N Weinstein
Han Liang

Cancer Research

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq.

2015-07-25

Per Qvist
Anto P. Rajkumar
Mette Nyegaard
Ole Mors

Ross Lazarus
Francesco Lescai
Jia Ju
Anders D Børglum
Qibin Li
Jane H Christensen

BMC Genomics

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia.

2015-07-25

Alex Widmer
Nicolas Blavet
Niklaus Zemp
Jos Käfer

H Blavet
A Muyle
R Cegan
C Deschamps
S Mousset
S Aubourg
R Bergero
D Charlesworth
R Hobza
G A B Marais

BMC Genomics

Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.

2015-07-28

Gil Omenn

Hong-Dong Li
Rajasree Menon
Brandon Govindarajoo
Bharat Panwar
Yang Zhang
Yuanfang Guan

Journal of Proteome Research

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

2015-07-30

Siamon Gordon

Kaur Alasoo
Fernando O Martinez
Christine Hale
Fiona Powrie
Gordon Dougan
Subhankar Mukhopadhyay
Daniel J Gaffney

Scientific Reports

Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks

2015-07-31

Anand Swaroop
Kohei Homma
Jizhong Zou
Matthew Brooks

Rossukon Kaewkhaw
Koray Dogan Kaya
Vijender Chaitankar
Mahendra Rao

Stem Cells

DNA hypomethylation-mediated activation of Cancer/Testis Antigen 45 (CT45) genes is associated with disease progression and reduced survival in epithelial ovarian cancer.

2015-08-01

Kunle Odunsi

Wa Zhang
Carter J Barger
Petra A Link
Paulette Mhawech-Fauceglia
Austin Miller
Stacey N Akers
Adam R Karpf

Epigenetics

Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer

2015-08-03

Mathias Uhlén
Linn Fagerberg
William M Gallagher
Karin Jirström

Gillian O'Hurley
Christer Busch
Björn M Hallström
Charlotte Stadler
Anna Tolf
Emma Lundberg
Jochen M Schwenk
Anders Bjartell
Fredrik Pontén

PLOS ONE

2015-08-03

Peter Hemmerich
Reinhard Guthke

Shiva Marthandan
Steffen Priebe
Mario Baumgart
Marco Groth
Alessandro Cellerino
Stephan Diekmann

BioMed Research International

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.

2015-08-03

Tahsin Stefan Barakat
Hendrik Marks
Wouter de Laat
Austin Smith

Hindrik H D Kerstens
Erik Splinter
René A M Dirks
Guido van Mierlo
Onkar Joshi
Shuang-Yin Wang
Tomas Babak
Cornelis A Albers
Tüzer Kalkan
Alice Jouneau
Joost Gribnau
Hendrik G Stunnenberg

Genome Biology

RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress.

2015-08-05

Yongqun He

Wenxiao Liu
Hao Dong
Jing Li
Qixing Ou
Yujin Lv
Xiaolei Wang
Zuoshuang Xiang
Qingmin Wu

Scientific Reports

Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.

2015-08-05

Carl J Schmidt

Liang Sun
Susan J Lamont
Amanda M Cooksey
Fiona McCarthy
Catalina O Tudor
K Vijay-Shanker
Rachael M DeRita
Max Rothschild
Chris Ashwell
Michael E Persia

Cell Stress & Chaperones

RNASeq in C. elegans Following Manganese Exposure.

2015-08-06

Michael Aschner

Nancy L Parmalee
Shahina B Maqbool
Bin Ye
Brent Calder
Aaron B Bowman

Current protocols in toxicology / editorial board, Mahin D. Maines (editor-in-chief) ... [et al.]

Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer

2015-08-07

Majid Kazemian

Min Ren
Jian-Xin Lin
Wei Liao
Rosanne Spolski
Warren J Leonard

Molecular Systems Biology

An RNA-Seq-based reference transcriptome for Citrus.

2015-08-11

Terol J

Francisco Tadeo
Daniel Ventimilla
Manuel Talon

Plant Biotechnology Journal

ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer.

2015-08-11

Laura L. Elo
Panu M Jaakkola

Fatemeh Seyednasrollah
Krista Rantanen

Nucleic Acids Research

Transcriptome profiling of larvae of the marine medaka Oryzias melastigma by Illumina RNA-seq.

2015-08-11

Jae-Seong Lee

Bo-Mi Kim
Beom-Soon Choi
Hui-Soo Kim
Jae-Sung Rhee
Doris W T Au
Rudolf S S Wu
Ik-Young Choi

Marine Genomics

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.

2015-08-12

Jun Fan
Fawaz Ghali
David A. Matthews
Andrew Jones

Shyamasree Saha
Gary Barker
Kate J Heesom
Conrad Bessant

Molecular & Cellular Proteomics

Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.

2015-08-13

Paola Bonfante

Valentina Fiorilli
Marta Vallino
Chiara Biselli
Antonella Faccio
Paolo Bagnaresi

Frontiers in Plant Science

Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype'.

2015-08-14

Ana Conesa

Victoria Morin-Adeline
Kai Mueller
Jan Šlapeta

Veterinary Parasitology

The identification and characterization of novel transcripts from RNA-seq data.

2015-08-17

Stefanie Dimmeler
Tyler Weirick
Shizuka Uchida

Giuseppe Militello
Raphael Müller
David John

Briefings in Bioinformatics

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.

2015-08-18

Andrea Barta
Yamile Marquez
Maria Kalyna
Geoffrey Michael Gadd

John W S Brown
Craig G Simpson

The Plant Cell

The mRNA expression of soluble urokinase plasminogen activator surface receptor in human adipose tissue is positively correlated with body mass index.

2015-08-18

Kok Gan Chan

Hien Fuh Ng
Kin Fah Chin
Yun Fong Ngeow

Genome

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.

2015-08-19

Guo-Li Ming
Hongjun Song
Daniel A Berg
David Nauen

Jaehoon Shin
Yunhua Zhu
Joseph Y Shin
Juan Song
Michael A Bonaguidi
Grigori Enikolopov
Kimberly M Christian

Cell Stem Cell

Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei.

2015-08-19

Ibonne Aydee García Romero
Dolly Montoya Castaño
Silvia Restrepo

Uriel Alonso Hurtado Páez
Fabio Ancizar Aristizábal Gutiérrez

PLOS ONE

Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.

2015-08-19

Dmitry A Ovchinnikov
Deanne M. Taylor
Ernst J. Wolvetang

Yu Hasegawa
Laurence de Torrenté
Jessica C Mar

PLOS Genetics

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

2015-08-19

Mihaela Pertea
Steven Salzberg

Tsung-Cheng Chang
Sungyul Lee
Joshua T Mendell

Genome Research

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.

2015-08-20

Steven E. Brenner
Brenton R. Graveley

Angela N Brooks
Michael O Duff
Gemma May
Li Yang
Mohan Bolisetty
Jane Landolin
Ken Wan
Jeremy Sandler
Benjamin W Booth
Susan E Celniker

Genome Research

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.

2015-08-20

Tim Xiaoming Hu
Ignacio del Valle
Kay Elder
Paul Robson

Paul Blakeley
Norah M E Fogarty
Sissy E Wamaitha
Philip Snell
Leila Christie
Kathy K Niakan

Development

Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.

2015-08-22

Jérôme Gouzy
Pascal Gamas
Corinne Da Silva

Susete Alves-Carvalho
Grégoire Aubert
Sébastien Carrère
Corinne Cruaud
Anne-Lise Brochot
Françoise Jacquin
Anthony Klein
Chantal Martin
Karen Boucherot
Jonathan Kreplak
Sandra Moreau
Patrick Wincker
Judith Burstin

The Plant Journal

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

2015-08-24

Christina Kendziorski

Ning Leng
Li-Fang Chu
Chris Barry
Yuan Li
Jeea Choi
Xiaomao Li
Peng Jiang
Ron M Stewart
James A Thomson

Nature Methods

Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis.

2015-08-24

Po-Jung Huang
Petrus Tang

Kuo-Yang Huang
Fu-Man Ku
Wei-Hung Cheng
Chi-Ching Lee
Lichieh Julie Chu
Chih-Chieh Cheng
Yi-Kai Fang
Hsueh-Hsia Wu

Antimicrobial Agents and Chemotherapy

Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection.

2015-08-25

Jin Kyo Jung

Won Kyong Cho
Sen Lian
Sang-Min Kim
Bo Yoon Seo
Kook-Hyung Kim

PLOS ONE

Identification of miRNAs in Bovine Endometrium through RNAseq and Prediction of Regulated Pathways.

2015-08-25

Soroush Sharbati

S E Palma-Vera
R Einspanier

Reproduction in Domestic Animals

MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.

2015-08-25

Karsten Suhre
Anja M Billing
Anna Halama

Pankaj Kumar
Shahina Hayat
Manish Gupta
Noha A Yousri
Gregory M Smith

BioMed Research International

Fast and accurate approximate inference of transcript expression from RNA-seq data.

2015-08-26

Antti Honkela

James Hensman
Panagiotis Papastamoulis
Peter Glaus
Antti Honkela
Magnus Rattray

Bioinformatics

Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205

2015-08-26

Piergiuseppe De Berardinis

Luciana D'Apice
Valerio Costa
Rossella Sartorius
Maria Trovato
Marianna Aprile

Journal of Immunology Research

Altered Exosomal RNA Profiles in Bronchoalveolar Lavage from Lung Transplants with Acute Rejection

2015-08-26

Aric Gregson
David Sayah

Aki Hoji
Patil Injean
Steven T Poynter
Claudia Briones
Vyacheslav Palchevskiy
S Sam Weigt
Michael Y Shino
Ariss Derhovanessian
Rajan Saggar
David Ross
Abbas Ardehali
Joseph P Lynch
John A Belperio

American Journal of Respiratory and Critical Care Medicine

Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy.

2015-08-26

Natalia Rodríguez-Muela
Shi-Yan Ng
Lee L Rubin
John L. Rinn

Boon Seng Soh
David G Hendrickson
Feodor Price

Cell Stem Cell

RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior

2015-08-27

Ana Conesa
Sven Krappmann
Gerhard H Braus

Henriette Irmer
Sonia Tarazona
Christoph Sasse
Patrick Olbermann
Jürgen Loeffler

BMC Genomics

The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.

2015-08-27

Josep F. Abril
Pedro Martinez

Jonatan L Gabre
Helen Nilsson Sköld
Olga Ortega-Martinez

Marine Genomics

RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226.

2015-08-28

K Ulaganathan

Mettu Madhavi Reddy

Genomics Data

Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators

2015-08-28

Deyou Zheng
Ales Cvekl

Jian Sun
Shira Rockowitz
Daniel Chauss
Ping Wang
Marc Kantorow

Molecular Vision

Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts

2015-09

Brett Trost
Anthony Kusalik

Catherine A Moir
Zoe E Gillespie
Jennifer A Mitchell
Christopher H Eskiw

Royal Society Open Science

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation

2015-09

Jessica A Goodheart
Allen Collins

Adam L Bazinet
Michael P Cummings

Royal Society Open Science

Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes.

2015-09-01

Peter Walker
Julio Rodriguez-Andres
Jean-bernard Duchemin

Prasad N Paradkar
Lee Trinidad

PLOS Pathogens

RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.

2015-09-01

Oliver Berkowitz
James Whelan

Xinhua Zhang
Jaime A Teixeira da Silva
Muhan Zhang
Guohua Ma
Jun Duan

Frontiers in Plant Science

Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia.

2015-09-01

Kristen H Taylor
Stephanie McKay

Md Almamun
Benjamin T Levinson
Annette C van Swaay
Nathan T Johnson
Gerald L Arthur
J Wade Davis

Epigenetics

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

2015-09-02

Aviv Regev
Rahul Satija
Roi Avraham
Alex K. Shalek

Nathan Haseley
Douglas Brown
Cristina Penaranda
Humberto B Jijon
John J Trombetta
Ramnik J Xavier
Deborah T Hung

Cell

RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection

2015-09-02

Claudia Pommerenke

Esther Wilk
Ashutosh K Pandey
Sarah Rebecca Leist
Bastian Hatesuer
Matthias Preusse
Junxi Wang
Klaus Schughart

BMC Genomics

Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

2015-09-02

Wolfgang Sadee

Roshan Mascarenhas
Maciej Pietrzak
Ryan M Smith
Amy Webb
Danxin Wang
Audrey C Papp
Julia K Pinsonneault
Michal Seweryn
Grzegorz Rempala

PLOS ONE

Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss

2015-09-02

Scott M Sternson
Henry FE
Ken Sugino
Tozer A
Branco T

eLife

HiCdat: a fast and easy-to-use Hi-C data analysis tool.

2015-09-03

Ueli Grossniklaus
Stefan Grob
Marc W Schmid

BMC Bioinformatics

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data

2015-09-03

Katharina E. Hayer
Gregory R Grant

Angel Pizarro
Nicholas F Lahens
John B Hogenesch

Bioinformatics

Errors in RNA-Seq quantification affect genes of relevance to human disease.

2015-09-03

Mick Watson

Christelle Robert

Genome Biology

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer.

2015-09-03

Namshin Kim

Byungkuk Min
Sunwha Cho
Jung Sun Park
Yun-Gyeong Lee
Yong-Kook Kang

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

2015-09-04

Frank Emmert-Streib

Yasir Rahmatallah
Galina Glazko

Briefings in Bioinformatics

Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.

2015-09-04

Jun-Jun Liu

Rona N Sturrock
Richard A Sniezko
Holly Williams
Ross Benton
Arezoo Zamany

BMC Genomics

Function and Regulation of Cph2 in Candida albicans.

2015-09-04

Pierre Baldi

Shelley Lane
Pietro Di Lena
Kati Tormanen
Haoping Liu

Eukaryotic Cell

RNA-seq analysis of the whole transcriptome of MDA-MB-231 mammary carcinoma cells exposed to the antimetastatic drug NAMI-A.

2015-09-04

Alberto Pallavicini

Alberta Bergamo
Marco Gerdol
Marianna Lucafò
Chiara Pelillo
Marilena Battaglia
Gianni Sava

Metallomics

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.

2015-09-08

Michael R. Barnes

Zhilong Jia
Xiang Zhang
Naiyang Guan
Xiaochen Bo
Zhigang Luo

PLOS ONE

Systematic identification of factors for provirus silencing in embryonic stem cells

2015-09-09

George Q. Daley
Chadi A El Farran
Yinghui Li
Matthew C. Lorincz

Bin Xia Yang
Hong Chao Guo
Tao Yu
Hai Tong Fang
Hao Fei Wang
Sharon Schlesinger
Yu Fen Samantha Seah
Germaine Yen Lin Goh
Suat Peng Neo
Vinay Tergaonkar
Tit-Meng Lim
Lingyi Chen
Jayantha Gunaratne
James J Collins
Stephen P Goff
Hu Li
Frederic A Bard
Yuin-Han Loh

Cell

Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.

2015-09-11

Aurélie Auguste
S Caburet
Sabine Sarnacki

Laurianne Bessière
Anne-Laure Todeschini
Jaime Prat
Emanuela D'angelo
Pierre De La Grange
Olivier Ariste
Fréderic Lemoine
Bérangère Legois
Charles Sultan
Alain Zider
Louise Galmiche
Nicolas Kalfa
Reiner A Veitia

Human Molecular Genetics

Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain.

2015-09-11

Andreas Knapp
Rolf Daniel

Rong Gao
Dagmar Krysciak
Katrin Petersen
Christian Utpatel
Christel Schmeisser
Sonja Voget
Karl-Erich Jaeger
Wolfgang R Streit

Applied and Environmental Microbiology

The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4(+) T-cells.

2015-09-11

Vanessa A Evans
David Powell
Sharon R. Lewin

Nitasha A Kumar
Karey Cheong
Candida da Fonseca Pereira
Jenny Anderson
Paul U Cameron

Retrovirology

The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent

2015-09-13

Andreas Hildebrandt
Marie-Luise Winz
Sunny Sharma
Yuri Motorin
Mark Helm

Ralf Hauenschild
Lyudmil Tserovski
Katharina Schmid
Kathrin Thüring
Karl-Dieter Entian
Ludivine Wacheul
Denis L J Lafontaine
James Anderson
Juan Alfonzo
Andres Jäschke

Nucleic Acids Research

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.

2015-09-15

Christian Rödelsperger
P Baskaran
Gabriel V. Markov

Christian Rödelsperger
Neel Prabh
Vahan Serobyan
Antje Hirsekorn
Christoph Dieterich

BMC Evolutionary Biology

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq

2015-09-16

Alicia Oshlack
Nadia M Davidson
Craig A. Smith
Andrew H Sinclair

Katie L Ayers
Luke S Lambeth

BMC Genomics

RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH

2015-09-16

Jens Nielsen
Verena Siewers
SungSoo Kim

Eugene Fletcher
Amir Feizi

Microbial Cell Factories

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.

2015-09-17

Estelle Proux-Wéra
Erik Andreasson

Itziar Frades
Kibrom B Abreha
Åsa Lankinen
Erik Alexandersson

Frontiers in Plant Science

Tools and best practices for data processing in allelic expression analysis.

2015-09-17

Tuuli Lappalainen
Pejman Mohammadi

Stephane E Castel
Ami Levy-Moonshine
Eric Banks

Genome Biology

RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs.

2015-09-17

Eric Ochomo
Mariangela Bonnizoni
Guiyun Yan

William Augustine Dunn
Monica Britton
Yaw Afrane
Guofa Zhou
Joshua Hartsel
Ming-Chieh Lee
Jiabao Xu
Andrew Githeko
Joseph Fass

Parasites & Vectors

Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea

2015-09-17

Cassandra G. Extavour

Carrie A Whittle

RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi.

2015-09-17

Louis Bernier

Martha Nigg
Jérôme Laroche
Christian R Landry

In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing

2015-09-18

Alexander Meissner

Carlos A Aguilar
Anna Shcherbina
Darrell O Ricke
Ramona Pop
Christopher T Carrigan
Casey A Gifford
Maria L Urso
Melissa A Kottke

Scientific Reports

Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.

2015-09-21

Jan Provazník
Konrad Schöttner
Rodolphe Poupardin

Jaroslava Korbelová
David Doležel
Dinko Pavlinic
Vladimír Beneš
Vladimír Koštál

BMC Genomics

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

2015-09-21

Sarah Teichmann
Aleksandra A Kolodziejczyk
Florian Buettner

Jason C H Tsang
Yong Yu
Shannon Burke
Cui Wang
Liming Lu
Pentao Liu

Genome Biology

Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.

2015-09-22

Andrey Ptitsyn

Ramzi Temanni
Christelle Bouchard
Peter A V Anderson

PLOS ONE

Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq.

2015-09-22

Qi Chen

Junchao Shi
Xin Li
Xiudeng Zheng
Ying Zhang
Jie Qiao
Fuchou Tang
Yi Tao
Qi Zhou
Enkui Duan

Development

Transcriptome Profiling of Pediatric Core Binding Factor AML.

2015-09-23

George Komatsoulis

Chih-Hao Hsu
Cu Nguyen
Chunhua Yan
Rhonda E Ries
Qing-Rong Chen
Ying Hu
Fabiana Ostronoff
Derek L Stirewalt
George Komatsoulis
Shawn Levy
Daoud Meerzaman
Soheil Meshinchi

PLOS ONE

Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection

2015-09-23

Luis Pedro Coelho
Ana Domingos
Alejandro Cabezas-Cruz

Renato Pinheiro-Silva
Lara Borges
James J Valdés
Virgílio do Rosário
José de la Fuente

Parasites & Vectors

Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.

2015-09-23

Soraya Seedat

Stefanie Malan-Müller
Lorren Fairbairn
Willie M U Daniels
Mahjoubeh Jalali Sefid Dashti
Edward J Oakeley
Marc Altorfer
Martin Kidd
Junaid Gamieldien
Sîan Megan Joanna Hemmings

Metabolic Brain Disease

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.

2015-09-24

David Posada
Rebeca Moreira
Carlos Canchaya

Patricia Pereiro
Antonio Figueras
Beatriz Novoa

BMC Genomics

Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies

2015-09-24

Helen L Wright

Huw B Thomas
Robert J Moots
Steven W Edwards

PLOS ONE

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.).

2015-09-25

RANJEET RANJAN KUMAR
Viswanathan Chinnusamy

Suneha Goswami
Sushil K Sharma
Yugal K Kala
Gyanendra K Rai
Dwijesh C Mishra
Monendra Grover
Gyanendra P Singh
Himanshu Pathak
Anil Rai
Raj D Rai

OMICS: A Journal of Integrative Biology

Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica).

2015-09-29

Heebal Kim

Kelsey Caetano-Anolles
Minseok Seo
Sandra Rodriguez-Zas
Jae-Don Oh
Jae Yong Han
Kichoon Lee
Tae Sub Park
Sangsu Shin
Zhang Jiao Jiao
Mrinmoy Ghosh
Dong Kee Jeong
Seoae Cho
Ki-Duk Song
Hak-Kyo Lee

PLOS ONE

De novo transcriptome profiling of highly purified human lymphocytes primary cells

2015-09-29

Sergio Abrignani
Massimiliano Pagani
Grazisa Rossetti
Ilaria Panzeri

Raoul J P Bonnal
Valeria Ranzani
Alberto Arrigoni
Serena Curti
Paola Gruarin

Scientific Data

Transcriptome Characteristics and X-Chromosome Inactivation Status in Cultured Rat Pluripotent Stem Cells.

2015-09-29

Irina S. Zakharova
Sergey P Medvedev
Fedor Kolpakov
Suren M Zakian
Alexander Karaskov

Evgeniya A Vaskova
Anastasiya E Sorokina
Artem A Nemudryy
Evgeniy A Elisaphenko
Alexander I Shevchenko
Elena A Kizilova
Antonina I Zhelezova
Ivan S Evshin
Ruslan N Sharipov
Julia M Minina
Natalia S Zhdanova
Igor I Khegay
Gennadiy T Sukhikh
Evgeniy A Pokushalov
Valentin V Vlasov
Ludmila N Ivanova

Stem Cells and Development

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification.

2015-10-01

Edward R. Dougherty

Jason Knight
Ivan Ivanov
Karen Triff
Robert Chapkin

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript.

2015-10-01

Tõnu Esko
Carla Giner-Delgado
Marta Puig
Magdalena Gayà-Vidal
David Castellano

Lorena Pantano
David Izquierdo
José Ignacio Lucas-Lledó
Chikashi Terao
Fumihiko Matsuda
Mario Cáceres

PLOS Genetics

SRSF1-Regulated Alternative Splicing in Breast Cancer

2015-10-01

Frédéric H-T Allain
Adrian Robert Krainer
Antoine Cléry

Olga Anczuków
Martin Akerman
Jie Wu
Chen Shen
Nitin H Shirole
Amanda Raimer
Shuying Sun
Mads A Jensen
Yimin Hua

Molecular Cell

Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.

2015-10-01

Carine Van Lint
Benoît Van Driessche
Julie Hanotel
Ian Quigley
Aurore Thelie
Alessandra Pierani
Michael Schubert

Simon Desiderio
Benoit Van Driessche
Anthony Rodari
Mark D Borromeo
Sadia Kricha
François Lahaye
Jenifer Croce
Gustavo Cerda-Moya
Jesús Ordoño Fernandez
Barbara Bolle
Katharine E Lewis
Maike Sander
Jane E Johnson
Christopher R Kintner
Tomas Pieler
Kristine A Henningfeld
Eric J Bellefroid
Claude Van Campenhout

Development

Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone.

2015-10-01

Dharani M Sontam
Peter Tsai

Elwyn C Firth
Mark H Vickers
Justin M O'Sullivan

Physiological Reports

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.

2015-10-01

Aviv Regev
Itay Tirosh

Monika S Kowalczyk
Itay Tirosh
Dirk Heckl
Tata Nageswara Rao
Atray Dixit
Brian J Haas
Rebekka K Schneider
Amy J Wagers
Benjamin L Ebert

Genome Research

Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case.

2015-10-01

Matthew Meyerson
Andrew L. Kung

Birgit Knoechel
Ami Bhatt
Li Pan
Chandra S Pedamallu
Eric Severson
Alejandro Gutierrez
David M Dorfman
Frank C Kuo
Michael Kluk
Patrick Zweidler-McKay
Stephen C Blacklow
Daniel J DeAngelo
Jon C Aster

Cold Spring Harbor molecular case studies

Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity.

2015-10-01

Marcel E. Dinger

Jesper L V Maag
Debabrata Panja
Ida Sporild
Sudarshan Patil
Dominik C Kaczorowski
Clive R Bramham
Karin Wibrand

Frontiers in Neuroscience

BrowserGenome.org: web-based RNA-seq data analysis and visualization.

2015-10-01

Jonathan Schmid-Burgk
Veit Hornung

Nature Methods

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.

2015-10-01

Tim Xiaoming Hu

Paul Blakeley
Norah M E Fogarty
Ignacio Del Valle
Sissy E Wamaitha
Kay Elder
Philip Snell
Leila Christie
Paul Robson
Kathy K Niakan

Development

Functional development of the adult ovine mammary gland--insights from gene expression profiling.

2015-10-05

Amy M Paten
Sam W Peterson
Elizabeth J. Duncan
Peter Dearden

Sarah J Pain
Paul R Kenyon
Hugh T Blair

BMC Genomics

Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.

2015-10-05

Norbert Perrimon

Mary-Lee Dequéant
Delphine Fagegaltier
Yanhui Hu
Kerstin Spirohn
Amanda Simcox
Gregory J Hannon

Proceedings of the National Academy of Sciences of the United States of America

RNA-Seq analysis for indigo biosynthesis pathway genes in Indigofera tinctoria and Polygonum tinctorium.

2015-10-05

Sanjog T Thul

Bijaya K Sarangi
Yoshiko Minami

Genomics Data

Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context.

2015-10-05

Spencer Diamond

Ryan K Shultzaberger
Joseph S Boyd
Ralph J Greenspan
Susan S Golden

Annual Review of Genetics

Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes.

2015-10-05

Dan Nettleton

Andrew Lithio

Journal of Agricultural, Biological, and Environmental Statistics

Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.

2015-10-05

Susan Fanayan
Ling Yen Lee

Julia Fangfei Yan
Hoguen Kim
Seul-Ki Jeong
Hyoung-Joo Lee
Manveen K Sethi
Ronald C Beavis
Hogune Im
Michael P Snyder
Matan Hofree
Trey Ideker
Shiaw-Lin Wu
Young-Ki Paik
William S Hancock

Journal of Proteome Research

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.

2015-10-05

Samuel J Allon

Brian S Cole
Iulia Tapescu
Michael J Mallory
Jinsong Qiu
Robert J Lake
Hua-Ying Fan
Xiang-Dong Fu
Kristen W Lynch

RNA

Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).

2015-10-06

Matthias Heinig

Sebastian Schafer
Kui Miao
Craig C Benson
Stuart A Cook
Norbert Hubner

Current protocols in human genetics / editorial board, Nicholas C, Dracapoli ... [et al.]

Transition from somatic embryo to friable embryogenic callus in cassava: dynamic changes in cellular structure, physiological status, and gene expression profiles.

2015-10-06

Peng Zhang

Qiuxiang Ma
Wenzhi Zhou

Frontiers in Plant Science

Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells.

2015-10-06

Dana Koludrovic
Gabrielle Mengus
Irwin Davidson

Patrick Laurette
Thomas Strub
Céline Keime
Madeleine Le Coz
Sebastien Coassolo
Lionel Larue

PLOS Genetics

Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells

2015-10-06

Vincenzo Cardinale
Guido Carpino
Domenico Alvaro

Tsunekazu Oikawa
Eliane Wauthier
Timothy A Dinh
Sara R Selitsky
Andrea Reyna-Neyra
Ronald Levine
David Klimstra
Eugenio Gaudio
Nancy Carrasco
Praveen Sethupathy
Lola M Reid

Nature Communications

Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy.

2015-10-06

Oyuna S. Kozhevnikova

Darya V Telegina
Elena E Korbolina
Nikita I Ershov
Nataliya G Kolosova

Cell Cycle

A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data.

2015-10-07

Chong Wang

Fangfang Liu
Peng Liu

Journal of Agricultural, Biological, and Environmental Statistics

RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

2015-10-07

Chuming Chen
Larry A. Cogburn
Michel J Duclos

Christopher W Resnyk
Hongzhan Huang
Cathy H Wu
Jean Simon
Elisabeth Le Bihan-Duval

PLOS ONE

The androgen receptor controls expression of the cancer-associated sTn antigen and cell adhesion through induction of ST6GalNAc1 in prostate cancer.

2015-10-07

Daniel Vodák
David J Elliott
Hing Y Leung
Rolf Inge Skotheim

Jennifer Munkley
Sebastian Oltean
Brian T Wilson
Karen E Livermore
Yan Zhou
Eleanor Star
Vasileios I Floros
Bjarne Johannessen
Bridget Knight
Paul McCullagh
John McGrath
Malcolm Crundwell
Craig N Robson
Lorna W Harries
Prabhakar Rajan
Ian G Mills

Oncotarget

The membrane proteome of male gametophyte in Solanum lycopersicum.

2015-10-08

Enrico Schleiff
Arindam Ghatak
Palak Chaturvedi
Wolfram Weckwerth

Puneet Paul
Mario Selymesi
Anida Mesihovic
Klaus-Dieter Scharf
Stefan Simm

Journal of Proteomics

B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data.

2015-10-08

Joel M Guthridge
Judith A. James

Mikhail G Dozmorov
Nicolas Dominguez
Krista Bean
Susan R Macwana
Virginia Roberts
Edmund Glass

Bioinformatics and Biology Insights

Profiling RNA editing in human tissues: towards the inosinome Atlas

2015-10-09

Graziano Pesole
Anna Maria D'Erchia
Ernesto Picardi

Caterina Manzari
Francesca Mastropasqua
Italia Aiello

Scientific Reports

Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin

2015-10-09

Jordan Chang

Yuan Lu
William T Boswell
Mikki Boswell
Kaela L Caballero
Ronald B Walter

Comparative Biochemistry and Physiology C: Toxicology and Pharmacology

Novel RNA variants in colorectal cancers.

2015-10-12

Andreas M Hoff
Torfinn Nome
Ragnhild A. Lothe
Rolf Inge Skotheim

Bjarne Johannessen
Sharmini Alagaratnam
Sen Zhao
Marthe Løvf
Anne C Bakken
Merete Hektoen
Anita Sveen

Oncotarget

A basal stem cell signature identifies aggressive prostate cancer phenotypes.

2015-10-12

Robert Baertsch

Bryan A Smith
Artem Sokolov
Vladislav Uzunangelov
Yulia Newton
Kiley Graim
Colleen Mathis
Donghui Cheng
Joshua M Stuart
Owen N Witte

Proceedings of the National Academy of Sciences of the United States of America

Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.

2015-10-12

David J Waxman

Tisha Melia
Pengying Hao
Feyza Yilmaz

Molecular and Cellular Biology

RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis.

2015-10-12

Avneesh Kumar
Jagdeep Kaur

Sunil Kumar
Shikha Kalra
Baljinder Singh
Kashmir Singh

Functional and Integrative Genomics

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.

2015-10-12

Brian D Lehmann
David C Samuels

Yan Guo
Shilin Zhao
Quanhu Sheng
Mingsheng Guo
Jennifer Pietenpol
Yu Shyr

BioMed Research International

Assessing Transcription Regulatory Elements To Evaluate the Expression Status of Missing Protein Genes on Chromosomes 11 and 19.

2015-10-12

Zhe Ren
Shaohang Xu

Nannan Kong
Yang Zhou
Yamei Deng
Yang Fan
Yue Zhang
Liang Lin
Yan Ren
Quanhui Wang
Jin Zi
Bo Wen
Siqi Liu

Journal of Proteome Research

FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.

2015-10-12

Charles J Vaske
Stephen Benz

Christina Yau
Laurence Meyer
Gary Scott
Brian Egan
Paul Labhart
Nader Pourmand
Christopher C Benz

Breast Cancer Research and Treatment

Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague

2015-10-13

Nikolas M Stasulli
William E. Goldman

Kara R Eichelberger
Paul A Price
Roger D Pechous
Stephanie A Montgomery
Joel S Parker

mBio

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

2015-10-13

Waqas Ahmed Malik
Dan Nettleton
Hans-Peter Piepho

Nina Opitz
Caroline Marcon
Anja Paschold
Andrew Lithio
Ronny Brandt
Frank Hochholdinger

Journal of Experimental Botany

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.

2015-10-13

James M Heather
Benny Chain

Katharine Best
Theres Oakes
John Shawe-Taylor

Scientific Reports

Dynamic association rules for gene expression data analysis

2015-10-14

Wen-Hsiung Li

Shu-Chuan Chen
Tsung-Hsien Tsai
Cheng-Han Chung

BMC Genomics

Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model

2015-10-14

Mukesh Kumar

Ji-Ae Kim
Seul-Ki Park
Chan-Hee Lee
Ok Sarah Shin

Oncotarget

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.

2015-10-14

Jörg Vogel
Lars Barquist

Annual Review of Genetics

RNA-Seq workflow: gene-level exploratory analysis and differential expression.

2015-10-14

Simon Anders
Wolfgang Huber
Michael I Love

Vladislav Kim

F1000Research

Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.

2015-10-16

Peter Redder
Julien Prados

Vanessa Khemici
Patrick Linder

PLOS Genetics

Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes.

2015-10-16

Sabeeha Merchant
Stefan Schmollinger
María Esther Pérez-Pérez
Crysten E Blaby-Haas
Stéphane D Lemaire

Ian K Blaby
Sorel Fitz-Gibbon

The Plant Journal

Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells

2015-10-17

Rebekah M Samsonraj
Drew M Titmarsh
Emily T Camilleri

Ling Ling
Torben Helledie
Ren Jie Chua
Oliver Dreesen
Christian Dombrowski
David A Rider
Mario Galindo
Ian Lee
Wanjin Hong
James H Hui
Victor Nurcombe
Andre J van Wijnen
Simon M Cool

Gene

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment.

2015-10-19

Deyou Zheng

Ping Wang
Mingyan Lin
Erika Pedrosa
Anastasia Hrabovsky
Zheng Zhang
Wenjun Guo
Herbert M Lachman

Molecular Autism

Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq.

2015-10-19

Jennifer L Graham
Rebecca Chalkley
Alastair Droop

Caroline Conway
Preetha Chengot
Catherine Daly
Lisa Ross
Pamela Rabbitts
Lucy F Stead

Oncotarget

Functional analysis of NtMPK2 uncovers its positive role in response to Pseudomonas syringae pv. tomato DC3000 in tobacco.

2015-10-19

Qingyou Xia

Xingtan Zhang
Genhong Wang
Junping Gao
Mengyun Nie
Wenshan Liu

Plant Molecular Biology

Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer.

2015-10-20

Sean D McGrath
Marcel E. Dinger
Elizabeth D. Williams
Gregor Tevz
Jyotsna Batra

Ryan Demeter
Vincent Magrini
Varinder Jeet
Anja Rockstroh
Stephen McPherson
John Lai
Nenad Bartonicek
Jiyuan An
Melanie L Lehman
Colleen C Nelson

Molecular and Cellular Endocrinology

Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes.

2015-10-21

Peter Dearden

Miriam L Sharpe
Gregory Gimenez
Kurt L Krause

BMC Genomics

Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis.

2015-10-21

Karinna Rubio-Peña
Sylvain Foissac
Eric Cornes
J Cerón

Laura Fontrodona
David Aristizábal-Corrales
Silvia Torres
Francisco J García-Rodríguez
Xènia Serrat
David González-Knowles
Montserrat Porta-De-La-Riva

RNA

The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.

2015-10-21

Linn Fagerberg
Mathias Uhlén

Agata Zieba
Evelina Sjöstedt
Matts Olovsson
Björn M Hallström
Linda Oskarsson
Karolina Edlund
Anna Tolf
Fredrik Ponten

OMICS: A Journal of Integrative Biology

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

2015-10-22

Aleksandra A Kolodziejczyk
John C Marioni
Sarah Teichmann
Jong Kyoung Kim

Tomislav Ilicic

Nature Communications

A Diencephalic Dopamine Source Provides Input to the Superior Colliculus, where D1 and D2 Receptors Segregate to Distinct Functional Zones.

2015-10-22

Martha Constantine-Paton
Rory Kirchner
Yasunobu Murata
Sung-Yon Kim

Andrew D Bolton
Andrew Young
Tru Dang
Yuchio Yanagawa

Cell Reports

HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse.

2015-10-23

Jeffrey R Mann
David L. Adelson
Lee H Wong
Hamish S. Scott
Moira O'bryan

Shu Ly Lim
Zhi Peng Qu
R Daniel Kortschak
David M Lawrence
Joel Geoghegan
Anna-Lena Hempfling
Martin Bergmann
Christopher C Goodnow
Christopher J Ormandy
Duangporn Jamsai

PLOS Genetics

Menadione-Induced Oxidative Stress Re-Shapes the Oxylipin Profile of Aspergillus flavus and Its Lifestyle.

2015-10-23

Walter Sanseverino

Marco Zaccaria
Matteo Ludovici
Simona Marianna Sanzani
Antonio Ippolito
Riccardo Aiese Cigliano
Marzia Scarpari
Valeria Scala
Corrado Fanelli
Massimo Reverberi

Toxins

Circularization restores signal recognition particle RNA functionality in Thermoproteus

2015-10-24

L Randau

André Plagens
Michael Daume
Julia Wiegel

eLife

Mapping 3' transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq.

2015-10-26

Petr Kotlík

Silvia Marková
Karolína Filipi
Jeremy B Searle

BMC Genomics

IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival.

2015-10-26

Phillip Dexheimer

Allie K Adams
Lyndsey C Bolanos
Rebekah A Karns
Bruce J Aronow
Kakajan Komurov
Anil G Jegga
Keith A Casper
Yash J Patil
Keith M Wilson
Daniel T Starczynowski
Susanne I Wells

Oncotarget

Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.

2015-10-27

Hao Zhang

Zhixiu Wang
Qinggang Li
Yangzom Chamba
Bo Zhang
Peng Shang
Changxin Wu

PLOS ONE

A Database of microRNA Expression Patterns in Xenopus laevis

2015-10-27

Sara Lopez-Gomollon
Simon Moxon
Tamas Dalmay

Ayisha Ahmed
Nicole J Ward
Camille Viaut
Matthew L Tomlinson
Ilya Patrushev
Michael J Gilchrist
Dario Dotlic
Andrea E Münsterberg
Grant N Wheeler

PLOS ONE

RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.

2015-10-27

Bauke Ylstra
Pieter Wesseling
Jan Koster

Myron G Best
Nik Sol
Irsan Kooi
Jihane Tannous
Bart A Westerman
François Rustenburg
Pepijn Schellen
Heleen Verschueren
Edward Post
Najim Ameziane
Josephine Dorsman
Egbert F Smit
Henk M Verheul
David P Noske
Jaap C Reijneveld
R Jonas A Nilsson
Bakhos A Tannous
Thomas Wurdinger

Cancer Cell

Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.

2015-10-28

Nedeljka N. Rosic
David I Kline
Chon-Kit Kenneth Chan
Sophie Dove
David Edwards
Ove Hoegh-Guldberg

Paulina Kaniewska
Edmund Yew Siang Ling

PLOS ONE

Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

2015-10-28

Igor V Grigoriev
Kazuo Ishii
Yuichi Sakamoto
Kerrie Barry

Hajime Muraguchi
Kiwamu Umezawa
Mai Niikura
Makoto Yoshida
Toshinori Kozaki
Kiyota Sakai
Motoyuki Shimizu
Kiyoshi Nakahori
Cindy Choi
Chew Yee Ngan
Eika Lindquist
Anna Lipzen
Andrew Tritt
Sajeet Haridas
Patricia J Pukkila

PLOS ONE

Sxl-Dependent, tra/tra2-Independent Alternative Splicing of the Drosophila melanogaster X-Linked Gene found in neurons.

2015-10-28

David Sturgill

Xia Sun
Haiwang Yang
Brian Oliver
Leonard Rabinow
Marie-Laure Samson

Transcriptomic analysis of global changes in cytokine expression in mouse spleens following acute Toxoplasma gondii infection.

2015-10-28

Xing-Quan Zhu
Si-Yang Huang
Dong-Hui Zhou

Jun-Jun He
Jun Ma
Hui-Qun Song
Jin-Lei Wang

Parasitology Research

A high-throughput RNA-seq approach to profile transcriptional responses

2015-10-29

Xiaoquan Wen
Francesca Luca
Roger Pique-Regi

G A Moyerbrailean
G O Davis
C T Harvey
D Watza

Scientific Reports

RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species

2015-10-30

Wenqin Wang
Joachim Messing

Wei Zhang
Yongrui Wu
Pal Maliga

PLOS ONE

ccmGDB: a database for cancer cell metabolism genes

2015-10-30

Feixiong Cheng

Pora Kim
Junfei Zhao
Zhongming Zhao

Nucleic Acids Research

The vitamin D-dependent transcriptome of human monocytes.

2015-10-30

Veijo Nurminen
Antonio Neme
Carsten Carlberg

Sabine Seuter

The Journal of Steroid Biochemistry and Molecular Biology

Activation of AhR-mediated toxicity pathway by emerging pollutants polychlorinated diphenyl sulfides.

2015-10-30

John P Giesy
Pu Xia
Rui Zhang
Guanyong Su
Zunyao Wang
Xiaowei Zhang

Junjiang Zhang
Yang Wu
Jie Xia
Jiamin Zhang
Daniel L Villeneuve
Hongxia Yu

Chemosphere

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

2015-10-30

Casey S. Greene

Jeffrey A Thompson
Jie Tan

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

2015-10-30

Casey S. Greene

Jeffrey A Thompson
Jie Tan

Comparative blood transcriptome analysis in idiopathic and LRRK2 G2019S-associated Parkinson's disease.

2015-10-31

Carlos Prieto

Jon Infante
María Sierra
Pascual Sánchez-Juan
Isabel González-Aramburu
Coro Sánchez-Quintana
José Berciano
Onofre Combarros
Jesús Sainz

Neurobiology of Aging

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

2015-11

Silvana Konermann
Eugene Koonin

Sergey Shmakov
Omar O. Abudayyeh
Kira S. Makarova
Yuri I. Wolf
Jonathan S. Gootenberg
Ekaterina Semenova
Leonid Minakhin
Julia Joung
Konstantin Severinov
Feng Zhang

Molecular Cell

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes.

2015-11-01

Mamuka Kvaratskhelia
Stephen H. Hughes

Parmit Kumar Singh
Matthew R Plumb
Andrea L Ferris
James R Iben
Xiaolin Wu
Hind J Fadel
Brian T Luke
Caroline Esnault
Eric M Poeschla
Henry L Levin

Genes & Development

Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions.

2015-11-01

Faraz Khosravi Mardakheh

Angela Paul
Sandra Kümper
Amine Sadok
Hugh Paterson
Afshan Mccarthy
Yinyin Yuan
Christopher J Marshall

Developmental Cell

SOX9 modulates the expression of key transcription factors required for heart valve development.

2015-11-02

Olivia Alder
Pamela A. Hoodless

Victoria C Garside
Rebecca Cullum
Daphne Y Lu
Ryan Vander Werff
Mikhail Bilenky
Yongjun Zhao
Steven J M Jones
Marco A Marra
T Michael Underhill

Development

Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types.

2015-11-02

Juan Bernal

Pilar Gil-Ibañez
Francisco García-García
Joaquín Dopazo
Beatriz Morte

Cerebral Cortex

Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

2015-11-04

Rachael Brust

Benjamin W Okaty
Morgan E Freret
Benjamin D Rood
Morgan L Hennessy
Danielle deBairos
Jun Chul Kim
Melloni N Cook
Susan M Dymecki

Neuron

The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.

2015-11-04

Dragos Scarlet
Reinhard Ertl
Christine Aurich

Ralf Steinborn

PLOS ONE

Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth.

2015-11-05

Bertrand Servin

Agnes Bonnet
Philippe Mulsant
Beatrice Mandon-Pepin

PLOS ONE

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

2015-11-05

Zhikun Zhao
Qichao Yu
Liang Wu
Yong Hou
Karsten Kristiansen
Huanming Yang
Xiuqing Zhang

Xiaolong Zhang
Ling Wang
Bo Li
Guibo Li
Michael Dean
Yanhui Wang
Xinxin Lin
Weijian Rao
Zhanlong Mei
Yang Li
Runze Jiang
Huan Yang
Fuqiang Li
Guoyun Xie
Liqin Xu
Kui Wu
Jie Zhang
Jianghao Chen
Ting Wang
Yingrui Li
Jian Wang
Xun Xu

GigaScience

A multi-omic analysis of human naïve CD4+ T cells.

2015-11-06

Danielle Thierry-Mieg
Tai-Chung Huang
Sneha M Pinto
Jun Zhong
Luigi Marchionni
Jean Thierry-Mieg
Min-Sik Kim

Christopher J Mitchell
Derese Getnet
Srikanth S Manda
Praveen Kumar
Raja Sekhar Nirujogi
Mio Iwasaki
Patrick G Shaw
Xinyan Wu
Raghothama Chaerkady
Arivusudar Marimuthu
Babylakshmi Muthusamy
Nandini A Sahasrabuddhe
Rajesh Raju
Caitlyn Bowman
Ludmila Danilova
Jevon Cutler
Dhanashree S Kelkar
Charles G Drake
T S Keshava Prasad
Peter N Murakami
Alan F Scott
Leming Shi
Rafael Irizarry
Leslie Cope
Yasushi Ishihama
Charles Wang
Harsha Gowda
Akhilesh Pandey

BMC Systems Biology

Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data

2015-11-07

Charles M. Perou

Yi-Juan Hu
Wei Sun
Jung-Ying Tzeng

Journal of the American Statistical Association

Host Transcriptional Profiling at Early and Later Stages of the Compatible Interaction Between Phaseolus vulgaris and Meloidogyne incognita.

2015-11-09

Mário Massayuki Inomoto
Maria Lucia Carneiro Vieira

Luciane Santini
Carla de Freitas Munhoz
Mauro Ferreira Bonfim
Marcelo Mendes Brandão

Phytopathology

RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens

2015-11-09

Jesse D Riordan
Adam J. Dupuy

Nuri A Temiz
Branden S Moriarity
Natalie K Wolf
David A Largaespada
Aaron L Sarver

Genome Research

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

2015-11-09

Albin Sandelin
Timo Lassmann
Bogumil Kaczkowski
Hideya Kawaji
Masayoshi Itoh
Piero Carninci
Yoshihide Hayashizaki
Robin Andersson

Yuji Tanaka
Alistair R R Forrest
FANTOM5 Consortium

Cancer Research

Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways.

2015-11-09

Ruben Boon
Alex van Vliet
Sarah-maria Fendt
Nick van Gastel
Catherine Verfaillie
Peter Carmeliet

Javed K Manesia
Zhuofei Xu
Dorien Broekaert
Guy Eelen
Thomas Vanwelden
Steve Stegen
Alberto Pascual-Montano
Geert Carmeliet
Satish Khurana

Stem Cell Research

STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA.

2015-11-09

Aviv Regev

Andrew Venteicher
Itay Tirosh
Christine Hebert
Leah Escalante
Brian Nahed
Daniel Cahill
William Curry
Robert Martuza
Bradley Bernstein
David Louis
Mario Suva

Neuro-Oncology

A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues.

2015-11-10

Nicolas Bertin

Jocelyn Y H Choy
Priscilla L S Boon
Melissa J Fullwood

Scientific Data

An effective analytic method for detecting tissue-specific genes in RNA-seq experiments.

2015-11-10

Xiaohua Douglas Zhang

Guoqing Zhao
Qiao Li
I-Ming Wang
Xiaoqiao Liu
Xiangzhong Fang

Pharmacogenomics

Cancer genetics: RNA-seq for blood-based pan-cancer diagnostics.

2015-11-10

Liesbet Lieben

Nature Reviews Genetics

REST-Governed Gene Expression Profiling in a Neuronal Cell Model Reveals Novel Direct and Indirect Processes of Repression and Up-Regulation.

2015-11-10

Davide Cittaro

Jose M Garcia-Manteiga
Silvia Bonfiglio
Lucrezia Folladori
Maria L Malosio
Dejan Lazarevic
Elia Stupka
Jacopo Meldolesi

Frontiers in Cellular Neuroscience

Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.

2015-11-11

Joseph A. Sisneros

Joshua Faber-Hammond
Manoj P Samanta
Elizabeth A Whitchurch
Dustin Manning
Allison B Coffin

PLOS ONE

A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins

2015-11-11

Andreas Gogol-Döring

Catrin Stutika
Laura Botschen
Mario Mietzsch
Stefan Weger
Mirjam Feldkamp
Wei Chen
Regine Heilbronn

Journal of Virology

Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties.

2015-11-11

Ludovico Dreni
Massimo Galbiati
Lucia Colombo
Martin M. Kater

Nahuel González-Schain
Lovely M F Lawas
Sigrid Heuer
Krishna S V Jagadish

Plant and Cell Physiology

RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium

2015-11-12

Shabarinath Srikumar
Siân V Owen
Carsten Kröger
Karsten Hokamp

Magali Hébrard
Aoife Colgan
Sathesh K Sivasankaran
Andrew D S Cameron
Jay C D Hinton

PLOS Pathogens

Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration.

2015-11-13

Luke A. Wiley
Budd A. Tucker
Todd E. Scheetz
Robert F. Mullins
Elliott H Sohn
Edwin M. Stone

Shemin Zeng
S Scott Whitmore
Megan J Riker

The Journal of Pathology

Diagnosis: RNA-seq for blood-based pan-cancer diagnostics.

2015-11-13

Liesbet Lieben

Nature Reviews Cancer

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis

2015-11-14

Gareth D Weedall

Helen Irving
Margaret A Hughes
Charles S Wondji

BMC Genomics

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

2015-11-16

Marc K. Halushka

Alexander S Baras
Christopher J Mitchell
Jason R Myers
Simone Gupta
Lien-Chun Weng
John M Ashton
Toby C Cornish
Akhilesh Pandey

PLOS ONE

Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.

2015-11-16

Peter Dervan

Amanda E Hargrove
Thomas F Martinez
Alissa A Hare
Alexis A Kurmis
John W Phillips
Sudha Sud
Kenneth J Pienta

PLOS ONE

Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.

2015-11-16

Vitaly Citovsky

Elena García-Cano
Shimpei Magori
Qi Sun
Zehong Ding
Sondra G Lazarowitz

PLOS ONE

High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells

2015-11-16

Mathias Müller

Priyank Shukla
Claus Vogl
Barbara Wallner
Doris Rigler
Sabine Macho-Maschler

BMC Genomics

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

2015-11-17

Buket Baddal
Raffaele A. Calogero

Alessandro Muzzi
Stefano Censini
Giulia Torricelli
Silvia Guidotti
Anna R Taddei
Antonello Covacci
Mariagrazia Pizza
Rino Rappuoli
Marco Soriani
Alfredo Pezzicoli

mBio

RNA-seq is a valuable complement of conventional diagnostic tools in newly diagnosed AML patients

2015-11-17

Vera Magistroni
Carlo Gambacorti-Passerini

Rocco Piazza
Caterina Cecchetti
Alessandra Pirola
Carla Donandoni
Diletta Fontana
Caterina Mezzatesta
Benedetta Bianchi
Lorenza Borin
Monica Fumagalli

American Journal of Hematology

Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq.

2015-11-18

Wannes Dermauw
Thomas Van Leeuwen
Ralf Nauen
Luc Tirry

Sabina Bajda
Robert Greenhalgh
Richard M Clark

BMC Genomics

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome

2015-11-18

Mick Watson
Ronan Kapetanovic
Dario Beraldi
Alan Archibald
David A Hume

Christelle Robert

BMC Genomics

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity

2015-11-18

Aviv Regev
Chuan Wu
Gerd Meyer zu Hörste

Chao Wang
Nir Yosef
Jellert Gaublomme
Youjin Lee
Clary B Clish
Jim Kaminski
Sheng Xiao
Mathias Pawlak
Yasuhiro Kishi
Nicole Joller
Katarzyna Karwacz
Chen Zhu
Maria Ordovas-Montanes
Asaf Madi
Ivo Wortman
Toru Miyazaki
Raymond A Sobel
Hongkun Park
Vijay K Kuchroo

Cell

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

2015-11-18

Pier Paolo Pandolfi
Aviv Regev
Rahul Satija
Chuan Wu
Alex K. Shalek
Li V. Yang

Jellert T Gaublomme
Nir Yosef
Youjin Lee
Rona S Gertner
Tak Mak
Vijay K Kuchroo
Hongkun Park

Cell

A Three-Dimensional Cell Culture Model To Study Enterovirus Infection of Polarized Intestinal Epithelial Cells.

2015-11-18

Carolyn Coyne

Coyne G Drummond
Cheryl A Nickerson

mSphere

Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force.

2015-11-22

Joanna Nowak
Katarzyna Połtowicz
Artur Gurgul
Katarzyna Ropka-Molik
Katarzyna Piórkowska

K Żukowski

Animal Genetics

Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly.

2015-11-23

Peter A. Bain
Alexie Papanicolaou

Anupama Kumar

PLOS ONE

Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.

2015-11-23

Romain Lavaud
Jonathan Flye-Sainte-Marie
Fred Jean
Vianney Pichereau
Melody S Clark

Sébastien Artigaud
Joëlle Richard
Michael A S Thorne
Lloyd S Peck

BMC Genomics

RNA-Seq and Mass-Spectrometry-Based Lipidomics Reveal Extensive Changes of Glycerolipid Pathways in Brown Adipose Tissue in Response to Cold.

2015-11-24

Susanne Mandrup

Ann-Britt Marcher
Anne Loft
Ronni Nielsen
Terhi Vihervaara
Jesper Grud Skat Madsen
Marko Sysi-Aho
Kim Ekroos

Cell Reports

Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.

2015-11-25

Zofia Szweykowska-Kulinska

Ge Qu
Katarzyna Kruszka
Patrycja Plewka
Shu-Yi Yang
Tzyy-Jen Chiou
Artur Jarmolowski
Manuel Echeverria
Wojciech M Karlowski

BMC Genomics

Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum.

2015-11-25

Evelien M. Bunnik

Xueqing Maggie Lu
Neeti Pokhriyal
Sara Nasseri
Stefano Lonardi
Karine G Le Roch

BMC Genomics

Different mechanisms of resistance modulate sulfite tolerance in wine yeasts.

2015-11-28

Chiara Nadai
Alessio Giacomini
Viviana Corich
Laura Treu
Stefano Campanaro

Applied Microbiology and Biotechnology

Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome

2015-12

Nina Papavasiliou
Monica Mugnier
Erik W. Debler

Danae Schulz
Eda-Margaret Paulsen
Hee-Sook Kim
Chun-wa W Chung
David F Tough
Inmaculada Rioja
Rab K Prinjha
F Nina Papavasiliou

PLOS Biology

mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis)

2015-12-01

Herman Silva

Jorge E Aedo
Jonathan Maldonado
Víctor Aballai
Juan M Estrada
Macarena Bastias-Molina
Claudio Meneses
Cristian Gallardo-Escarate
Alfredo Molina
Juan A Valdés

BMC Genomics

Ig Superfamily Ligand and Receptor Pairs Expressed in Synaptic Partners in Drosophila.

2015-12-01

Liming Tan
Kelvin Xi Zhang
Matthew Y Pecot
Sonal Nagarkar-Jaiswal
Pei-Tseng Lee
Shin-ya Takemura
Jason M McEwen
Aljoscha Nern
Shuwa Xu
Wael Tadros
Zhenqing Chen
Kai Zinn
Hugo J. Bellen
Marta Morey
S Lawrence Zipursky

Cell

Exposure to sixty minutes of hyperoxia upregulates myocardial humanins in patients with coronary artery disease - a pilot study.

2015-12-01

Joel Starkopf

I Karu
P Tahepold
A Ruusalepp
E Reimann
S Koks

Journal of Physiology and Pharmacology

Nitro-Fatty Acids in Plant Signaling: Nitro-Linolenic Acid Induces the Molecular Chaperone Network in Arabidopsis.

2015-12-01

Francisco J. Corpas

Capilla Mata-Pérez
Beatriz Sánchez-Calvo
María N Padilla
Juan C Begara-Morales
Francisco Luque
Manuel Melguizo
Jaime Jiménez-Ruiz
Jesús Fierro-Risco
Antonio Peñas-Sanjuán
Raquel Valderrama
Juan B Barroso

Plant Physiology

Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression

2015-12-02

Konrad Förstner
Thomas A Kohl

Ebrahim M. Abda
Dagmar Krysciak
Ines Krohn-Molt
Uwe Mamat
Christel Schmeisser
Ulrich E. Schaible
Stefan Nieman
Wolfgang R. Streit

Frontiers in Microbiology

Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress.

2015-12-04

Maria Manuela Coelho
Ana R. Grosso

Tiago Filipe Jesus
Vera Maria Fonseca Almeida-Val

Journal of Thermal Biology

The Schistosome Esophagus Is a 'Hotspot' for Microexon and Lysosomal Hydrolase Gene Expression: Implications for Blood Processing

2015-12-07

Leandro Xavier Neves
Leonardo P Farias
Sandy J Macdonald
Ricardo DeMarco

R Alan Wilson
Xiao Hong Li
Juliana Vitoriano-Souza
Luciana C C Leite
Sally James
Peter D Ashton
William Castro Borges

PLOS Neglected Tropical Diseases

Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives

2015-12-08

Wen-Hsiung Li

Ping Wu
Chen Siang Ng
Jie Yan
Yung-Chih Lai
Chih-Kuan Chen
Yu-Ting Lai
Siao-Man Wu
Jiun-Jie Chen
Weiqi Luo
Randall B Widelitz
Cheng-Ming Chuong

Proceedings of the National Academy of Sciences of the United States of America

Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs

2015-12-08

Antony M Jose

Andrew L Blumenfeld

RNA

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

2015-12-08

Shaun Jackman

René L Warren
Ewan A Gibb
Benjamin P Vandervalk
Hamid Mohamadi
Justin Chu
Anthony Raymond
Stephen Pleasance
Robin Coope
Mark R Wildung
Carol E Ritland
Jean Bousquet
Steven J M Jones
Joerg Bohlmann
Inanç Birol

Genome Biology and Evolution

RNAseq analysis for the diagnosis of muscular dystrophy.

2015-12-08

Michael D. Wilson
Cynthia Hawkins

Hernan Gonorazky
Minggao Liang
Beryl Cummings
Monkol Lek
Johann Micallef
Raveen Basran
Ronald Cohn
Daniel MacArthur
Christian R Marshall
Peter N Ray
James J Dowling

Annals of clinical and translational neurology

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.

2015-12-09

Aleksandra A Miranda-CasoLuengo
Kévin Rue-Albrecht
Brendan Loftus
David E. MacHugh
A Aulicino

Adam M Dinan
John A Browne

BMC Genomics

Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis

2015-12-09

David H Hall

Juan Wang
Rachel Kaletsky
Malan Silva
April Williams
Leonard A Haas
Rebecca J Androwski
Jessica N Landis
Cory Patrick
Alina Rashid
Dianaliz Santiago-Martinez
Maria Gravato-Nobre
Jonathan Hodgkin
Coleen T Murphy
Maureen M Barr

Current Biology

RNA-seq reveals post-transcriptional regulation of Drosophila insulin-like peptide dilp8 and the neuropeptide-like precursor Nplp2 by the exoribonuclease Pacman/XRN1.

2015-12-09

Christopher Jones

Amy L Pashler
Benjamin P Towler
Sophie R Robinson
Sarah F Newbury

Nucleic Acids Research

Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach.

2015-12-09

Christiane Hertz-Fowler
David A. Matthews
Julian Hiscox
John Barr
John G Kenny

Waleed Aljabr
Olivier Touzelet
Georgios Pollakis
Weining Wu
Diane C Munday
Margaret Hughes
Rachel Fearns

Journal of Virology

Transcriptome profiling of human FoxP3+ regulatory T cells

2015-12-10

Cuong K. Nguyen

Ravikiran Bhairavabhotla
Yong C Kim
Deborah D Glass
Thelma M Escobar
Mira C Patel
Rami Zahr
Gokhul K Kilaru
Stefan A Muljo
Ethan M Shevach

Human Immunology

Rapamycin reduces fibroblast proliferation without causing quiescence and induces STAT5A/B-mediated cytokine production.

2015-12-10

Anthony Kusalik

Zoe E Gillespie
Kimberly MacKay
Michelle Sander
Brett Trost
Wojciech Dawicki
Aruna Wickramarathna
John Gordon
Mark Eramian
Ian R Kill
Joanna M Bridger
Jennifer A Mitchell
Christopher H Eskiw

Nucleus

RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits.

2015-12-10

Lucas B Carey

eLife

Comparative transcriptome analysis reveals molecular strategies of oriental river prawn Macrobrachium nipponense in response to acute and chronic nitrite stress.

2015-12-11

Jian G. Qin

Zhixin Xu
Tongyu Li
Erchao Li
Ke Chen
Zhili Ding
Liqiao Chen
Jinyun Ye

Fish and Shellfish Immunology

Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection.

2015-12-13

Shikai Liu

Lin Song
Chao Li
Yangjie Xie
Jiaren Zhang
Jun Yao
Chen Jiang
Yun Li
Zhanjiang Liu

Fish and Shellfish Immunology

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.

2015-12-14

Daniel J Gaffney

Natsuhiko Kumasaka
Andrew J Knights

Nature Genetics

Comparative Transcriptome Analysis in the Hepatopancreas Tissue of Pacific White Shrimp Litopenaeus vannamei Fed Different Lipid Sources at Low Salinity.

2015-12-15

Jian G. Qin

Ke Chen
Erchao Li
Zhixin Xu
Tongyu Li
Chang Xu
Liqiao Chen

PLOS ONE

ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing in vivo

2015-12-15

Mark R Cookson

Allissa A Dillman
Dagmar Galter

RNA Biology

Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.

2015-12-15

Laure Bally-Cuif
Chirag Nepal
Yavor Hadzhiev
Marion Coolen
Jesper B. Andersen
Boris Lenhard
Piero Carninci

Delphine Cussigh
Piotr Mydel
Vidar M Steen
Ferenc Müller

Nucleic Acids Research

A human haploid gene trap collection to study lncRNAs with unusual RNA biology

2015-12-15

Irena Vlatkovic

Aleksandra E Kornienko
Jürgen Neesen
Denise P Barlow
Florian M Pauler

RNA Biology

Adeno-associated virus gene therapy vector scAAVIGF-I for transduction of equine articular chondrocytes and RNA-seq analysis.

2015-12-16

Richard Slayden

D D Hemphill
C W McIlwraith
R J Samulski
L R Goodrich

Osteoarthritis and Cartilage

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.

2015-12-16

Antonio Scialdone
Luis R. Saraiva
Darren W. Logan
John C Marioni

Ximena Ibarra-Soria
Mona Khan
Masayo Omura
Peter Mombaerts

Scientific Reports

Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression

2015-12-16

Guo-Li Ming
Hongjun Song
Jun Wan

Yaxue Zeng
Bing Yao
Jaehoon Shin
Li Lin
Namshik Kim
Qifeng Song
Shuang Liu
Yijing Su
Junjie U Guo
Luoxiu Huang
Hao Wu
Jiang Qian
Xiaodong Cheng
Heng Zhu
Peng Jin

Molecular Cell

Ectopic expression of TAPETUM DETERMINANT1 affects ovule development in Arabidopsis.

2015-12-17

Chong Tang

Jian Huang
Asela J Wijeratne
Tianyu Zhang
Rebecca E Fenelon
Heather A Owen
Dazhong Zhao

Journal of Experimental Botany

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing

2015-12-18

Gwenola Tosser-Klopp
Beatriz Gutierrez-Gil
Gwenola Tosser-Klopp
Juan J Arranz

Aroa Suárez-Vega
Christophe Klopp
Christèle Robert-Granie

Scientific Reports

Canonical pathways, networks and transcriptional factor regulation by clinical strains of Mycobacterium tuberculosis in pulmonary alveolar epithelial cells.

2015-12-18

William Bishai
Manormoney Pillay

Nontobeko E Mvubu
Balakrishna Pillay
Junaid Gamieldien

Tuberculosis

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes

2015-12-21

Sten Linnarsson

János Fuzik
Amit Zeisel
Zoltán Máté
Daniela Calvigioni
Yuchio Yanagawa
Gábor Szabó
Tibor Harkany

Nature Biotechnology

Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types

2015-12-21

Christoph Bock
Johanna Klughammer
Ekaterine Berishvili
Andreas Spittler

Jin Li
Matthias Farlik
Thomas Penz
Charlotte Barbieux
Stefan Kubicek

EMBO Reports

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

2015-12-22

Svante Pääbo
Farhath Badsha
Barbara Treutlein
Madeline Lancaster
Juergen A Knoblich
Marta Florio

J Gray Camp
Sabina Kanton
Tobias Gerber
Michaela Wilsch-Bräuninger
Eric Lewitus
Alex Sykes
Wulf Hevers
Robert Lachmann
Wieland B Huttner

Proceedings of the National Academy of Sciences of the United States of America

Meta-analysis of RNA-seq expression data across species, tissues and studies.

2015-12-22

Peter H Sudmant

Maria S Alexis
Christopher B Burge

Genome Biology

RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway.

2015-12-22

Elizabeth S. Haswell

Darron R Luesse
Margaret E Wilson

Frontiers in Plant Science

Multidimensional Genome-wide Analyses Show Accurate FVIII Integration by ZFN in Primary Human Cells

2015-12-22

Ajit Johnson Nirmal
Jaichandran Sivalingam
Sebastian Maurer-Stroh

Dimitar Kenanov
Hao Han
Wai Har Ng
Sze Sing Lee
Jeyakumar Masilamani
Toan Thang Phan
Oi Lian Kon

Molecular Therapy

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

2015-12-23

Jeremy Chien
Wei Zhang
Baolin Wu

Jae-Woong Chang
Lilong Lin
Kay Minn
Jeongsik Yong
Hui Zheng
Rui Kuang

PLOS Computational Biology

Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.).

2015-12-23

Marcio Gilberto Cardoso Costa

Andresa Muniz Pedrosa
Cristina de Paula Santos Martins
Luana Pereira Gonçalves

PLOS ONE

Elimination of Chromosomal Island SpyCIM1 from Streptococcus pyogenes Strain SF370 Reverses the Mutator Phenotype and Alters Global Transcription

2015-12-23

Scott V Nguyen

Christina Hendrickson
Chad W Euler
Maliha Rahman
Kimberly A McCullor
Catherine J King
Vincent A Fischetti
W Michael McShan

PLOS ONE

Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting

2015-12-23

Tzumin Lee
Ching-po Yang
Chi-Cheng Fu
Ken Sugino
Zhiyong Liu
Qingzhong Ren
Ling-Yu Liu
Xiaohao Yao
Luke P Lee

Development

WheatExp: an RNA-seq expression database for polyploid wheat.

2015-12-24

Jorge Dubcovsky

Stephen Pearce
Hans Vazquez-Gross
Sayer Y Herin
David Hane
Yi Wang
Yong Q Gu

BMC Plant Biology

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.

2015-12-28

Miguel Beato del Rosal
Marc A. Martí‐Renom

Gireesh K Bogu
Pedro Vizán
Lawrence W Stanton
Luciano Di Croce

Molecular and Cellular Biology

Anti-inflammatory therapies of amyotrophic lateral sclerosis guided by immune pathways

2015-12-28

Matteo Pellegrini

Larry Lam
Ramesh C Halder
Dennis J Montoya
Liudmilla Rubbi
Arturo Rinaldi
Bien Sagong
Sarah Weitzman
Rachel Rubattino
Ram Raj Singh
Milan Fiala

American journal of neurodegenerative disease

Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions.

2015-12-29

Héctor Corrada Bravo
Najib El-sayed

Laura A L Dillon
Rahul Suresh
Kwame Okrah
David M Mosser

BMC Genomics

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.

2015-12-30

Mark D. Robinson
Michael I Love

Charlotte Soneson

F1000Research

Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq

2015-12-31

Ricardo DeMarco
Joao Carlos Setubal
Sergio Verjovski-Almeida

Letícia Anderson
Murilo S Amaral
Felipe Beckedorff
Lucas F Silva
Bianca Dazzani
Katia C Oliveira
Giulliana T Almeida
Monete R Gomes
David S Pires

PLOS Neglected Tropical Diseases

Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders

2016

Graham Plastow
Tim A. McAllister

Ou Wang
Guanxiang Liang
Kim Stanford
Brent Selinger
Le Luo Guan

PLOS ONE

A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq

2016

Eric J. Nestler

Tianyuan Wang
Janine H Santos
Jian Feng
David C Fargo
Li Shen
Gonzalo Riadi
Elizabeth Keeley
Zachary S Rosh
Richard P Woychik

PLOS ONE

Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay

2016

Syed A. Hashsham
Hui Li
James Tiedje

Benli Chai
Tamara V Tsoi
Shoko Iwai
Cun Liu
Jordan A Fish
Cheng Gu
Timothy A Johnson
Gerben Zylstra
Brian J Teppen
Stephen A Boyd
James R Cole

PLOS ONE

Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

2016

Christopher R. Myers

Eli Bogart

PLOS ONE

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla

2016

Samuel Owen Purvine

Peter H Waltman
Jian Guo
Emily Nahas Reistetter
Charles K Ansong
Marijke J van Baren
Chee-Hong Wong
Chia-Lin Wei
Richard D Smith
Stephen J Callister
Joshua M Stuart
Alexandra Z Worden

PLOS ONE

Contrasting Potato Foliage and Tuber Defense Mechanisms against the Late Blight Pathogen Phytophthora infestans

2016

Liangliang Gao
James M Bradeen

PLOS ONE

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation

2016

Rolf Backofen
Ralf Gilsbach
Björn A Grüning

David K Kranzhöfer
Thomas G Nührenberg
Lutz Hein

PLOS ONE

Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling

2016

Masaki Morita
Eva Knoch
Go Hirai
Mami Yamazaki
Mikiko Sodeoka
Kazuki Saito

Atsushi Fukushima
Michimi Nakamura
Hideyuki Suzuki
Tetsuya Mori
Naoyuki Umemoto

Frontiers in Plant Science

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings

2016

Won Cheol Yim
John Cushman

Chih-Pin Chiang
Ying-Hsuan Sun
Miwa Ohnishi
Tetsuro Mimura
Hungchen E Yen

Frontiers in Plant Science

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

2016

Byrappa Venkatesh
Yu Huang
Jose V. Lopez
Guillermo Ortí
Keith A. Crandall

Ying Sun
Xiaofeng Li
Carole C Baldwin
Zhuocheng Zhou
Zhixiang Yan
Yong Zhang
Xiaomeng Zhao
Min Wang
Alex Wong
Chao Fang
Xinhui Zhang
Hai Huang
Kirk Kilfoyle
Qiong Shi

GigaScience

Identifying stably expressed genes from multiple RNA-Seq data sets

2016

Jeff H. Chang
Sarah Emerson

Bin Zhuo
Yanming Di

PeerJ

Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition

2016

Kengo Sato

Tatsumu Inatsuki
Yasubumi Sakakibara

Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data

2016

Jordi Abante
Charles D. Johnson

Noushin Ghaffari
Raminder Singh
Philip D. Blood

Computational Methods for Quality Check, Preprocessing and Normalization of RNA-Seq Data for Systems Biology and Analysis

2016

Haja N. Kadarmideen

Gianluca Mazzoni

Forkhead Box C1 Regulates Human Primary Keratinocyte Terminal Differentiation

2016-01-01

Lianghua Bin

Liehua Deng
Hengwen Yang
Leqing Zhu
Xiao Wang
Michael G. Edwards
Brittany Richers
Donald Y. M. Leung

PLOS ONE

Analysis of RNA-Seq Data Using TopHat and Cufflinks.

2016-01-01

Sreya Ghosh
Chon-Kit Kenneth Chan

Methods in Molecular Biology

Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data.

2016-01-01

Cécile Neuvéglise

Hugo Devillers
Nicolas Morin

Methods in Molecular Biology

Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells.

2016-01-01

Brigitte Galliot
Y Wenger

W Buzgariu

Philosophical Transactions of the Royal Society B

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.

2016-01-01

Gordon K Smyth

Aaron T L Lun
Yunshun Chen

Methods in Molecular Biology

Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses.

2016-01-01

Finn Skou Pedersen

Martin Sokol
Karen Margrethe Jessen
Finn Skou Pedersen

Acta Pathologica et Microbiologica Scandinavica

RNA-Seq as a Tool to Study the Tumor Microenvironment.

2016-01-01

Guillaume Bourque

Pudchalaluck Panichnantakul
Mathieu Bourgey
Alexandre Montpetit
Yasser Riazalhosseini

Methods in Molecular Biology

In Silico Methods to Identify Exapted Transposable Element Families.

2016-01-01

Guillaume Bourque

LeeAnn Ramsay

Methods in Molecular Biology

Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.

2016-01-01

Geraldine Butler

Can Wang
Markus S Schröder
Stephen Hammel

Methods in Molecular Biology

Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill.

2016-01-01

Vicent Pelechano

Stefan Wilkening
Lars M Steinmetz

Methods in Molecular Biology

Analysis RNA-seq and Noncoding RNA.

2016-01-01

Sergio Abrignani
Massimiliano Pagani

Alberto Arrigoni
Valeria Ranzani
Grazisa Rossetti
Ilaria Panzeri
Raoul J P Bonnal

Methods in Molecular Biology

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.

2016-01-05

Zhen-Xia Chen

Yanzhu Lin
Kseniya Golovnina
Hang Noh Lee
Yazmin L Serrano Negron
Hina Sultana
Brian Oliver
Susan T Harbison

BMC Genomics

2016-01-05

Satyan Chintawar
Alice Giustacchini
Mahito Nakanishi
Sally A. Cowley

Adam E Handel
Tatjana Lalic
Emma Whiteley
Jane Vowles
Karene Argoud
Paul Sopp
Rory Bowden
Sarah Newey
Colin Akerman
Chris P Ponting
M Zameel Cader

Human Molecular Genetics

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

2016-01-06

Paul Blainey
Gregory Szeto
Alex K. Shalek

Robert J Kimmerling
Jennifer W Li
Alex S Genshaft
Samuel W Kazer
Kristofor R Payer
Jacob de Riba Borrajo
Darrell J Irvine
Scott R Manalis

Nature Communications

Tunable protein synthesis by transcript isoforms in human cells

2016-01-06

Jennifer Doudna
Stephen N Floor

eLife

OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data

2016-01-06

Christina Kendziorski

Ning Leng
Jeea Choi
Li-Fang Chu
James A Thomson
Ron Stewart

Bioinformatics

HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT).

2016-01-06

Yuichi Mitobe
Masao Matsuoka
Keiko Yasuma

Jun-ichirou Yasunaga
Keiko Takemoto
Kenji Sugata
Norihiro Takenouchi
Masanori Nakagawa
Yutaka Suzuki

PLOS Pathogens

Acute Exposure to Tris(1,3-dichloro-2-propyl) Phosphate (TDCIPP) Causes Hepatic Inflammation and Leads to Hepatotoxicity in Zebrafish.

2016-01-08

John P Giesy
Robert J Letcher

Chunsheng Liu
Guanyong Su
Guangyu Li
Ira Agrawal
Jing Li
Liqin Yu
Jianghua Wang
Zhiyuan Gong

Scientific Reports

The Female Post-Mating Response Requires Genes Expressed in the Secondary Cells of the Male Accessory Gland in Drosophila melanogaster

2016-01-08

Mariana Wolfner

Jessica L Sitnik
Dragan Gligorov
Robert K Maeda
François Karch

Genetics

Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish.

2016-01-08

Eric Peatman
Luyang Sun
Shikai Liu

Ailu Chen
Ruijia Wang
Lisui Bao
Chen Jiang
Chao Li
Yun Li
Qifan Zeng
Zhanjiang Liu

Molecular Genetics and Genomics

Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.

2016-01-10

Robert J. Beynon
Victoria M Harman
Philip Brownridge
Claire E. Eyers
Simon J. Hubbard

Craig Lawless
Stephen W Holman
Karin Lanthaler
Rachel Watkins
Dean E Hammond
Rebecca L Miller
Paul F G Sims
Christopher M Grant

Molecular & Cellular Proteomics

NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data.

2016-01-11

Jingyi Jessica Li

Yuting Ye

BMC Genomics

A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity.

2016-01-11

Robin Dowell

Timothy Read
Phillip A Richmond

PLOS Genetics

Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice.

2016-01-11

John Quackenbush
Kristen T Rooney
Monica P Goldklang
Francesca Polverino
Suzanne M Cloonan
Kimberly Glass

Maria E Laucho-Contreras
Abhiram R Bhashyam
Morgan Cervo
Maria A Pabón
Csaba Konrad
Ilias I Siempos
Elizabeth Perez
Kenji Mizumura
Manik C Ghosh
Harikrishnan Parameswaran
Niamh C Williams
Zhi-Hua Chen
Guo-Cheng Yuan
Stephen C Moore
Dawn L Demeo
Tracey A Rouault
Jeanine M D'Armiento
Eric A Schon
Giovanni Manfredi
Ashfaq Mahmood
Edwin K Silverman
Caroline A Owen
Augustine M K Choi

Nature Medicine

Keratin 12 missense mutation induces the unfolded protein response and apoptosis in Meesmann epithelial corneal dystrophy.

2016-01-11

Sarah D Atkinson
David G Courtney
Ebbe Toftgaard Poulsen
Deena M Leslie Pedrioli
Christian Cole
Johnny Moore
Jan J. Enghild

Edwin H A Allen
Laura Mairs
Davide Schiroli
Eleonora Maurizi
Robyn P Hickerson
John James
Helen Murgatroyd
Frances J D Smith
Carrie MacEwen
M Andrew Nesbit
W H Irwin McLean
C B Tara Moore

Human Molecular Genetics

Adipose tissue RNASeq reveals novel gene-nutrient interactions following n-3 PUFA supplementation and evoked inflammation in humans.

2016-01-11

Jane Ferguson
Muredach P. Reilly

Chenyi Xue
Yu Hu
Mingyao Li

Journal of Nutritional Biochemistry

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

2016-01-11

John C Marioni
Aleksandra A Kolodziejczyk
Jong Kyoung Kim
Sarah Teichmann

Tomislav Ilicic

Nature Communications

RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins.

2016-01-11

Evan S Bardot
Jonas Ibn-Salem
Michael L Piacentino

Daniel T Zuch
Julie Fishman
Sviatlana Rose
Emily E Speranza
Christy Li
Jia Yu
Oliver Chung
Janani Ramachandran
Patrick Ferrell
Vijeta Patel
Arlene Reyna
Hajerah Hameeduddin
James Chaves
Finnegan B Hewitt
David Lee
Amanda B Core
John D Hogan
Jessica L Keenan
Lingqi Luo
Jasmin Coulombe-Huntington
Todd A Blute
Ekaterina Oleinik
Albert J Poustka
Cynthia A Bradham

Development

The power and promise of RNA-seq in ecology and evolution.

2016-01-12

Michael A. Black
Neil J. Gemmell
Erica V Todd

Molecular Ecology

Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.

2016-01-13

Rajeev Kumar Varshney

Rohini Garg
Rama Shankar
Bijal Thakkar
Himabindu Kudapa
Lakshmanan Krishnamurthy
Nitin Mantri
Sabhyata Bhatia
Mukesh Jain

Scientific Reports

Repeated exposure to neurotoxic levels of chlorpyrifos alters hippocampal expression of neurotrophins and neuropeptides.

2016-01-13

Young Lee
Jonathan D Stallings
Pamela Lein

John A Lewis
Danielle L Ippolito
Naissan Hussainzada
David A Jackson

Toxicology

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect.

2016-01-13

Christine Vogel

Philip J Uren
Emad Bahrami-Samani
Patricia Rosa de Araujo
Mei Qiao
Suzanne C Burns
Andrew D Smith
Luiz O F Penalva

RNA Biology

FRAMA: from RNA-seq data to annotated mRNA assemblies.

2016-01-14

Matthias Platzer

Martin Bens
Arne Sahm
Marco Groth
Niels Jahn
Michaela Morhart
Susanne Holtze
Thomas B Hildebrandt
Karol Szafranski

BMC Genomics

RNA-Seq Reveals OTA-Related Gene Transcriptional Changes in Aspergillus carbonarius.

2016-01-14

Donato Gerin

Rita M De Miccolis Angelini
Stefania Pollastro
Francesco Faretra

PLOS ONE

Choline Kinase Alpha (CHKα) as a Therapeutic Target in Pancreatic Ductal Adenocarcinoma: Expression, Predictive Value, and Sensitivity to Inhibitors.

2016-01-14

Miriam Marqués
Eithne Costello
Juan C. Lacal
Francisco X Real

José M Mazarico
Victor J Sánchez-Arévalo Lobo
Rosy Favicchio
William Greenhalf
Enrique Carrillo-de Santa Pau
Eric Aboagye

Molecular Cancer Therapeutics

Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions.

2016-01-15

Trupti Joshi
Babu Valliyodan

Li Song
Silvas Prince
Joao V Maldonado dos Santos
Jiaojiao Wang
Li Lin
Jinrong Wan
Yongqin Wang
Dong Xu
Henry T Nguyen

BMC Genomics

Dosage Compensation in the African Malaria Mosquito Anopheles gambiae.

2016-01-18

Graham Rose
Luca Ferretti

Elzbieta Krzywinska
Jan Kim
Loic Revuelta
Jaroslaw Krzywinski

Genome Biology and Evolution

IL-36R signalling activates intestinal epithelial cells and fibroblasts and promotes mucosal healing in vivo.

2016-01-18

Stefan Wirtz
Georg Schett

Kristina Scheibe
Ingo Backert
Axel Hueber
Michael Vieth
Hans Christian Probst
Tobias Bopp
Markus F Neurath
Clemens Neufert

Gut

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

2016-01-20

Konrad Förstner
Jörg Vogel
Alexander Westermann
Fabian Amman
Lars Barquist
Peter F. Stadler
Yanjie Chao
Richard Reinhardt

Leon N. Schulte
Lydia Müller

Nature

Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery.

2016-01-20

Gabriel Wajnberg

Fabio Passetti

Expert Opinion on Drug Discovery

Identification of novel noncoding transcripts in telomerase-negative yeast using RNA-seq.

2016-01-20

David Zappulla

Rachel O Niederer
Nickolas Papadopoulos

Scientific Reports

Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1.

2016-01-20

Kylene Kehn-Hall
Jonathan D. Dinman

Alan Baer
Lindsay Lundberg
Danielle Swales
Nicole Waybright
Chelsea Pinkham
Jonathan L Jacobs

Journal of Virology

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

2016-01-21

Casey S. Greene

Jeffrey A Thompson
Jie Tan

PeerJ

Hepatic transcriptomic and metabolic responses of hybrid striped bass (Morone saxatilis×Morone chrysops) to acute and chronic hypoxic insult.

2016-01-21

Eric Peatman

Benjamin H Beck
S Adam Fuller
Chao Li
Bartholomew W Green
Honggang Zhao
Steven D Rawles
Carl D Webster

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing

2016-01-22

Kyung-Woon Kim

Won-Young Lee
Jeong Tae Do
Chankyu Park
Jin Hoi Kim
Hak-Jae Chung
Chang-Hyun Gil
Nam-Hyung Kim
Hyuk Song

PLOS ONE

RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots.

2016-01-22

Lucélia Donatti

V C S Pankievicz
D Camilios-Neto
P Bonato
E Balsanelli
M Z Tadra-Sfeir
H Faoro
L S Chubatsu
G Wajnberg
F Passetti
R A Monteiro
F O Pedrosa
E M Souza

Plant Molecular Biology

Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea.

2016-01-23

Aamir W Khan
Vanika Garg
Rajeev Kumar Varshney

Gaurav Agarwal
Himabindu Kudapa
Dadakhalandar Doddamani
Lekha T Pazhamala
Mahendar Thudi
Suk-Ha Lee

Plant Biotechnology Journal

Social defeat leads to changes in the endocannabinoid system: An overexpression of calreticulin and motor impairment in mice.

2016-01-24

Vincenzo Di Marzo
Stephan Lorenzen
Fabiana Piscitelli

J Tomas-Roig
V Gil
J A Del Río
T P Moore
H Agbemenyah
G Salinas-Riester
C Pommerenke
T Beißbarth
S Hoyer-Fender
U Havemann-Reinecke

Behavioural Brain Research

Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructure

2016-01-25

Masahira Hattori

Shuhei Ota
Kenshiro Oshima
Tomokazu Yamazaki
Sangwan Kim
Zhe Yu
Mai Yoshihara
Kohei Takeda
Tsuyoshi Takeshita
Aiko Hirata
Kateřina Bišová
Vilém Zachleder
Shigeyuki Kawano
Masahira Hattori

Biotechnology for Biofuels

Cascade: an RNA-seq visualization tool for cancer genomics.

2016-01-25

Aaron Shifman

Radia M Johnson
Brian T Wilhelm

BMC Genomics

De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma.

2016-01-25

Peter W Harrison
Paulino Martínez

Abul Farah Md Hasanuzzaman
Diego Robledo
Antonio Gómez-Tato
Jose A Alvarez-Dios
Asunción Cao
Sergio Fernández-Boo
Antonio Villalba
Belén G Pardo

Journal of Invertebrate Pathology

A survey of best practices for RNA-seq data analysis

2016-01-26

Ana Conesa
Michał Wojciech Szcześniak
Pedro Madrigal
David Gomez-Cabrero

Sonia Tarazona
Alejandra Cervera
Andrew McPherson
Daniel J. Gaffney
Laura L. Elo
Xuegong Zhang
Ali Mortazavi

Genome Biology

The Phenazine 2-Hydroxy-Phenazine-1-Carboxylic Acid Promotes Extracellular DNA Release and Has Broad Transcriptomic Consequences in Pseudomonas chlororaphis 30-84.

2016-01-26

Jun Myoung Yu

Dongping Wang
Robert J Dorosky
Leland S Pierson
Elizabeth A Pierson

PLOS ONE

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments.

2016-01-27

Jie Yao

Feinan Wu
Brennan G Olson

Journal of Visualized Experiments

Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals.

2016-01-27

Matteo Pellegrini

Kelvin Xi Zhang
Liming Tan
S Lawrence Zipursky
Jason M McEwen

Cell Reports

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.

2016-01-28

Fabian Amman
Michael T. Wolfinger
Andreas Dötsch
Susanne Häussler
Udo Bläsi

Muralidhar Tata
Nicole Roschanski
Elisabeth Sonnleitner

PLOS ONE

Gene expression under thermal stress varies across a geographical range expansion front.

2016-01-28

Rachael Y. Dudaniec
Maren Wellenreuther
Erik I Svensson
Bengt Hansson

Lesley T Lancaster
Pallavi Chauhan

Molecular Ecology

RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

2016-01-29

Vimalkumar Velayudhan
Audrey M Michel

James P A Mullan
Patrick B F O'Connor
Claire A Donohue
Pavel V Baranov

RNA Biology

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks.

2016-01-29

Deyou Zheng

Rebecca A Nebel
Dejian Zhao
Erika Pedrosa
Jill Kirschen
Herbert M Lachman
Brett S Abrahams

PLOS ONE

Single-cell Transcriptome Study as Big Data

2016-02

Pingjian Yu

Wei Lin

Genomics Proteomics and Bioinformatics

Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses

2016-02

Mario Arteaga-Vazquez
Shih-Shun Lin
Kimitsune Ishizaki
Katsuyuki T. Yamato
Takayuki Kohchi
John L. Bowman

Pin-Chun Lin
Chia-Wei Lu
Bing-Nan Shen
Guan-Zong Lee
Li-Yu Daisy Liu
Syuan-Fei Hong
Chu-Fang Lo
Gong-Min Su
Sabine Zachgo
Felix Althoff
Mizuki Takenaka

Plant and Cell Physiology

Expression of mRNA Encoding Mcu and Other Mitochondrial Calcium Regulatory Genes Depends on Cell Type, Neuronal Subtype, and Ca2+ Signaling

2016-02-01

Owen Dando
Peter C Kind
Giles E. Hardingham

Nóra M Márkus
Philip Hasel
Jing Qiu
Karen F S Bell
Samuel Heron
T Ian Simpson

PLOS ONE

Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters.

2016-02-01

Michael A Gorin

Kevin J Cheung
Veena Padmanaban
Vanesa Silvestri
Koen Schipper
Joshua D Cohen
Amanda N Fairchild
James E Verdone
Kenneth J Pienta
Joel S Bader
Andrew J Ewald

Proceedings of the National Academy of Sciences of the United States of America

Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components

2016-02-01

Laurence Florens
Gaye L Hattem
Michael P. Washburn

Mahadevan Lakshminarasimhan
Gina Boanca
Charles A S Banks
Ana E Gabriel
Brad D Groppe
Christine Smoyer
Kate E Malanowski
Allison Peak

Molecular & Cellular Proteomics

In silico prediction of the G-protein coupled receptors expressed during the metamorphic molt of Sagmariasus verreauxi (Crustacea: Decapoda) by mining transcriptomic data: RNA-seq to repertoire.

2016-02-02

Tomer Ventura
Quinn P Fitzgibbon
Gregory G Smith

Sean J Buckley

General and Comparative Endocrinology

H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus

2016-02-02

Michelle A. Petri

Zhe Zhang
Lihua Shi
Noor Dawany
Judith Kelsen
Kathleen E Sullivan

Clinical epigenetics

WHITE PANICLE1, a Val-tRNA Synthetase Regulating Chloroplast Ribosome Biogenesis in Rice, Is Essential for Early Chloroplast Development.

2016-02-02

Yunlong Wang
William Terzaghi

Chunming Wang
Ming Zheng
Jia Lyu
Yang Xu
Xiaohui Li
Mei Niu
Wuhua Long
Di Wang
HaiYang Wang
Yihua Wang
Jianmin Wan

Plant Physiology

Transcriptome Analysis of Murine Olfactory Sensory Neurons during Development Using Single Cell RNA-Seq.

2016-02-02

Hanns Hatt
Günter Gisselmann

Paul Scholz
Benjamin Kalbe
Fabian Jansen
Janine Altmueller
Christian Becker
Julia Mohrhardt
Benjamin Schreiner
Guenter Gisselmann
Sabrina Osterloh

Chemical Senses

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis

2016-02-04

Robert B Abramovitch

Benjamin K Johnson
Matthew B Scholz
Tracy K Teal

BMC Bioinformatics

Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage.

2016-02-04

Sophie Piperno-Neumann
Sergio Roman-Roman
Franck Tirode
Marc-Henri Stern
Martin Dutertre

Samar Alsafadi
Alexandre Houy
Aude Battistella
Tatiana Popova
Michel Wassef
Emilie Henry
Angelos Constantinou

Nature Communications

Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing

2016-02-05

Benjamin King

Thomas S Lisse
Sandra Rieger

Scientific Reports

Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.

2016-02-05

Hendrik Marks
Tahsin Stefan Barakat
Wouter de Laat

Hindrik H D Kerstens
Erik Splinter
René A M Dirks
Guido van Mierlo
Onkar Joshi
Shuang-Yin Wang
Tomas Babak
Cornelis A Albers
Tüzer Kalkan
Austin Smith
Alice Jouneau
Joost Gribnau
Hendrik G Stunnenberg

Genome Biology

Implementation of an Open Source Software solution for Laboratory Information Management and automated RNAseq data analysis in a large-scale Cancer Genomics initiative using BASE with extension package Reggie

2016-02-06

Johan Vallon-Christersson

Jari Hakkinen
Nicklas Nordborg
Olle Mansson

Differences in Host Cell Invasion and Salmonella Pathogenicity Island 1 Expression between Salmonella enterica Serovar Paratyphi A and Nontyphoidal S. Typhimurium

2016-02-08

Michael McClelland

Dana Elhadad
Prerak Desai
Guntram A Grassl
Galia Rahav
Ohad Gal-Mor

Infection and Immunity

Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers

2016-02-09

Anja M Billing
Johannes Graumann
Karsten Suhre
Hisham Ben Hamidane

Shaima S Dib
Richard J Cotton
Aditya M Bhagwat
Pankaj Kumar
Shahina Hayat
Noha A Yousri
Neha Goswami
Arash Rafii

Scientific Reports

New insights into the Plasmodium vivax transcriptome using RNA-Seq.

2016-02-09

Bruce Russell
Zbynek Bozdech
François H Nosten
Nicholas P J Day
Nicholas John White
Mallika Imwong
Sachel Mok

Lei Zhu
Anchalee Jaidee
Peter R Preiser

Scientific Reports

Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

2016-02-09

Elizabeth Theusch
Wolfgang Sadee

A Chhibber
C E French
S W Yee
E R Gamazon
X Qin
A Webb
A C Papp
A Wang
C Q Simmons
A Konkashbaev
A S Chaudhry
K Mitchel
D Stryke
T E Ferrin
S T Weiss
D L Kroetz
D A Nickerson
R M Krauss
A L George
E G Schuetz
M W Medina
N J Cox
S E Scherer
K M Giacomini
S E Brenner

The Pharmacogenomics Journal

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

2016-02-10

Shailesh Kumar

Angie Duy Vo
Fujun Qin
Hui Li

Scientific Reports

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.

2016-02-10

Auda A. Eltahla
Simone Rizzetto
Rowena A Bull
Katherine Kedzierska
Andrew R. Lloyd
Brigid D Betz-Stablein

Mehdi R Pirozyan
Vanessa Venturi
Fabio Luciani

Immunology & Cell Biology

A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq

2016-02-11

Annemie Van der Linden

Sandra Steyaert
Jolien Diddens
Jeroen Galle
Ellen De Meester
Sarah De Keulenaer
Antje Bakker
Nina Sohnius-Wilhelmi
Carolina Frankl-Vilches
Wim Van Criekinge
Wim Vanden Berghe
Tim De Meyer

Scientific Reports

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data

2016-02-11

Gunnar Rätsch

André Kahles
Cheng Soon Ong
Yi Zhong

Bioinformatics

Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method.

2016-02-11

Yohei Kirino

Shozo Honda
Keisuke Morichika

Nature Protocols

Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.

2016-02-12

Ryszard Przewłocki
Michał Korostyński

Marcin Piechota
Joanna Ficek
Andrzej Tomski

BMC Bioinformatics

Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer

2016-02-12

Vinod Yadav
Howard Li
Teresa T Nguyen

Joanna M Poczobutt
Subhajyoti De
Trisha R Sippel
Mary C M Weiser-Evans
Raphael A Nemenoff

Journal of Immunology

Single-cell transcriptome analysis of endometrial tissue.

2016-02-13

Juha Kere
M Vera-Rodriguez
Triin Laisk-Podar
Shintaro Katayama
Andres Salumets

K Krjutškov
M Saare
D Lubenets
K Samuel
H Teder
E Einarsdottir

Human Reproduction

Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing.

2016-02-13

Nora Fernandez-Jimenez

Davide Degli Esposti
Hector Hernandez-Vargas
Catherine Voegele
Nora Fernandez-Jimenez
Nathalie Forey
Brigitte Bancel
Florence Le Calvez-Kelm
James McKay
Philippe Merle
Zdenko Herceg

Oncotarget

Molecular signatures of age-associated chronic degeneration of shoulder muscles.

2016-02-14

Wibowo Arindrarto
Yotam Raz
Szymon M Kiełbasa
Peter A.C. 't Hoen

Jan Ferdinand Henseler
Arjen Kolk
Zuotian Tatum
Niels Kuipers Groosjohan
Nisha E Verwey
Jochem Nagels
Rob G H H Nelissen
Vered Raz

Oncotarget

An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes

2016-02-16

Kathryn J Boor
Martin Wiedmann

Yichang Liu
Renato Hohl Orsi
Veronica Guariglia-Oropeza

BMC Genomics

Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit.

2016-02-16

Leonardo Tenori
Claudio Luchinat

Dubravka Cukrov
Monica Zermiani
Stefano Brizzolara
Alessandro Cestaro
Francesco Licausi
Claudio Santucci
Hans Van Veen
Andrea Zuccolo
Benedetto Ruperti
Pietro Tonutti

Frontiers in Plant Science

Classification of low quality cells from single-cell RNA-seq data

2016-02-17

Aleksandra A Kolodziejczyk
Davis J McCarthy
Frederik Otzen Bagger
John C Marioni
Jong Kyoung Kim
Sarah Teichmann

Tomislav Ilicic

Genome Biology

Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection.

2016-02-17

Thomas Wicker

Tim Kamber
Jan P Buchmann
Joël F Pothier
Theo H M Smits
Brion Duffy

Scientific Reports

Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

2016-02-17

Xianzhi Lin
Xinshu Xiao

Yun-Hua Esther Hsiao
Jae Hoon Bahn
Tak-Ming Chan
Rena Wang

Genome Research

Molluscum Contagiosum Virus Transcriptome in Abortively Infected Cultured Cells and a Human Skin Lesion

2016-02-17

Bernard Moss

Jorge D Mendez-Rios
Zhilong Yang
Karl J Erlandson
Jeffrey I Cohen
Craig A Martens
Daniel P Bruno
Stephen F Porcella

Journal of Virology

The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis.

2016-02-17

Feng Ding

Peng Cui
Tao Chen
Tao Qin
Zhenyu Wang
Hao Chen
Liming Xiong

The Plant Cell

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

2016-02-18

Jennifer Erwin

Suguna Rani Krishnaswami
Rashel V Grindberg
Mark Novotny
Pratap Venepally
Benjamin Lacar
Kunal Bhutani
Sara B Linker
Son Pham
Jeremy A Miller
Rebecca Hodge
James K McCarthy
Martin Kelder
Jamison McCorrison
Brian D Aevermann
Francisco Diez Fuertes
Richard H Scheuermann
Jun Lee
Ed S Lein
Nicholas Schork
Michael J McConnell
Fred H Gage
Roger S Lasken

Nature Protocols

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.

2016-02-18

Anders Hamsten
Per Tornvall
Jacob Odeberg

Daniel Edsgärd
Maria Jesus Iglesias
Sarah-Jayne Reilly
Olof Emanuelsson

Scientific Reports

The Nuclear Receptor, RORγ, Regulates Pathways Necessary for Breast Cancer Metastasis.

2016-02-18

Tae Gyu Oh
Bipul R. Acharya
Shu-Ching Mary Wang
Christine Clarke
Alpha S. Yap

Joel M Goode
J Dinny Graham
George E O Muscat

EBioMedicine

Hemocytome: deep sequencing analysis of mosquito blood cells in Indian malarial vector Anopheles stephensi.

2016-02-22

Rajnikant Dixit

Tina Thomas
Tanwee Das De
Punita Sharma
Suman Lata
Priyanka Saraswat
Kailash C Pandey

Gene

RNA-seq analysis of clinical-grade osteochondral allografts reveals activation of early response genes.

2016-02-22

Annalise Noelle Larson

Yang Lin
Eric A Lewallen
Emily T Camilleri
Carolina A Bonin
Dakota L Jones
Amel Dudakovic
Catalina Galeano-Garces
Wei Wang
Marcel J Karperien
Diane L Dahm
Michael J Stuart
Bruce A Levy
Jay Smith
Daniel B Ryssman
Jennifer J Westendorf
Hee-Jeong Im
Andre J van Wijnen
Scott M Riester
Aaron J Krych

Journal of Orthopaedic Research

The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli.

2016-02-22

Michael T. Wolfinger

Martina Sauert
Oliver Vesper
Christian Müller
Konstantin Byrgazov
Isabella Moll

Nucleic Acids Research

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality.

2016-02-23

Yankel Gabet

Rachel E Bell
Tamar Golan
Danna Sheinboim
Hagar Malcov
David Amar
Avi Salamon
Tamar Liron
Sahar Gelfman
Ron Shamir
Carmit Levy

Genome Research

Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan.

2016-02-24

Matthias Platzer

Mario Baumgart
Steffen Priebe
Marco Groth
Nils Hartmann
Uwe Menzel
Luca Pandolfini
Philipp Koch
Marius Felder
Michael Ristow
Christoph Englert
Reinhard Guthke
Alessandro Cellerino

Cell systems

Nitric oxide release from nitro-fatty acids in Arabidopsis roots.

2016-02-24

Francisco J. Corpas

Capilla Mata-Pérez
Beatriz Sánchez-Calvo
Juan C Begara-Morales
María N Padilla
Raquel Valderrama
Juan B Barroso

Plant Signaling and Behavior

Isolation of the protein and RNA content of active sites of transcription from mammalian cells.

2016-02-25

Argyris Papantonis
Karsten Rippe
Ian M. Carr
Maïwen Caudron-Herger

Svitlana Melnik
Lilija Brant
Peter R Cook

Nature Protocols

Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line.

2016-02-26

Mathias Heikenwalder
Hans Lehrach
Martin Kerick
Ralf Herwig
Lubor Borsig

Felix Broecker
Christopher Hardt
Bernd Timmermann
Andrea Wunderlich
Michal R Schweiger
Karin Moelling

FEBS Journal

TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-autonomously in Caenorhabditis elegans.

2016-02-26

Peter Swoboda
Katie C McCallum
Juan Carlos Fierro-González
Bin Liu
Antonio Miranda-Vizuete
Danielle A Garsin

Swathi Arur

Genetics

Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.

2016-02-27

Nicolas Terrapon
Christopher J Fields
Evelyne Forano
Bernard Henrissat

Jordane Despres
Pascale Lepercq
Sophie Comtet-Marre
Grégory Jubelin
Carl J Yeoman
Margret E Berg Miller
Carine Le Bourvellec
Catherine M G C Renard
Bryan A White
Pascale Mosoni

BMC Genomics

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data.

2016-02-29

Mihails Delmans

Martin Hemberg

BMC Bioinformatics

Overlapping cell population expression profiling and regulatory inference in C. elegans.

2016-02-29

Arjun Raj

Joshua Burdick
Travis Walton
Elicia Preston
Amanda Zacharias
John Isaac Murray

BMC Genomics

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.

2016-02-29

Jason A. Hackney
Florian Gnad
David J. Sugarbaker

Raphael Bueno
Eric W Stawiski
Leonard D Goldstein
Steffen Durinck
Assunta De Rienzo
Zora Modrusan
Thong T Nguyen
Bijay S Jaiswal
Lucian R Chirieac
Daniele Sciaranghella
Nhien Dao
Corinne E Gustafson
Kiara J Munir
Amitabha Chaudhuri
Ravi Gupta
Joseph Guillory
Karen Toy
Connie Ha
Ying-Jiun Chen
Jeremy Stinson
Subhra Chaudhuri
Na Zhang
Thomas D Wu
Frederic J de Sauvage
William G Richards
Somasekar Seshagiri

Nature Genetics

Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells

2016-03

Carmen Sandoval-Espinosa

Tomasz J. Nowakowski
Alex A. Pollen
Elizabeth Di Lullo
Marina Bershteyn
Arnold R. Kriegstein

Cell Stem Cell

Human MicroRNA miR-532-5p Exhibits Antiviral Activity against West Nile Virus via Suppression of Host Genes SESTD1 and TAB3 Required for Virus Replication

2016-03

A Slonchak
Alexander A. Khromykh

Rory P Shannon
Gabor Pali

Journal of Virology

The impact of oil spill to lung health--Insights from an RNA-seq study of human airway epithelial cells

2016-03-01

Erik K Flemington

Yao-Zhong Liu
Astrid M Roy-Engel
Melody C Baddoo
Guangdi Wang
He Wang

Gene

GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.

2016-03-01

Doron Lancet

Shani Ben-Ari Fuchs
Iris Lieder
Gil Stelzer
Yaron Mazor
Ella Buzhor
Sergey Kaplan
Yoel Bogoch
Inbar Plaschkes
Alina Shitrit
Noa Rappaport
Asher Kohn
Ron Edgar
Liraz Shenhav
Marilyn Safran
Yaron Guan-Golan
David Warshawsky
Ronit Shtrichman

OMICS: A Journal of Integrative Biology

Characterizing Milk Production Related Genes in Holstein Using RNA-seq

2016-03-01

Heebal Kim

Minseok Seo
Hyun-Jeong Lee
Kwondo Kim
Kelsey Caetano-Anolles
Jin Young Jeong
Sungkwon Park
Young Kyun Oh
Seoae Cho

Asian-Australasian Journal of Animal Sciences

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.

2016-03-01

Andrew Mungall

Hye-Jung E Chun
Emilia L Lim
Alireza Heravi-Moussavi
Saeed Saberi
Karen L Mungall
Mikhail Bilenky
Annaick Carles
Kane Tse
Inna Shlafman
Kelsey Zhu
Jenny Q Qian
Diana L Palmquist
An He
William Long
Rodrigo Goya
Michelle Ng
Veronique G LeBlanc
Erin Pleasance
Nina Thiessen
Tina Wong
Eric Chuah
Yong-Jun Zhao
Jacquie E Schein
Daniela S Gerhard
Michael D Taylor
Richard A Moore
Yussanne Ma
Steven J M Jones
Elizabeth J Perlman
Martin Hirst
Marco A Marra

Cancer Cell

Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness.

2016-03-01

Paolo Zambonelli

E Gaffo
M Zappaterra
S Bortoluzzi
R Davoli

Animal Genetics

Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns.

2016-03-02

Xin Wei
Linhai Wang

Donghua Li
Yanxin Zhang
Yuan Gao
Jingyin Yu
Xiurong Zhang

PLOS ONE

FgSsn3 kinase, a component of the mediator complex, is important for sexual reproduction and pathogenesis in Fusarium graminearum

2016-03-02

Huiquan Liu

Shulin Cao
Shijie Zhang
Chaofeng Hao
Jin-Rong Xu
Qiaojun Jin

Scientific Reports

Erratum to: 'Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq'.

2016-03-02

Alicia Oshlack

Katie L Ayers
Luke S Lambeth
Nadia M Davidson
Andrew H Sinclair
Craig A Smith

BMC Genomics

Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression.

2016-03-02

Timothy J Pullen

Richard M Denton
Craig T Armstrong
Kate J Heesom
Guy A Rutter

Biochemical Journal

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions

2016-03-03

Takanori Maruta
Kazuharu Arakawa

Yuta Yoshida
Takuya Tomiyama
Masaru Tomita
Takahiro Ishikawa

BMC Genomics

Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks

2016-03-03

Alejandro Villar-Briones

Alejandro Reyes-Bermudez
Catalina Ramirez-Portilla
Michio Hidaka
Alexander S Mikheyev

Genome Biology and Evolution

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

2016-03-04

Maria Byrne

Jennifer W Israel
Megan L Martik
Elizabeth C Raff
Rudolf A Raff
David R McClay
Gregory A Wray

PLOS Biology

Early alterations on photosynthesis-related parameters in Chlamydomonas reinhardtii cells exposed to atrazine: A multiple approach study.

2016-03-04

Marta Seoane
Marta Esperanza
Concepción Herrero
Carmen Rioboo
Ángeles Cid

Science of the Total Environment

Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b.

2016-03-05

Jérémie Piton
Jérémie Piton
Claudia Sala

Andrej Benjak
Swapna Uplekar
Ming Zhang
Stewart T Cole

BMC Genomics

Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae).

2016-03-06

Josephine A Reinhardt
Gerald Wilkinson

Richard H Baker
Apurva Narechania
Rob DeSalle
Philip M Johns

Genome Biology and Evolution

Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae.

2016-03-07

Octávio S. Paulo
Ana Cabral
Ana Vieira
Ana Sofia Pires
Vitor Varzea
Andreia Loureiro
Helena Azinheira
Helena Oliveira
Dora Batista
Maria do Céu Silva

Joana Fino
Pedro Talhinhas
Pilar Moncada

PLOS ONE

Comparative analysis of human and mouse transcriptomes of Th17 cell priming.

2016-03-07

Brigitta Stockinger
Sini Rautio
Ubaid Ullah
Zhi Chen
Helena Ahlfors
Harri Lähdesmäki
Tarmo Äijö

Soile Tuomela
Viveka Öling
Verna Salo
Saara Hämälistö
Subhash K Tripathi
Omid Rasool
Hayssam Soueidan
Lodewyk Wessels
Riitta Lahesmaa

Oncotarget

Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.

2016-03-07

Shikai Liu

Xiaoxu Zhou
Jun Cui
Derong Kong
He Sun
Chenlei Gu
Hongdi Wang
Xuemei Qiu
Yaqing Chang
Zhanjiang Liu
Xiuli Wang

PeerJ

RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt

2016-03-08

Mariangela Hungria

Francisco Pérez-Montaño
Pablo Del Cerro
Irene Jiménez-Guerrero
Francisco Javier López-Baena
Maria Teresa Cubo
Mariangela Hungria
Manuel Megías
Francisco Javier Ollero

BMC Genomics

Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL

2016-03-08

Paul Stothard

Martine Schroyen
Christopher Eisley
James E Koltes
Eric Fritz-Waters
Igseo Choi
Graham S Plastow
Leluo Guan
Hua Bao
Arun Kommadath
James M Reecy
Joan K Lunney
Robert R R Rowland
Jack C M Dekkers
Christopher K Tuggle

BMC Genomics

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq.

2016-03-08

Claudio Varotto
Nicola La Porta
Gaurav Sablok
Violeta Velikova

Yuan Fu
Michele Poli
Bo Wang
Yanchun Liang
Francesco Loreto
Mingai Li

Biotechnology for Biofuels

Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia.

2016-03-08

Mats Hellström

Tatjana Pandzic
Jimmy Larsson
Liqun He
Snehangshu Kundu
Kenneth Ban
Muhammad Akhtar-Ali
Anders R Hellström
Anna Schuh
Ruth Clifford
Stuart J Blakemore
Jonathan C Strefford
Tycho Baumann
Armando Lopez-Guillermo
Elias Campo
Viktor Ljungström
Larry Mansouri
Richard Rosenquist
Tobias Sjöblom

Clinical Cancer Research

Striatal mRNA expression patterns underlying peak dose L-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat.

2016-03-08

Michael A. Black

L M Smith
L C Parr-Brownlie
E J Duncan
N J Gemmell
P K Dearden
J N J Reynolds

Neuroscience

Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.

2016-03-09

Robert Dantzer

Dianelys Gonzalez-Pena
Scott E Nixon
Jason C O'Connor
Bruce R Southey
Marcus A Lawson
Robert H McCusker
Tania Borras
Debbie Machuca
Alvaro G Hernandez
Keith W Kelley
Sandra L Rodriguez-Zas

PLOS ONE

Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation.

2016-03-09

Chenyu Huang

Jingyu Wang
Fengling Chen
Longwei Liu
Chunxiao Qi
Bingjie Wang
Xiaojun Yan
Wei Hou
Michael Q Zhang
Yang Chen
Yanan Du

Biomaterials

Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications

2016-03-10

Michaela Willi
Hubert Hackl
Gregor Wenning
Werner Poewe

Simon Schafferer
Rimpi Khurana
Violetta Refolo
Serena Venezia
Edith Sturm
Paolo Piatti
Clara Hechenberger
Roman Kessler
Ronald Gstir
Anne Krogsdam
Alexandra Lusser
Alexander Hüttenhofer
Nadia Stefanova

PLOS ONE

Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses

2016-03-10

Jean-Marc Schwartz
Timothy E. Hardingham

S L Dunn
J Soul
S Anand
R P Boot-Handford

Osteoarthritis and Cartilage

High E6 Gene Expression Predicts for Distant Metastasis and Poor Survival in Patients With HPV-Positive Oropharyngeal Squamous Cell Carcinoma.

2016-03-10

Christopher R Spencer
Rebecca D. Chernock

Shariq S Khwaja
Callie Baker
Wesley Haynes
Hiram Gay
Wade Thorstad
Douglas R Adkins
Brian Nussenbaum
James S Lewis
Xiaowei Wang

International Journal of Radiation Oncology Biology Physics

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

2016-03-11

David E. MacHugh
Kévin Rue-Albrecht
Stephen V. Gordon

Paul A McGettigan
Belinda Hernández
Nicolas C Nalpas
David A Magee
Andrew C Parnell

BMC Bioinformatics

Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster

2016-03-11

Fang-Hua Chu
Wen-Hsiung Li

Mei-Ju May Chen
Li-Kai Chen
Yu-Shing Lai
Yu-Yu Lin
Dung-Chi Wu
Yi-An Tung
Kwei-Yan Liu
Hsueh-Tzu Shih
Yi-Jyun Chen
Yan-Liang Lin
Li-Ting Ma
Jian-Long Huang
Po-Chun Wu
Ming-Yi Hong
June-Tai Wu
Chien-Yu Chen

BMC Genomics

The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity.

2016-03-11

Catriona P Harkins
Sharon Peacock

Ben Warne
Simon R Harris
Alexandra Vatsiou
Nicola Stanley-Wall
Julian Parkhill
Tracy Palmer
Matthew T G Holden

BMC Genomics

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing.

2016-03-11

Elliott D. Kieff

Lijuan Hu
Zhirui Lin
Yanheng Wu
Juqin Dong
Bo Zhao
Yanbing Cheng
Peiyu Huang
Lihua Xu
Tianliang Xia
Dan Xiong
Hongbo Wang
Manzhi Li
Ling Guo
Yixin Zeng
Qian Zhong
Musheng Zeng

Frontiers of medicine

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.

2016-03-12

Francois Sabot
Yves Vigouroux

K N Ta
H Adam
S De Mita
A Ghesquière
N V Do
P Gantet
S Jouannic

Rice

A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.

2016-03-14

Christopher R. Myers

Jay N Worley
Marina A Pombo
Yi Zheng
Diane M Dunham
Zhangjun Fei
Gregory B Martin

BMC Genomics

CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.

2016-03-14

Sarven Sabunciyan

Li Song
Liliana Florea

Nucleic Acids Research

Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells

2016-03-15

Damien Balestrino
Nicolas Parisot

Cyril Guilhen
Nicolas Charbonnel
Nathalie Gueguen
Agnès Iltis
Christiane Forestier

BMC Genomics

Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target

2016-03-15

Lucy F Stead
Terence Rabbitts

Jennifer Town
Helio Pais
Sally Harrison
Carole Bataille
Wilawan Bunjobpol
Jing Zhang

Proceedings of the National Academy of Sciences of the United States of America

Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways.

2016-03-17

Héctor Candela

Tali Mandel
Udi Landau
Lior Asis
Einat Zelinger
Cristel C Carles
Leor Eshed Williams

Development

A mutation in the tuft mouse disrupts TET1 activity and alters the expression of genes that are crucial for neural tube closure.

2016-03-17

Scott Lozanoff

Keith S K Fong
Robert B Hufnagel
Vedbar S Khadka
Michael J Corley
Alika K Maunakea
Ben Fogelgren
Zubair M Ahmed

Disease Models & Mechanisms

Systems Biology of Metabolic Regulation by Estrogen Receptor Signaling in Breast Cancer.

2016-03-17

Zeynep Madak-Erdogan

Yiru Chen Zhao

Journal of Visualized Experiments

Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis.

2016-03-17

Yu Gao

Feifei Wang
Brian E Eisinger
Laurel E Kelnhofer
Emily M Jobe
Xinyu Zhao

Cerebral Cortex

Identification by FFPE RNA-Seq of a new recurrent inversion leading to RBM10-TFE3 fusion in renal cell carcinoma with subtle TFE3 break-apart FISH pattern.

2016-03-21

Eric Pasmant

Pierre-Alexandre Just
Franck Letourneur
Christelle Pouliquen
Florence Dome
Anne Audebourg
Philippe Biquet
Michel Vidaud
Benoit Terris
Mathilde Sibony

Genes, Chromosomes and Cancer

De Novo Transcriptome Sequencing of Desert Herbaceous Achnatherum splendens (Achnatherum) Seedlings and Identification of Salt Tolerance Genes

2016-03-23

Lizhe An

Jiangtao Liu
Yuelong Zhou
Changxin Luo
Yun Xiang

Genes

Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula.

2016-03-23

Edward M. De Robertis

Yi Ding
Gabriele Colozza
Kelvin Zhang
Yuki Moriyama
Diego Ploper
Eric A Sosa
Maria D J Benitez

Developmental Biology

Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy.

2016-03-23

Traude H. Beilharz
Thomas Preiss

R Soetanto
C J Hynes
H R Patel
D T Humphreys
M Evers
G Duan
B J Parker
S K Archer
J L Clancy
R M Graham
N J Smith

Biochimica et Biophysica Acta

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.

2016-03-24

Stephanie McKay

Aimee L Benjamin
Benjamin B Green
Brian A Crooker
David E Kerr

BMC Genomics

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo.

2016-03-24

David Sturgill

D Quénet
Y Dalal

Methods in Enzymology

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

2016-03-25

Mark Bender Gerstein

Fei He
Shinjae Yoo
Daifeng Wang
Sunita Kumari
Doreen Ware
Sergei Maslov

The Plant Journal

Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

2016-03-25

Karin Troell
Staffan G Svärd

Elin Einarsson
Marc P Hoeppner
Manfred Grabherr
Ulf Ribacke

PLOS Neglected Tropical Diseases

Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq.

2016-03-28

Amy E Young
Laercio R Porto-Neto

Kristina L Weber
Bryan T Welly
Alison L Van Eenennaam
Antonio Reverter
Gonzalo Rincon

PLOS ONE

Transcriptomic and epigenomic characterization of the developing bat wing.

2016-03-28

Nicola Illing
Zoe Gill
Nadav Ahituv

Walter L Eckalbar
Stephen A Schlebusch
Mandy K Mason
Ash V Parker
Betty M Booker
Sierra Nishizaki
Christiane Muswamba-Nday
Elizabeth Terhune
Kimberly A Nevonen
Nadja Makki
Tara Friedrich
Julia E VanderMeer
Katherine S Pollard
Lucia Carbone
Jeff D Wall
Nicola Illing

Nature Genetics

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

2016-03-28

Geoffrey J. Barton
Gordon G Simpson
Nicholas Schurch
Christian Cole
Tom Owen-Hughes
Karim Gharbi
Mark Blaxter

Pietá Schofield
Marek Gierliński
Alexander Sherstnev
Vijender Singh
Nicola Wrobel

RNA

A mutation in SLC22A4 encoding an organic cation transporter expressed in the cochlea strial endothelium causes human recessive non-syndromic hearing loss DFNB60

2016-03-29

Bouthaina Hammami
Mustafa Tekin

Mariem Ben Said
M'hamed Grati
Takahiro Ishimoto
Bing Zou
Imen Chakchouk
Qi Ma
Qi Yao
Denise Yan
Rahul Mittal
Noritaka Nakamichi
Abdelmonem Ghorbel
Lingling Neng
Xiao Rui Shi
Yukio Kato
Saber Masmoudi
Zhongmin Lu
Mounira Hmani
Xuezhong Liu

Human Genetics

Prognostic and Functional Significance of MAP4K5 in Pancreatic Cancer.

2016-03-29

Nancy Azizian

Oliver H Wang
Ming Guo
Michela Capello
Defeng Deng
Fenglin Zang
Jason Fry
Matthew H Katz
Jason B Fleming
Jeffrey E Lee
Robert A Wolff
Samir Hanash
Huamin Wang
Anirban Maitra

PLOS ONE

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes.

2016-03-29

Roberto Galizi
Omar S Akbari
Sergey Koren
Changde Cheng
Tony Nolan
Adam Phillippy
Andrea Crisanti
Nikolai Windbichler

Andrew Brantley Hall
Philippos-Aris Papathanos
Atashi Sharma
Lauren Assour
Nicholas H Bergman
Alessia Cagnetti
Tania Dottorini
Elisa Fiorentini
Jonathan Hnath
Xiaofang Jiang
Diane Radune
Maria V Sharakhova
Aaron Steele
Vladimir A Timoshevskiy
Simo Zhang
Matthew W Hahn
Scott J Emrich
Igor V Sharakhov
Zhijian Jake Tu
Nora J Besansky

Proceedings of the National Academy of Sciences of the United States of America

Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression.

2016-03-31

Hilde Van Esch
Janine M van Gils
Anton Jan van Zonneveld
Ton J Rabelink
Ilze Bot

Ruben G de Bruin
Lily Shiue
Jurriën Prins
Hetty C de Boer
Anjana Singh
W Samuel Fagg
Jacques M G J Duijs
Sol Katzman
Adriaan O Kraaijeveld
Stefan Böhringer
Wai Y Leung
Szymon M Kielbasa
John P Donahue
Patrick H J van der Zande
Rick Sijbom
Carla M A van Alem
Cees van Kooten
J Wouter Jukema
Hilal Kazan
Erik A L Biessen
Manuel Ares
Eric P van der Veer

Nature Communications

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

2016-03-31

Igor V Grigoriev
Jane Grimwood
Hang Yu
Charles Bachy
Samuel Owen Purvine

Marijke J van Baren
Emily Nahas Reistetter
Jane Grimwood
Sebastian Sudek
Camille Poirier
Thomas J Deerinck
Alan Kuo
Chee-Hong Wong
Richard D Smith
Stephen J Callister
Chia-Lin Wei
Jeremy Schmutz
Alexandra Z Worden

BMC Genomics

Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis

2016-03-31

Qiaosheng Guo

Yuanyuan Miao
Zaibiao Zhu
Yunhao Zhu
Xiaohua Yang
Yuan Sun

Frontiers in Plant Science

Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors.

2016-03-31

Hikmet Budak
Burcu Alptekin

Functional and Integrative Genomics

Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

2016-04-01

Masao Watanabe

Toru Kudo
Yohei Sasaki
Shin Terashima
Noriko Matsuda-Imai
Tomoyuki Takano
Misa Saito
Maasa Kanno
Soichi Ozaki
Keita Suwabe
Go Suzuki
Makoto Matsuoka
Seiji Takayama
Kentaro Yano

Genes and Genetic Systems

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

2016-04-01

Aviv Regev
Itay Tirosh
Alex K. Shalek
Peter K. Sorger
Orit Rozenblatt-Rosen
Keith Flaherty

Itay Tirosh
Benjamin Izar
Sanjay M Prakadan
Marc H Wadsworth
Daniel Treacy
John J Trombetta
Asaf Rotem
Christopher Rodman
Christine Lian
George Murphy
Mohammad Fallahi-Sichani
Ken Dutton-Regester
Jia-Ren Lin
Ofir Cohen
Parin Shah
Diana Lu
Alex S Genshaft
Travis K Hughes
Carly G K Ziegler
Samuel W Kazer
Aleth Gaillard
Kellie E Kolb
Alexandra-Chloé Villani
Cory M Johannessen
Aleksandr Y Andreev
Eliezer M Van Allen
Monica Bertagnolli
Ryan J Sullivan
Dennie T Frederick
Judit Jané-Valbuena
Charles H Yoon
Levi A Garraway

Science

Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation.

2016-04-01

Lunzhi Dai
Dongjun Chung
Minjia Tan
David B. Lombard

Zhongyu Xie
Di Zhang
Zhanyun Tang
He Huang
Shankang Qi
Jingya Li
Gozde Colak
Yue Chen
Chunmei Xia
Chao Peng
Haibin Ruan
Matt Kirkey
Danli Wang
Lindy M Jensen
Oh Kwang Kwon
Sangkyu Lee
Scott D Pletcher
Kevin P White
Hongyu Zhao
Jia Li
Robert G Roeder
Xiaoyong Yang
Yingming Zhao

Molecular Cell

Transcriptome sequencing reveals e-cigarette vapor and mainstream-smoke from tobacco cigarettes activate different gene expression profiles in human bronchial epithelial cells.

2016-04-04

Michael P. Timko

Yifei Shen
Michael J Wolkowicz
Tatyana Kotova
Lonjiang Fan

Scientific Reports

Near-optimal probabilistic RNA-seq quantification.

2016-04-04

Lior Pachter
Harold Pimentel
Páll Melsted

Nicolas L Bray

Nature Biotechnology

De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products.

2016-04-04

Amit Rai
Mami Yamazaki
Kazuki Saito

R Han
M Nakamura
H Suzuki
H Takahashi

Methods in Enzymology

The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet (Setaria italica (L.) P. Beauv)

2016-04-04

James Schnable

Xiaotong Liu
Sha Tang
Guanqing Jia
Haixia Su
Chanjuan Tang
Hui Zhi
Xianmin Diao

Journal of Experimental Botany

Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas

2016-04-05

Yoel Sadovsky

Shinichiro Yabe
Andrei P Alexenko
Mitsuyoshi Amita
Ying Yang
Danny J Schust
Toshihiko Ezashi
R Michael Roberts

Proceedings of the National Academy of Sciences of the United States of America

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.

2016-04-05

Sten Linnarsson
Alvaro Plaza Reyes
Björn Reinius
Qiaolin Deng
Rickard Sandberg

Sophie Petropoulos
Daniel Edsgärd
Sarita Pauliina Panula
Simone Codeluppi
Fredrik Lanner

Cell

Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

2016-04-05

Vadivel Ganapathy

Rajneesh Pathania
Sabarish Ramachandran
Gurusamy Mariappan
Priyanka Thakur
Huidong Shi
Jeong-Hyeon Choi
Santhakumar Manicassamy
Ravindra Kolhe
Puttur D Prasad
Suash Sharma
Bal L Lokeshwar
Muthusamy Thangaraju

Cancer Research

Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma.

2016-04-06

Qiang Gong
Philippe Gaulard

Can Küçük
Xiaozhou Hu
Bei Jiang
Adam Cornish
Timothy McKeithan
Wing C Chan

The American Journal of Pathology

Upregulation of hydroxysteroid sulfotransferase 2B1b promotes hepatic oval cell proliferation by modulating oxysterol-induced LXR activation in a mouse model of liver injury.

2016-04-06

Joe Yeong
Sifeng Chen

Zhengyang Wang
Xiaoming Yang
Liang Chen
Xiuling Zhi
Hanyu Lu
Yanxia Ning
Lianhua Yin
Xinhong Wang
Xiaobo Li

Archives of Toxicology

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules.

2016-04-11

Gert Jan C Veenstra
Stefan Hoppler

Yukio Nakamura
Eduardo de Paiva Alves

Development

RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis.

2016-04-12

Amit Rai
Mami Yamazaki
Kazuki Saito

Hiroki Takahashi
Michimi Nakamura
Mareshige Kojoma
Hideyuki Suzuki

Frontiers in Plant Science

Understanding metabolite transport and metabolism in C4 plants through RNA-seq.

2016-04-12

Andrea Bräutigam

Urte Schlüter
Alisandra K Denton

Current Opinion in Plant Biology

Refined Pichia pastoris reference genome sequence.

2016-04-12

Ruth Birner-Gruenberger
Kasey J Day
Anton Glieder

Lukas Sturmberger
Thomas Chappell
Martina Geier
Florian Krainer
Ursa Vide
Sara Trstenjak
Anja Schiefer
Toby Richardson
Leah Soriaga
Barbara Darnhofer
Benjamin S Glick
Ilya Tolstorukov
James Cregg
Knut Madden

Journal of Biotechnology

Erratum for Baddal et al., Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk.

2016-04-12

Buket Baddal

Alessandro Muzzi
Stefano Censini
Raffaele A Calogero
Giulia Torricelli
Silvia Guidotti
Anna R Taddei
Antonello Covacci
Mariagrazia Pizza
Rino Rappuoli
Marco Soriani
Alfredo Pezzicoli

mBio

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

2016-04-13

John L. Rinn

Leonardo M R Ferreira
Torsten B Meissner
Tarjei S Mikkelsen
William Mallard
Charles W O'Donnell
Tamara Tilburgs
Hannah A B Gomes
Raymond Camahort
Richard I Sherwood
David K Gifford
Chad A Cowan
Jack L Strominger

Proceedings of the National Academy of Sciences of the United States of America

Single-cell analysis of long non-coding RNAs in the developing human neocortex.

2016-04-14

Jonathan Weissman

Siyuan John Liu
Tomasz J Nowakowski
Alex A Pollen
Jan H Lui
Max A Horlbeck
Frank J Attenello
Daniel He
Arnold R Kriegstein
Aaron A Diaz
Daniel A Lim

Genome Biology

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

2016-04-15

Jesse Gillis

Sara Ballouz

PLOS Computational Biology

Beyond comparisons of means: understanding changes in gene expression at the single-cell level.

2016-04-15

John C Marioni
Catalina A Vallejos
Sylvia Richardson

Genome Biology

A Class of Diacylglycerol Acyltransferase 1 Inhibitors Identified by a Combination of Phenotypic High-throughput Screening, Genomics, and Genetics

2016-04-16

Herbert Waldmann
Mathias Beller
Thomas O Eichmann

Kirsten Tschapalda
Ya-Qin Zhang
Li Liu
Kseniya Golovnina
Thomas Schlemper
Madhu Lal-Nag
Urmila Sreenivasan
John McLenithan
Slava Ziegler
Carole Sztalryd
Achim Lass
Douglas Auld
Brian Oliver
Zhuyin Li
Min Shen
Matthew B Boxer

EBioMedicine

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.

2016-04-16

Gregory E Crawford

Christopher L Frank
Dinesh Manandhar
Raluca Gordân

Epigenetics & Chromatin

Burkholderia pseudomallei Capsule Exacerbates Respiratory Melioidosis but Does Not Afford Protection against Antimicrobial Signaling or Bacterial Killing in Human Olfactory Ensheathing Cells.

2016-04-18

Glen C Ulett

Samantha J Dando
Deepak S Ipe
Michael Batzloff
Matthew J Sullivan
David K Crossman
Michael Crowley
Emily Strong
Stephanie Kyan
Sophie Y Leclercq
Jenny A K Ekberg
James St John
Ifor R Beacham

Infection and Immunity

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

2016-04-19

Carolyn O'Connor
Jerika Barron
Baptiste N Jaeger
Jennifer Erwin

Benjamin Lacar
Sara B Linker
Suguna Krishnaswami
Martijn Kelder
Sarah Parylak
Apuã Paquola
Pratap Venepally
Mark Novotny
Conor Fitzpatrick
Jonathan Y Hsu
David Husband
Michael J McConnell
Roger Lasken
Fred H Gage

Nature Communications

Beta-Poisson model for single-cell RNA-seq data analyses.

2016-04-19

Trung N. Vu
Krishna R Kalari

Quin F Wills
Nifang Niu
Liewei Wang
Mattias Rantalainen
Yudi Pawitan

Bioinformatics

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

2016-04-19

John P. Bannantine

Randy J Hempel
Judith R Stabel

PLOS ONE

Insights into the Mechanisms Underlying Ultraviolet-C Induced Resveratrol Metabolism in Grapevine (V. amurensis Rupr.) cv. "Tonghua-3"

2016-04-19

Hao Wang

Xiangjing Yin
Stacy D Singer
Hengbo Qiao
Yajun Liu
Chen Jiao
Zhi Li
Zhangjun Fei
Yuejin Wang
Chonghui Fan
Xiping Wang

Frontiers in Plant Science

TNF is a key cytokine mediating neutrophil cytotoxic activity in breast cancer patients.

2016-04-20

Larry Norton

Elizabeth Comen
Paulina Wojnarowicz
Venkatraman E Seshan
Riddhi Shah
Courtney Coker
Robert Benezra

NPJ breast cancer

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome.

2016-04-20

Cheong Xin Chan
Mark A. Ragan

A R Mohamed
V Cumbo
S Harii
C Shinzato
D G Bourne
B L Willis
E E Ball
N Satoh
D J Miller

Molecular Ecology

Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar "Svilena".

2016-04-21

Jochen Kumlehn

Felix Seifert
Sandra Bössow
Heike Gnad
Stefan Scholten

BMC Plant Biology

Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners.

2016-04-21

Bruna Lancia Zampieri
Enrique Medina-Acosta

Antônio Francisco Alves da Silva
Filipe Brum Machado
Érika Cristina Pavarino
Joice Matos Biselli-Périco
Ronaldo da Silva Francisco Junior
Pedro Thyago Mozer Rodrigues
Douglas Terra Machado
Cíntia Barros Santos-Rebouças
Maria Gomes Fernandes
Susana Marina Chuva de Sousa Lopes
Álvaro Fabricio Lopes Rios

PLOS ONE

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.

2016-04-21

Yisrael Parmet

Dena Leshkowitz
Ester Feldmesser
Gilgi Friedlander
Ghil Jona
Elena Ainbinder
Shirley Horn-Saban

PLOS ONE

Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells

2016-04-21

Manuel Mattheisen
Jessica Johnson
Gerard Cagney
Kristen J. Brennand
Douglas Ruderfer
David R Cotter

Aaron Topol
Shijia Zhu
Brigham J Hartley
Jane English
Mads E Hauberg
Ben Readhead
Ngoc Tran
Chelsea Ann Rittenhouse
Anthony Simone
Yoav Hadas
Peter A Gochman
Ying-Chih Wang
Hardik Shah
Judith Rapoport
Fred H Gage
Joel T Dudley
Pamela Sklar
Gang Fang

Cell Reports

RNA-seq analysis of early enteromyxosis in turbot (Scophthalmus maximus): new insights into parasite invasion and immune evasion strategies.

2016-04-21

Ariadna Sitjà-Bobadilla
Paolo Ronza
Ana Paula Losada
Belén G Pardo
Paulino Martínez

Diego Robledo
Roberto Bermúdez
María Isabel Quiroga

International Journal for Parasitology

A benchmark for RNA-seq quantification pipelines.

2016-04-23

Mingxiang Teng
Michael I Love

Carrie A Davis
Sarah Djebali
Alexander Dobin
Brenton R Graveley
Sheng Li
Christopher E Mason
Sara Olson
Dmitri Pervouchine
Cricket A Sloan
Xintao Wei
Lijun Zhan
Rafael A Irizarry

Genome Biology

Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis

2016-04-25

Benjamin King

Elaine C Lee
Heejung Kim
Jennifer Ditano
Dacie Manion
Kevin Strange

PLOS ONE

Survey of cryptic unstable transcripts in yeast.

2016-04-26

Robin Dowell

Jessica M Vera

BMC Genomics

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.

2016-04-26

Mark S Cembrowski
Lihua Wang
Ken Sugino
Brenda C Shields
Nelson Spruston

eLife

A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus.

2016-04-26

Nicholas R Waters

David J Samuels
Ranjan K Behera
Jonathan Livny
Kyu Y Rhee
Marat R Sadykov
Shaun R Brinsmade

Molecular Microbiology

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

2016-04-27

John C Marioni

Aaron T L Lun
Karsten Bach

Genome Biology

RNA-seq Identification of RACGAP1 as a Metastatic Driver in Uterine Carcinosarcoma.

2016-04-27

Deyou Zheng

Shijun Mi
Mingyan Lin
Jurriaan Brouwer-Visser
Jennifer Heim
David Smotkin
Tiffany Hebert
Marc J Gunter
Gary L Goldberg
Gloria S Huang

Clinical Cancer Research

Transcriptional changes of mouse splenocyte organelle components following acute infection with Toxoplasma gondii.

2016-04-27

Xing-Quan Zhu

Jun-Jun He
Jun Ma
Fa-Cai Li
Hui-Qun Song
Min-Jun Xu

Experimental Parasitology

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.

2016-04-28

Aviv Regev
Yaron de Leeuw
Leon Anavy
Itai Yanai
Orit Rozenblatt-Rosen

Tamar Hashimshony
Naftalie Senderovich
Gal Avital
Agnes Klochendler
Dave Gennert
Shuqiang Li
Kenneth J Livak
Yuval Dor

Genome Biology

Structural and transcriptomic response to antenatal corticosteroids in an Erk3-null mouse model of respiratory distress.

2016-04-30

Kjersti M Aagaard

Braden K Pew
R Alan Harris
Elena Sbrana
Milenka Cuevas Guaman
Cynthia Shope
Rui Chen
Sylvain Meloche

American Journal of Obstetrics and Gynecology

Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults.

2016-05

Toshiaki Yujiri
Masahito Kawazu
Eisei Kondo

Takahiko Yasuda
Shinobu Tsuzuki
Fumihiko Hayakawa
Shinya Kojima
Toshihide Ueno
Naoto Imoto
Shinji Kohsaka
Akiko Kunita
Koichiro Doi
Toru Sakura
Katsumichi Fujimaki
Yasunori Ueda
Yasutaka Aoyama
Shigeki Ohtake
Junko Takita
Eirin Sai
Masafumi Taniwaki
Mineo Kurokawa
Shinichi Morishita
Masashi Fukayama
Hitoshi Kiyoi
Yasushi Miyazaki
Tomoki Naoe
Hiroyuki Mano

Nature Genetics

The Staphylococcus aureus Global Regulator MgrA Modulates Clumping and Virulence by Controlling Surface Protein Expression

2016-05

Heidi A Crosby
Wilmara Salgado-Pabón
Patrick M. Schlievert

Joseph A Merriman
Jessica M King
Alexander R Horswill

PLOS Pathogens

RNA-sequencing study of peripheral blood monocytes in chronic periodontitis

2016-05-01

Melody Baddoo
Hong-Wen Deng
Erik K Flemington

Yao-Zhong Liu
Pooja Maney
Jyoti Puri
Yu Zhou
Melody Baddoo
Michael Strong
Yu-Ping Wang

Gene

Wishbone identifies bifurcating developmental trajectories from single-cell data.

2016-05-02

Dana Pe'er

Manu Setty
Michelle D Tadmor
Shlomit Reich-Zeliger
Omer Angel
Tomer Meir Salame
Pooja Kathail
Kristy Choi
Sean Bendall
Nir Friedman
Dana Pe'er

Nature Biotechnology

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure.

2016-05-02

Yong-Guan Zhu

Yingjiao Zhang
Songcan Chen
Xiuli Hao
Jian-Qiang Su
Ximei Xue
Yu Yan
Jun Ye

Frontiers in Microbiology

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq.

2016-05-03

Alessandro Cellerino
Matthias Platzer

S Marthandan
M Baumgart
S Priebe
M Groth
J Schaer
C Kaether
R Guthke
S Diekmann
P Hemmerich

PLOS ONE

Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton

2016-05-03

Thibaut Léger
Róbert Šuťák
Jean-Michel Camadro
Chris Bowler

Gaëlle Lelandais
Ivo Scheiber
Javier Paz-Yepes
Jean-Claude Lozano
Hugo Botebol
Jana Pilátová
Vojtěch Žárský
Pierre-Louis Blaiseau
François-Yves Bouget
Emmanuel Lesuisse

BMC Genomics

Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs.

2016-05-03

Anne Van den Broeke
Arsène Burny
Nicolas Rosewick

Keith Durkin
Maria Artesi
Vincent Hahaut
Philip Griebel
Natasa Arsic
Michel Georges
Anne Van den Broeke

Retrovirology

Single-Cell Genomics for Virology

2016-05-04

Amalio Telenti

Angela Ciuffi
Sylvie Rato

Viruses

The Trichoderma atroviride putative transcription factor Blu7 controls light responsiveness and tolerance.

2016-05-04

Alfredo Herrera-Estrella

José E Cetz-Chel
Edgar Balcázar-López
Edgardo U Esquivel-Naranjo

BMC Genomics

Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level.

2016-05-04

Nicolas Terrapon
Christopher J Fields
Evelyne Forano
Bernard Henrissat

Jordane Despres
Pascale Lepercq
Sophie Comtet-Marre
Gregory Jubelin
Christophe Chambon
Carl J Yeoman
Margaret E Berg Miller
Eric Martens
Bryan A White
Pascale Mosoni

BMC Genomics

Modeling Doxorubicin-Induced Cardiotoxicity in Human Pluripotent Stem Cell Derived-Cardiomyocytes

2016-05-04

Michael R. Hayden

Agnes Maillet
Kim Tan
Xiaoran Chai
Singh N Sadananda
Ashish Mehta
Jolene Ooi
Mahmoud A Pouladi
Sujoy Ghosh
Winston Shim
Liam R Brunham

Scientific Reports

NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes.

2016-05-04

Nikki A. Copeland

Andrew S Marriott
Olga Vasieva
Yongxiang Fang
Alexander G McLennan
Nigel J Jones

PLOS ONE

Exploiting single-cell expression to characterize co-expression replicability

2016-05-06

Jesse Gillis

Megan Crow
Anirban Paul
Sara Ballouz
Z Josh Huang

Genome Biology

Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks.

2016-05-09

Gregory Poland

Bahareh Rahmani
Michael T Zimmermann
Diane E Grill
Richard B Kennedy
Ann L Oberg
Bill C White
Brett A McKinney

Frontiers in Genetics

Recovery of high-quality RNA from laser capture microdissected human and rodent pancreas.

2016-05-10

Peter C Butler

Alexandra E Butler
Aleksey V Matveyenko
David Kirakossian
Johanna Park
Tatyana Gurlo

Journal of histotechnology

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

2016-05-10

John K. Colbourne
Christoph R Haag
Mikko J Frilander
Dieter Ebert
Anurag Chaturvedi
Jouni Kvist
J Asselman
Ellen Decaestecker
Luisa Orsini
Adam Petrusek
Ram Podicheti

Donald Gilbert
Mieke Jansen
James B Brown
Omid Shams Solari
Katina I Spanier
Douglas Rush
Karel A C De Schamphelaere
Christian Laforsch
Andrew P Beckerman
Tom J Little
Michael E Pfrender
Luc De Meester

Scientific Data

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report.

2016-05-10

Dan J. Stein
Anne Uhlmann

M S Breen
C M Nday
S J Glatt
M Mitt
A Metsalpu
N Illing

Translational Psychiatry

Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma.

2016-05-10

Ling-Wen Ding
Anand Mayakonda
Liang Xu

Yan-Yi Jiang
De-Chen Lin
Masaharu Hazawa
Wen-Wen Chien
Ye Chen
Jin-Fen Xiao
William Senapedis
Erkan Baloglu
Deepika Kanojia
Li Shang
Xin Xu
Henry Yang
Jeffrey W Tyner
Ming-Rong Wang
H Phillip Koeffler

Gut

RNA-Seq of Huntington's disease patient myeloid cells reveals innate transcriptional dysregulation associated with proinflammatory pathway activation.

2016-05-11

Sarah J. Tabrizi

James R C Miller
Kitty K Lo
Ralph Andre
Davina J Hensman Moss
Ulrike Träger
Timothy C Stone
Lesley Jones
Peter Holmans
Vincent Plagnol

Human Molecular Genetics

Persistent Alterations in Microglial Enhancers in a Model of Chronic Pain.

2016-05-11

Douglas M. Lopes
Athanasios Didangelos
Franziska Denk

Megan Crow
Stephen B McMahon

Cell Reports

RNA-Seq Analysis Reveals Genes Underlying Different Disease Responses to Porcine Circovirus Type 2 in Pigs.

2016-05-12

Shijin Jiang

Yanping Li
Hao Liu
Pengfei Wang
Liyuan Wang
Yi Sun
Gen Liu
Ping Zhang
Li Kang
Yunliang Jiang

PLOS ONE

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation

2016-05-12

Tapio Lönnberg
Valentina Proserpio
Giacomo Donati
Kedar N Natarajan
Oliver Billker
Mario Nicodemi
Sarah Teichmann

Andrea Piccolo
Liora Haim-Vilmovsky
Gozde Kar
Valentine Svensson
Jhuma Pramanik
Weichao Zhai
Xiuwei Zhang
Melis Kayikci
Jurij Kotar
Andrew N J McKenzie
Ruddy Montandon
Steven Woodhouse
Pietro Cicuta

Genome Biology

An updated human snoRNAome.

2016-05-12

Mihaela Zavolan
Jana Hertel
Stephanie Kehr
Peter F. Stadler

Hadi Jorjani
Dominik J Jedlinski
Rafal Gumienny
Andreas R Gruber

Nucleic Acids Research

Dual Identification and Analysis of Differentially Expressed Transcripts of Porcine PK-15 Cells and Toxoplasma gondii during in vitro Infection.

2016-05-13

Xing-Quan Zhu
Dong-Hui Zhou

Chun-Xue Zhou
Hany M Elsheikha
Qing Liu
Xun Suo

Frontiers in Microbiology

The transcriptome of mouse central nervous system myelin.

2016-05-13

Sudhir Thakurela
Hauke Werner

Angela Garding
Ramona B Jung
Christina Müller
Sandra Goebbels
Robin White
Vijay K Tiwari

Scientific Reports

Polycomb repressive complex 1 controls uterine decidualization.

2016-05-16

Artem Barski
Anil G. Jegga

Fenghua Bian
Fei Gao
Andrey V Kartashov
Sanjoy K Das

Scientific Reports

Molecular Mechanisms of Malignant Transformation by Low Dose Cadmium in Normal Human Bronchial Epithelial Cells.

2016-05-17

Steven Shen

Laura Cartularo
Thomas Kluz
Lisa Cohen
Max Costa

PLOS ONE

De Novo Sequencing and Transcriptome Analysis of Pleurotus eryngii subsp. tuoliensis (Bailinggu) Mycelia in Response to Cold Stimulation.

2016-05-17

Songnian Hu

Yong-Ping Fu
Yuan Liang
Yue-Ting Dai
Chen-Tao Yang
Ming-Zheng Duan
Zhuo Zhang
Zhi-Wu Zhang
Yu Li

Molecules

Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance.

2016-05-17

Matteo Pellegrini

Hanwei Zhang
Kris Prado
Kelvin X Zhang
Elizabeth M Peek
Jane Lee
Xiaoyan Wang
Jiaoti Huang
Gang Li
Arnold I Chin

Clinical Cancer Research

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.

2016-05-18

Lawrence H. Uricchio

Noah A Zaitlen
Chun Jimmie Ye
John S Witte
Ryan D Hernandez

Genome Research

Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy.

2016-05-18

Yaobo Xu
Aurora Gomez-Duran
Rita Horvath
Veronika Boczonadi

Michele Giunta
Shimon Edvardson
Markus Schuelke
Orly Elpeleg
Juliane S Müller

Human Molecular Genetics

The Proteasome Stress Regulon Is Controlled by a Pair of NAC Transcription Factors in Arabidopsis.

2016-05-18

Richard D Vierstra

Nicholas P Gladman
Richard S Marshall
Kwang-Hee Lee

The Plant Cell

Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing.

2016-05-18

David K. Crossman

Ivan K Popov
Taejoon Kwon
Michael R Crowley
John B Wallingford
Chenbei Chang

Developmental Biology

Hair-Cell Mechanotransduction Persists in TRP Channel Knockout Mice.

2016-05-19

Artur A Indzhykulian

Xudong Wu
Paul D Niksch
Roxanna M Webber
Miguel Garcia-Gonzalez
Terry Watnick
Jing Zhou
Melissa A Vollrath
David P Corey

PLOS ONE

Novel non-canonical role of STAT1 in Natural Killer cell cytotoxicity.

2016-05-19

Christopher Gerner
Andrea Majoros
Eva Maria Putz
Eva M Putz
Mathias Müller

Dagmar Gotthardt
Michaela Prchal-Murphy
Eva Maria Zebedin-Brandl
Daniela Alexandra Fux
Andreas Schlattl
Robert D Schreiber
Sebastian Carotta
Thomas Decker
Veronika Sexl

OncoImmunology

Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance.

2016-05-21

Gary J Muehlbauer

Yadong Huang
Lin Li
Kevin P Smith

BMC Genomics

Group II mGluRs suppress hyperexcitability in mouse and human nociceptors.

2016-05-21

Pradipta R Ray
Theodore J. Price

Steve Davidson
Judith P Golden
Bryan A Copits
Sherri K Vogt
Manouela V Valtcheva
Robert E Schmidt
Andrea Ghetti
Robert W Gereau

Pain

Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis.

2016-05-23

Mark Q Martindale

Leslie S Babonis
Joseph F Ryan

BMC Evolutionary Biology

A Laser Dissection-RNAseq Analysis Highlights the Activation of Cytokinin Pathways by Nod Factors in the Medicago truncatula Root Epidermis.

2016-05-23

Jérôme Gouzy
Ludovic Cottret
Anna Kisiala
Pascal Gamas

Marie-Françoise Jardinaud
Stéphane Boivin
Nathalie Rodde
Olivier Catrice
Agnes Lepage
Sandra Moreau
Brice Roux
Erika Sallet
Mathias Brault
R J Neil Emery
Florian Frugier

Plant Physiology

Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis.

2016-05-23

Mukesh Kumar

Mahdi Belcaid
Vivek R Nerurkar

Scientific Reports

Rho GTPase Transcriptome Analysis Reveals Oncogenic Roles for Rho GTPase-Activating Proteins in Basal-like Breast Cancers

2016-05-23

Charles M. Perou

Campbell D Lawson
Cheng Fan
Natalia Mitin
Nicole M Baker
Samuel D George
David M Graham
Keith Burridge
Channing J Der
Kent L Rossman

Cancer Research

Small molecule inhibition of cAMP response element binding protein in human acute myeloid leukemia cells.

2016-05-23

Matteo Pellegrini

B Mitton
H-D Chae
K Hsu
R Dutta
G Aldana-Masangkay
R Ferrari
K Davis
B C Tiu
A Kaul
N Lacayo
G Dahl
F Xie
B X Li
M R Breese
E M Landaw
G Nolan
S Romanov
X Xiao
K M Sakamoto

Leukemia

Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus.

2016-05-23

Erich Bornberg-Bauer

David Haase
Jenny K Rieger
Anika Witten
Monika Stoll
Martin Kalbe
Alexander Schmidt-Drewello
Jörn P Scharsack
Thorsten B H Reusch

Zoology

Prediction and Quantification of Splice Events from RNA-Seq Data

2016-05-24

Robert Gentleman

Leonard D Goldstein
Yi Cao
Gregoire Pau
Michael Lawrence
Thomas D Wu
Somasekar Seshagiri

PLOS ONE

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells

2016-05-24

Vincent Schulz

Laurie A Steiner
Yelena Makismova
Kimberly Lezon-Geyda
Patrick G Gallagher

PLOS ONE

Female rat transcriptome response to infraorbital nerve transection differs from that of males: RNA-seq.

2016-05-25

John J Orczyk

Richard Batka
Ashleigh Gore
Michelena Maio-Lexa
Akhil Kulkarni
Preston E Garraghty

The Journal of Comparative Neurology

Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin.

2016-05-26

Jiayin Li

Xiaoya Tao
Li Li
Linchun Mao
Zisheng Luo
Zia Ullah Khan
Tiejin Ying

PLOS ONE

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts

2016-05-26

Lior Pachter

Vasilis Ntranos
Govinda M Kamath
Jesse M Zhang
David N Tse

Genome Biology

JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells.

2016-05-26

Thomas G Beach

Yuxin Li
Xusheng Wang
Ji-Hoon Cho
Timothy I Shaw
Zhiping Wu
Bing Bai
Hong Wang
Suiping Zhou
Gang Wu
Jinghui Zhang
Junmin Peng

Journal of Proteome Research

Phosphorus remobilization from rice flag leaves during grain filling: an RNA-seq study.

2016-05-26

Tobias Kretzschmar
Abdul Baten

Kwanho Jeong
Daniel L E Waters
Omar Pantoja
Cecile C Julia
Matthias Wissuwa
Sigrid Heuer
Terry J Rose

Plant Biotechnology Journal

RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4

2016-05-26

Jason Gertz
Donald J Buchsbaum

Marie K Kirby
Ryne C Ramaker
Nicholas S Davis
Bobbi E Johnston
Patsy G Oliver
Katherine C Sexton
Edward W Greeno
John D Christein
Martin J Heslin
James A Posey
William E Grizzle
Selwyn M Vickers
Sara J Cooper
Richard M Myers

Molecular Oncology

Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans.

2016-05-26

Christina A Cuomo
Robert T Wheeler
Michelle D Leach
Rhys A Farrer
Kaeling Tan
Leah E Cowen
Alistair J P Brown

Zhengqiang Miao
Louise A Walker
Koon Ho Wong

Nature Communications

An atlas of gene expression and gene co-regulation in the human retina.

2016-05-27

Luisa Cutillo
Sandro Banfi
Diego di Bernardo
Annamaria Carissimo
Michele Pinelli
Diego Ponzin

Ching-Hung Lai
Margherita Mutarelli
Maria Nicoletta Moretti
Marwah Veer Singh
Marianthi Karali
Diego Carrella
Mariateresa Pizzo
Francesco Russo
Stefano Ferrari
Claudia Angelini

Nucleic Acids Research

Landscape of tumor-infiltrating T cell repertoire of human cancers

2016-05-30

Nir Hacohen

Bo Li
Taiwen Li
Jean-Christophe Pignon
Binbin Wang
Jinzeng Wang
Sachet A Shukla
Ruoxu Dou
Qianming Chen
F Stephen Hodi
Toni K Choueiri
Catherine Wu
Sabina Signoretti
Jun S Liu
X Shirley Liu

Nature Genetics

Resistance to docetaxel in prostate cancer is associated with androgen receptor activation and loss of KDM5D expression

2016-05-31

Philip W. Kantoff

Kazumasa Komura
Seong Ho Jeong
Kunihiko Hinohara
Fangfang Qu
Xiaodong Wang
Masayuki Hiraki
Haruhito Azuma
Gwo-Shu Mary Lee
Christopher J. Sweeney

Proceedings of the National Academy of Sciences of the United States of America

The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p

2016-05-31

Cei Abreu-Goodger
Xin Yan
Sudhir Gopal Tattikota
Gergely Nagy
Eva Varallyay
Laszlo Nagy

Zsolt Czimmerer
Tamas Varga
Mate Kiss
Cesaré Ovando Vázquez
Quang Minh Doan-Xuan
Dominik Rückerl
Zsuzsanna S Nagy
Bence Daniel
Szilard Poliska
Attila Horvath
Matthew N Poy
Judith E Allen
Zsolt Bacso

Genome Medicine

Combined physiological, transcriptome, and cis-regulatory element analyses indicate that key aspects of ripening, metabolism, and transcriptional program in grapes (Vitis vinifera L.) are differentially modulated accordingly to fruit size

2016-05-31

Darren Wong

R Lopez Gutierrez
N Dimopoulos
G A Gambetta
S D Castellarin

BMC Genomics

Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

2016-05-31

Gane Ka-Shu Wong
Michael Melkonian
Caroline Rempe
Mark W. Chase

Thomas S Lane
Jack Davitt
Margaret E Staton
Yanhui Peng
Douglas Edward Soltis
Michael Melkonian
Michael Deyholos
James H Leebens-Mack
Carl J Rothfels
Dennis Stevenson
Sean W Graham
Jun Yu
Tao Liu
J Chris Pires
Patrick P Edger
Yong Zhang
Yinlong Xie
Ying Zhu
Eric Carpenter
C Neal Stewart

BMC Biotechnology

Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis.

2016-05-31

Julia A. Horsfield
Shinichi Nakagawa
Aniruddha Chatterjee
Malgorzata Lagisz

Euan J Rodger
Li Zhen
Peter A Stockwell
Elizabeth J Duncan
Justin Jeyakani
Sinnakaruppan Mathavan
Yuichi Ozaki

Gene

Bluetongue Virus NS4 Protein Is an Interferon Antagonist and a Determinant of Virus Virulence

2016-06-01

Anna Janowicz
Marco Caporale
Massimo Palmarini

Maxime Ratinier
Andrew E Shaw
Gerald Barry
Quan Gu
Luigina Di Gialleonardo
Mariana Varela
Richard E Randall

Journal of Virology

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq

2016-06-01

James C Mullikin

Stephen W Hartley

Nucleic Acids Research

The contribution of cell cycle to heterogeneity in single-cell RNA-seq data.

2016-06-01

Andrew McDavid

Greg Finak
Raphael Gottardo

Nature Biotechnology

ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells

2016-06-01

Kristian Helin
Marco Cammisa
Gaetano Verde
Aditya Sankar
Robert Feil
Andrea Riccio

Vincenzo Riso
Harpreet Kukreja
Zahra Anvar
Angela Sparago
Basilia Acurzio
Shraddha Lad
Enza Lonardo
Annalisa Fico
Claudia Angelini
Giovanna Grimaldi

Nucleic Acids Research

Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data.

2016-06-02

Janine E. Deakin
Kristine Hardy
Alexie Papanicolaou
Stephen D. Sarre

Alexandra Livernois
Renae Domaschenz
Arthur Georges
Sudha Rao
Tariq Ezaz

Immunogenetics

Transcriptome Profiling Identifies Multiplexin as a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance During Drosophila Visual Development

2016-06-03

Vikki M. Weake

Jingqun Ma
Kaelan J Brennan
Mitch R D'Aloia
Pete E Pascuzzi

Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)

2016-06-06

Allen Collins

Ehsan Kayal
Bastian Bentlage

RNA Biology

RNA-seq Analysis of δ9-Tetrahydrocannabinol-treated T Cells Reveals Altered Gene Expression Profiles That Regulate Immune Response and Cell Proliferation.

2016-06-06

Mitzi Nagarkatti

Xiaoming Yang
Marpe Bam
Prakash S Nagarkatti

Journal of Biological Chemistry

Erratum to: Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.

2016-06-06

Christopher J Fields
Evelyne Forano
Bernard Henrissat

Jordane Despres
Pascale Lepercq
Sophie Comtet-Marre
Grégory Jubelin
Carl J Yeoman
Margret E Berg Miller
Nicolas Terrapon
Carine Le Bourvellec
Catherine M G C Renard
Bryan A White
Pascale Mosoni

BMC Genomics

Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

2016-06-07

Mark Lathrop
Diana Zelenika
Naftali Kaminski

Tasha E Fingerlin
Weiming Zhang
Ivana V Yang
Hannah C Ainsworth
Pamela H Russell
Rachel Z Blumhagen
Marvin I Schwarz
Kevin K Brown
Mark P Steele
James E Loyd
Gregory P Cosgrove
David A Lynch
Steve Groshong
Harold R Collard
Paul J Wolters
Williamson Z Bradford
Karl Kossen
Scott D Seiwert
Roland M du Bois
Christine Kim Garcia
Megan S Devine
Gunnar Gudmundsson
Helgi J Isaksson
Yingze Zhang
Kevin F Gibson
Lisa H Lancaster
Toby M Maher
Philip L Molyneaux
Athol U Wells
Miriam F Moffatt
Moises Selman
Annie Pardo
Dong Soon Kim
James D Crapo
Barry J Make
Elizabeth A Regan
Dinesha S Walek
Jerry J Daniel
Yoichiro Kamatani
Elissa Murphy
Keith Smith
David McKean
Brent S Pedersen
Janet Talbert
Julia Powers
Cheryl R Markin
Kenneth B Beckman
Brian Freed
Carl D Langefeld
David A Schwartz

BMC Genetics

CRAF R391W is a melanoma driver oncogene

2016-06-08

Bartosz Chmielowski
Antoni Ribas
Anastasia Lomova
Bjoern Titz
Thomas Graeber

Mohammad Atefi
Jennifer Tsoi
Earl Avramis
Allison Le
Charles Ng
Amanda Lassen
Michael Friedman

Scientific Reports

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

2016-06-08

Moritz Mall
Barbara Treutlein
Marius Wernig

Qian Yi Lee
J Gray Camp
Winston Koh
Seyed Ali Mohammad Shariati
Sopheak Sim
Norma F Neff
Jan M Skotheim
Stephen R Quake

Nature

Reduced Expression of Histone Methyltransferases KMT2C and KMT2D Correlates with Improved Outcome in Pancreatic Ductal Adenocarcinoma

2016-06-08

Frances R Balkwill
Jun Wang
Claude Chelala
Jude Fitzgibbon

Joshua B N Dawkins
Eleni Maniati
James A Heward
Lola Koniali
Hemant M Kocher
Sarah A Martin
Richard P Grose

Cancer Research

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

2016-06-09

Marie-Agnès Dillies

Hugo Varet
Loraine Brillet-Guéguen
Jean-Yves Coppée

PLOS ONE

Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410.

2016-06-09

Gautam Dantas

Aki Yoneda
Bruce J Wittmann
Jeremy D King
Robert E Blankenship

Photosynthesis Research

A unique stylopod patterning mechanism by Shox2-controlled osteogenesis.

2016-06-10

Marco Osterwalder
Axel Visel

Wenduo Ye
Yingnan Song
Zhen Huang
Anja Ljubojevic
Jue Xu
Brent Bobick
Samuel Abassah-Oppong
Ningsheng Ruan
Ross Shamby
Diankun Yu
Lu Zhang
Chen-Leng Cai
Yanding Zhang
John Cobb
YiPing Chen

Development

RTFBSDB: an integrated framework for transcription factor binding site analysis.

2016-06-10

Charles G Danko

Zhong Wang
André L Martins

Bioinformatics

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

2016-06-11

Anand Swaroop
Rinki Ratnapriya

Vijender Chaitankar
Gökhan Karakülah
Felipe O Giuste
Matthew J Brooks

Progress in Retinal and Eye Research

Candida albicans Transcriptional Profiling Within Biliary Fluid From a Patient With Cholangitis, Before and After Antifungal Treatment and Surgical Drainage

2016-06-11

Nathan L Clark

Cornelius J Clancy
Camille Meslin
Hassan Badrane
Shaoji Cheng
Liliana C Losada
William C Nierman
Pascalis Vergidis
M Hong Nguyen

Open forum infectious diseases

Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals

2016-06-13

Juan A. Bernal
Ferdinand Marlétaz
Ignacio Maeso
Thomas L Dunwell
Manuel Irimia

Chris D R Wyatt
Borbála Vető
Shan Quah
Peter W H Holland

BMC Biology

RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome

2016-06-13

Paulina Carmona-Mora

Susan M Corley
Cesar P Canales
Veronica Mendoza-Reinosa
Annemiek Beverdam
Edna C Hardeman
Marc R Wilkins
Stephen J Palmer

BMC Genomics

Boiler: lossy compression of RNA-seq alignments using coverage vectors.

2016-06-13

Ben Langmead

Jacob Pritt

Nucleic Acids Research

Getting Useful Information from RNA-Seq Contaminants: A Case of Study in the Oil-Collecting Bee Tetrapedia diversipes Transcriptome.

2016-06-13

Maria C. Arias

Natalia de Souza Araujo
Alexandre Rizzo Zuntini

OMICS: A Journal of Integrative Biology

Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein.

2016-06-14

Keith D Rivera

Victoria L M Herrera
Martin Steffen
Ann Marie Moran
Glaiza A Tan
Khristine A Pasion
Darryl J Pappin
Nelson Ruiz-Opazo

BMC Molecular Biology

Characterization of RON protein isoforms in pancreatic cancer: implications for biology and therapeutics.

2016-06-14

Carsten Schultz-Fademrecht

Jeffery Chakedis
Randall French
Michele Babicky
Dawn Jaquish
Evangeline Mose
Peter Cheng
Patrick Holman
Haleigh Howard
Jaclyn Miyamoto
Paula Porras
Zakk Walterscheid
Christina Esdar
Oliver Schadt
Jan Eickhoff
Andrew M Lowy

Oncotarget

Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression.

2016-06-14

Edward C. Holmes

Kurtis H Feng
Miao Sun
Sho Iketani
Colin R Parrish

Virology

Genome-wide analysis of pentatricopeptide-repeat proteins of an aquatic plant.

2016-06-15

Wenqin Wang
Joachim Messing

Yongrui Wu

Planta

Transcriptome Display During Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis.

2016-06-15

Shikai Liu
Rex Dunham

Qifan Zeng
Jun Yao
Yu Zhang
Zihao Yuan
Chen Jiang
Ailu Chen
Qiang Fu
Baofeng Su
Zhanjiang Liu

Biology of Reproduction

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

2016-06-17

Monther Alhamdoosh
Matthew E Ritchie
Gordon K Smyth

Charity W Law
Shian Su

F1000Research

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

2016-06-19

Takashi Gojobori
Kazuho Ikeo

Masakazu Ishikawa
Ikuko Yuyama
Hiroshi Shimizu
Masafumi Nozawa

Genome Biology and Evolution

Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress.

2016-06-20

Martin L Hibberd

Wenwei Lin
Paola Florez de Sessions
Garrett Hor Keong Teoh
Ahmad Naim Nazri Mohamed
Yuan O Zhu
Vanessa Hui Qi Koh
Michelle Lay Teng Ang
Peter C Dedon
Sylvie Alonso

Infection and Immunity

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

2016-06-20

Gordon K Smyth

Yunshun Chen
Aaron T L Lun

F1000Research

GATA6 regulates EMT and tumour dissemination, and is a marker of response to adjuvant chemotherapy in pancreatic cancer.

2016-06-20

Marina Pajic
Andrew Biankin
John P Neoptolemos
Paola Martinelli
Nelson Dusetti
Francisco X Real
Eithne Costello
Markus Büchler

Enrique Carrillo-de Santa Pau
Trevor Cox
Bruno Sainz
William Greenhalf
Lorenzo Rinaldi
Paula Ghaneh
Núria Malats
Juan Iovanna

Gut

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

2016-06-21

Jorge Dubcovsky
Néstor Kippes
Juan Manuel Debernardi

Stephen Pearce
Andrew Chen

BMC Plant Biology

2016-06-21

Anne-Marie Cleton-Jansen
Emily T Camilleri
Annalise Noelle Larson

Scott M Riester
Jorge Torres-Mora
Amel Dudakovic
Wei Wang
Fuhua Xu
Roman R Thaler
Jared M Evans
René Zwartbol
Inge H Briaire-de Bruijn
Avudaiappan Maran
Andrew L Folpe
Carrie Y Inwards
Peter S Rose
Thomas C Shives
Michael J Yaszemski
Franklin H Sim
David R Deyle
Mario A Galindo
Arjen G H Cleven
Andre M Oliveira
Anne-Marie Cleton-Jansen
Judith V M G Bovée
Andre J van Wijnen

Journal of Orthopaedic Research

The activation of OR51E1 causes growth suppression of human prostate cancer cells.

2016-06-21

Hanns Hatt
Günter Gisselmann
Désirée Maßberg

Désirée Maßberg
Nikolina Jovancevic
Anne Offermann
Annika Simon
Aria Baniahmad
Sven Perner
Thanakorn Pungsrinont
Katarina Luko
Stathis Philippou
Burkhard Ubrig
Markus Heiland
Lea Weber
Janine Altmüller
Christian Becker
Günter Gisselmann
Lian Gelis

Oncotarget

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation.

2016-06-21

Zoltan Simandi
Laszlo Nagy

Attila Horvath
Peter Nagy

Journal of Visualized Experiments

Sequencing, de novo assembly and annotation of a pink bollworm larval midgut transcriptome.

2016-06-22

Yves Carrière
Bruce E Tabashnik

Erica E Tassone
Gina Zastrow-Hayes
John Mathis
Mark E Nelson
Gusui Wu
J Lindsey Flexner
Jeffrey A Fabrick

GigaScience

The Ensembl gene annotation system.

2016-06-23

Bronwen Aken
Laura Clarke
Kevin L Howe
Magali Ruffier
Paul Flicek
Felix Kokocinski
Amonida Zadissa
Daniel N Murphy
Carlos García Girón
Rishi Nag
Julio Fernandez Banet
Thibaut Hourlier
Andreas K Kähäri
Susan Fairley
Konstantinos Billis
Fergal J Martin
Simon White

Sarah Ayling
Daniel Barrell
Valery Curwen
Michael Schuster
Y Amy Tang
Jan-Hinnerk Vogel
Stephen M J Searle

Database

The long intergenic non-coding RNA CCR492 functions as a let-7 competitive endogenous RNA to regulate c-Myc expression.

2016-06-23

Raffaele A. Calogero
Francesco Neri

Mara Maldotti
Danny Incarnato
Anna Krepelova
Stefania Rapelli
Francesca Anselmi
Caterina Parlato
Giulia Basile
Daniela Dettori
Salvatore Oliviero

Biochimica et Biophysica Acta

Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation.

2016-06-24

Christine M. Sambles

Sarah E Barchinger
Sahand Pirbadian
Carol S Baker
Kar Man Leung
Nigel J Burroughs
Mohamed Y El-Naggar
John H Golbeck

Applied and Environmental Microbiology

Integrating transcriptome and proteome profiling: Strategies and applications.

2016-06-25

Dhirendra Kumar

Gourja Bansal
Ankita Narang
Trayambak Basak
Tahseen Abbas
Debasis Dash

Proteomics

Expression of Bcl-2 genes in channel catfish after bacterial infection and hypoxia stress.

2016-06-25

Shikai Liu

Zihao Yuan
Jun Yao
Qifan Zeng
Suxu Tan
Zhanjiang Liu

Developmental and Comparative Immunology

Blood lipids influence DNA methylation in circulating cells.

2016-06-27

Cornelia M. van Duijn
André Uitterlinden
Gonneke Willemsen
Cisca Wijmenga
Daria V. Zhernakova
Marc Jan Bonder
Lude Franke
Koen F Dekkers
Roderick C Slieker
Jenny van Dongen
Rick Jansen
Dorret Boomsma
Peter A.C. 't Hoen
Pieternella E Slagboom
Albert Hofman
Leonard H van den Berg
Jan H Veldink
Coenraad Dirk Adriaan Stehouwer
Casper G. Schalkwijk
Jouke-Jan Hottenga

Maarten van Iterson
Matthijs H Moed
Michiel van Galen
Hailiang Mei
Joris Deelen
Diana van Heemst
Carla J H van der Kallen
Ettje F Tigchelaar
Alexandra Zhernakova
Joyce van Meurs
Marleen M J van Greevenbroek
BIOS Consortium
Erik W van Zwet
J Wouter Jukema
Bastiaan T Heijmans

Genome Biology

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia

2016-06-29

Juha Kere
Elisabet Einarsdottir
Kaarel Krjutškov
Anna-Elina Lehesjoki
Shintaro Katayama

Inken Körber
Elisabet Einarsdottir
Paula Hakala
Tarja Joensuu

PLOS ONE

A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration

2016-06-29

Benjamin King

Viravuth P Yin

PLOS ONE

Long-read sequencing and de novo assembly of a Chinese genome

2016-06-30

Francoise Thibaud-Nissen

Lingling Shi
Yunfei Guo
Chengliang Dong
John Huddleston
Hui Yang
Xiaolu Han
Aisi Fu
Quan Li
Na Li
Siyi Gong
Katherine E Lintner
Qiong Ding
Zou Wang
Jiang Hu
Depeng Wang
Feng Wang
Lin Wang
Gholson J Lyon
Yongtao Guan
Yufeng Shen
Oleg V Evgrafov
James A Knowles
Francoise Thibaud-Nissen
Valerie Schneider
Chack-Yung Yu
Libing Zhou
Evan E Eichler
Kwok-Fai So
Kai Wang

Nature Communications

CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma.

2016-06-30

Matteo Pellegrini
Diana L Moughon
Junhui Hu

Shiruyeh Schokrpur
Peijun Liu
Lucia C Lin
Kip Hermann
Serghei Mangul
Wei Guan
Hua Xu
Lily Wu

Scientific Reports

Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia

2016-07

Benjamin J Ainscough
Elaine Mardis
Katie M Campbell
Benjamin J Ainscough
Kilannin Krysiak
Zachary L Skidmore
Sean D McGrath
Christopher A. Miller
Avinash Ramu
Catrina Fronick

Malachi Griffith
Obi L Griffith
Matthew J Christopher
Jeffery M Klco
Tamara L Lamprecht
Alex H Wagner
Robert Lesurf
Jasreet Hundal
Jin Zhang
Nicholas C Spies
David E Larson
Sharon E Heath
Shelly O'Laughlin
Robert S Fulton
Vincent Magrini
Scott M Smith
Christopher A Maher
Jacqueline E Payton
Jason R Walker
James M Eldred
Matthew J Walter
Daniel C Link
Timothy A Graubert
Peter Westervelt
Shashikant Kulkarni
John F DiPersio
Richard K Wilson
Timothy J Ley

Experimental Hematology

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae

2016-07

Sam Griffiths-Jones
Samina Naseeb

Katarzyna B Hooks
Steven Parker
Daniela Delneri

Genetics

State-feedback control of Partially-Observed Boolean Dynamical Systems using RNA-seq time series data

2016-07

Mahdi Imani

Ulisses Braga-Neto

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.

2016-07-01

Huidong Chen
Luca Pinello

Lan Jiang
Guo-Cheng Yuan

Genome Biology

A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab.

2016-07-01

Susan C. Short
Josie Hayes
David R. Westhead
Martin J van den Bent

Helene Thygesen
Walter Gregory
Pim J French
Sean E Lawler

Molecular Oncology

Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients.

2016-07-01

Matteo Pellegrini

Larry Lam
Lydia Chin
Ramesh C Halder
Bien Sagong
Sam Famenini
James Sayre
Dennis Montoya
Liudmilla Rubbi
Milan Fiala

FASEB Journal

The synovial microenvironment of osteoarthritic joints alters RNA-seq expression profiles of human primary articular chondrocytes.

2016-07-01

Annalise Noelle Larson

Eric A Lewallen
Carolina A Bonin
Xin Li
Jay Smith
Marcel Karperien
David G Lewallen
Simon M Cool
Jennifer J Westendorf
Aaron J Krych
Alexey A Leontovich
Hee-Jeong Im
Andre J van Wijnen

Gene

Comparison of methods to detect differentially expressed genes between single-cell populations.

2016-07-03

Laura L. Elo

Maria K Jaakkola
Fatemeh Seyednasrollah
Arfa Mehmood

Briefings in Bioinformatics

Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease.

2016-07-04

Maurice A Curtis
Henry J. Waldvogel
Christopher A Ross

Lan Lin
Juw Won Park
Shyam Ramachandran
Yida Zhang
Yu-Ting Tseng
Shihao Shen
Richard L M Faull
Juan C Troncoso
Olga Pletnikova
Beverly L Davidson
Yi Xing

Human Molecular Genetics

Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.

2016-07-05

Brage Storstein Andresen
Adrian Robert Krainer

Gitte H Bruun
Thomas K Doktor
Jonas Borch-Jensen
Akio Masuda
Kinji Ohno

BMC Biology

Long noncoding RNAs in B-cell development and activation.

2016-07-05

Andreas Heger
Chris Ponting
Jennifer Müller

Tiago F Brazão
Jethro S Johnson
Victor L J Tybulewicz

Blood

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome

2016-07-05

Gwenola Tosser-Klopp
Gwenola Tosser-Klopp

Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
Christophe Klopp
Juan-José Arranz

Scientific Data

Pho4 mediates phosphate acquisition in Candida albicans and is vital for stress resistance and metal homeostasis

2016-07-06

Janet Quinn
Elizabeth A. Veal
Donna M MacCallum
Herrero-de-Dios CM
Alistair J P Brown

Mélanie A C Ikeh
Stavroula L Kastora
Alison M Day
Emma Tarrant
Kevin J Waldron
A Peter Banks
Judith M Bain
David Lydall
Lars P Erwig

Molecular Biology of the Cell

Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function.

2016-07-06

Gerhard G Thallinger
Brigitte Gasser
Diethard Mattanovich

Minoska Valli
Nadine E Tatto
Armin Peymann
Clemens Gruber
Nils Landes
Heinz Ekker
Alexandra B Graf

FEMS Yeast Research

Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq.

2016-07-07

Dieter Egli

Uri Weissbein
Maya Schachter
Nissim Benvenisty

Nature Communications

Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41.

2016-07-07

Mitchell Machiela
Stephen Chanock

Pierre Bigot
Leandro M Colli
Lea Jessop
Timothy A Myers
Julie Carrouget
Sarah Wagner
David Roberson
Caroline Eymerit
Daniel Henrion

Nature Communications

Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups.

2016-07-07

Ayelet Avraham

Dvir Netanely
Ayelet Avraham
Adit Ben-Baruch
Ella Evron
Ron Shamir

Breast Cancer Research

Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer

2016-07-09

Jason H. Moore

Runmin Wei
Immaculata De Vivo
Sijia Huang
Xun Zhu
Harvey Risch
Herbert Yu
Lana X Garmire

Oncotarget

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association.

2016-07-11

Melody Baddoo
Erik K Flemington

Michael J Strong
Eugene Blanchard
Zhen Lin
Cindy A Morris
Melody Baddoo
Christopher M Taylor
Marcus L Ware

Acta neuropathologica communications

RNASeq analysis reveals biological processes governing the clinical behaviour of endometrioid and serous endometrial cancers

2016-07-12

Rajmohan Murali
Jorge Reis-Filho
Britta Weigelt
Salvatore Piscuoglio

Christophe Lemetre
Begoña Vieites
Charlotte K Y Ng
Anne M Schultheis
Caterina Marchiò
Maria A Lopez-García
Jose C Palacios
Achim A Jungbluth
Luigi M Terracciano

European Journal of Cancer

A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation.

2016-07-12

José Tomás Matus

Darren Chern Jan Wong
Rudolf Schlechter
Alessandro Vannozzi
Janine Höll
Ibrahim Hmmam
Jochen Bogs
Giovanni Battista Tornielli
Simone Diego Castellarin

DNA Research

Design and expression of peptides with antimicrobial activity against Salmonella typhimurium.

2016-07-12

Alessandro Weisz
Ilaria Granata
Francesca Rizzo

Amalia Porta
Anna Maria Petrone
Silvana Morello
Domenico Memoli
Bruno Maresca

Cellular Microbiology

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

2016-07-12

Julien Bobe

Cédric Cabau
Frédéric Escudié
Anis Djari
Yann Guiguen
Christophe Klopp

A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq.

2016-07-13

Tetsuo Kobayashi

Takaaki Kojima
Emi Kunitake
Kunio Ihara
Hideo Nakano

PLOS ONE

Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq.

2016-07-14

Barbara Treutlein
Thomas C. Südhof
Marc V Fuccillo
Özgün Gökçe
Robert Malenka

Geoff Stanley
Norma F Neff
Gray J Camp
Patrick E Rothwell
Stephen R Quake

Cell Reports

Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells.

2016-07-15

Alessandro Simonati
Maciej Lalowski

Francesco Pezzini
Laura Bettinetti
Francesca Di Leva
Marzia Bianchi
Elisa Zoratti
Rosalba Carrozzo
Filippo M Santorelli
Massimo Delledonne

Cellular and Molecular Neurobiology

RNA editing generates cellular subsets with diverse sequence within populations.

2016-07-15

Theodore Papamarkou
Violeta Rayon-Estrada

Dewi Harjanto
Chris J Oates
Violeta Rayon-Estrada
F Nina Papavasiliou
Anastasia Papavasiliou

Nature Communications

Abstract 105: Bioinformatic analysis of RNA-Seq data to search for novel diagnostic/prognostic biomarkers of pancreatic ductal adenocarcinoma

2016-07-15

Joao Carlos Setubal

Omar J. Sosa
Vinícius F. Paixão
Eduardo M. Reis

Cancer Research

Increase of Alternatively Activated Antigen Presenting Cells in Active Experimental Autoimmune Encephalomyelitis.

2016-07-16

Frauke Zipp

Beatrice Wasser
Gautam Pramanik
Moritz Hess
Matthias Klein
Felix Luessi
Klaus Dornmair
Tobias Bopp
Esther Witsch

Journal of Neuroimmune Pharmacology

Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel

2016-07-19

Eviatar Nevo

Kexin Li
Huihua Wang
Zhenyuan Cai
Liuyang Wang
Qinqin Xu
Matěj Lövy
Zhenlong Wang

Proceedings of the National Academy of Sciences of the United States of America

Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.

2016-07-19

Babu Valliyodan
Rupesh K. Deshmukh
Rajeev Kumar Varshney
Gunvant Patil

Wei Chen
Qiuming Yao
Gaurav Agarwal
Li Lin
Biao Wang
Yongqin Wang
Silvas J Prince
Li Song
Dong Xu
Yongqiang C An
Henry T Nguyen

Frontiers in Plant Science

Full Spectrum of LPS Activation in Alveolar Macrophages of Healthy Volunteers by Whole Transcriptomic Profiling.

2016-07-19

Miguel Pinilla-Vera
Robert M Tighe

Zeyu Xiong
Yutong Zhao
Jing Zhao
Michael P Donahoe
Suchitra Barge
William T Horne
Jay K Kolls
Bryan J McVerry
Anastasiya Birukova
W Michael Foster
John Hollingsworth
Anuradha Ray
Rama Mallampalli
Prabir Ray
Janet S Lee

PLOS ONE

Contextual fear conditioning induces differential alternative splicing.

2016-07-19

Ted Abel
John N Koberstein
Shane G. Poplawski
Lucia Peixoto
Davide Risso

Giulia S Porcari
Mathieu E Wimmer
Anna G McNally
Keiko Mizuno
K Peter Giese
Snehajyoti Chatterjee
Terence P Speed

Neurobiology of Learning and Memory

Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression.

2016-07-20

Markus Hohenfellner
Holger Sültmann
Boris Hadaschik

Julia M A Pickl
Diana Tichy
Vladimir Y Kuryshev
Yanis Tolstov
Michael Falkenstein
Julia Schüler
Daniel Reidenbach
Agnes Hotz-Wagenblatt
Glen Kristiansen
Wilfried Roth
Stefan Duensing
Doreen Heckmann

Oncotarget

SLC9A9 Co-expression modules in autism-associated brain regions.

2016-07-21

Stephen Faraone

Jameson Patak
Jonathan L Hess
Yanli Zhang-James
Stephen J Glatt

Autism Research

A Splice Defect in the EDA Gene in Dogs with an X-Linked Hypohidrotic Ectodermal Dysplasia (XLHED) Phenotype

2016-07-22

Tosso Leeb
Gila Zur

Dominik P Waluk
Ronnie Kaufmann
Monika M Welle
Vidhya Jagannathan
Cord Drögemüller
Eliane J Müller
Arnaud Galichet

Deep transcriptomic profiling reveals the similarity between endothelial cells cultured under static and oscillatory shear stress conditions

2016-07-22

Hanjoong Jo

Congzhen Qiao
Fan Meng
Inhwan Jang
Y Eugene Chen
Jifeng Zhang

Physiological Genomics

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

2016-07-25

Marie-France Sagot

Hélène Lopez-Maestre
Lilia Brinza
Camille Marchet
Janice Kielbassa
Sylvère Bastien
Mathilde Boutigny
David Monnin
Adil El Filali
Claudia Marcia Carareto
Cristina Vieira
Franck Picard
Natacha Kremer
Fabrice Vavre
Vincent Lacroix

Nucleic Acids Research

PR2S2Clust: Patched RNA-seq read segments' structure-oriented clustering.

2016-07-25

Ashis Kumer Biswas

Jean X Gao

Journal of Bioinformatics and Computational Biology

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

2016-07-27

Olivier Elemento

David Redmond
Asaf Poran

Genome Medicine

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles.

2016-07-27

Chongzhi Zang
Su Wang
Housheng Hansen He

Tengfei Xiao
Jingyu Fan
Shenglin Mei
Qian Qin
Qiu Wu
Xujuan Li
Kexin Xu
Myles Brown
Clifford A Meyer
X Shirley Liu

Genome Research

Novel genes on rat chromosome 10 are linked to body fat mass, preadipocyte number and adipocyte size.

2016-07-27

Matthias Blüher
Michael Stumvoll

A Weingarten
L Turchetti
K Krohn
I Klöting
M Kern
P Kovacs
M Blüher
N Klöting

International Journal of Obesity

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.

2016-07-28

Jeremy Luban

Alan Derr
Chaoxing Yang
Rapolas Zilionis
Alexey Sergushichev
David M Blodgett
Sambra Redick
Rita Bortell
David M Harlan
Sebastian Kadener
Dale L Greiner
Allon Klein
Maxim N Artyomov
Manuel Garber

Genome Research

FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis.

2016-07-28

Xuemei Chen

Dongming Li
Xing Fu
Lin Guo
Zhigang Huang
Yongpeng Li
Yang Liu
Zishan He
Xiuwei Cao
Xiaohan Ma
Meicheng Zhao
Guohui Zhu
Langtao Xiao
Haiyang Wang
Renyi Liu
Xigang Liu

Proceedings of the National Academy of Sciences of the United States of America

Characterization of circular RNAs in human, mouse and rat hearts.

2016-07-28

Thomas Meitinger
Stephan Nothjunge
Stefan Engelhardt

Stanislas Werfel
Thomas Schwarzmayr
Tim-Matthias Strom

Journal of Molecular and Cellular Cardiology

Single-Cell RNAseq Reveals That Pancreatic β-Cells From Very Old Male Mice Have a Young Gene Signature.

2016-07-28

Andrew J Murphy

Yurong Xin
Haruka Okamoto
Jinrang Kim
Min Ni
Christina Adler
Katie Cavino
Erqian Na
George D Yancopoulos
Calvin Lin
Jesper Gromada

Endocrinology

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.

2016-07-28

Aviv Regev

Naomi Habib
Yinqing Li
Matthias Heidenreich
Lukasz Swiech
Inbal Avraham-Davidi
John J Trombetta
Cynthia Hession
Feng Zhang

Science

Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia

2016-08

Nenad Sestan
Jernej Mlakar
Marco Onorati

Zhen Li
Fuchen Liu
André M.M. Sousa
Naoki Nakagawa
Mingfeng Li
Maria Teresa Dell’Anno
Forrest O. Gulden
Sirisha Pochareddy
Andrew T.N. Tebbenkamp
Wenqi Han
Mihovil Pletikos
Tianliuyun Gao
Ying Zhu
Candace Bichsel
Luis Varela
Klara Szigeti-Buck
Steven Lisgo
Yalan Zhang
Anze Testen
Xiao-Bing Gao
Mara Popovic
Marie Flamand
Stephen M. Strittmatter
Leonard K. Kaczmarek
E.S. Anton
Tamas L. Horvath
Brett D. Lindenbach

Cell Reports

Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells

2016-08

François-Loïc Cosset
Saadi Khochbin
Apirat Chaikuad
Stefan Knapp
Matthieu Gérard
Fayçal Boussouar
Anouk Emadali
Minjia Tan
Sophie Rousseaux

Yuichi Morozumi
Mahya Jamshidikia
Gozde Colak
Huang He
Litong Nie
Carlo Petosa
Maud de Dieuleveult
Sandrine Curtet
Anne-Laure Vitte
Clothilde Rabatel
Alexandra Debernardi
Els Verhoeyen
Norbert Schweifer
Davide Gianni
Marta Gut
Philippe Guardiola
Yingming Zhao

Journal of molecular cell biology

Tensor decomposition for multiple-tissue gene expression experiments

2016-08-01

Jonathan Marchini
Ana Viñuela
Kerrin S. Small
Mark McCarthy

Victoria Hore
Alfonso Buil
Julian Knight

Nature Genetics

Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors

2016-08-01

John Quackenbush
Emily MacDuffie

Kevin M Elias
Megan M Emori
Thomas Westerling
Henry Long
Anna Budina-Kolomets
Fugen Li
Michelle R Davis
Alexander Holman
Brian Lawney
Matthew L Freedman
Myles Brown
Ronny Drapkin

JCI insight

Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer.

2016-08-01

Marcin Cieślik

Sudhanshu Shukla
Xiang Zhang
Yashar S Niknafs
Lanbo Xiao
Rohit Mehra
Ashley Ross
Edward Schaeffer
Bhavna Malik
Shuling Guo
Susan M Freier
Huynh-Hoa Bui
Javed Siddiqui
Xiaojun Jing
Xuhong Cao
Saravana M Dhanasekaran
Felix Y Feng
Arul M Chinnaiyan
Rohit Malik

Neoplasia

Neuraminidase A-Exposed Galactose Promotes Streptococcus pneumoniae Biofilm Formation during Colonization.

2016-08-01

Sean C Daugherty

Krystle A Blanchette
Anukul T Shenoy
Jeffrey Milner
Ryan P Gilley
Erin McClure
Cecilia A Hinojosa
Nikhil Kumar
Luke J Tallon
Sandra Ott
Samantha J King
Daniela M Ferreira
Stephen B Gordon
Hervé Tettelin
Carlos J Orihuela

Infection and Immunity

142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis.

2016-08-01

Aviv Regev
Itay Tirosh
Brian V. Nahed

Andrew Sean Venteicher
Itay Tirosh
Christine Hebert
Leah Escalante
Robert L Martuza
William T Curry
Daniel P Cahill
Bradley Bernstein
David N Louis
Mario Suva

Neurosurgery

Strong down-regulation of glycophorin genes: A host defense mechanism against rotavirus infection.

2016-08-01

Alberto Gómez-Carballa
Miriam Cebey-López
Jose Gomez-Rial
Antonio Salas
Federico Martinón-Torres

Guillermo Marco-Puche
Juan Carlos Triviño
Irene Rivero-Calle
Lucía Vilanova-Trillo
Carmen Rodríguez-Tenreiro

Infection, Genetics and Evolution

Optimized design and analysis of preclinical intervention studies in vivo

2016-08-02

Jukka Westermarck
Mikael Jumppanen
Sari Mäkelä
Teemu D Laajala
Tero Aittokallio

Riikka Huhtaniemi
Vidal Fey
Amanpreet Kaur
Matias Knuuttila
Eija Aho
Riikka Oksala
Matti Poutanen

Scientific Reports

The Sinorhizobium fredii HH103 MucR1 Global Regulator Is Connected With the nod Regulon and Is Required for Efficient Symbiosis With Lotus burttii and Glycine max cv. Williams.

2016-08-02

Susanne Zehner
Miguel A Rodríguez-Carvajal
José-María Vinardell

Sebastián Acosta-Jurado
Cynthia Alias-Villegas
Pilar Navarro-Gómez
Piedad Del Socorro Murdoch
María J Soto
Francisco-Javier Ollero
José E Ruiz-Sainz
Michael Göttfert

Molecular Plant-Microbe Interactions

The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes.

2016-08-02

David Roy Smith

Matheus Sanitá Lima
Laura C Woods
Matthew W Cartwright

Molecular Ecology Resources

Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly.

2016-08-03

Oliver Rackham
Aleksandra Filipovska
Nils-Göran Larsson

Jakob D Busch
Stanka Matic
Stefan J Siira
Irina Kuznetsova
Ilian Atanassov
Judith A Ermer
Anne-Marie J Shearwood
Tara R Richman
James B Stewart
Arnaud Mourier
Dusanka Milenkovic

Cell Reports

Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells.

2016-08-03

William Bishai
Manormoney Pillay

Nontobeko Eunice Mvubu
Balakrishna Pillay
Junaid Gamieldien

Developmental and Comparative Immunology

microRNA-132/212 deficiency enhances Aβ production and senile plaque deposition in Alzheimer's disease triple transgenic mice.

2016-08-03

Maxime P Vallée
Sébastien S. Hébert
Frédéric Calon

Julia Hernandez-Rapp
Sara Rainone
Claudia Goupil
Véronique Dorval
Pascal Y Smith
Martine Saint-Pierre
Emmanuel Planel
Arnaud Droit
Francesca Cicchetti

Scientific Reports

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

2016-08-04

Philip Rosenstiel

Wentao Yang
Hinrich Schulenburg

BMC Genomics

Modulatory Effects of Sex Steroids Progesterone and Estradiol on Odorant Evoked Responses in Olfactory Receptor Neurons.

2016-08-05

Hanns Hatt
Günter Gisselmann

Ninthujah Kanageswaran
Maximilian Nagel
Paul Scholz
Julia Mohrhardt
Günter Gisselmann

PLOS ONE

Identification of genes differentially regulated by vitamin D deficiency that alter lung pathophysiology and inflammation in allergic airways disease.

2016-08-05

Rachel E Foong
Anthony Bosco
Prue H Hart
Graeme R. Zosky
Anthony Kicic
Shelley Gorman

Niamh M Troy

American Journal of Physiology - Lung Cellular and Molecular Physiology

Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α).

2016-08-05

Michael A. Skinner

Efstathios S Giotis
Rebecca C Robey
Natalie G Skinner
Christopher D Tomlinson
Stephen Goodbourn

Veterinary Research

scphaser: haplotype inference using single-cell RNA-seq data

2016-08-06

Björn Reinius
Rickard Sandberg

Daniel Edsgärd

Bioinformatics

Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements.

2016-08-08

Itunuoluwa Isewon
Jelili Oyelade

Efejiro Ashano
Ezekiel Adebiyi

F1000Research

Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay

2016-08-08

Matthew Berriman

Zhigang Lu
Florian Sessler
Nancy Holroyd
Steffen Hahnel
Thomas Quack
Christoph G Grevelding

Scientific Reports

RNA-seq analysis identifies key long non-coding RNAs connected to the pathogenesis of alcohol-associated head and neck squamous cell carcinoma.

2016-08-08

Jessica Wang-Rodriguez

Vicky Yu
Pranav Singh
Elham Rahimy
Hao Zheng
Selena Z Kuo
Elizabeth Kim
Weg M Ongkeko

Oncology Letters

Spliced synthetic genes as internal controls in RNA sequencing experiments.

2016-08-08

Lars K. Nielsen
John Mattick
Simon A Hardwick
Ira Deveson

Wendy Y Chen
Ted Wong
James Blackburn
Stacey B Andersen
Tim R Mercer

Nature Methods

Vacuolar Chloride Fluxes Impact Ion Content and Distribution during Early Salinity Stress.

2016-08-08

Enrico Martinoia

Ulrike Baetz
Cornelia Eisenach
Takayuki Tohge
Alexis De Angeli

Plant Physiology

Transcriptional Profiling of Cultured, Embryonic Epicardial Cells Identifies Novel Genes and Signaling Pathways Regulated by TGFβR3 In Vitro.

2016-08-09

Daniel M DeLaughter

Daniel M DeLaughter
Cynthia R Clark
Danos C Christodoulou
Christine E Seidman
H Scott Baldwin
J G Seidman
Joey V Barnett

PLOS ONE

Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma.

2016-08-09

Chia-Lang Hsu
Wen-Ming Hsu
Hsuan-Cheng Huang

Divya Sahu
Chen-Ching Lin
Tz-Wen Yang
Shinn-Ying Ho
Hsueh-Fen Juan

Oncotarget

Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming.

2016-08-10

Tatyana B Nesterova
Claire Rougeulle
Irene Cantone
Matthias Merkenschlager

Hakan Bagci
Dirk Dormann
Gopuraja Dharmalingam
Neil Brockdorff
Celine Vallot
Edith Heard
Ronan Chaligne
Amanda G Fisher

Nature Communications

Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators.

2016-08-11

David J Waxman

Junjie Wu
Marie Jordan

BMC Cancer

Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves.

2016-08-11

Paul Stothard

Guanxiang Liang
Nilusha Malmuthuge
Hua Bao
Philip J Griebel
Le Luo Guan

BMC Genomics

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi.

2016-08-11

Davide Spadaro

Slavica Matić
Paolo Bagnaresi
Chiara Biselli
Luigi Orru'
Greice Amaral Carneiro
Ilenia Siciliano
Giampiero Valé
Maria Lodovica Gullino

BMC Genomics

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

2016-08-11

Steven Salzberg
Mihaela Pertea

Daehwan Kim
Geo M Pertea
Jeffrey T Leek

Nature Protocols

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

2016-08-11

Robert M. Waterhouse
Thorsten Burmester
Ioannis Michalopoulos
Julio Rozas
Ramesh T Gunaratna
Suyog S Kuwar
Xiaolong Cao
Tom K Walsh
Seung-Joon Ahn
Adriana Briscoe
Yannick Pauchet
Alexie Papanicolaou
Ewald Grosse-Wilde
Guillaume Tetreau
René Feyereisen
John G Oakeshott
Gary W. Blissard
Lars S Jermiin
Susan J Brown
Bill S. Hansson
Haobo Jiang

Michael R Kanost
Estela L Arrese
Yun-Ru Chen
Sanjay Chellapilla
Marian R Goldsmith
David G Heckel
Nicolae Herndon
Jiaxin Qu
Jose L Soulages
Heiko Vogel
James Walters
Francisca C Almeida
Chunju An
Peshtewani Aqrawi
Anne Bretschneider
William B Bryant
Sascha Bucks
Hsu Chao
Germain Chevignon
Jayne M Christen
David F Clarke
Neal T Dittmer
Laura C F Ferguson
Spyridoula Garavelou
Karl H J Gordon
Yi Han
Frank Hauser
Yan He
Hanna Heidel-Fischer
Ariana Hirsh
Yingxia Hu
Hongbo Jiang
Divya Kalra
Christian Klinner
Christopher König
Christie Kovar
Ashley R Kroll
Sandy L Lee
Rüdiger Lehman
Kai Li
Zhaofei Li
Hanquan Liang
Shanna Lovelace
Zhiqiang Lu
Jennifer H Mansfield
Kyle J McCulloch
Tittu Mathew
Brian Morton
Donna M Muzny
David Neunemann
Fiona Ongeri
Ling-Ling Pu
Ioannis Pyrousis
Xiang-Jun Rao
Amanda Redding
Charles Roesel
Alejandro Sanchez-Gracia
Sarah Schaack
Aditi Shukla
Yang Wang
Guang-Hua Xiong
Walther Traut
Kim C Worley
Di Wu
Wenbi Wu
Yuan-Qing Wu
Xiufeng Zhang
Zhen Zou
Hannah Zucker
Rollie J Clem
Cornelis J P Grimmelikhuijzen
Stavros J Hamodrakas
Elisabeth Huguet
Que Lan
Herman K Lehman
Marce Lorenzen
Hans Merzendorfer
David B Morton
Subbaratnam Muthukrishnan
Will Palmer
Yoonseong Park
A Lorena Passarelli
Lawrence M Schwartz
Wendy Smith
Agnes Southgate
Andreas Vilcinskas
Richard Vogt
Ping Wang
John Werren
Xiao-Qiang Yu
Jing-Jiang Zhou
Steven E Scherer
Stephen Richards

Insect Biochemistry and Molecular Biology

NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies.

2016-08-11

Thomas Eder
Florian Grebien
Thomas Rattei

Bioinformatics

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

2016-08-12

Konrad Förstner
Cynthia Sharma
Jörg Soppa
Friedhelm Pfeiffer

Julia Babski
Karina A. Haas
Daniela Näther-Schindler
Matthias Hammelmann
Rolf Hilker
Anke Becker
Anita Marchfelder

BMC Genomics

A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report.

2016-08-12

Daniel C Swan

David J Barnes
Edward Hookway
Nick Athanasou
Takeshi Kashima
Udo Oppermann
Simon Hughes
Dietrich Lueerssen
John Anson
A Bassim Hassan

BMC Cancer

Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice.

2016-08-12

Jason Munshi-South

Jonathan L Richardson

Seminars in Cell & Developmental Biology

Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons

2016-08-16

Thomas C. Südhof
Robert Malenka

Csaba Földy
Spyros Darmanis
Jason Aoto
Stephen R Quake

Proceedings of the National Academy of Sciences of the United States of America

Proteolysis-a characteristic of tumor-initiating cells in murine metastatic breast cancer.

2016-08-16

Marie Follo
Melanie Boerries
Hauke Busch
Thomas Reinheckel

Larissa E Hillebrand
Fee Bengsch
Jochen Hochrein
Jan Hülsdünker
Julia Bender

Oncotarget

Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity.

2016-08-16

Victoria Arango

S P Pantazatos
Y-Y Huang
G B Rosoklija
A J Dwork
J J Mann

Molecular Psychiatry

Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals.

2016-08-16

Thorsten Burmester

Andrej Fabrizius
Daniel Andre
Tilmann Laufs
Anne Bicker
Stefan Reuss
Elena Porto
Thomas Hankeln

Neuroscience

REST is a hypoxia-responsive transcriptional repressor

2016-08-17

Miguel Cavadas
Carsten C Scholz
Zsolt Fabian
Alex Cheong
Murtaza M Tambuwala

Marion Mesnieres
Bianca Crifo
Mario C Manresa
Andrew C Selfridge
Ciara E Keogh
Karen A Nolan
Liliane M A Rocha
Stuart Brown
Anita Wdowicz
Danielle Corbett
Keith J Murphy
Catherine Godson
Eoin P Cummins
Cormac T Taylor

Scientific Reports

Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq.

2016-08-17

Katarzyna Goljanek-Whysall

Mandy Jayne Peffers
John Collins
Yongxiang Fang
Michael Rushton
John Loughlin
Carole Proctor
Peter David Clegg

PLOS ONE

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome.

2016-08-17

Hadas Keren-Shaul

Meital Gury-BenAri
Christoph A Thaiss
Nicolas Serafini
Deborah R Winter
Amir Giladi
David Lara-Astiaso
Maayan Levy
Tomer Meir Salame
Assaf Weiner
Eyal David
Hagit Shapiro
Mally Dori-Bachash
Meirav Pevsner-Fischer
Erika Lorenzo-Vivas
Hadas Keren-Shaul
Franziska Paul
Alon Harmelin
Gérard Eberl
Shalev Itzkovitz
Amos Tanay
James P Di Santo
Eran Elinav
Ido Amit

Cell

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm.

2016-08-17

Christina Kendziorski

Li-Fang Chu
Ning Leng
Jue Zhang
Zhonggang Hou
Daniel Mamott
David T Vereide
Jeea Choi
Ron Stewart
James A Thomson

Genome Biology

Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORγ Axis Regulating Proliferation in β Cells.

2016-08-17

Jens Juul Holst
Susanne Mandrup
Bjørk Ditlev Larsen
Louise T Dalgaard
Pierre Maechler

Søren Fisker Schmidt
Jesper Grud Skat Madsen
Kari Østerli Frafjord
Lars la Cour Poulsen
Sofia Salö
Michael Boergesen
Anne Loft
Maria Stahl Madsen

Cell Reports

C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides.

2016-08-17

Han Wang
Erich M Schwarz
Paul W. Sternberg

Ravi D Nath
Elly S Chow

Current Biology

Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis.

2016-08-19

Ole Ammerpohl
Johanna Klughammer

Markus Tschurtschenthaler
Priyadarshini Kachroo
Femke-Anouska Heinsen
Timon Erik Adolph
Malte Christoph Rühlemann
Felix Albert Offner
Felix Krueger
Sébastien Smallwood
Silke Szymczak
Arthur Kaser
Andre Franke

Scientific Reports

Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis.

2016-08-22

Svetlana N Dedysh
Anastasia A. Ivanova

Carl-Eric Wegner
Yongkyu Kim
Werner Liesack

Molecular Ecology

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

2016-08-23

Daphne Ezer
Berthold Göttgens

Victoria Moignard
Boris Adryan

PLOS Computational Biology

RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns.

2016-08-23

Brage Storstein Andresen
Adrian Robert Krainer

Thomas Koed Doktor
Yimin Hua
Henriette Skovgaard Andersen
Sabrina Brøner
Ying Hsiu Liu
Anna Wieckowska
Maja Dembic
Gitte Hoffmann Bruun

Nucleic Acids Research

Identification of novel regulators of developmental hematopoiesis using Endoglin regulatory elements as molecular probes.

2016-08-23

Rahul Roychoudhuri
Jason Wong
Elaine Dzierzak
Julie Thoms

Rabab Nasrallah
Eva M Fast
Parham Solaimani
Kathy Knezevic
Alexia Eliades
Rahima Patel
Roshana Thambyrajah
Ashwin Unnikrishnan
Dominik Beck
Chris S Vink
Aileen Smith
Mairi Shepherd
David Kent
Fabian Paul
Julia Klippert
Annette Hammes
Thomas Willnow
Bertie Göttgens
Leonard I Zon
George Lacaud
Valerie Kouskoff
John E Pimanda

Blood

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.

2016-08-24

Jonathan S. Serody
Benjamin G Vincent
Charles M. Perou

Lisle E Mose
Sara R Selitsky
Lisa M Bixby
David L Marron
Michael D Iglesia
Joel S Parker

Bioinformatics

An integrative transcriptomic atlas of organogenesis in human embryos.

2016-08-24

Dave Gerrard
Neil A. Hanley

Andrew A Berry
Rachel E Jennings
Karen Piper Hanley
Nicoletta Bobola

eLife

Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.

2016-08-25

Washington Mio
Benedikt Hallgrímsson

Joanne B Cole
Mange Manyama
Emmanuel Kimwaga
Joshua Mathayo
Jacinda R Larson
Denise K Liberton
Ken Lukowiak
Tracey M Ferrara
Sheri L Riccardi
Mao Li
Washington Mio
Michaela Prochazkova
Trevor Williams
Hong Li
Kenneth L Jones
Ophir D Klein
Stephanie A Santorico
Benedikt Hallgrimsson
Richard A Spritz

PLOS Genetics

DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome

2016-08-25

Karin Buiting
Samuel G. Jacobson
Corey T Watson
Thomas H Wassink
Noah Zaitlen

Ricky S Joshi
Paras Garg
Tuuli Lappalainen
Nidha Azam
Daniel Ho
Xin Li
Stylianos E Antonarakis
Han G Brunner
Sau Wai Cheung
Bradford Coffee
Thomas Eggermann
David Francis
Joep P Geraedts
Giorgio Gimelli
Cedric Le Caignec
Nicole de Leeuw
Thomas Liehr
Deborah J Mackay
Stephen B Montgomery
Alistair T Pagnamenta
Peter Papenhausen
David O Robinson
Claudia Ruivenkamp
Charles Schwartz
Bernhard Steiner
David A Stevenson
Urvashi Surti
Andrew J Sharp

American Journal of Human Genetics

Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells

2016-08-25

Bo Wen

Xiwen Lin
Miao Han
Lu Cheng
Jian Chen
Zhuqiang Zhang
Ting Shen
Min Wang
Ting Ni
Chunsheng Han

RNA Biology

Maf1-mediated regulation of yeast RNA polymerase III is correlated with CCA addition at the 3' end of tRNA precursors.

2016-08-26

Dominika Wichtowska
Marek Żywicki
Grzegorz Kudła
Wojciech M Karlowski
Magdalena Rakowska-Boguta

Przemysław Nuc

Gene

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

2016-08-26

Feixiong Cheng
Bairong Shen

Chuang Liu
Zhongming Zhao

BMC Systems Biology

Erratum to: A survey of best practices for RNA-seq data analysis.

2016-08-26

Laura L. Elo
David Gomez-Cabrero

Ana Conesa
Pedro Madrigal
Sonia Tarazona
Alejandra Cervera
Andrew McPherson
Michal Wojciech Szcześniak
Daniel J Gaffney
Xuegong Zhang
Ali Mortazavi

Genome Biology

Inferring expressed genes by whole-genome sequencing of plasma DNA.

2016-08-29

Peter Ulz
Gerhard G Thallinger
Michael R. Speicher

Martina Auer
Ricarda Graf
Karl Kashofer
Stephan W Jahn
Luca Abete
Gunda Pristauz
Edgar Petru
Jochen B Geigl
Ellen Heitzer

Nature Genetics

Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18

2016-08-30

Janine Altmüller
Hanns Hatt
Günter Gisselmann
Christa E Müller

Caroline Flegel
Felix Vogel
Adrian Hofreuter
Sebastian Wojcik
Clara Schoeder
Katarzyna Kieć-Kononowicz
Norbert H Brockmeyer
Christian Becker
Günter Gisselmann

Scientific Reports

Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα.

2016-08-30

Bart Staels
Réjane Paumelle
Karolien De Bosscher
Lode De Cauwer
Michał Pawlak
Nathalie Hennuyer

Dariusz Ratman
Viacheslav Mylka
Nadia Bougarne
Sandrine Caron
Jonathan Thommis
Mark H Rider
Claude Libert
Sam Lievens
Jan Tavernier

Nucleic Acids Research

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

2016-08-31

John C Marioni
Davis J McCarthy

Aaron T L Lun

F1000Research

RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease

2016-09-01

Claudia B Monteiro-Vitorello

Patricia D C Schaker
Alessandra C Palhares
Lucas M Taniguti
Leila P Peters
Silvana Creste
Karen S Aitken
Marie-Anne Van Sluys
João P Kitajima
Maria L C Vieira

PLOS ONE

Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians.

2016-09-01

Annika Guse
Christian R. Voolstra

Iliona Wolfowicz
Sebastian Baumgarten
Philipp A Voss
Elizabeth A Hambleton
Masayuki Hatta

Scientific Reports

Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells.

2016-09-01

Theodore J Perkins

Jair Bar
Mohamed S Hasim
Tabassom Baghai
Nima Niknejad
David J Stewart
Harmanjatinder S Sekhon
Patrick J Villeneuve
Jim Dimitroulakos

Neoplasia

Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP.

2016-09-01

Andrei Rozanski

Wânia Rezende Lima
Giulliana Tessarin-Almeida
Kleber S Parreira
Miriam S Moraes
David C Martins
Ronaldo F Hashimoto
Pedro A F Galante
Célia R S Garcia

Genes & Cancer

ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells.

2016-09-01

Stefanie Dimmeler
Tyler Weirick
Shizuka Uchida

Raphael Müller
David John
Giuseppe Militello
Wei Chen

Scientific Reports

Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.

2016-09-01

Sarah Diermeier

Kung-Chi Chang
Susan M Freier
Junyan Song
Osama El Demerdash
Alexander Krasnitz
Frank Rigo
C Frank Bennett
David L Spector

Cell Reports

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.

2016-09-01

Sten Linnarsson
Björn Reinius
Fredrik Lanner
Rickard Sandberg

Sophie Petropoulos
Daniel Edsgärd
Qiaolin Deng
Sarita Pauliina Panula
Simone Codeluppi
Alvaro Plaza Reyes

Cell

A full-body transcriptome and proteome resource for the European common carp.

2016-09-02

Hans J Jansen
Christiaan V. Henkel

I C R M Kolder
S J van der Plas-Duivesteijn
G Tan
G F Wiegertjes
M Forlenza
A T Guler
D Y Travin
M Nakao
T Moritomo
I Irnazarow
J T den Dunnen
S Y Anvar
R P Dirks
M Palmblad
B Lenhard
H P Spaink

BMC Genomics

Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

2016-09-04

Andrew E Jaffe
Jeffrey T. Leek
Ben Langmead
Abhinav Nellore

Leonardo Collado-Torres
José Alquicira-Hernández
Christopher Wilks
Jacob Pritt
James Morton

Bioinformatics

Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells.

2016-09-06

Anja M Billing
Johannes Graumann
Karsten Suhre
Hisham Ben Hamidane

Aditya M Bhagwat
Richard J Cotton
Shaima S Dib
Pankaj Kumar
Shahina Hayat
Neha Goswami
Arash Rafii

Journal of Proteomics

RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response.

2016-09-07

Corinne Berthonneche
Sven Bergmann

Andrea Prunotto
Brian J Stevenson
Fanny Schüpfer
Jacques S Beckmann
Fabienne Maurer

BMC Genomics

Pro-invasive Effect of Proto-oncogene PBF Is Modulated by an Interaction with Cortactin.

2016-09-07

Vicki E Smith
Erica Gentilin
Martin L. Read
H Mehanna

Rachel J Watkins
Waraporn Imruetaicharoenchoke
Neil Sharma
Vikki L Poole
Sukhchain Bansal
Emy Bosseboeuf
Rachel Fletcher
Hannah R Nieto
Ujjal Mallick
Allan Hackshaw
Kristien Boelaert
Christopher J McCabe

The Journal of Clinical Endocrinology and Metabolism

Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology

2016-09-08

Haja N. Kadarmideen
Marcin Sikora
Mariusz Pierzchała
Horbańczuk Jarosław Olav

Chandra Shekhar Pareek
Rafał Smoczyński
Piotr Dziuba
Paweł Błaszczyk
Paulina Walendzik
Tomasz Grzybowski
Agnieszka Szostak
Magdalena Ogluszka
Lech Zwierzchowski
Urszula Czarnik
Leyland Fraser
Przemysław Sobiech
Krzysztof Wąsowicz
Brian Gelfand
Yaping Feng
Dibyendu Kumar

PLOS ONE

TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.

2016-09-08

Gaye L Hattem
Michael P. Washburn

Charles A S Banks
Gina Boanca
Zachary T Lee
Cassandra G Eubanks
Allison Peak
Lauren E Weems
Juliana J Conkright

Molecular & Cellular Proteomics

Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum.

2016-09-08

Dario Cantu

Mélanie Massonnet
Abraham Morales-Cruz
Rosa Figueroa-Balderas
Daniel P Lawrence
Kendra Baumgartner

Molecular Plant Pathology

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

2016-09-08

John C Marioni

Aaron TL Lun

Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation.

2016-09-09

Andreas Gogol-Döring

Catrin Stutika
Mario Mietzsch
Stefan Weger
Madlen Sohn
Wei Chen
Regine Heilbronn

PLOS ONE

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.

2016-09-10

Sharmila Bhattacharya

Shannon Hateley
Ravikumar Hosamani
Shilpa R Bhardwaj
Lior Pachter

Genomics

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

2016-09-12

Roderic Guigó i Serra
Martin Oti
Pedro G Ferreira
Michael Sammeth
Philip Rosenstiel
Anna Esteve-Codina

Matthias Barann
Thomas Wieland
Suzana Ezquina
Marc R Friedländer
Manuel A Rivas
GEUVADIS Consortium
Tim M Strom
Tuuli Lappalainen

Scientific Reports

Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta

2016-09-12

Dehong Hu

Jiwei Zhang
Gerald N Presley
Kenneth E Hammel
Jae-San Ryu
Jon R Menke
Melania Figueroa
Galya Orr
Jonathan S Schilling

Proceedings of the National Academy of Sciences of the United States of America

Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum.

2016-09-12

Shigehiro Kuraku
Masahiko Hibi

Miki Takeuchi
Shingo Yamaguchi
Yoshimasa Sakakibara
Takuto Hayashi
Koji Matsuda
Yuichiro Hara
Chiharu Tanegashima
Takashi Shimizu

The Journal of Comparative Neurology

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

2016-09-13

Sohiya Yotsukura

David A duVerle
Seitaro Nomura
Hiroyuki Aburatani
Koji Tsuda

BMC Bioinformatics

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

2016-09-13

Aldons Jake Lusis
Matteo Pellegrini
Eleazar Eskin
Yehudit Hasin-Brumshtein
Anneke Brümmer
Paul D. Piehowski
Xinshu Xiao

Arshad H Khan
Farhad Hormozdiari
Calvin Pan
Brian W Parks
Vladislav A Petyuk
Richard D Smith
Desmond J Smith

eLife

Tissue enrichment analysis for C. elegans genomics.

2016-09-13

Paul W. Sternberg

David Angeles-Albores
Raymond Y N Lee
Juancarlos Chan

BMC Bioinformatics

Zinc finger protein 407 overexpression upregulates PPAR target gene expression and improves glucose homeostasis in mice.

2016-09-13

Dave Bridges
David A. Buchner

Alyssa Charrier
Li Wang
Erin J Stephenson
Siddharth V Ghanta
Chih-Wei Ko
Colleen M Croniger

American Journal of Physiology - Endocrinology and Metabolism

Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation

2016-09-13

Lily G Fogg
Tapio Lönnberg
Ismail Sebina
Frederik Otzen Bagger
Ashraful Haque
Sarah Teichmann

Valentine Svensson
Kylie R James
Daniel Fernandez-Ruiz
Ruddy Montandon
Megan S F Soon
Michael J T Stubbington
Max Zwiessele
Neil Lawrence
Fernando Souza-Fonseca- Guimaraes
William R Heath
Oliver Billker
Oliver Stegle

Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues.

2016-09-15

Sergio Esposito

Lauralie Mangeot-Peter
Sylvain Legay
Jean-Francois Hausman
Gea Guerriero

International Journal of Molecular Sciences

MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins.

2016-09-15

Marc Boutry

Sylvain Legay
Gea Guerriero
Christelle André
Cédric Guignard
Emmanuelle Cocco
Sophie Charton
Owen Rowland
Jean-Francois Hausman

New Phytologist

Alternative Splicing May Not Be the Key to Proteome Complexity

2016-09-16

Alfonso Valencia

Michael L. Tress
Federico Abascal

Trends in Biochemical Sciences

Regulation of X-linked gene expression during early mouse development by Rlim

2016-09-19

Aviv Regev
Alex K. Shalek
Oliver J Rando

Feng Wang
JongDae Shin
Jeremy M Shea
Jun Yu
Ana Bošković
Meg Byron
Xiaochun Zhu
Jeanne B Lawrence
Eduardo M Torres
Lihua J Zhu
Ingolf Bach

eLife

The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions.

2016-09-19

Matthieu D Lavigne

Aikaterini Nanou
Chrisavgi Toumpeki
Vassiliki Lazou
Jeroen Demmers
Triantafillos Paparountas
Dimitris Thanos
Eleni Katsantoni

Nucleic Acids Research

Transcriptomic profiles of the upper olfactory rosette in cultured and wild Senegalese sole (Solea senegalensis) males.

2016-09-20

Elvira Fatsini
Manuel Manchado

R Bautista
N J Duncan

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Standardizing unique molecular identifiers in SAM flags would benefit more than RNA-Seq

2016-09-20

Elisha Roberson

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

2016-09-21

Lana Garmire

Olivier B. Poirion
Xun Zhu
Travers Ching
Lana Garmire

Frontiers in Genetics

The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth.

2016-09-21

Erich M Schwarz
Michael Krieg
Robert O'Hagan
Paul W. Sternberg

Dean Lockhead
Sebastian Bellotti
Maureen M Barr
Alexander R Dunn
Miriam B Goodman

Molecular Biology of the Cell

Long non-coding RNAs in human early embryonic development and their potential in ART.

2016-09-21

John De Vos

Julien Bouckenheimer
Said Assou
Sébastien Riquier
Cyrielle Hou
Nicolas Philippe
Caroline Sansac
Thierry Lavabre-Bertrand
Thérèse Commes
Jean-Marc Lemaître
Anthony Boureux

Human Reproduction Update

Probiotic Enterococcus faecalis Symbioflor® down regulates virulence genes of EHEC in vitro and decrease pathogenicity in a Caenorhabditis elegans model.

2016-09-21

Klaus Neuhaus

Marina C Lamparter
Benjamin Zölch
Richard Landstorfer
Svenja Simon
Britta Spanier
Matthias A Ehrmann
Rudi F Vogel

Archives of Microbiology

P08.40 RNAseq of paired primary and recurrent glioblastoma samples

2016-09-21

Susan C. Short

L. F. Stead
A. Bruns
R. Morton
S. Harrison
A. Chakrabarty
A. Ismail
H. King
K. Ashton
K. Syed

Neuro-Oncology

SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

2016-09-22

Ivan Kel
Alessandra Mezzelani
Luciano Milanesi

Zisong Chang
Nadia Galluccio
Margherita Romeo
Stefano Beretta
Luisa Diomede
Christoph Dieterich
Ivan Merelli

Molecular BioSystems

A Global Analysis of the Polygalacturonase Gene Family in Soybean (Glycine max).

2016-09-22

Fanjiang Kong

Feifei Wang
Xia Sun
Xinyi Shi
Hong Zhai
Changen Tian
Baohui Liu
Xiaohui Yuan

PLOS ONE

C14orf132 gene is possibly related to extremely low birth weight

2016-09-22

Triin Viltrop
Andres Salumets
Sulev Kõks
Ene Reimann

Airi Tiirats
Margit Nõukas

BMC Genetics

2016-09-22

Cornelia M. van Duijn
André Uitterlinden
Cisca Wijmenga
Jenny van Dongen
Rick Jansen
Eco de Geus
Morris A Swertz
Dorret Boomsma
Albert Hofman
Leonard H van den Berg
Jan H Veldink
Coenraad Dirk Adriaan Stehouwer
Casper G. Schalkwijk

Roderick C Slieker
Maarten van Iterson
René Luijk
Marian Beekman
Daria V Zhernakova
Matthijs H Moed
Hailiang Mei
Michiel van Galen
Patrick Deelen
Marc Jan Bonder
Alexandra Zhernakova
Ettje F Tigchelaar
Carla J H van der Kallen
Diana van Heemst
Joris Deelen
Joyce van Meurs
Peter A C 't Hoen
Lude Franke
Marleen M J van Greevenbroek
BIOS consortium
P Eline Slagboom
Bastiaan T Heijmans

Genome Biology

A perspective on single cell behavior during infection

2016-09-22

Roi Avraham

Deborah T Hung

Gut microbes

A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans.

2016-09-23

Czerwinski M
Natarajan A
Barske L
Loren L Looger
Capel B

Developmental Biology

Pre-mRNA splicing repression triggers abiotic stress signaling in plants.

2016-09-24

Stefan T Arold
Sahar Alshareef
Yu Ling
Hiroaki Fujii
Jorge Lozano-Juste
Paula Duque
Ahmed Moustafa
Magdy M. Mahfouz
Pedro L Rodriguez

Haroon Butt
Lixin Li
Aya A Galal
Afaque A Momin
Manal Tashkandi
Dale N Richardson

The Plant Journal

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

2016-09-26

Svante Pääbo
Farhath Badsha
Barbara Treutlein
Zhisong He

Felipe Mora-Bermúdez
Sabina Kanton
J Gray Camp
Benjamin Vernot
Kathrin Köhler
Birger Voigt
Keisuke Okita
Tomislav Maricic
Robert Lachmann
Wieland B Huttner

eLife

Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity.

2016-09-26

Aviv Regev
Chuan Wu
Norio Chihara

Yasuhiro Kishi
Takaaki Kondo
Sheng Xiao
Nir Yosef
Jellert Gaublomme
Chao Wang
Nicole Joller
Vijay K Kuchroo

Journal of Experimental Medicine

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

2016-09-26

Rickard Sandberg
Daniel Ramsköld
Björn Reinius
Qiaolin Deng

Jeff E Mold
Per Johnsson
Jakob Michaëlsson
Jonas Frisén

Nature Genetics

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.

2016-09-26

Michael I Love

John B Hogenesch
Rafael A Irizarry

Nature Biotechnology

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species.

2016-09-27

Weizhong Li

R Alexander Richter
Yunsup Jung
Qiyun Zhu
Robert W Li

BMC Genomics

Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection.

2016-09-27

Jan-Willem Veening
Jelle Slager

Rieza Aprianto
Siger Holsappel

Genome Biology

Consensus Analysis of Whole Transcriptome Profiles from Two Breast Cancer Patient Cohorts Reveals Long Non-Coding RNAs Associated with Intrinsic Subtype and the Tumour Microenvironment.

2016-09-29

James R. Bradford
Angela Cox

Philip Bernard
Nicola J Camp

PLOS ONE

Mammalian Period represses and de-represses transcription by displacing CLOCK-BMAL1 from promoters in a Cryptochrome-dependent manner.

2016-09-29

Aziz Sancar

Yi-Ying Chiou
Yanyan Yang
Naim Rashid
Rui Ye
Christopher P Selby

Proceedings of the National Academy of Sciences of the United States of America

Flexible expressed region analysis for RNA-seq with derfinder.

2016-09-29

Leonardo Collado-Torres
Andrew E Jaffe
Jeffrey T. Leek
Ben Langmead
Abhinav Nellore

Alyssa C Frazee
Christopher Wilks
Michael I Love
Rafael A Irizarry

Nucleic Acids Research

Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway.

2016-09-29

Sarah Teichmann
Xi Chen
Gabrielle Belz

Yong Yu
Jason C H Tsang
Cui Wang
Simon Clare
Juexuan Wang
Cordelia Brandt
Leanne Kane
Lia S Campos
Liming Lu
Andrew N J McKenzie
Gordon Dougan
Pentao Liu

Nature

Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors that Can Function as a Cell of Origin for Prostate Cancer.

2016-09-29

Hsueh-Ping Chao
Dingxiao Zhang
Yue Lu

Kevin Lin
Kiera Rycaj
Yi Zhong
Tammy Calhoun-Davis
Jianjun Shen
Dean G Tang

Stem Cells Translational Medicine

Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA.

2016-09-29

Gaurav Sablok

Xiaoyong Sun
Lin Wang
Jiechao Ding
Yanru Wang
Jiansheng Wang
Xiaoyang Zhang
Yulei Che
Ziwei Liu
Xinran Zhang
Jiazhen Ye
Jie Wang
Zhiping Deng
Hongwei Zhao

FEBS Letters

Downregulation of sphingosine kinase-1 induces protective tumor immunity by promoting M1 macrophage response in melanoma.

2016-09-30

Nathalie Andrieu-Abadie
Bruno Ségui
Jean-Christophe Marine
Nicole Therville
Mona Diab-Assaf

Marguerite Mrad
Caroline Imbert
Virginie Garcia
Florian Rambow
Stéphane Carpentier
Thierry Levade
Rania Azar
Céline Colacios

Oncotarget

Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection

2016-10

Sassan Asgari

Kayvan Etebari
Sultan Asad
Guangmei Zhang

PLOS Neglected Tropical Diseases

Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study

2016-10

Pritish Kumar Varadwaj

Rashmi Tripathi
Apoorva Soni

Non-coding RNA Research

Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics.

2016-10-01

Peter Ladurner

Marcelo Rodrigues
Thomas Ostermann
Leopold Kremeser
Herbert Lindner
Christian Beisel
Eugene Berezikov
Bert Hobmayer

Biofouling

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.

2016-10-01

Sten Linnarsson
Peter Lönnerberg
Lars E Borm
Daniel Gyllborg
Enrique M Toledo
Kaneyasu Nishimura
Ernest Arenas
Roger A. Barker

Gioele La Manno
Simone Codeluppi
Carmen Salto
Amit Zeisel
Simon R W Stott
J Carlos Villaescusa
Jesper Ryge

Cell

Profiling the macrofilaricidal effects of flubendazole on adult female Brugia malayi using RNAseq.

2016-10-01

Lucienne Tritten
Steven A Williams
Jianguo Xia

Maeghan O'Neill
Cristina Ballesteros
Erica Burkman
Weam I Zaky
Andrew Moorhead
Timothy G Geary

International Journal for Parasitology: Drugs and Drug Resistance

Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells.

2016-10-01

Rebecca Resnick
Sujatha Jagannathan
Silvère M van der Maarel

Sean C Shadle
Lauren Snider
Rabi N Tawil
Robert K Bradley
Stephen J Tapscott

Human Molecular Genetics

Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

2016-10-01

Tom Owen-Hughes

Nicholas J Schurch
Pietà Schofield
Marek Gierliński
Christian Cole
Alexander Sherstnev
Vijender Singh
Nicola Wrobel
Karim Gharbi
Gordon G Simpson
Mark Blaxter
Geoffrey J Barton

RNA

Correlation of an epigenetic mitotic clock with cancer risk

2016-10-03

Diana Kuh
Andrew Wong

Zhen Yang
Dirk S Paul
Vardhman K Rakyan
R David Leslie
Shijie C Zheng
Martin Widschwendter
Stephan Beck
Andrew E Teschendorff

Genome Biology

Developmental effects of fipronil on Japanese Medaka (Oryzias latipes) embryos.

2016-10-03

Bruce D. Hammock

Scott D Wagner
Tomofumi Kurobe
Bruce G Hammock
Chelsea H Lam
Gary Wu
Natalia Vasylieva
Shirley J Gee
Bruce D Hammock
Swee J Teh

Chemosphere

Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology

2016-10-04

Cedric Bardy

M van den Hurk
B Kakaradov
J A Erwin
B N Jaeger
R V Hernandez
T Eames
A A Paucar
M Gorris
C Marchand
R Jappelli
J Barron
A K Bryant
M Kellogg
R S Lasken
B P F Rutten
H W M Steinbusch
G W Yeo
F H Gage

Molecular Psychiatry

Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant

2016-10-06

Sherif Edris

Ahmed Bahieldin
Ahmed Atef
Nour O Gadalla
Hani M Ali
Sabah M Hassan
Magdy A Al-Kordy
Ahmed M Ramadan
Rania M Makki
Abdulrahman S M Al-Hajar
Fotouh M El-Domyati

BMC Plant Biology

Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.

2016-10-07

Sagiv Shifman
Eyal Ben-David
Aldons Jake Lusis
Eleazar Eskin

Eun Yong Kang
Lisa J Martin
Serghei Mangul
Warin Isvilanonda
Jennifer Zou
Buhm Han

Genetics

Psoriasis-Specific RNA Isoforms Identified by RNA-Seq Analysis of 173,446 Transcripts.

2016-10-07

Ene Reimann
Sulev Kõks

Maris Keermann
Ele Prans
Kristi Abram
Helgi Silm
Gea Kõks
Kulli Kingo

Frontiers in medicine

The Molecular Circuit Regulating Tooth Development in Crocodilians.

2016-10-07

A Abdelhamid

S Tsai
M K Khan
A Elkarargy
R B Widelitz
C M Chuong
P Wu

Journal of Dental Research

Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling.

2016-10-08

Charles R. Farber
Jerome I Rotter

Margareta D Pisarska
Marzieh Akhlaghpour
Bora Lee
Gillian M Barlow
Ning Xu
Erica T Wang
Aaron J Mackey
Stephen S Rich
Yii-der I Chen
Mark O Goodarzi
Seth Guller
John Williams

Prenatal Diagnosis

Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets.

2016-10-11

Brian C Searle

Rachel M Gittelman
Ohad Manor
Joshua M Akey

Genetics

Transcriptomic alterations in Sitophilus zeamais in response to allyl isothiocyanate fumigation.

2016-10-11

Xing Zhang

Chao Zhang
Zhiqing Ma
Hua Wu

Pesticide Biochemistry and Physiology

Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis.

2016-10-11

Kenneth L McClain

Rikhia Chakraborty
Thomas M Burke
Oliver A Hampton
Daniel J Zinn
Karen Phaik Har Lim
Harshal Abhyankar
Brooks Scull
Vijetha Kumar
Nipun Kakkar
David A Wheeler
Angshumoy Roy
Poulikos I Poulikakos
Miriam Merad
D Williams Parsons
Carl E Allen

Blood

Comparative RNA-Seq profiling of berry development between table grape 'Kyoho' and its early-ripening mutant 'Fengzao'.

2016-10-12

Da-Long Guo

Fei-Fei Xi
Yi-He Yu
Xiao-Yu Zhang
Guo-Hai Zhang
Gan-Yuan Zhong

BMC Genomics

Tubulin C-terminal Post-translational Modifications Do Not Occur in Wood Forming Tissue of Populus

2016-10-13

Hao Hu

Xi Gu
Liang-Jiao Xue
Prashant S Swamy
Scott A Harding
Chung-Jui Tsai

Frontiers in Plant Science

The defence-associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias.

2016-10-13

Donald M. Gardiner
Jonathan J Powell
Robert Henry

Timothy L Fitzgerald
Jiri Stiller
Paul J Berkman
John M Manners
Kemal Kazan

Plant Biotechnology Journal

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells

2016-10-14

Lieve Umans
Steven Goossens
Leo A van Grunsven
Danny Huylebroeck
Wilfred F J van IJcken
Geert Berx
Ruben Dries

Agata Stryjewska
Tim Pieters
Griet Verstappen
Andrea Conidi
Kathleen Coddens
Annick Francis
Lieve Umans
Frank G Grosveld
Jody J Haigh

Stem Cells

Genetic divergence in the transcriptional engram of chronic alcohol abuse: A laser-capture RNA-seq study of the mouse mesocorticolimbic system.

2016-10-15

Robert W. Williams
Megan K Mulligan

Khyobeni Mozhui
Ashutosh K Pandey
Maren L Smith
Suzhen Gong
Jesse Ingels
Michael F Miles
Marcelo F Lopez
Lu Lu

Alcohol

Growth and maturation of heart valves leads to changes in endothelial cell distribution, impaired function, decreased metabolism and reduced cell proliferation.

2016-10-15

Samir N. Ghadiali

Lindsey J Anstine
Chris Bobba
Joy Lincoln

Journal of Molecular and Cellular Cardiology

The alternatively-included 11a sequence modifies the effects of Mena on actin cytoskeletal organization and cell behavior

2016-10-17

Douglas A Lauffenburger

Michele Balsamo
Chandrani Mondal
Guillaume Carmona
Leslie M McClain
Daisy N Riquelme
Jenny Tadros
Duan Ma
Eliza Vasile
John S Condeelis
Frank B Gertler

Scientific Reports

Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A.

2016-10-17

Daisuke Kaida
Maxwell Burroughs
Yoshihide Hayashizaki

Rei Yoshimoto
Masaaki Furuno
A Maxwell Burroughs
Shohei Noma
Harukazu Suzuki
Yumi Kawamura
Akila Mayeda
Minoru Yoshida

RNA

Dynamic translation regulation in Caulobacter cell cycle control.

2016-10-17

Jonathan Weissman

Jared M Schrader
Gene-Wei Li
W Seth Childers
Adam M Perez
Lucy Shapiro
Harley H McAdams

Proceedings of the National Academy of Sciences of the United States of America

Human melanomas and ovarian cancers overexpressing mechanical barrier molecule genes lack immune signatures and have increased patient mortality risk.

2016-10-18

Ileana S Mauldin
George Coukos
Craig Slingluff

Elise P Salerno
Davide Bedognetti
Donna H Deacon
Sofia M Shea
Joel Pinczewski
Joseph M Obeid
Ena Wang
Thomas F Gajewski
Francesco M Marincola

OncoImmunology

The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro.

2016-10-18

Tracy L Rimington
Amanda P Henry
Andrew Wardlaw
Ian P. Hall
Suzanne Miller
Stuart G. Parker
Charlotte E Bolton
Anders Malarstig
Erik Melén

Emily Hodge
Alexander K Kheirallah
Charlotte K Billington
Sangita K Bhaker
Ma'en Obeidat
Simon K Merid
Caroline Swan
Catherine Gowland
Carl P Nelson
Ceri E Stewart
Iain Kilty
Miriam F Moffatt
Ian Sayers

PLOS ONE

High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes.

2016-10-18

Horn DA

Sebastian Hutchinson
Lucy Glover

BMC Genomics

Expression and prognostic significance of the autoimmune regulator gene in breast cancer cells.

2016-10-18

Francesca Bianchi
Lucia Sfondrini
Michele Sommariva
Tiziana Triulzi
Loris De Cecco
Andrea Balsari

Sandra Romero-Cordoba
Elda Tagliabue

Cell Cycle

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)

2016-10-19

Rajeev Kumar Varshney

Lekha T Pazhamala
Gaurav Agarwal
Prasad Bajaj
Vinay Kumar
Akanksha Kulshreshtha
Rachit K Saxena

PLOS ONE

The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development.

2016-10-20

Julie Rodor
David R. FitzPatrick

Eduardo Eyras
Javier F Cáceres

RNA Biology

A Study of TP53 RNA Splicing Illustrates Pitfalls of RNA-seq Methodology.

2016-10-20

Peter Tsai
Cristin G. Print
Roger R. Reddel

Sunali Mehta
Annette Lasham
Hamish Campbell
Antony Braithwaite

Cancer Research

RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection

2016-10-20

Bienyameen Baker

Gina Leisching
Ray-Dean Pietersen
Carel van Heerden
Paul van Helden
Ian Wiid

Virulence

Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq

2016-10-21

Jennifer A Kearney

Nicole A Hawkins
Nicole J Zachwieja
Alison R Miller
Lyndsey L Anderson

PLOS Genetics

Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells

2016-10-24

Mikael Huss

Yuanjun Ma
Yali Miao
Zhuochun Peng
Johanna Sandgren
Teresita Díaz De Ståhl
Lena Lennartsson
Yanling Liu
Monica Nistér
Sten Nilsson
Chunde Li

SpringerPlus

Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum.

2016-10-24

Niti Kumar

Deeksha Bhartiya
Vandna Chawla
Sourav Ghosh
Ravi Shankar

Genomics

Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.

2016-10-24

Octávio S. Paulo
Patrícia Gomes de Almeida
João Lucas Coito
Miguel Ramos
Jorge Cunha
Margarida Rocheta
Maria Manuela Ribeiro Costa

Joana Fino
Helena Silva
Sara Amâncio

Plant Molecular Biology

Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes.

2016-10-25

Javier De Las Rivas
Ricardo Assunção Vialle

Katia de Paiva Lopes
Francisco José Campos-Laborie
José Miguel Ortega

BMC Genomics

The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets.

2016-10-25

Ana Tereza Ribeiro de Vasconcelos
Pablo Ivan Pereira Ramos

Márlon Grégori Flores Custódio
Guadalupe Del Rosario Quispe Saji
Thiago Cardoso
Gisele Lucchetti da Silva
Graziela Braun
Willames M B S Martins
Raquel Girardello
Elmer Fernández
Ana Cristina Gales
Marisa Fabiana Nicolás

BMC Genomics

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.

2016-10-25

Christina Kendziorski

Keegan D Korthauer
Li-Fang Chu
Michael A Newton
Yuan Li
James Thomson
Ron Stewart

Genome Biology

RNA-Seq-based analysis of differential gene expression associated with hepatitis C virus infection in a cell culture.

2016-10-25

Marek Figlerowicz

Anna Hojka-Osinska
Lucyna Budzko
Agnieszka Zmienko
Agnieszka Rybarczyk
Patrick Maillard
Agata Budkowska
Paulina Jackowiak

Acta Biochimica Polonica

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process

2016-10-26

Thanh Nguyen

Asim Bhatti
Samuel Yang
Saeid Nahavandi

PLOS ONE

Developmental transcriptome of resting cell formation in Mycobacterium smegmatis.

2016-10-26

Hans-Joachim Mollenkopf
Martin Gengenbacher
Swaine L Chen
Thomas Dick

Mu-Lu Wu
Jade C S Chung
Stefan H E Kaufmann

BMC Genomics

A Multifaceted Role for Myd88-Dependent Signaling in Progression of Murine Mammary Carcinoma.

2016-10-27

Maureen A Carey

Mary J Higgins
Antonio Serrano
Kofi Y Boateng
Victoria A Parsons
Tiffany Phuong
Alyssa Seifert
Jacob M Ricca
Kyle C Tucker
Alec S Eidelman
Robert A Kurt

Breast cancer : basic and clinical research

Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq.

2016-10-27

Dehong Hu
Ronald Taylor

Hugh D Mitchell
Lye Meng Markillie
William B Chrisler
Matthew J Gaffrey
Craig J Szymanski
Yumei Xie
Eric S Melby
Alice Dohnalkova
Eva K Grate
Scott K Cooley
Jason E McDermott
Alejandro Heredia-Langner
Galya Orr

ACS Nano

Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.

2016-10-27

Malin Parmar
Sara Nolbrant
Agnete Kirkeby
Rickard Sandberg

Nigel Kee
Nikolaos Volakakis
Lina Dahl
Helena Storvall
Laura Lahti
Åsa K Björklund
Linda Gillberg
Eliza Joodmardi
Thomas Perlmann

Cell Stem Cell

Early molecular events during retinoic acid induced differentiation of neuromesodermal progenitors.

2016-10-28

Thomas J. Cunningham
Gregg Duester

Alexandre Colas

Biology Open

RNA-Seq: RNA Conversion to cDNA and Amplification.

2016-11-01

Elaine Mardis

Elaine Mardis
W Richard McCombie

Cold Spring Harbor Protocols

Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics.

2016-11-01

Po-Jung Huang
Petrus Tang

Yi-Kai Fang
Kun-Yi Chien
Kuo-Yang Huang
Wei-Hung Cheng
Fu-Mann Ku
Rose Lin
Ting-Wen Chen
Cheng-Hsun Chiu

OMICS: A Journal of Integrative Biology

Molecular phenotyping of infection-associated small non-coding RNAs.

2016-11-01

Alexander Westermann
Jörg Vogel
Lars Barquist

Philosophical Transactions of the Royal Society B

Identification of Differential Gene Expression Patterns after Acute Exposure to High and Low Doses of Low-LET Ionizing Radiation in a Reconstituted Human Skin Tissue.

2016-11-01

Ronald Taylor

Susan C Tilton
Lye Meng Markillie
Spencer Hays
David L Stenoien

Radiation Research

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.

2016-11-01

Jens Nielsen
Verena Siewers

Eugene Fletcher
Amir Feizi
Markus M M Bisschops
Björn M Hallström
Sakda Khoomrung

Metabolic Engineering

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.

2016-11-02

Daniel P Cahill
Rahul Satija
Itay Tirosh
Aviv Regev
Orit Rozenblatt-Rosen
Aanand A Patel
Christopher W Mount
Brian V. Nahed
Michelle Monje
Gad Getz

Andrew S Venteicher
Christine Hebert
Leah E Escalante
Anoop P Patel
Keren Yizhak
Jonathan M Fisher
Christopher Rodman
Mariella G Filbin
Cyril Neftel
Niyati Desai
Jackson Nyman
Benjamin Izar
Christina C Luo
Joshua M Francis
Maristela L Onozato
Nicolo Riggi
Kenneth J Livak
Dave Gennert
William T Curry
Robert L Martuza
Ravindra Mylvaganam
A John Iafrate
Matthew P Frosch
Todd R Golub
Miguel N Rivera
Bradley E Bernstein
David N Louis
Mario L Suvà

Nature

The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem.

2016-11-03

Peter Frommolt

Anneke Frerichs
Rahere Thoma
Ali Taleb Abdallah
Wolfgang Werr
John William Chandler

BMC Genomics

LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development

2016-11-03

Bernice E. Morrow

Deanna Acosta
Susmita Bagchi
Pilib Ó Broin
Daniel Hollern
Silvia E Racedo
Rani S Sellers
John M Greally
Aaron Golden
Eran Andrechek
Teresa Wood
Cristina Montagna

Scientific Reports

The ribosome-engaged landscape of alternative splicing.

2016-11-07

Robert J Weatheritt

Timothy Sterne-Weiler
Benjamin J Blencowe

Nature Structural & Molecular Biology

RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks.

2016-11-08

Jan Perner
Veronika Urbanová

Jan Provazník
Jana Schrenková
José M C Ribeiro
Petr Kopáček

Scientific Reports

ROCK signalling induced gene expression changes in mouse pancreatic ductal adenocarcinoma cells.

2016-11-08

Michael F. Olson

Nicola Rath
Gabriela Kalna
William Clark

Scientific Data

BRM Promoter Polymorphisms and Survival of Advanced Non-Small Cell Lung Cancer Patients in the Princess Margaret Cohort and CCTG BR.24 Trial.

2016-11-08

Geoffrey Liu
Ming-Sound Tsao
Bingshu E Chen

Sinead Cuffe
Shermi Liang
Lu Cheng
Yonathan Brhane
Xin Qiu
David W Cescon
Jeffrey Bruce
Zhuo Chen
Dangxiao Cheng
Devalben Patel
Brandon C Tse
Scott A Laurie
Glenwood Goss
Natasha B Leighl
Rayjean Hung
Penelope A Bradbury
Lesley Seymour
Frances A Shepherd
Wei Xu
David N Reisman

Clinical Cancer Research

Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.

2016-11-09

Daniel Hebenstreit

Nathan Archer
Mark D Walsh
Vahid Shahrezaei

Cell systems

Single-Cell Resolution of Temporal Gene Expression during Heart Development.

2016-11-09

Daniel M DeLaughter

Daniel M DeLaughter
Alexander G Bick
Hiroko Wakimoto
David McKean
Joshua M Gorham
Irfan S Kathiriya
John T Hinson
Jason Homsy
Jesse Gray
William Pu
Benoit G Bruneau
J G Seidman
Christine E Seidman

Developmental Cell

Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa.

2016-11-09

Krzysztof Palczewski

Yuanyuan Chen
Matthew J Brooks
Linn Gieser
Anand Swaroop

Pharmacological Research

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.

2016-11-09

Uwe Ohler

Song Li
Masashi Yamada
Xinwei Han
Philip N Benfey

Developmental Cell

Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting.

2016-11-11

Tomas Marques-Bonet
Marta Sanchez-Delgado
Isabel Iglesias-Platas
Enrique Vidal
Jose Medrano
Ronald Bontrop

Franck Court
Ana Monteagudo-Sánchez
Alex Martin-Trujillo
Chiharu Tayama
Ivanela Kondova
Maria Eugenia Poo-Llanillo
Kazuhiko Nakabayashi
Carlos Simón
David Monk

PLOS Genetics

Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch.

2016-11-11

Aimée M Dudley

Gareth A Cromie
Zhihao Tan
Michelle Hays
Eric W Jeffery

In vitro toxicity of pirimiphos-methyl in Atlantic salmon hepatocytes.

2016-11-11

Pål A. Olsvik

Marc H G Berntssen
Liv Søfteland

Toxicology in Vitro

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.

2016-11-12

Ryan Lister
James Whelan

Reena Narsai
David Secco
Matthew D Schultz
Joseph R Ecker

The Plant Journal

MicroRNA profiling of human intermediate monocytes.

2016-11-13

Loems Ziegler-Heitbrock

Adam M Zawada
Lu Zhang
Insa E Emrich
Kyrill S Rogacev
Nicolas Krezdorn
Björn Rotter
Danilo Fliser
Yvan Devaux
Loems Ziegler-Heitbrock
Gunnar H Heine

Immunobiology

Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont

2016-11-14

Nancy A. Moran

J Elijah Powell
Sean P Leonard
Waldan K Kwong
Philipp Engel

Proceedings of the National Academy of Sciences of the United States of America

RNAseq profiling of primary microglia and astrocyte cultures in near-term ovine fetus: A glial in vivo-in vitro multi-hit paradigm in large mammalian brain.

2016-11-14

Patrick Burns

M Cortes
M Cao
H L Liu
C Moore
G Fecteau
A Desrochers
L B Barreiro
J P Antel
M G Frasch

Journal of Neuroscience Methods

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.

2016-11-14

Jörg Vogel
Leon N Schulte
Lei Li
Silke Appenzeller

Antoine-Emmanuel Saliba
Alexander J Westermann
Daphne A C Stapels
Sophie Helaine

Nature Microbiology

Organ- and Growing Stage-Specific Expression of Solanesol Biosynthesis Genes in Nicotiana tabacum Reveals Their Association with Solanesol Content.

2016-11-15

Yanhua Liu
Michael P. Timko

Ning Yan
Hongbo Zhang
Zhongfeng Zhang
John Shi
Yongmei Du
Xinmin Liu

Molecules

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion

2016-11-15

Deyou Zheng

Mingyan Lin
Erika Pedrosa
Anastasia Hrabovsky
Jian Chen
Benjamin R Puliafito
Stephanie R Gilbert
Herbert M Lachman

BMC Systems Biology

Patterns of Transposable Element Expression and Insertion in Cancer.

2016-11-16

Lavanya Rishishwar

Evan A Clayton
Lu Wang
Jianrong Wang
John F McDonald
I King Jordan

Frontiers in molecular biosciences

Aging is associated with impaired angiogenesis, but normal microvascular network structure, in the rat mesentery.

2016-11-18

Melody Baddoo

Richard S Sweat
David C Sloas
Scott A Stewart
Malwina Czarny-Ratajczak
James R Eastwood
Ariana D Suarez-Martinez
Mohammad S Azimi
Hope E Burks
Lee O Chedister
Leann Myers
Walter L Murfee

American Journal of Physiology - Heart and Circulatory Physiology

Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments

2016-11-20

Walter L. Ruzzo

Daniel C. Jones
Kavitha T. Kuppusamy
Nathan J. Palpant
Xinxia Peng
Charles E. Murry
Hannele Ruohola-Baker

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis

2016-11-21

Manuel Kleiner
Nicole Dubilier

Juliane Wippler
Christian Lott
Alexander Gruhl
Paul E Abraham
Richard J Giannone
Jacque C Young
Robert L Hettich

BMC Genomics

Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling

2016-11-21

Javier De Las Rivas
Fermin Sanchez-Guijo

Beatriz Roson-Burgo
Consuelo Del Cañizo

BMC Genomics

Predicting causal variants affecting expression using whole genome sequence and RNA-seq from multiple human tissues

2016-11-21

Kerrin S. Small

Andrew Anand Brown
Ana Viñuela
Olivier Delaneau
Timothy Spector
Emmanouil Dermitzakis

Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity

2016-11-22

Vera Gorbunova
Siming Ma
Charles F. Burant

Akhil Upneja
Andrzej Galecki
Yi-Miau Tsai
Sasha Raskind
Quanwei Zhang
Zhengdong D Zhang
Andrei Seluanov
Clary B Clish
Richard A Miller
Vadim N Gladyshev

eLife

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

2016-11-22

Jonathan Weissman

Joshua G Dunn

BMC Genomics

5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves.

2016-11-22

Yohei Kirino

Megumi Shigematsu

RNA

Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data

2016-11-25

David R. Westhead

Nisar A Shar
M S Vijayabaskar

Molecular Cancer

Tsetse fly tolerance to T. brucei infection: transcriptome analysis of trypanosome-associated changes in the tsetse fly salivary gland

2016-11-25

Jan Van Den Abbeele
Guy Caljon

Irina Matetovici

BMC Genomics

RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk.

2016-11-25

Alessandra Crisà
Bianca Moioli
Giovanni Chillemi

Fabrizio Ferrè

BMC Veterinary Research

Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq.

2016-11-26

Manfred Schartl
Barbara Treutlein
Dirk Schadendorf

Tobias Gerber
Edith Willscher
Henry Loeffler-Wirth
Lydia Hopp
Manfred Schartl
Ulf Anderegg
Gray Camp
Hans Binder
Manfred Kunz

Oncotarget

Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors.

2016-11-28

Yumei Li
Jia-Yu Chen

Lei Lei
Shou-Yu Yan
Ran Yang
Ye Bu
Nannan Chang
Qinchao Zhou
Xiaojun Zhu
Chuan-Yun Li
Jing-Wei Xiong

Nucleic Acids Research

A comprehensive approach to expression of L1 loci.

2016-11-28

Melody Baddoo
Erik K Flemington

Prescott Deininger
Maria E Morales
Travis B White
Melody Baddoo
Dale J Hedges
Geraldine Servant
Sudesh Srivastav
Madison E Smither
Monica Concha
Dawn L DeHaro
Victoria P Belancio

Nucleic Acids Research

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

2016-11-29

Matthew E Ritchie
Gordon K Smyth

Aliaksei Z Holik
Charity W Law
Ruijie Liu
Zeya Wang
Wenyi Wang
Jaeil Ahn
Marie-Liesse Asselin-Labat

Nucleic Acids Research

Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model.

2016-11-29

Alberto Bosque
David M. Margolis

Cory H White
Bastiaan Moesker
Nadejda Beliakova-Bethell
Laura J Martins
Celsa A Spina
Douglas D Richman
Vicente Planelles
Christopher H Woelk

PLOS Pathogens

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation.

2016-11-30

Jibin Sun

Yueming Zhu
Peng Chen
Yunjuan Bao
Yan Men
Yan Zeng
Jiangang Yang
Yuanxia Sun

Scientific Reports

A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior.

2016-12-01

Gavin Clowry
David J Elliott
Yoseph Barash
Mauro Santibanez-Korev

Ingrid Ehrmann
Matthew R Gazzara
Vittoria Pagliarini
Caroline Dalgliesh
Mahsa Kheirollahi-Chadegani
Yaobo Xu
Eleonora Cesari
Marina Danilenko
Marie Maclennan
Kate Lowdon
Tanja Vogel
Piia Keskivali-Bond
Sara Wells
Heather Cater
Philippe Fort
Silvia Middei
Claudio Sette
Mark O Cunningham

Cell Reports

The Lair: a resource for exploratory analysis of published RNA-Seq data.

2016-12-01

Lior Pachter
Harold Pimentel
Páll Melsted

Pascal Sturmfels
Nicolas Bray

BMC Bioinformatics

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors.

2016-12-01

Yankun Yang

Yang Sun
Wenwen Guo
Fen Wang
Feng Peng
Xiaofeng Dai
Xiuxia Liu
Zhonghu Bai

PLOS ONE

InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.

2016-12-01

Thomas F. Meyer
Lukas Rajkowitsch

Konstantin Okonechnikov
Aki Imai-Matsushima
Alexander Seitz
Fernando Garcia-Alcalde

PLOS ONE

QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments.

2016-12-01

Ralf Herwig
Holger Sültmann

Matthias Lienhard
Sabrina Grasse
Jana Rolff
Steffen Frese
Uwe Schirmer
Michael Becker
Stefan Börno
Bernd Timmermann
Lukas Chavez
Gunda Leschber
Iduna Fichtner
Michal R Schweiger

Nucleic Acids Research

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

2016-12-01

Nir Friedman
Jenny Chen
Jonathan Weissman

Atray Dixit
Oren Parnas
Biyu Li
Charles P Fulco
Livnat Jerby-Arnon
Nemanja D Marjanovic
Danielle Dionne
Tyler Burks
Britt Adamson
Thomas M Norman

Cell

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

2016-12-01

Aviv Regev
Marco Y. Hein
Jonathan Weissman

Britt Adamson
Thomas M Norman
Marco Jost
Min Y Cho
James K Nuñez
Yuwen Chen
Jacqueline E Villalta
Luke A Gilbert
Max A Horlbeck
Ryan A Pak
Andrew N Gray
Carol A Gross
Atray Dixit
Oren Parnas

Cell

Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile.

2016-12-01

Weiqing Wang

Huaishan Wang
Kangle Zhai
Yingchao Xue
Jia Yang
Qi Yang
Yi Fu
Yu Hu
Fang Liu
Lianxian Cui
Hui Chen
Jianmin Zhang
Wei He

PLOS ONE

Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations.

2016-12-01

Peter Frommolt
Alvaro Rada-Iglesias

Rizwan Rehimi
Milos Nikolic
Sara Cruz-Molina
Christina Tebartz
Esther Mahabir
Mathieu Clément-Ziza

Cell Reports

Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer.

2016-12-01

John Greally
Katalin Susztak
Shizheng Huang
Niraj Shenoy

Tushar D Bhagat
Yiyu Zou
Jihwan Park
Matthew B Palmer
Caroline Hu
Weijuan Li
Orsolya Giricz
Gaurav Choudhary
Yiting Yu
Yi-An Ko
María C Izquierdo
Ae Seo Deok Park
Nishanth Vallumsetla
Remi Laurence
Robert Lopez
Masako Suzuki
James Pullman
Justin Kaner
Benjamin Gartrell
A Ari Hakimi
Bharvin Patel
Karim Benhadji
Kith Pradhan
Amit Verma

Journal of Biological Chemistry

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56.

2016-12-01

Michelle Craig Barton
Abhinav K Jain
Lalit Patel
Kendra Allton

Yuanxin Xi
Ryan McCarthy
Kadir C Akdemir
Bruce Aronow
Chunru Lin
Wei Li
Liuqing Yang

Molecular Cell

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.

2016-12-01

Alexander van Oudenaarden
Hadas Keren-Shaul

Diego Adhemar Jaitin
Assaf Weiner
Ido Yofe
David Lara-Astiaso
Hadas Keren-Shaul
Eyal David
Tomer Meir Salame
Amos Tanay
Ido Amit

Cell

MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize.

2016-12-02

Blake Meyers

Guo-Ling Nan
Jixian Zhai
Siwaret Arikit
Darren Morrow
John Fernandes
Lan Mai
Nhi Nguyen
Virginia Walbot

Development

How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome?

2016-12-02

Kimon Froussios
Nicholas Schurch
Marek Gierlinski
Geoffrey J. Barton

Katarzyna Mackinnon
Céline Duc
Gordon G Simpson

Transcriptomic Analysis of Mouse Cochlear Supporting Cell Maturation Reveals Large-Scale Changes in Notch Responsiveness Prior to the Onset of Hearing.

2016-12-05

Andrew K. Groves
Zhandong Liu

Juan C Maass
Rende Gu
Tiantian Cai
Ying-Wooi Wan
Silvia C Cantellano
Joanna S T Asprer
Hongyuan Zhang
Hsin-I Jen
Renée K Edlund

PLOS ONE

Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line.

2016-12-05

Richard Simpson

Maoshan Chen
Rong Xu
Hong Ji
David W Greening
Alin Rai
Keiichi Izumikawa
Hideaki Ishikawa
Nobuhiro Takahashi

Scientific Reports

Identification of context-dependent expression quantitative trait loci in whole blood.

2016-12-05

Lude Franke
Harm-Jan Westra
André Uitterlinden
Cornelia M. van Duijn
Cisca Wijmenga
Wibowo Arindrarto
Patrick Deelen
Marc Jan Bonder
Jenny van Dongen
Yang Li
Rick Jansen
Marian Beekman
Morris A Swertz
Dorret Boomsma
Peter A.C. 't Hoen
Albert Hofman
Leonard H van den Berg
Jan H Veldink
Coenraad Dirk Adriaan Stehouwer
Casper G. Schalkwijk
Jouke-Jan Hottenga

Daria V Zhernakova
Martijn Vermaat
Maarten van Iterson
Michiel van Galen
Peter van 't Hof
Hailiang Mei
Freerk van Dijk
Jeroen van Rooij
Marijn Verkerk
P Mila Jhamai
Matthijs Moed
Szymon M Kielbasa
Jan Bot
Irene Nooren
René Pool
Carla J H van der Kallen
Alexandra Zhernakova
Ettje F Tigchelaar
Niek de Klein
Joris Deelen
Diana van Heemst
André G Uitterlinden
Marleen M J van Greevenbroek
P Eline Slagboom
Aaron Isaacs
Joyce B J van Meurs
Bastiaan T Heijmans

Nature Genetics

Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection.

2016-12-05

James P Scott-Browne

Isaac F López-Moyado
Sara Trifari
Victor Wong
Lukas Chavez
Anjana Rao
Renata M Pereira

Immunity

Loss of Rearranged L-Myc Fusion (RLF) results in defects in heart development in the mouse.

2016-12-05

Pamela M. Pollock

L M Bourke
G Del Monte-Nieto
J E Outhwaite
V Bharti
D G Simmons
A Adam
S S J Hur
G J Maghzal
E Whitelaw
R Stocker
C M Suter
R P Harvey
S K Harten

Differentiation

Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection

2016-12-06

Mary F Fontana
Chioma Anidi
Charles C. Kim

Gabrielly L de Melo
Rebecca Hamburger
Chris Y Kim
So Youn Lee
Jennifer Pham

PLOS Pathogens

Identification of senescence-associated circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1

2016-12-07

Amaresh C Panda
Myriam Gorospe
Kotb Abdelmohsen

Ioannis Grammatikakis
Kyoung Mi Kim
Supriyo De
Jennifer L Martindale
Rachel Munk
Xiaoling Yang

Nucleic Acids Research

Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq.

2016-12-07

Subhash J Jakhesara
Chaitanya G. Joshi

Prakash G Koringa
Neelam M Nathani

3 Biotech

Acfs: accurate circRNA identification and quantification from RNA-Seq data.

2016-12-08

Tim Conrad

Xintian You

Scientific Reports

Catalase deletion promotes prediabetic phenotype in mice.

2016-12-08

Kristofer S Fritz

Claire Heit
Stephanie Marshall
Surrendra Singh
Xiaoqing Yu
Georgia Charkoftaki
Hongyu Zhao
David J Orlicky
David C Thompson
Vasilis Vasiliou

Free Radical Biology and Medicine

Single-cell barcoding and sequencing using droplet microfluidics.

2016-12-08

David Zemmour

Rapolas Zilionis
Juozas Nainys
Adrian Veres
Virginia Savova
Allon M Klein
Linas Mazutis

Nature Protocols

Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport.

2016-12-08

Breandan N Kennedy

Victor L Jensen
Stephen Carter
Anna A W M Sanders
Chunmei Li
Julie Kennedy
Tiffany A Timbers
Jerry Cai
Noemie Scheidel
Ryan D Morin
Michel R Leroux
Oliver E Blacque

PLOS Genetics

Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae.

2016-12-09

Clícia Grativol

Ailton B Santa Brigida
Cristian A Rojas
Elvismary M de Armas
Júlio O P Entenza
Flávia Thiebaut
Marcelo de F Lima
Laurent Farrinelli
Adriana S Hemerly
Sérgio Lifschitz
Paulo C G Ferreira

PLOS ONE

Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism.

2016-12-09

Rita Benítez

Miriam Ayuso
Almudena Fernández
Yolanda Núñez
Beatriz Isabel
Ana I Fernández
Ana I Rey
Antonio González-Bulnes
Juan F Medrano
Ángela Cánovas
Clemente J López-Bote
Cristina Óvilo

PLOS ONE

Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq.

2016-12-09

Yan Li

Jinlong Zhang
Jiaxue Wang
Wei Jiang
Juge Liu
Songnan Yang
Junyi Gai

Frontiers in Plant Science

Cardiac inflammation in genetic dilated cardiomyopathy caused by MYBPC3 mutation.

2016-12-09

Sakthivel Sadayappan
Anil G. Jegga

Thomas L Lynch
Mohamed Ameen Ismahil
Michael J Zilliox
Christian Troidl
Sumanth D Prabhu

Journal of Molecular and Cellular Cardiology

Simulation-based comprehensive benchmarking of RNA-seq aligners.

2016-12-12

Katharina E. Hayer
Gregory R Grant

Giacomo Baruzzo
Eun Ji Kim
Barbara Di Camillo
Garret A FitzGerald

Nature Methods

Prediction and prioritization of neoantigens: integration of RNA sequencing data with whole-exome sequencing.

2016-12-13

Osamu Ohara

Takahiro Karasaki
Kazuhiro Nagayama
Hideki Kuwano
Jun-Ichi Nitadori
Masaaki Sato
Masaki Anraku
Akihiro Hosoi
Hirokazu Matsushita
Masaki Takazawa
Jun Nakajima
Kazuhiro Kakimi

Cancer Science

Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states.

2016-12-14

Jiapei Yuan

Yang Yang
Yu-Cheng T Yang
Zhi John Lu
Jingyi Jessica Li

Nucleic Acids Research

Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection.

2016-12-14

Marvin Whiteley

Apollo Stacy
Nader Abraham
Peter Jorth

PLOS Pathogens

Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets.

2016-12-14

Thorsten Bischler

Ping-Kun Hsieh
Marcus Resch
Quansheng Liu
Hock Siew Tan
Patricia L Foley
Anika Hartleib
Cynthia M Sharma
Joel G Belasco

Journal of Biological Chemistry

Characterization of a TUTase/RNase complex required for Drosophila gametogenesis.

2016-12-14

Jiayu Wen
Eric C Lai

Ching-Jung Lin
Fernando Bejarano
Fuqu Hu
Diane Bortolamiol-Becet
Lijuan Kan
Piero Sanfilippo

RNA

FAM13A is associated with non-small cell lung cancer (NSCLC) progression and controls tumor cell proliferation and survival.

2016-12-14

Arif B. Ekici

Felix Eisenhut
Lisanne Heim
Sonja Trump
Susanne Mittler
Nina Sopel
Katerina Andreev
Fulvia Ferrazzi
Ralf Rieker
Rebekka Springel
Vera L Assmann
Matthias Lechmann
Sonja Koch
Marina Engelhardt
Christina Warnecke
Denis I Trufa
Horia Sirbu
Arndt Hartmann
Susetta Finotto

OncoImmunology

SLICE: determining cell differentiation and lineage based on single cell entropy.

2016-12-19

Erik L Bao

Minzhe Guo
Michael Wagner
Jeffrey A Whitsett
Yan Xu

Nucleic Acids Research

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development.

2016-12-20

Lay Teng Ang
Anshul Kundaje

Pang Wei Koh
Rahul Sinha
Amira A Barkal
Rachel M Morganti
Angela Chen
Irving L Weissman
Kyle M Loh

Scientific Data

Limb patterning genes and heterochronic development of the emu wing bud.

2016-12-20

Alicia Oshlack
Nadia M Davidson
Craig A. Smith
Claire E. Hirst
David M Lambert

Peter G Farlie
Kelly N Roeszler

EvoDevo

Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans

2016-12-21

Aurélien Vigneron

Amy F Savage
Nikolay G Kolev
Joseph B Franklin
Serap Aksoy
Christian Tschudi

PLOS ONE

A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing.

2016-12-21

Robert J. Meagher

Zachary W Bent
Kunal Poorey
Annette E LaBauve
Rachelle Hamblin
Kelly P Williams

PLOS ONE

Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater.

2016-12-21

Wataru Iwasaki

Yoshio Takei
Marty K-S Wong
Supriya Pipil
Haruka Ozaki
Yutaka Suzuki
Makoto Kusakabe

American Journal of Physiology - Regulatory, Integrative and Comparative Physiology

Logic programming to infer complex RNA expression patterns from RNA-seq data.

2016-12-22

Stefanie Dimmeler
Yuliya Ponomareva
Tyler Weirick
Shizuka Uchida

Giuseppe Militello
David John
Claudia Döring

Briefings in Bioinformatics

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.

2016-12-22

Tommy Kaplan

Markus Nevil
Eliana R Bondra
Katharine N Schulz
Melissa M Harrison

Genetics

CYP716A179 functions as a triterpene C-28 oxidase in tissue-cultured stolons of Glycyrrhiza uralensis.

2016-12-22

Toshiya Muranaka
Kazuki Saito

Keita Tamura
Hikaru Seki
Hideyuki Suzuki
Mareshige Kojoma

Plant Cell Reports

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.

2016-12-23

Vivek Krishnakumar
Erik S Ferlanti
Jason R Miller
Matthew Vaughn

Sergio Contrino
Chia-Yi Cheng
Irina Belyaeva
Gos Micklem
Christopher D Town
Agnes P Chan

Plant and Cell Physiology

Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders

2016-12-23

Thomas Freeman
Barbara Shih
Arne N Akbar

Ajit J Nirmal
Denis J Headon
Neil A Mabbott

The Journal of Pathology

RNA sequencing of archived neonatal dried blood spots.

2016-12-24

Marie Bækvad-Hansen
Jonas Bybjerg-Grauholm
Mads Vilhelm Hollegaard

Christian Munch Hagen
Sok Kean Khoo
Maria Louise Johannesen
Christine Søholm Hansen
Michael Christiansen
David Michael Hougaard

Molecular Genetics and Metabolism Reports

Alternative splicing in tomato pollen in response to heat stress.

2016-12-26

Enrico Schleiff

Mario Keller
Yangjie Hu
Anida Mesihovic
Sotirios Fragkostefanakis
Stefan Simm

DNA Research

Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.

2016-12-27

Matteo Pellegrini
Davide Carnevali
Anastasia Conti

Giorgio Dieci

DNA Research

Transcriptomic gene profiling of porcine muscle tissue depending on histological properties.

2016-12-27

Artur Gurgul
Katarzyna Ropka-Molik
Katarzyna Piórkowska

Anna Bereta
Kacper Żukowski
Grzegorz Żak

Animal Science Journal

Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer.

2016-12-28

Alex Zhavoronkov

Anastasiya Vladimirovna Snezhkina
George Sergeevich Krasnov
Andrew Rostislavovich Zaretsky
Kirill Mikhailovich Nyushko
Alexey Alexandrovich Moskalev
Irina Yurievna Karpova
Anastasiya Isaevna Afremova
Anastasiya Valerievna Lipatova
Dmitriy Vladimitovich Kochetkov
Maria Sergeena Fedorova
Nadezhda Nikolaevna Volchenko
Asiya Fayazovna Sadritdinova
Nataliya Vladimirovna Melnikova
Dmitry Vladimirovich Sidorov
Anatoly Yurievich Popov
Dmitry Valerievich Kalinin
Andrey Dmitrievich Kaprin
Boris Yakovlevich Alekseev
Alexey Alexandrovich Dmitriev
Anna Viktorovna Kudryavtseva

BMC Genomics

Succession of splicing regulatory elements determines cryptic 5΄ss functionality.

2016-12-29

Emanuele Buratti

Anna-Lena Brillen
Katrin Schöneweis
Lara Walotka
Linda Hartmann
Lisa Müller
Johannes Ptok
Wolfgang Kaisers
Gereon Poschmann
Kai Stühler
Stephan Theiss
Heiner Schaal

Nucleic Acids Research

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

2016-12-30

Kasper D. Hansen
Leonardo Collado-Torres
Andrew E Jaffe
Jeffrey T. Leek
Ben Langmead
Abhinav Nellore

Jean-Philippe Fortin
José Alquicira-Hernández
Siruo Wang
Robert A Phillips Iii
Nishika Karbhari

Genome Biology

2017

I-Hsuan Lin

Yi-Fan Chen
Ming-Ta Hsu

PLOS ONE

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

2017

Luisa Pereira
Nuno A. Fonseca

Bruno Cavadas
Joana Ferreira
Rui Camacho

Advances in Intelligent Systems and Computing

Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.

2017-01-01

Rohit jain

Sushma Naithani
Pankaj Jaiswal

Methods in Molecular Biology

Coupled Proliferation and Apoptosis Maintain the Rapid Turnover of Microglia in the Adult Brain

2017-01-01

Olga Garaschuk
Amanda Sierra
Yajie Liang
Diego Gómez-Nicola
Zoltán Molnár
Mark S Cragg

Katharine Askew
Kaizhen Li
Adrian Olmos-Alonso
Fernando Garcia-Moreno
Philippa Richardson
Tom Tipton
Mark A Chapman
Kristoffer Riecken
Sol Beccari
V Hugh Perry

Cell Reports

Simple Analysis of Deposited Gene Expression Datasets for the Non-Bioinformatician: How to Use GEO for Fibrosis Research.

2017-01-01

Lam C. Tsoi

Yang Guo
Richard Townsend

Methods in Molecular Biology

Some Thoughts on Experimental Design.

2017-01-01

Claudio Daniel Stern

Methods in Molecular Biology

RNA-Seq investigations of human post-mortem trigeminal ganglia.

2017-01-01

Danielle Thierry-Mieg
Stephen J Raithel
Jean Thierry-Mieg

Danielle M LaPaglia
Matthew R Sapio
Peter D Burbelo
Danielle Thierry-Mieg
Christopher E Ramsden
Michael J Iadarola
Andrew J Mannes

Cephalalgia

Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

2017-01-01

Thomas Derrien

Sarah Djebali
Valentin Wucher
Sylvain Foissac
Christophe Hitte
Evan Corre

Methods in Molecular Biology

Understanding development and stem cells using single cell-based analyses of gene expression.

2017-01-01

Patrick Cahan

Pavithra Kumar
Yuqi Tan

Development

RNA-Seq in the Collaborative Cross.

2017-01-01

Michael Gale
Courtney Wilkins

Richard Green
Martin T Ferris

Methods in Molecular Biology

Analysis of EBV Transcription Using High-Throughput RNA Sequencing.

2017-01-01

Melody Baddoo
Tina O'Grady
Erik K Flemington

Melody Baddoo

Methods in Molecular Biology

Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation.

2017-01-01

Sergio Abrignani

Valeria Ranzani
Alberto Arrigoni
Grazisa Rossetti
Ilaria Panzeri
Raoul J P Bonnal
Massimiliano Pagani

Methods in Molecular Biology

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging.

2017-01-01

Rickie Patani
Jernej Ule
John Anthony Hardy
Mina Ryten
North American Brain Expression Consortium
Mark R Cookson

Lilach Soreq
UK Brain Expression Consortium
Jamie Rose
Eyal Soreq
Daniah Trabzuni
Colin Smith

Cell Reports

Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo

2017-01-01

Linus T-Y Tsai

Hyun Cheol Roh
Anna Lyubetskaya
Danielle Tenen
Manju Kumari
Evan D Rosen

Cell Reports

RNA-Seq Data Analysis Protocol: Combining In-House and Publicly Available Data.

2017-01-01

Marc W Schmid

Methods in Molecular Biology

Optimized Whole Transcriptome Profiling of Motor Axons.

2017-01-01

Michael Sendtner

Lena Saal-Bauernschubert
Michael Briese

Methods in Molecular Biology

Analysis of Mitochondrial RNA-Processing Defects in Patient-Derived Tissues by qRT-PCR and RNAseq.

2017-01-01

Johannes A Mayr
Holger Prokisch

Robert Kopajtich

Methods in Molecular Biology

Genetic screens: Combining CRISPR perturbations and RNA-seq.

2017-01-01

Darren J. Burgess

Nature Reviews Genetics

Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.

2017-01-02

Andrea Bräutigam

Alisandra K Denton
Janina Maß
Canan Külahoglu
Martin J Lercher
Andreas P M Weber

Journal of Experimental Botany

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.

2017-01-03

Roderic Guigó i Serra
Emilio Palumbo
A Rastrojo

Bernardo Rodríguez-Martín
Santiago Marco-Sola
Thasso Griebel
Paolo Ribeca
Graciela Alonso
Begoña Aguado
Sarah Djebali

BMC Genomics

An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity.

2017-01-03

Matthew M Schaefers
Deborah R Yoder-Himes
Damien Roux

Tiffany L Liao
Nicole M Boisvert
Gregory P Priebe

PLOS Pathogens

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.

2017-01-03

Markus Landthaler
Christoph Dieterich
Emanuel Wyler
Uwe Ohler

Michael Piechotta

BMC Bioinformatics

A three-lncRNA signature derived from the Atlas of ncRNA in cancer (TANRIC) database predicts the survival of patients with head and neck squamous cell carcinoma.

2017-01-03

Ze-Guang Han

Wei Cao
Jian-Nan Liu
Zeqi Liu
Xu Wang
Tong Ji
Wan-Tao Chen
Xin Zou

Oral Oncology

Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle

2017-01-03

Eva M Murauer
Magali Taulan
Mireille Claustres
Sylvie Tuffery-Giraud

Anne-Laure Bougé
Emmanuelle Beyne
Julie Miro
Jessica Varilh
Michel Koenig

Scientific Reports

Blocking Tumor-Educated MSC Paracrine Activity Halts Osteosarcoma Progression.

2017-01-04

Sonia A. Melo
Roberta Bonafede
Anne-Marie Cleton-Jansen
Agostino Steffan
Massimo Dominici

S Rubina Baglio
Tonny Lagerweij
Maria Pérez-Lanzón
Xuan Dung Ho
Nicolas Léveillé
Anne-Marie Cleton-Jansen
Ekaterina S Jordanova
Laura Roncuzzi
Michelina Greco
Monique A J van Eijndhoven
Giulia Grisendi
Sinead M Lougheed
Tanja D de Gruijl
Nicoletta Zini
Silvia Cervo
Vincenzo Canzonieri
Aare Martson
Katre Maasalu
Sulev Köks
Tom Wurdinger
Nicola Baldini
D Michiel Pegtel

Clinical Cancer Research

In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways

2017-01-05

Konrad Förstner
Jörg Vogel
Lei Li
Kai Papenfort
Hans-Joachim Wieden
Richard Reinhardt

Yanjie Chao
Dylan Girodat
Nelly Said
Colin Corcoran
Michał Śmiga
Ben F Luisi

Molecular Cell

Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism

2017-01-05

Kerstin Kutsche
Stéphane Bézieau
Sébastien Küry

Frederike Leonie Harms
Katta M. Girisha
Andrew A. Hardigan
Fanny Kortüm
Anju Shukla
Malik Alawi
Ashwin Dalal
Lauren Brady
Mark Tarnopolsky
Lynne M. Bird
Sophia Ceulemans
Martina Bebin
Kevin M. Bowling
Susan M. Hiatt
Edward J. Lose
Michelle Primiano
Wendy K. Chung
Jane Juusola
Zeynep C. Akdemir
Matthew Bainbridge
Wu-Lin Charng
Margaret Drummond-Borg
Mohammad K. Eldomery
Ayman W. El-Hattab
Mohammed A. M. Saleh
Stéphane Bézieau
Benjamin Cogné
Bertrand Isidor
Sébastien Küry
James R. Lupski
Richard M. Myers
Gregory M. Cooper

American Journal of Human Genetics

iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.

2017-01-05

Giorgio Giurato
Francesca Rizzo
Roberta Tarallo
Alessandro Weisz
Luciano Milanesi

Riccardo Panero
Antonio Rinaldi
Domenico Memoli
Giovanni Nassa
Maria Ravo

Bioinformatics

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus

2017-01-05

Amy L Roberts
Ana Viñuela
Kerrin S. Small
Christopher A Odhams
Timothy J Vyse

Andrea Cortini
Lingyan Chen
Alfonso Buil
Emmanouil T Dermitzakis
David L Morris
Deborah S Cunninghame Graham

Human Molecular Genetics

SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention.

2017-01-05

Elisa Pesce
Sara Ricciardi
Stefano Biffo
Diego Luis Medina
Massimiliano Pagani

Piera Calamita
Annarita Miluzio
Arianna Russo
Farhat Khanim
Cristina Cheroni
Roberta Alfieri
Marilena Mancino
Chiara Gorrini
Grazisa Rossetti
Ivana Peluso
Johanna Rommens

PLOS Genetics

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells.

2017-01-05

Alicja Pacholewska

Eliane Marti
Tosso Leeb
Vidhya Jagannathan
Vincent Gerber

BMC Genomics

Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation.

2017-01-06

Dev Paudel

Ze Peng
Fengxia Liu
Liping Wang
Hai Zhou
Lubin Tan
James Maku
Maria Gallo
Jianping Wang

Scientific Reports

Single-cell transcriptomics of small microbial eukaryotes: limitations and potential.

2017-01-06

Karla B Heidelberg

Zhenfeng Liu
Sarah K Hu
Victoria Campbell
Avery O Tatters
David A Caron

The ISME Journal

The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq

2017-01-07

Sergi Padilla-Parra
William James

Quin F Wills
Esther Mellado-Gomez
Rory Nolan
Damien Warner
Eshita Sharma
John Broxholme
Benjamin Wright
Helen Lockstone
Mark Lynch
Michael Gonzales
Jay West
Anne Leyrat
Sarah Filippi
Chris Holmes
Michael D Moore
Rory Bowden

BMC Genomics

KANK1 inhibits cell growth by inducing apoptosis though regulating CXXC5 in human malignant peripheral nerve sheath tumors

2017-01-09

GuangJun Zhang

Zhibin Cui
Yingjia Shen
Kenny H Chen
Suresh K Mittal
Jer-Yen Yang

Scientific Reports

Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus.

2017-01-09

Sharon Rozovsky

Sai Siddarth Kalburge
Megan R Carpenter
E Fidelma Boyd

Infection and Immunity

Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome.

2017-01-09

Jeffrey S. Buzby

Shirley A Williams
Lana Schaffer
Steven R Head
Diane J Nugent

Cancer Genetics

Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion

2017-01-10

Victor Nizet
Bjørn Voldborg
Nathan E. Lewis

Xander M van Wijk
Simon Döhrmann
Björn M Hallström
Shangzhong Li
Brandon X Meng
Karen K McKee
Toin H van Kuppevelt
Peter D Yurchenco
Bernhard O Palsson
Jeffrey D Esko

mBio

A Hypothesis Testing Based Method for Normalization and Differential Expression Analysis of RNA-Seq Data.

2017-01-10

Jun Zhang

Yan Zhou
Guochang Wang
Han Li

PLOS ONE

Long noncoding RNA repertoire in chicken liver and adipose tissue

2017-01-10

Hervé Acloque
Fabrice Legeai
Kévin Muret
Thomas Derrien
Sandrine Lagarrigue

Christophe Klopp
Valentin Wucher
Diane Esquerré
Frédéric Lecerf
Colette Désert
Morgane Boutin
Frédéric Jehl
Elisabetta Giuffra
Sarah Djebali
Sylvain Foissac

Genetics Selection Evolution

Nitro-fatty acids in plant signaling: New key mediators of nitric oxide metabolism.

2017-01-10
2017-04-01

Francisco J. Corpas
Juan C Begara-Morales

Capilla Mata-Pérez
Beatriz Sánchez-Calvo
María N Padilla
Raquel Valderrama
Juan B Barroso

Redox Biology

Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures.

2017-01-11

Elba Serrano

V Bleu Knight

PeerJ

High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis.

2017-01-12

Takayoshi Yamamoto
Yuuri Yasuoka
Takuya Nakayama

Tatsuo Michiue
Toshiyasu Goto
Takafumi Ikeda
Kei Nagura
Masanori Taira
Tsutomu Kinoshita

Developmental Biology

Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum.

2017-01-12

Stanford Kwenda
Elena Osipova
Lucy Moleleki

Vladimir Gorshkov
Olga Petrova
Yuri Gogolev

PLOS ONE

Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response.

2017-01-12

Chi Nam Ignatius Pang
Dee A Carter

Yu-Wen Lai
Leona T Campbell
Sharon C-A Chen
Marc R Wilkins

Scientific Reports

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

2017-01-14

Davis J McCarthy

Kieran R Campbell
Aaron T L Lun
Quin F Wills

Bioinformatics

Effective detection of variation in single-cell transcriptomes using MATQ-seq.

2017-01-16

Chenghang Zong

Kuanwei Sheng
Wenjian Cao
Yichi Niu
Qing Deng

Nature Methods

PEDF Is Associated with the Termination of Chondrocyte Phenotype and Catabolism of Cartilage Tissue.

2017-01-16

Arif B. Ekici

P Klinger
S Lukassen
F Ferrazzi
T Hotfiel
B Swoboda
T Aigner
K Gelse

BioMed Research International

Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae.

2017-01-17

Christina A Cuomo

Su San Toh
Zehua Chen
David J Schultz
Michael H Perlin

Microbiology

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis

2017-01-18

Pär G Engström
Janne Lehtiö
Kaustuv Sanyal
Joseph Heitman
Teun Boekhout

Yafeng Zhu
Christian Tellgren-Roth
Charles D Baudo
John C Kennell
Sheng Sun
R Blake Billmyre
Markus S Schröder
Anna Andersson
Tina Holm
Benjamin Sigurgeirsson
Guangxi Wu
Sundar Ram Sankaranarayanan
Rahul Siddharthan
Joakim Lundeberg
Björn Nystedt
Thomas L Dawson
Annika Scheynius

Nucleic Acids Research

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey.

2017-01-18

Erich M Schwarz
Yen-Ping Hsueh
Frank C Schroeder
Paul W. Sternberg

Matthew R Gronquist
Ravi David Nath
Ching-Han Lee
Shalha Gharib

eLife

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

2017-01-18

Andreas Heger
Tom Smith
Ian Sudbery

Genome Research

Feasibility of sample size calculation for RNA-seq studies.

2017-01-18

Alicia Poplawski

Harald Binder

Briefings in Bioinformatics

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

2017-01-19

Lana Garmire

Xun Zhu
Travers Ching
Xinghua Pan
Sherman M Weissman
Lana Garmire

PeerJ

Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies.

2017-01-22

Arne Van Hoeck
Ronny Blust

Nele Horemans
Robin Nauts
May Van Hees
Hildegarde Vandenhove

Plant Science

Genome-wide identification and analysis of biotic and abiotic stress regulation of small heat shock protein (HSP20) family genes in bread wheat.

2017-01-22

Senthilkumar K Muthusamy
Viswanathan Chinnusamy

Monika Dalal
Kailash C Bansal

The Journal of Plant Physiology

The choreography of the chemical defensome response to insecticide stress: insights into the Anopheles stephensi transcriptome using RNA-Seq

2017-01-23

Claudio Bandi

Leone De Marco
Davide Sassera
Sara Epis
Valentina Mastrantonio
Marco Ferrari
Irene Ricci
Francesco Comandatore
Daniele Porretta
Sandra Urbanelli

Scientific Reports

A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine.

2017-01-23

Alycia Gardner

Isaac A Chaim
Jie Wu
Teruaki Iyama
David M Wilson
Leona D Samson

Nucleic Acids Research

RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development.

2017-01-24

Jinggui Fang

Lingfei Shangguan
Qian Mu
Xiang Fang
Kekun Zhang
Haifeng Jia
Xiaoying Li
Yiqun Bao

PLOS ONE

Single-cell epigenomic variability reveals functional cancer heterogeneity.

2017-01-24

Nathan C. Sheffield
William Greenleaf

Ulrike M Litzenburger
Jason D Buenrostro
Beijing Wu
Ying Shen
Arwa Kathiria
Howard Y Chang

Genome Biology

Large-scale analysis of branchpoint usage across species and cell lines.

2017-01-24

Allison J Taggart
William G Fairbrother

Chien-Ling Lin
Barsha Shrestha
Claire Heintzelman
Seongwon Kim

Genome Research

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model

2017-01-25

Matthew E Thornton

Kathy A Schall
Mubina Isani
Kathleen A Holoyda
Xiaogang Hou
Ching-Ling Lien
Brendan H Grubbs
Tracy C Grikscheit

BMC Genomics

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.

2017-01-25

Marc Dabad
Nuria de la Iglesia
Avelina Tortosa
Carmen Balaña
Anna Esteve-Codina

Oriol Arpi
Maria Martinez-García
Estela Pineda
Mar Mallo
Marta Gut
Cristina Carrato
Anna Rovira
Raquel Lopez
Sonia Del Barco
Simon Heath
Silvia Bagué
Teresa Ribalta
Francesc Alameda
GLIOCAT Group

PLOS ONE

Two-Way Chemical Communication between Artificial and Natural Cells.

2017-01-25

Luca Belmonte
Sheref S. Mansy

Roberta Lentini
Noël Yeh Martín
Michele Forlin
Jason Fontana
Michele Cornella
Laura Martini
Sabrina Tamburini
William E Bentley
Olivier Jousson

ACS Central Science

Guanylate-binding protein 1 (GBP1) contributes to the immunity of human mesenchymal stromal cells against Toxoplasma gondii.

2017-01-25

Geoff Hide
De-Hua Lai
Francisco J. Ayala

Aiping Qin
Qifa Liu
Weijun Huang
Ya-Ping Wu
Xiaoyong Chen
Sunxing Yan
Huimin Xia
Zhao-Rong Lun
Andy Peng Xiang

Proceedings of the National Academy of Sciences of the United States of America

Stably Expressed Genes Involved in Basic Cellular Functions.

2017-01-26

Vikrant Vijay

Kejian Wang
James C Fuscoe

PLOS ONE

Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis

2017-01-26

Lukas Kenner
Iveta Yotova

Emily Hsu
Catherine Do
Aulona Gaba
Matthias Sczabolcs
Sabine Dekan
Rene Wenzl
Benjamin Tycko

PLOS ONE

Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion.

2017-01-26

Céline Cruciani-Guglielmacci
Christophe Magnan
Lara Bellini
Robin Liechti
Ioannis Xenarios

Jessica Denom
Masaya Oshima
Neïké Fernandez
Priscilla Normandie-Levi
Xavier P Berney
Nadim Kassis
Claude Rouch
Julien Dairou
Tracy Gorman
David M Smith
Anna Marley
Dmitry Kuznetsov
Leonore Wigger
Frédéric Burdet
Anne-Laure Lefèvre
Isabelle Wehrle
Ingo Uphues
Tobias Hildebrandt
Werner Rust
Catherine Bernard
Alain Ktorza
Guy A Rutter
Raphael Scharfmann
Hervé Le Stunff
Bernard Thorens
Mark Ibberson

Molecular Metabolism

Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing.

2017-01-27

Allan B. Dietz

Amel Dudakovic
Martina Gluscevic
Christopher R Paradise
Halil Dudakovic
Farzaneh Khani
Roman Thaler
Farah S Ahmed
Xiaodong Li
Gary S Stein
Martin A Montecino
David R Deyle
Jennifer J Westendorf
Andre J van Wijnen

Gene

Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells.

2017-01-28

Justin L. Mott

Penn Muluhngwi
Kirsten Richardson
Joshua Napier
Eric C Rouchka
Carolyn M Klinge

Molecular and Cellular Endocrinology

MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi

2017-01-30

Timothy Casselli
Ata Abbas

Humaira Qureshi
Elizabeth Peterson
Danielle Perley
Emily Blake
Bradley Jokinen
Sergei Nechaev
John A Watt
Archana Dhasarathy
Catherine A Brissette

PLOS ONE

Comparative genomics of two jute species and insight into fibre biogenesis.

2017-01-30

Xuehua Wan

Md Shahidul Islam
Jennifer A Saito
Emdadul Mannan Emdad
Borhan Ahmed
Mohammad Moinul Islam
Abdul Halim
Quazi Md Mosaddeque Hossen
Md Zakir Hossain
Rasel Ahmed
Md Sabbir Hossain
Shah Md Tamim Kabir
Md Sarwar Alam Khan
Md Mursalin Khan
Rajnee Hasan
Nasima Aktar
Ummay Honi
Rahin Islam
Md Mamunur Rashid
Shaobin Hou
Taslima Haque
Muhammad Shafiul Azam
Mahdi Muhammad Moosa
Sabrina M Elias
A M Mahedi Hasan
Niaz Mahmood
Md Shafiuddin
Saima Shahid
Nusrat Sharmeen Shommu
Sharmin Jahan
Saroj Roy
Amlan Chowdhury
Ashikul Islam Akhand
Golam Morshad Nisho
Khaled Salah Uddin
Taposhi Rabeya
S M Ekramul Hoque
Afsana Rahman Snigdha
Sarowar Mortoza
Syed Abdul Matin
Md Kamrul Islam
M Z H Lashkar
Mahboob Zaman
Anton Yuryev
Md Kamal Uddin
Md Sharifur Rahman
Md Samiul Haque
Md Monjurul Alam
Haseena Khan
Maqsudul Alam

Nature Plants

Identification and evolutionary analysis of long non-coding RNAs in zebra finch.

2017-01-31

Chun-Ping Yu

Chih-Kuan Chen
Sung-Chou Li
Siao-Man Wu
Mei-Yeh Jade Lu
Yi-Hua Chen
Di-Rong Chen
Chen Siang Ng
Chau-Ti Ting
Wen-Hsiung Li

BMC Genomics

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

2017-01-31

Ellen Decaestecker
Luisa Orsini
John K. Colbourne

Donald Gilbert
Ram Podicheti
Mieke Jansen
James B Brown
Omid Shams Solari
Katina I Spanier
Douglas B Rusch
Jana Asselman
Karel A C De Schamphelaere
Dieter Ebert
Christoph R Haag
Jouni Kvist
Christian Laforsch
Adam Petrusek
Andrew P Beckerman
Tom J Little
Anurag Chaturvedi
Michael E Pfrender
Luc De Meester
Mikko J Frilander

Scientific Data

Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability

2017-02-01

Timothy L. Bailey
Melissa D Ilsley
Michael W Parker
Kevin R Gillinder
Michael J Landsberg
Joel P Mackay
Luanne L Peters
Andrew C Perkins

Danitza Nébor
Ravi Sachidanandam
Mathieu Lajoie
Graham W Magor
Michael R Tallack
Luke A Miles
Joel H Graber
James J Bieker

Nucleic Acids Research

Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms.

2017-02-01

Mohammad Nazim
Kinji Ohno

Akio Masuda
Mohammad Alinoor Rahman
Farhana Nasrin
Jun-Ichi Takeda
Kenji Ohe
Bisei Ohkawara
Mikako Ito

Nucleic Acids Research

Impact of exudative diathesis induced by selenium deficiency on LncRNAs and their roles in the oxidative reduction process in broiler chick veins.

2017-02-01

Changyu Cao

Ruifeng Fan
Jinxin Zhao
Xia Zhao
Jie Yang
Ziwei Zhang
Shiwen Xu

Oncotarget

An Intrinsic Transcriptional Program Underlying Synaptic Scaling during Activity Suppression

2017-02-01

Ege T Kavalali

Katie Schaukowitch
Austin L Reese
Seung-Kyoon Kim
Gokhul Kilaru
Jae-Yeol Joo
Tae-Kyung Kim

Cell Reports

USP39 Deubiquitinase Is Essential for KRAS Oncogene-driven Cancer.

2017-02-01

Víctor Quesada
Amaia Lujambio

Julia M Fraile
Eusebio Manchado
Diana Campos-Iglesias
Thomas R Webb
Scott W Lowe
Carlos López-Otín
José M P Freije

Journal of Biological Chemistry

Comparative Analysis of Single-Cell RNA Sequencing Methods.

2017-02-01

Swati Parekh
Beate Vieth
Björn Reinius

Christoph Ziegenhain
Amy Guillaumet-Adkins
Martha Smets
Heinrich Leonhardt
Holger Heyn
Ines Hellmann
Wolfgang Enard

Molecular Cell

CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes.

2017-02-01

Matt Kaeberlein

Carine Beaupere
Brian M Wasko
Jared Lorusso
Brian K Kennedy
Vyacheslav M Labunskyy

Cell Reports

RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.

2017-02-01

Jerome Bouquet
Theodore S Steiner
Charles Y. Chiu

Jennifer L Gardy
Scott Brown
Jacob Pfeil
Ruth R Miller
Muhammad Morshed
Antonio Avina-Zubieta
Kam Shojania
Mark McCabe
Shoshana Parker
Miguel Uyaguari
Scot Federman
Patrick Tang
Michael Otterstater
Rob Holt
Richard Moore
David M Patrick
Complex Chronic Disease Study Group

Clinical Infectious Diseases

The START App: a web-based RNAseq analysis and visualization resource.

2017-02-01

Jessica Minnier

Jonathan W Nelson
Jiri Sklenar
Anthony P Barnes

Bioinformatics

Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts.

2017-02-01

Kiran Padmanabhan
Christophe Papin

Aysegul Ors
Bertrand Favier
Yohan Roulland
Defne Dalkara
Mehmet Ozturk
Ali Hamiche
Stefan Dimitrov

Biochemistry and Cell Biology

Gene expression: Host-pathogen duels revealed by dual RNA-seq in vivo.

2017-02-01

Darren J. Burgess

Nature Reviews Genetics

Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.

2017-02-02

Leonid Padyukov
Lars Klareskog

Klementy Shchetynsky
Lina-Marcella Diaz-Gallo
Lasse Folkersen
Aase Haj Hensvold
Anca Irinel Catrina
Louise Berg

Arthritis Research and Therapy

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes.

2017-02-02

Shu Pan
Luke R Thompson
Rob Knight
Jennifer L Reed

Kiel Nikolakakis
Edward G Ruby

Environmental Microbiology

Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes.

2017-02-03

Eugene Kolker

Roger Higdon
Jessie Kala
Devan Wilkins
Julia Fangfei Yan
Manveen K Sethi
Liang Lin
Siqi Liu
Elizabeth Montague
Imre Janko
John Choiniere
Natali Kolker
William S Hancock
Susan Fanayan

Proteomes

miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis.

2017-02-03

Markus H Heim
Simonetta Bandiera
Diego Calabrese
Joachim Lupberger
Nathalie Pochet

Nicolaas Van Renne
Armando Andres Roca Suarez
Francois H T Duong
Claire Gondeau
Nelly Fontaine
Amina Ababsa
Tom Croonenborghs
Vito De Blasi
Patrick Pessaux
Tullio Piardi
Daniele Sommacale
Atsushi Ono
Kazuaki Chayama
Masashi Fujita
Hidewaki Nakagawa
Yujin Hoshida
Mirjam B Zeisel
Thomas F Baumert

Gut

RNA-seq in kinetoplastids: A powerful tool for the understanding of the biology and host-pathogen interactions.

2017-02-04

Juan D Ramírez

Luz Helena Patino

Infection, Genetics and Evolution

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

2017-02-06

Gregory P Way
Robert J Allaway
Casey S. Greene

Stephanie J Bouley
Camilo E Fadul
Yolanda Sanchez

BMC Genomics

Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis.

2017-02-06

Kathryn L. Lunetta
Josée Dupuis
Adam Labadorf

Seung Hoan Choi
Richard H Myers
Anita L DeStefano

BMC Bioinformatics

Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori.

2017-02-06

Qingyou Xia
Tingcai Cheng
Emmanuelle Jacquin-Joly

Huizhen Guo
Zhiwei Chen
Liang Jiang
Youbing Guo
Jianqiu Liu
Shenglong Li
Kiyoko Taniai
Kiyoshi Asaoka
Keiko Kadono-Okuda
Kallare P Arunkumar
Jiaqi Wu
Hirohisa Kishino
Huijie Zhang
Rakesh K Seth
Karumathil P Gopinathan
Nicolas Montagné
Marian R Goldsmith
Kazuei Mita

Insect Biochemistry and Molecular Biology

Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma.

2017-02-07

Mikhail G Dozmorov

Tara J Nulton
Amy L Olex
Iain M Morgan
Brad Windle

Oncotarget

PIGN gene expression aberration is associated with genomic instability and leukemic progression in acute myeloid leukemia with myelodysplastic features.

2017-02-07

Emmanuel K Teye
Jeffrey Pu
Thomas Abraham

Abigail Sido
Ping Xin
Niklas K Finnberg
Prashanth Gokare
Yuka I Kawasawa
Anna C Salzberg
Sara Shimko
Michael Bayerl
W Christopher Ehmann
David F Claxton
Witold B Rybka
Joseph J Drabick
Hong-Gang Wang
Wafik S El-Deiry
Robert A Brodsky
Raymond J Hohl

Oncotarget

RNA-seq Analysis of Cold and Drought Responsive Transcriptomes of Zea mays ssp. mexicana L.

2017-02-07

Meixue Zhou

Xiang Lu
Xuan Zhou
Yu Cao
David McNeil
Shan Liang
Chengwei Yang

Frontiers in Plant Science

Expression and splicing of ABC and SLC transporters in the human blood-brain barrier measured with RNAseq.

2017-02-07

Wolfgang Sadee

Adam M Suhy
Amy Webb
Audrey C Papp
Ethan G Geier

European Journal of Pharmaceutical Sciences

Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant.

2017-02-08

Irina Mohorianu
Tamas Dalmay

Vahid Omidvar
Yi Zheng
Zhangjun Fei
Anna Pucci
Andrea Mazzucato
Vendula Večeřová
Michaela Sedlářova
Martin Fellner

PLOS ONE

RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides

2017-02-09

Michael Rosbash
Katharine C Abruzzi

Abigail Zadina
Weifei Luo
Evelyn Wiyanto
Reazur Rahman
Fang Guo
Orie Shafer

PLOS Genetics

If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq.

2017-02-09

Carsten Kröger
Andrew Ds Cameron

Aoife M Colgan

Current Opinion in Microbiology

Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation.

2017-02-09

Melody Baddoo
Harrison M Penrose
Erik K Flemington

Sandra Heller
Chloe Cable
Debjani Biswas
Hani Nakhoul
Susan E Crawford
Suzana D Savkovic

FASEB Journal

Immortalized human myotonic dystrophy muscle cell lines to assess therapeutic compounds.

2017-02-10

Arnaud F Klein
Denis Furling
Vincent Mouly

Ludovic Arandel
Micaela Polay Espinoza
Magdalena Matloka
Audrey Bazinet
Damily De Dea Diniz
Naïra Naouar
Frédérique Rau
Arnaud Jollet
Frédérique Edom-Vovard
Kamel Mamchaoui
Mark Tarnopolsky
Jack Puymirat
Christophe Battail
Anne Boland
Jean-Francois Deleuze

Disease Models & Mechanisms

CirComPara: A Multi-Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA-seq Data.

2017-02-10

Stefania Bortoluzzi
Geertruy Te Kronnie
Enrico Gaffo

Annagiulia Bonizzato

Non-coding RNA

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.

2017-02-13

Alex K. Shalek
Rahul Satija

Todd M Gierahn
Marc H Wadsworth
Travis K Hughes
Bryan D Bryson
Andrew Butler
Sarah Fortune
J Christopher Love

Nature Methods

Subinhibitory Concentrations of Ciprofloxacin Enhance Antimicrobial Resistance and Pathogenicity of Enterococcus faecium.

2017-02-13

Maurizio Sanguinetti

Clara Sinel
Margherita Cacaci
Pierrick Meignen
François Guérin
Bryan W Davies
Jean-Christophe Giard
Vincent Cattoir

Antimicrobial Agents and Chemotherapy

Transcriptomic, cellular and life-history responses of Daphnia magna chronically exposed to benzotriazoles: Endocrine-disrupting potential and molting effects.

2017-02-14

Magali Houde

Maeva Giraudo
Mélanie Douville
Guillaume Cottin

PLOS ONE

A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus

2017-02-15

Xiaodong Fang

Xiaofang Geng
Wanshun Li
Haitao Shang
Qiang Gou
Fuchun Zhang
Xiayan Zang
Benhua Zeng
Jiang Li
Ying Wang
Ji Ma
Jianlin Guo
Jianbo Jian
Bing Chen
Zhigang Qiao
Minghui Zhou
Hong Wei
Cunshuan Xu

GigaScience

Endometrial factors similarly induced by IFNT2 and IFNTc1 through transcription factor FOXS1

2017-02-15

Kazuya Kusama

Rulan Bai
Keigo Nakamura
Sayaka Okada
Jiro Yasuda
Kazuhiko Imakawa

PLOS ONE

Variant discovery in the sheep milk transcriptome using RNA sequencing

2017-02-15

Gwenola Tosser-Klopp
Gwenola Tosser-Klopp
Juan J Arranz

Aroa Suárez-Vega
Beatriz Gutiérrez-Gil
Christophe Klopp

BMC Genomics

Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation.

2017-02-15

José Onuchic

Linglin Yu
Mingyang Lu
Dongya Jia
Jianpeng Ma
Eshel Ben-Jacob
Herbert Levine
Benny Abraham Kaipparettu

Cancer Research

Identification of a novel series of anti-inflammatory and anti-oxidative phospholipid oxidation products containing the cyclopentenone moiety in vitro and in vivo: Implication in atherosclerosis.

2017-02-15

Sotirios Tsimikas

Jianhong Lu
Shuyuan Guo
Xinli Xue
Qun Chen
Jing Ge
Yujuan Zhuo
Huiqin Zhong
Buxing Chen
Mingming Zhao
Wei Han
Takashi Suzuki
Mingjiang Zhu
Lin Xia
Claus Schneider
Timothy S Blackwell
Ned A Porter
Lemin Zheng
Huiyong Yin

Journal of Biological Chemistry

RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation

2017-02-16

Francesca Di Giallonardo
Pierre Roques
Andreas Suhrbier
Suresh Mahalingam

Natalie A. Prow
Wayne A. Schroder
Jonathan J. Ellis
Helen E. Cumming
Linden J. Gearing
Yee Suan Poo
Adam Taylor
Paul J. Hertzog
Linda Hueston
Roger Le Grand
Bing Tang
Thuy T. Le
Joy Gardner
Phillip I. Bird

PLOS Pathogens

Resolving host-pathogen interactions by dual RNA-seq.

2017-02-16
2017-02-01

Jörg Vogel
Lars Barquist

Alexander J Westermann

PLOS Pathogens

RNA-seq and metabolomic analyses of Akt1-mediated muscle growth reveals regulation of regenerative pathways and changes in the muscle secretome.

2017-02-16

Kenneth Walsh

Chia-Ling Wu
Yoshinori Satomi

BMC Genomics

Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs

2017-02-16

Scott E. Sattler

Teresa Donze-Reiner
Nathan A Palmer
Erin D Scully
Travis J Prochaska
Kyle G Koch
Tiffany Heng-Moss
Jeffrey D Bradshaw
Paul Twigg
Keenan Amundsen
Gautam Sarath

BMC Plant Biology

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies.

2017-02-16

Yann Guiguen
Julien Bobe

Cédric Cabau
Frédéric Escudié
Anis Djari
Christophe Klopp

PeerJ

Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses

2017-02-17

Deyou Zheng

Yao Shen
Milda Stanislauskas
Gen Li
Liang Liu

Scientific Reports

Epigenomics of human CD8 T cell differentiation and aging.

2017-02-17

Sabine Le Saux
Bin Hu
David Moskowitz
William Greenleaf

David W Zhang
Rolando E Yanes
Zhongde Ye
Jason D Buenrostro
Cornelia M Weyand
Jörg J Goronzy

Science immunology

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.

2017-02-20

Eric Peatman
Geoff Waldbieser
Terrence Tiersch
Acacia Alcivar-Warren
Wilawan Thongda
Brian P Bosworth
Shikai Liu
Rex Dunham

Aquaculture Genomics, Genetics and Breeding Workshop
Hisham Abdelrahman
Mohamed ElHady
Acacia Alcivar-Warren
Standish Allen
Rafet Al-Tobasei
Lisui Bao
Ben Beck
Harvey Blackburn
John Buchanan
Jesse Chappell
William Daniels
Sheng Dong
Evan Durland
Ahmed Elaswad
Marta Gomez-Chiarri
Kamal Gosh
Ximing Guo
Perry Hackett
Terry Hanson
Dennis Hedgecock
Tiffany Howard
Leigh Holland
Molly Jackson
Yulin Jin
Karim Kahlil
Thomas Kocher
Tim Leeds
Ning Li
Lauren Lindsey
Zhanjiang Liu
Kyle Martin
Romi Novriadi
Ramjie Odin
Yniv Palti
Dina Proestou
Guyu Qin
Benjamin Reading
Caird Rexroad
Steven Roberts
Mohamed Salem
Andrew Severin
Huitong Shi
Craig Shoemaker
Sheila Stiles
Suxu Tan
Kathy F J Tang
Wilawan Thongda
Terrence Tiersch
Joseph Tomasso
Wendy Tri Prabowo
Roger Vallejo
Hein van der Steen
Khoi Vo
Geoff Waldbieser
Hanping Wang
Xiaozhu Wang
Jianhai Xiang
Yujia Yang
Roger Yant
Zihao Yuan
Qifan Zeng
Tao Zhou

BMC Genomics

MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.

2017-02-21

Isidore Rigoutsos

Phillipe Loher
Aristeidis G Telonis

Scientific Reports

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

2017-02-22

Marie-France Sagot

Leandro Lima
Blerina Sinaimeri
Gustavo Sacomoto
Helene Lopez-Maestre
Camille Marchet
Vincent Miele
Vincent Lacroix

Algorithms for Molecular Biology

Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

2017-02-23

Thomas Rydzak
James G. Elkins
Adam Guss
Nancy Engle
Timothy Tschaplinski

Tobin J Verbeke
Richard J Giannone
Dawn M Klingeman
Steven D Brown
Robert L Hettich

Scientific Reports

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

2017-02-23

D Yap

Tyler Funnell
Shinya Tasaki
Arusha Oloumi
Shinsuke Araki
Esther Kong
Yusuke Nakayama
Christopher S Hughes
S-W Grace Cheng
Hirokazu Tozaki
Misa Iwatani
Satoshi Sasaki
Tomohiro Ohashi
Tohru Miyazaki
Nao Morishita
Daisuke Morishita
Mari Ogasawara-Shimizu
Momoko Ohori
Shoichi Nakao
Masatoshi Karashima
Masaya Sano
Aiko Murai
Toshiyuki Nomura
Noriko Uchiyama
Tomohiro Kawamoto
Ryujiro Hara
Osamu Nakanishi
Karey Shumansky
Jamie Rosner
Adrian Wan
Steven McKinney
Gregg B Morin
Atsushi Nakanishi
Sohrab Shah
Hiroyoshi Toyoshiba
Samuel Aparicio

Nature Communications

Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

2017-02-24

Haja N. Kadarmideen
Mariusz Pierzchała

Chandra Shekhar Pareek
Paweł Błaszczyk
Piotr Dziuba
Urszula Czarnik
Leyland Fraser
Przemysław Sobiech
Yaping Feng
Dibyendu Kumar

PLOS ONE

Can milk cell or skim milk miRNAs be used as biomarkers for early pregnancy detection in cattle?

2017-02-24

Benedikt Kirchner
Michael W Pfaffl

Corina I Schanzenbach
Susanne E Ulbrich

PLOS ONE

MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

2017-02-27

Kim-Anh Lê Cao

Florian Rohart
Aida Eslami
Nicholas Matigian
Stéphanie Bougeard
Kim-Anh Lê Cao

BMC Bioinformatics

Essentiality of mmpL3 and impact of its silencing on Mycobacterium tuberculosis gene expression.

2017-02-27

Riccardo Manganelli
Giorgio Palù

Giulia Degiacomi
Andrej Benjak
Jan Madacki
Francesca Boldrin
Roberta Provvedi
Jana Kordulakova
Stewart T Cole

Scientific Reports

Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions.

2017-02-27

Daniel M Stoebel

Ciaran Evans
Johanna Hardin

Briefings in Bioinformatics

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.

2017-02-28

Eva Hellström-Lindberg
Elisabet Einarsdottir
Kaarel Krjutškov
Francesco Marabita
Shintaro Katayama
Juha Kere
Karl Ekwall
Andreas Lennartsson

Magnus Tobiasson
Hani Abdulkadir
Ayla De Paepe
Mohsen Karimi
Michael Grövdal
Monika Jansson
Asmaa Ben Azenkoud
Lina Corddedu
Sören Lehmann
Eva Hellström-Lindberg
Johanna Ungerstedt

Oncotarget

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

2017-02-28

Klaus Neuhaus
Siegfried Scherer

Richard Landstorfer
Svenja Simon
Steffen Schober
Patrick R Wright
Cameron Smith
Rolf Backofen
Romy Wecko
Daniel A Keim

BMC Genomics

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

2017-02-28

Guillaume Bourque

LeeAnn Ramsay
Maria C Marchetto
Maxime Caron
Shu-Huang Chen
Stephan Busche
Tony Kwan
Tomi Pastinen
Fred H Gage

BMC Genomics

Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq.

2017-02-28

Marvin Whiteley

Erik L Hendrickson
David A C Beck
Daniel P Miller
Qian Wang
Richard J Lamont
Murray Hackett

Frontiers in Microbiology

Human Mesenchymal Stem Cell-Educated Macrophages Are a Distinct High IL-6-Producing Subset that Confer Protection in Graft-versus-Host-Disease and Radiation Injury Models.

2017-02-28

Andrea B Moffitt
Jaehyup Kim
Christian M. Capitini

Myriam N Bouchlaka
John A Kink
Debra D Bloom
Cassandra Love
Sandeep Dave
Peiman Hematti

Biology of Blood and Marrow Transplantation

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

2017-03-01

Tapio Lönnberg
Ismail Sebina
Frederik Otzen Bagger
Oliver Stegle
Kylie R James
Valentine Svensson
Ashraful Haque
William R Heath
Sarah Teichmann

Daniel Fernandez-Ruiz
Ruddy Montandon
Megan S F Soon
Lily G Fogg
Arya Sheela Nair
Urijah Liligeto
Michael J T Stubbington
Lam-Ha Ly
Max Zwiessele
Neil D Lawrence
Fernando Souza-Fonseca-Guimaraes
Patrick T Bunn
Christian R Engwerda
Oliver Billker

Science immunology

Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer.

2017-03-01

Jonathan R. Pollack

Xue Gong
Zurab Siprashvili
Okyaz Eminaga
Zhewei Shen
Yusuke Sato
Haruki Kume
Yukio Homma
Seishi Ogawa
Paul A Khavari
James D Brooks

Oncotarget

Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer.

2017-03-01

Elgene Lim
Wouter de Laat

Koen M A Dreijerink
Anna C Groner
Erica S M Vos
Alba Font-Tello
Lei Gu
David Chi
Jaime Reyes
Jennifer Cook
Charles Y Lin
Prakash K Rao
Henry W Long
Myles Brown

Cell Reports

Transcriptomic and histological responses of African rice (Oryza glaberrima) to Meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots.

2017-03-01

Janice de Almeida Engler
Tina Kyndt
Diana Fernandez

Anne-Sophie Petitot
Rana Haidar
Alexis Dereeper
Myriam Collin
Godelieve Gheysen

Annals of Botany

Hypomorphic Pathogenic Variants in TAF13 Are Associated with Autosomal-Recessive Intellectual Disability and Microcephaly.

2017-03-01

Heinrich Sticht
Igor Martianov
Fulvia Ferrazzi
Irwin Davidson
André Reis

Hasan Tawamie
Natalie Wohlfahrt
Rebecca Buchert
Gabrielle Mengus
Steffen Uebe
Luigi Janiri
Franz Wolfgang Hirsch
Johannes Schumacher
Roberto Colombo
Rami Abou Jamra

American Journal of Human Genetics

Dissecting common and divergent molecular pathways elicited by CdSe/ZnS quantum dots in freshwater and marine sentinel invertebrates.

2017-03-01

Beatriz Pelaz
Abuelmagd M. Abdelmonem
Angela Tino
Claudia Tortiglione

Alfredo Ambrosone
Modi Roopin
Lisa-Maria Ackermann
Lucia Mattera
Mariateresa Allocca
Markus Klapper
Wolfgang J Parak
Oren Levy

Nanotoxicology

DExD/H-box RNA helicase genes are differentially expressed between males and females during the critical period of male sex differentiation in channel catfish.

2017-03-01

Shikai Liu

Changxu Tian
Suxu Tan
Lisui Bao
Qifan Zeng
Yujia Yang
Xiaoxiao Zhong
Zhanjiang Liu

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.

2017-03-01

Daniel P Cahill
Itay Tirosh
Orit Rozenblatt-Rosen
Aviv Regev
Shawn M. Gillespie
Christopher W Mount
Brian V. Nahed
Michelle Monje
Gad Getz

Andrew S Venteicher
Christine Hebert
Keren Yizhak
Cyril Neftel
Mariella G Filbin
Volker Hovestadt
Leah E Escalante
McKenzie L Shaw
Christopher Rodman
Danielle Dionne
Christina C Luo
Hiranmayi Ravichandran
Ravindra Mylvaganam
Maristela L Onozato
Hiroaki Wakimoto
William T Curry
A John Iafrate
Miguel N Rivera
Matthew P Frosch
Todd R Golub
Priscilla K Brastianos
Anoop P Patel
David N Louis
Bradley E Bernstein
Mario L Suvà

Science

RED-ML: a novel, effective RNA editing detection method based on machine learning.

2017-03-02

Huanming Yang

Heng Xiong
Dongbing Liu
Qiye Li
Mengyue Lei
Liqin Xu
Liang Wu
Zongji Wang
Shancheng Ren
Wangsheng Li
Min Xia
Lihua Lu
Haorong Lu
Yong Hou
Shida Zhu
Xin Liu
Yinghao Sun
Jian Wang
Kui Wu
Xun Xu
Leo J Lee

GigaScience

Single-cell transcriptomics reveals specific RNA editing signatures in the human brain

2017-03-03

Graziano Pesole
Ernesto Picardi

David S Horner

RNA

Laser capture microdissection enables transcriptomic analysis of dividing and quiescent liver stages of Plasmodium relapsing species.

2017-03-03

Nathalie Dereuddre-Bosquet
Jean-François Franetich

Roger Cubi
Shruthi S Vembar
Anne Biton
Jean-Francois Franetich
Mallaury Bordessoulles
Daniel Sossau
Gigliola Zanghi
Henriette Bosson-Vanga
Magalie Benard
Alicia Moreno
Roger Le Grand
Artur Scherf
Dominique Mazier

Cellular Microbiology

A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis.

2017-03-03

Seisuke Kimura

Yaichi Kawakatsu
Hokuto Nakayama
Kaori Kaminoyama
Kaori Igarashi
Masaki Yasugi
Hiroshi Kudoh
Atsushi J Nagano
Kentaro Yano
Nakao Kubo

Journal of Plant Research

Molecular mechanism and structural basis of gain-of-function of STAT1 caused by pathogenic R274Q mutation.

2017-03-03

Atsushi Hijikata
Satoshi Okada

Ryoji Fujiki
Tsuyoshi Shirai
Masao Kobayashi

Journal of Biological Chemistry

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.

2017-03-06

Daniele Ramazzotti

Bo Wang
Junjie Zhu
Emma Pierson
Serafim Batzoglou

Nature Methods

Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis.

2017-03-06

Sarah A Boswell
Andrew Snavely

Heather M Landry
L Stirling Churchman
Jesse M Gray
Michael Springer

Nature Chemical Biology

Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition.

2017-03-07

Erez Y. Levanon
Eli Eisenberg

Nurit Gal-Mark
Lea Shallev
Sahar Sweetat
Michal Barak
Jin Billy Li
Oded Behar

Scientific Reports

Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment.

2017-03-07

Robert A Bonomo

Meredith S Wright
Michael R Jacobs
Mark D Adams

mBio

The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.

2017-03-07

Gediminas Valkiūnas
Elin Videvall
Olof Hellgren

Charlie K Cornwallis
Dag Ahrén
Vaidas Palinauskas

Molecular Ecology

The novel long non-coding RNA TALNEC2, regulates tumor cell growth and the stemness and radiation response of glioma stem cells.

2017-03-07

Simona Cazacu
Chaya Brodie

Shlomit Brodie
Hae Kyung Lee
Wei Jiang
Simona Cazacu
Cunli Xiang
Laila M Poisson
Indrani Datta
Steve Kalkanis
Doron Ginsberg

Oncotarget

TT-seq captures enhancer landscapes immediately after T-cell stimulation.

2017-03-07

Julien Gagneur
Björn Schwalb

Margaux Michel
Carina Demel
Benedikt Zacher
Stefan Krebs
Helmut Blum
Patrick Cramer

Molecular Systems Biology

Activation of odorant receptor in colorectal cancer cells leads to inhibition of cell proliferation and apoptosis.

2017-03-08

Hanns Hatt
Günter Gisselmann
S Hahn

Lea Weber
Klaudia Al-Refae
Juliane Ebbert
Peter Jägers
Janine Altmüller
Christian Becker
Günter Gisselmann

PLOS ONE

VCNet: Vector based gene Co-expression Network construction and its application to RNA-seq data.

2017-03-08

Nelson Leung-Sang Tang

Zengmiao Wang
Huaying Fang
Minghua Deng

Bioinformatics

Quantifying circular RNA expression from RNA-seq data using model-based framework.

2017-03-08

Tong Zhou
Eun-A Ko

Musheng Li
Xueying Xie
Jing Zhou
Mengying Sheng
Xiaofeng Yin
Wanjun Gu

Bioinformatics

Variation-preserving normalization unveils blind spots in gene expression profiling.

2017-03-09

Janeck J Scott-Fordsmand

Carlos P Roca
Susana I L Gomes
Mónica J B Amorim

Scientific Reports

Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress.

2017-03-09

Frédéric Partensky

Marie L Cuvelier
Jian Guo
Alejandra C Ortiz
Marijke J van Baren
Muhammad Akram Tariq
Alexandra Z Worden

PLOS ONE

Imiquimod has strain-dependent effects in mice and does not uniquely model human psoriasis.

2017-03-09

Mrinal K. Sarkar
Nicole L. Ward

William R Swindell
Kellie A Michaels
Andrew J Sutter
Doina Diaconu
Yi Fritz
Xianying Xing
Yun Liang
Alex Tsoi
Johann E Gudjonsson

Genome Medicine

Transcriptome and Functional Genomics Reveal the Participation of Adenine Phosphoribosyltransferase in Trypanosoma cruzi Resistance to Benznidazole.

2017-03-09

Omar Triana-Chávez

Paola García-Huertas
Ana María Mejía-Jaramillo
Laura González

Journal of Cellular Biochemistry

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase.

2017-03-09

Roxane Lestini
Kamel Djaout
Hubert F Becker
Hannu Myllykallio

Alice Héliou
Mireille Regnier

RNA Biology

Smooth muscle cell-specific deletion of Col15a1 unexpectedly leads to impaired development of advanced atherosclerotic lesions.

2017-03-10

Joshua T Butcher
Delphine Gomez
Brant E Isakson

Brittany G Durgin
Olga A Cherepanova
Themistoclis Karaoli
Gabriel F Alencar
Yu-Qing Zhou
Michelle P Bendeck
Gary K Owens
Jessica J Connelly

American Journal of Physiology - Heart and Circulatory Physiology

Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium.

2017-03-10

Simon Moxon
Jennifer Southgate
Sarah Bastkowski

Carl Fishwick
Janet Higgins
Lawrence Percival-Alwyn
Arianna Hustler
Joanna Pearson
David Swarbreck
Chris D Greenman

Cell Death & Differentiation

Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer

2017-03-10

Richard Weinshilboum

Arjun P Athreya
Krishna R Kalari
Junmei Cairns
Alan J Gaglio
Quin F Wills
Nifang Niu
Ravishankar K Iyer
Liewei Wang

Oncotarget

Lipid degradation promotes prostate cancer cell survival.

2017-03-11

Etienne Waelkens
Elai Davicioni
Nicholas Erho

Harri M Itkonen
Michael Brown
Alfonso Urbanucci
Gregory Tredwell
Chung Ho Lau
Stefan Barfeld
Claire Hart
Ingrid J Guldvik
Mandeep Takhar
Hannelore V Heemers
Katarzyna Bloch
Rita Derua
James L Mohler
Noel Clarke
Johan V Swinnen
Hector C Keun
Ole P Rekvig
Ian G Mills

Oncotarget

Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development.

2017-03-15

Robert Literman
Nicole Valenzuela

Srihari Radhakrishnan
Jennifer Neuwald
Andrew Severin
Nicole Valenzuela

PLOS ONE

Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data.

2017-03-15

Julian Brandl
Claus Kristensen
Lasse Ebdrup Pedersen
Helene Faustrup Kildegaard
Mikael Rørdam Andersen

Anne Mathilde Lund
Christian Schrøder Kaas

BMC Systems Biology

Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications.

2017-03-16

Habil Zare
Linda Chang

Amir Foroushani
Rupesh Agrahari
Roderick Docking
Gerben Duns
Monika Hudoba
Aly Karsan

BMC Medical Genomics

The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes.

2017-03-16

Andrew D. Paterson

Catherine P M Hayward
Minggao Liang
Subia Tasneem
Asim Soomro
John S Waye
Georges E Rivard
Michael D Wilson

PLOS ONE

Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons.

2017-03-16

Jingyi Jessica Li

Ruiqi Gao

BMC Genomics

Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia.

2017-03-16

Jan Gorodkin
Alexander Junge

Roza Zandi
Jakob Hull Havgaard
Jack Bernard Cowland

Gene

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis.

2017-03-17

Yuichi Sakamoto

Keiko Nakade
Shiho Sato
Kentaro Yoshida
Kazuhiro Miyazaki
Satoshi Natsume
Naotake Konno

Applied and Environmental Microbiology

Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines.

2017-03-17

Staffan G Svärd
Robin B. Gasser
Aaron R Jex

Brendan R E Ansell
Louise Baker
Samantha J Emery
Malcolm J McConville

Frontiers in Microbiology

Marginal likelihood estimation of negative binomial parameters with applications to RNA-seq data.

2017-03-19

Sarah Emerson

Luis León-Novelo
Claudio Fuentes

Biostatistics

Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem.

2017-03-20

Hernan G. Rosli

Marina A Pombo
Yi Zheng
Zhangjun Fei
Gregory B Martin

Scientific Reports

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells.

2017-03-20

Michael Kirschenbaum
Deyou Zheng

Ping Wang
Ryan Mokhtari
Erika Pedrosa
Can Bayrak
Herbert M Lachman

Molecular Autism

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.

2017-03-20

Elise T Courtois
Paul Robson

Huipeng Li
Debarka Sengupta
Yuliana Tan
Kok Hao Chen
Jolene Jie Lin Goh
Say Li Kong
Clarinda Chua
Lim Kiat Hon
Wah Siew Tan
Mark Wong
Paul Jongjoon Choi
Lawrence J K Wee
Axel M Hillmer
Iain Beehuat Tan
Shyam Prabhakar

Nature Genetics

Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously

2017-03-20

Jaclyn N Taroni
Casey S. Greene

Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s disease

2017-03-21

Davina J Hensman Moss
James R C Miller
Peter A.C. 't Hoen
Sarah J. Tabrizi

Flower MD
Lo KK
van Ommen GJ
Stone TC
Guinee A
Langbehn DR
Jones L
Plagnol V
van Roon-Mom WM
Holmans P

Scientific Reports

Discovery of novel determinants of endothelial lineage using chimeric heterokaryons.

2017-03-21

Wing Tak Wong
James K Chen
John P. Cooke

Gianfranco Matrone
XiaoYu Tian
Simion Alin Tomoiaga
Kin Fai Au
Shu Meng
Sayumi Yamazoe
Daniel Sieveking
Kaifu Chen
David M Burns
Helen M Blau

eLife

Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq.

2017-03-21

Jianbo Pan

Yi Huang
Dunyan Chen
Jiaying Zheng
Funan Qiu
Feng Li
Yanan Wu
Wenbing Wu
Xiaoli Huang
Jiang Qian

Oncotarget

Activation of Epithelial Signal Transducer and Activator of Transcription 1 by Interleukin 28 Controls Mucosal Healing in Mice With Colitis and Is Increased in Mucosa of Patients With Inflammatory Bowel Disease.

2017-03-22

Arif B. Ekici

Mircea T Chiriac
Barbara Buchen
Alexandra Wandersee
Gheorghe Hundorfean
Claudia Günther
Yvonne Bourjau
Sean E Doyle
Benjamin Frey
Christian Büttner
Benno Weigmann
Raja Atreya
Stefan Wirtz
Christoph Becker
Jürgen Siebler
Markus F Neurath

Gastroenterology

Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo.

2017-03-23

Marcel E. Dinger

Jesper L V Maag
Dominik C Kaczorowski
Debabrata Panja
Timothy J Peters
Clive R Bramham
Karin Wibrand

BMC Genomics

Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.

2017-03-23

Gungor Budak
Sarath Chandra Janga

Rajneesh Srivastava

RNA

Cytochrome P450 Monooxygenase CYP716A141 is a Unique β-Amyrin C-16β Oxidase Involved in Triterpenoid Saponin Biosynthesis in Platycodon grandiflorus.

2017-03-23

Toshiya Muranaka
Kazuki Saito

Keita Tamura
Yuga Teranishi
Shinya Ueda
Hideyuki Suzuki
Noriaki Kawano
Kayo Yoshimatsu
Nobuo Kawahara
Hikaru Seki

Plant and Cell Physiology

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

2017-03-24

Peter Lund

M S Salleh
G Mazzoni
J K Höglund
D W Olijhoek
P Løvendahl
H N Kadarmideen

BMC Genomics

Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome

2017-03-27

Gos Micklem
Marcus C Davis

Melinda S Modrell
Mike Lyne
Adrian R Carr
Harold H Zakon
David Buckley
Alexander S Campbell
Clare Vh Baker

eLife

SC3: consensus clustering of single-cell RNA-seq data

2017-03-27

Mauricio Barahona
Tallulah Andrews
Kedar N Natarajan
Kristina Kirschner
Anthony R Green
Wolf Reik

Vladimir Yu Kiselev
Michael T Schaub
Andrew Yiu
Tamir Chandra
Martin Hemberg

Nature Methods

Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata.

2017-03-27

Nicholas A. Robinson
Ira R Cooke
Jan Strugnell

Brett P Shiel
Nathan E Hall

Marine Biotechnology

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives.

2017-03-28

Kenneth Daily
Phillip Dexheimer
Winston Hide
Lynn Schriml
Alexander R. Pico

Shannan J Ho Sui
Lynn M Schriml
Nathan Salomonis
Robin Schroll
Stacy Bush
Mehdi Keddache
Christopher Mayhew
Samad Lotia
Thanneer M Perumal
Kristen Dang
Lorena Pantano
Elke Grassman
Diana Nordling
Antonis K Hatzopoulos
Punam Malik
Jose A Cancelas
Carolyn Lutzko
Bruce J Aronow
Larsson Omberg

Scientific Data

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae.

2017-03-28

John L. Williams

Bouabid Badaoui
André Fougeroux
Fabien Petit
Anna Anselmo
Chiara Gorni
Marco Cucurachi
Antonella Cersini
Anna Granato
Giusy Cardeti
Giovanni Formato
Franco Mutinelli
Elisabetta Giuffra
Sara Botti

PLOS ONE

Erratum: Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle.

2017-03-28

Mireille Claustres
Sylvie Tuffery-Giraud

Anne-Laure Bougé
Eva Murauer
Emmanuelle Beyne
Julie Miro
Jessica Varilh
Magali Taulan
Michel Koenig

Scientific Reports

Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress

2017-03-29

Dejian Zhao
Deyou Zheng

Ryan Mokhtari
Erika Pedrosa
Rayna Birnbaum
Herbert M Lachman

Molecular Autism

Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq.

2017-03-30

Sara Lustigman
Thomas R Unnasch

Alexandra Grote
Denis Voronin
Tao Ding
Alan Twaddle
Elodie Ghedin

PLOS Neglected Tropical Diseases

Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle.

2017-03-30

Mogens Sandø Lund

Lingzhao Fang
Goutam Sahana
Guosheng Su
Ying Yu
Shengli Zhang
Peter Sørensen

Scientific Reports

Top2b is involved in the formation of outer segment and synapse during late-stage photoreceptor differentiation by controlling key genes of photoreceptor transcriptional regulatory network.

2017-03-30

Ronald P Hart

Ying Li
Hailing Hao
Mavis R Swerdel
Hyeon-Yeol Cho
Ki-Bum Lee
Yi Lisa Lyu
Li Cai

Journal of Neuroscience Research

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.

2017-04-01

Aviv Regev
Rahul Satija
Nir Hacohen
Gary Reynolds
Andrew Butler
Shiwei Zheng
Orit Rozenblatt-Rosen

Alexandra-Chloé Villani
Siranush Sarkizova
Karthik Shekhar
James Fletcher
Morgane Griesbeck
Suzan Lazo
Laura Jardine
David Dixon
Emily Stephenson
Emil Nilsson
Ida Grundberg
David McDonald
Andrew Filby
Weibo Li
Philip L De Jager
Andrew A Lane
Muzlifah Haniffa

Science

Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling.

2017-04-01

Mick Watson
Venugopal Nair

William N Mwangi
Deepali Vasoya
Lydia B Kgosana

Journal of General Virology

An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation.

2017-04-01

Diego Balboa
Salla Keskitalo
Markku Varjosalo
Noel G Morgan

Jonna Saarimäki-Vire
Mark A Russell
Juha Saarikettu
Matias Kinnunen
Amrinder Malhi
Cristina Valensisi
Colin Andrus
Solja Eurola
Heli Grym
Jarkko Ustinov
Kirmo Wartiovaara
R David Hawkins
Olli Silvennoinen
Timo Otonkoski

Cell Reports

Characterization of RBP9 and RBP10, two developmentally regulated RNA-binding proteins in Trypanosoma brucei.

2017-04-01

Luis M De Pablos
Janaina de Freitas Nascimento
Jack D Sunter

Steve Kelly
Mark Carrington

Open Biology

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.

2017-04-01

Matthias Heinig
Caroline C Friedel

Kathrin Davari
Johannes Lichti
Christian Gallus
Franziska Greulich
N Henriette Uhlenhaut
Elke Glasmacher

Cell Reports

Functional Enhancer Screening in Single Cells.

2017-04-01

Bas van Steensel

Joris van Arensbergen

Molecular Cell

Reproducible RNA-seq analysis using recount2.

2017-04-01

Kasper D. Hansen
Leonardo Collado-Torres
Andrew E Jaffe
Jeffrey T. Leek
Ben Langmead
Abhinav Nellore

Kai Kammers
Shannon E Ellis
Margaret A Taub

Nature Biotechnology

Osteoblast-specific deletion of Hrpt2/Cdc73 results in high bone mass and increased bone turnover.

2017-04-03

Bin Tean Teh

Casey J Droscha
Cassandra R Diegel
Nicole J Ethen
Travis A Burgers
Mitchell J McDonald
Kevin A Maupin
Agni S Naidu
PengFei Wang
Bart O Williams

Bone

Intranuclear Actin Structure Modulates Mesenchymal Stem Cell Differentiation.

2017-04-03

Rebekah M Samsonraj

Buer Sen
Gunes Uzer
Zhihui Xie
Cody McGrath
Maya Styner
Amel Dudakovic
Andre J van Wijnen
Janet Rubin

Stem Cells

An immunoaffinity-based method for isolating ultrapure adult astrocytes based on ATP1B2 targeting by the ACSA-2 antibody.

2017-04-03

Takashi Saito

Mykhailo Y Batiuk
Filip de Vin
Sandra I Duqué
Chen Li
Takaomi Saido
Mark Fiers
T Grant Belgard
Matthew G Holt

Journal of Biological Chemistry

The Transcriptome of Leishmania major Developmental Stages in Their Natural Sand Fly Vector

2017-04-04

Najib El-sayed

Ehud Inbar
V Keith Hughitt
Laura A L Dillon
Kashinath Ghosh
David L Sacks

mBio

Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.

2017-04-04

Dana Pe'er

Keara Lane
David Van Valen
Mialy M DeFelice
Derek N Macklin
Takamasa Kudo
Ariel Jaimovich
Ambrose Carr
Tobias Meyer
Dana Pe'er
Stéphane C Boutet
Markus W Covert

Cell systems

Transcriptome profiling of Arabian horse blood during training regimens.

2017-04-05

Artur Gurgul
Katarzyna Ropka-Molik
Katarzyna Piórkowska

Monika Stefaniuk-Szmukier
Kacper Żukowski
Monika Bugno-Poniewierska

BMC Genetics

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury.

2017-04-05

Matthew D. MacManes

American Journal of Physiology - Renal Physiology

Spontaneous lung metastasis formation of human Merkel cell carcinoma cell lines transplanted into scid mice.

2017-04-05

Max Heiland

Jill Knips
Manja Czech-Sioli
Michael Spohn
Ingrid Moll
Adam Grundhoff
Udo Schumacher
Nicole Fischer

International Journal of Cancer

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.

2017-04-05

Célia Jeronimo

Nicole Uwimana
Pierre Collin
Benjamin Haibe-Kains
François Robert

Nucleic Acids Research

Genome-wide RNA-seq of iPSC-derived motor neurons indicates selective cytoskeletal perturbation in Brown-Vialetto disease that is partially rescued by riboflavin.

2017-04-06

Enrico Bertini
Nereo Bresolin
Andreina Bordoni

Federica Rizzo
Agnese Ramirez
Claudia Compagnucci
Sabrina Salani
Valentina Melzi
Francesco Fortunato
Alessia Niceforo
Giacomo P Comi
Monica Nizzardo
Stefania Corti

Scientific Reports

LncATLAS database for subcellular localization of long noncoding RNAs.

2017-04-06

Roderic Guigó i Serra
Antoni Hermoso
Rory Johnson
David Mas-Ponte
Joana Carlevaro-Fita
Emilio Palumbo

RNA

The functional genomic studies of curcumin.

2017-04-06

Lukasz B Huminiecki
Horbańczuk Jarosław Olav
Atanas G. Atanasov

Seminars in Cancer Biology

ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data

2017-04-06

Jean-Philippe Vert

Davide Risso
Fanny Perraudeau
Svetlana Gribkova
Sandrine Dudoit

De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue.

2017-04-07

Muredach P. Reilly
Xuan Zhang

Chenyi Xue
Hanrui Zhang
Jane F Ferguson
Ying Wang
Christine C Hinkle
Mingyao Li

Physiological Genomics

Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.

2017-04-07

Celia Greenwood

Marie Hudson
Sasha Bernatsky
Ines Colmegna
Maximilien Lora
Tomi Pastinen
Kathleen Klein Oros

Epigenetics

Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion.

2017-04-08

Philippe Froguel
Mickaël Canouil
Odile Poulain-Godefroy
Lorella Marselli
Amar Abderrahmani
Amélie Bonnefond

Fatou K Ndiaye
Ana Ortalli
Marlène Huyvaert
Clara Salazar-Cardozo
Cécile Lecoeur
Marie Verbanck
Valérie Pawlowski
Raphaël Boutry
Emmanuelle Durand
Iandry Rabearivelo
Olivier Sand
Julie Kerr-Conte
Vikash Chandra
Raphaël Scharfmann
Piero Marchetti
François Pattou

Molecular Metabolism

Analysis of Purified Pancreatic Islet Beta and Alpha Cell Transcriptomes Reveals 11β-Hydroxysteroid Dehydrogenase (Hsd11b1) as a Novel Disallowed Gene.

2017-04-10

Timothy J Pullen
Guy A. Rutter

Mark O Huising

Frontiers in Genetics

Stem Cell-Intrinsic, Seven-up-Triggered Temporal Factor Gradients Diversify Intermediate Neural Progenitors.

2017-04-10

Tzumin Lee
Qingzhong Ren
Ching-po Yang
Zhiyong Liu
Ken Sugino
Kent Mok
Yisheng He
Masayoshi Ito
Aljoscha Nern
Hideo Otsuna

Current Biology

CRISPR/Cas9-mediated targeted gene correction in amyotrophic lateral sclerosis patient iPSCs.

2017-04-11

Juan Carlos Izpisúa Belmonte

Lixia Wang
Fei Yi
Lina Fu
Jiping Yang
Si Wang
Zhaoxia Wang
Keiichiro Suzuki
Liang Sun
Xiuling Xu
Yang Yu
Jie Qiao
Ze Yang
Yun Yuan
Jing Qu
Guang-Hui Liu

Protein & cell

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.

2017-04-11

Heribert Hirt

Runxuan Zhang
Cristiane P G Calixto
Yamile Marquez
Peter Venhuizen
Nikoleta A Tzioutziou
Wenbin Guo
Mark Spensley
Juan Carlos Entizne
Dominika Lewandowska
Sara Ten Have
Nicolas Frei Dit Frey
Allan B James
Hugh G Nimmo
Andrea Barta
Maria Kalyna
John W S Brown

Nucleic Acids Research

Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development.

2017-04-11

Mehari Endale
Erik L Bao

Shawn Ahlfeld
Xiaoting Chen
Jenna Green
Zach Bess
Matthew T Weirauch
Yan Xu
Anne Karina Perl

Developmental Biology

Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes.

2017-04-13

Oliver Voigt
Maja Adamska
Gert Wörheide

Marcin Adamski
André Kittelmann
Lukardis Wencker

Scientific Reports

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress.

2017-04-13

Jibin Zhang
Carl J Schmidt

Susan J Lamont

BMC Genomics

Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels.

2017-04-13

Sam Buckberry
Quenten P. Schwarz

Rachael Lumb
Genevieve Secker
David Lawrence

BMC Developmental Biology

Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices.

2017-04-13

Elaine Fuchs

Hanseul Yang
Rene C Adam
Yejing Ge
Zhong L Hua

Cell

Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.

2017-04-13

Fan Guo
Jie Qiao

Li Li
Ji Dong
Liying Yan
Jun Yong
Xixi Liu
Yuqiong Hu
Xiaoying Fan
Xinglong Wu
Hongshan Guo
Xiaoye Wang
Xiaohui Zhu
Rong Li
Jie Yan
Yuan Wei
Yangyu Zhao
Wei Wang
Yixin Ren
Peng Yuan
Zhiqiang Yan
Boqiang Hu
Lu Wen
Fuchou Tang

Cell Stem Cell

Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study.

2017-04-14

Steve Bird
Maria Forlenza

Gregory Jacobson
Simon Muncaster
Koen Mensink
Nick Elliot
Grant Broomfield
Beth Signal

Developmental and Comparative Immunology

Reprogramming towards totipotency is greatly facilitated by synergistic effects of small molecules

2017-04-15

Kei Miyamoto
John Gurdon

Yosuke Tajima
Koki Yoshida
Mami Oikawa
Rika Azuma
George E Allen
Tomomi Tsujikawa
Tomomasa Tsukaguchi
Charles R Bradshaw
Jerome Jullien
Kazuo Yamagata
Kazuya Matsumoto
Masayuki Anzai
Hiroshi Imai
Masayasu Yamada

Biology Open

Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations

2017-04-17

Umesh Wankhade
Kartik Shankar

Ying Zhong
Ping Kang
Maria Alfaro
Sree V Chintapalli
Keshari M Thakali

PLOS ONE

A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response.

2017-04-17

Robin Dowell

K Audrey Audetat
Matthew D Galbraith
Aaron T Odell
Thomas Lee
Ahwan Pandey
Joaquin M Espinosa
Dylan J Taatjes

Molecular and Cellular Biology

SCnorm: robust normalization of single-cell RNA-seq data.

2017-04-17

Christina Kendziorski
Michael Newton
Rhonda Bacher

Li-Fang Chu
Ning Leng
Audrey P Gasch
James A Thomson
Ron M Stewart

Nature Methods

Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.

2017-04-17

Susanne Schneiker-Bekel
Alfred Pühler
Jörn Kalinowski

Timo Wolf
Susanne Schneiker-Bekel
Armin Neshat
Vera Ortseifen
Daniel Wibberg
Till Zemke

Journal of Biotechnology

Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages.

2017-04-18

Xinchao Wang

Xinyuan Hao
Yajun Yang
Chuan Yue
Lu Wang
David P Horvath

Frontiers in Plant Science

Reduced changes in protein compared to mRNA levels across non-proliferating tissues

2017-04-18

Karen B Avraham

Kobi Perl
Kathy Ushakov
Yair Pozniak
Ofer Yizhar-Barnea
Yoni Bhonker
Shaked Shivatzki
Tamar Geiger
Ron Shamir

BMC Genomics

Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties.

2017-04-19

Roland H. Friedel
Rut Tejero
Robert Sebra

Jessica Tome-Garcia
German Nudelman
Raymund L Yong
Huaien Wang
Mary Fowkes
Margret Magid
Martin Walsh
Violeta Silva-Vargas
Elena Zaslavsky
Fiona Doetsch
Nadejda M Tsankova

Stem Cell Reports

LncRNA-Six1 Encodes a Micropeptide to Activate Six1 in Cis and Is Involved in Cell Proliferation and Muscle Growth.

2017-04-20

Bahareldin A Abdalla

Bolin Cai
Zhenhui Li
Manting Ma
Zhijun Wang
Peigong Han
Qinghua Nie
Xiquan Zhang

Frontiers in Physiology

Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus

2017-04-21

Jason E Podrabsky

Amie L Romney

EvoDevo

Direct comparison of distinct naive pluripotent states in human embryonic stem cells.

2017-04-21

Dieter Deforce

S Warrier
M Van der Jeught
G Duggal
L Tilleman
E Sutherland
J Taelman
M Popovic
S Lierman
S Chuva De Sousa Lopes
A Van Soom
L Peelman
F Van Nieuwerburgh
D I M De Coninck
B Menten
P Mestdagh
J Van de Sompele
P De Sutter
B Heindryckx

Nature Communications

Genome-Wide Investigation of Biofilm Formation in Bacillus cereus.

2017-04-21

Yun Chen

Fang Yan
Yiyang Yu
Kevin Gozzi
Jian-Hua Guo
Yunrong Chai

Applied and Environmental Microbiology

Whole transcriptome profiling of the human hippocampus suggests an involvement of the KIBRA rs17070145 polymorphism in differential activation of the MAPK signaling pathway.

2017-04-22

Isabelle Schrauwen
Ignazio Stefano Piras
Thomas G Beach

Jonida Krate
Jason J Corneveaux
Geidy E Serrano
Lucia Sue
Matthew J Huentelman

Hippocampus

Draft genome of the lined seahorse, Hippocampus erectus.

2017-04-22

Geng Qin
Byrappa Venkatesh

Qiang Lin
Ying Qiu
Ruobo Gu
Meng Xu
Jia Li
Chao Bian
Huixian Zhang
Yanhong Zhang
Wei Luo
Jieming Chen
Xinxin You
Mingjun Fan
Min Sun
Pao Xu
Junming Xu
Hongtuo Fu
Qiong Shi

GigaScience

Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery.

2017-04-24

Jason H. Moore

Nathaniel M Crabtree
John F Bowyer
Nysia I George

BioData Mining

IL-10 improves cardiac remodeling after myocardial infarction by stimulating M2 macrophage polarization and fibroblast activation.

2017-04-24

Merry L. Lindsey
Andriy Yabluchanskiy

Mira Jung
Yonggang Ma
Rugmani Padmanabhan Iyer
Kristine Y DeLeon-Pennell
Michael R Garrett

Basic Research in Cardiology

Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models.

2017-04-25

Crispin J. Miller
Caroline Dive

Garima Khandelwal
María Romina Girotti
Christopher Smowton
Sam Taylor
Christopher Wirth
Marek Dynowski
Kristopher K Frese
Ged Brady
Richard Marais

Molecular Cancer Research

Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples.

2017-04-26

Maris Laan
Kristiina Rull
Siim Sõber

Mario Reiman

FASEB Journal

Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation.

2017-04-26

Andrew Routh

Ping Ji
Elizabeth Jaworski
Zheng Xia
Wei Li
Eric J Wagner

Nucleic Acids Research

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

2017-04-27

Lior Pachter
Harold Pimentel
Lynn Yi

PLOS ONE

miRNA-mRNA network involved in folliculogenesis interactome: systems biology approach.

2017-04-27

Ali Najafi

Abolfazl Bahrami
Seyed Reza Miraie-Ashtiani
Mostafa Sadeghi

Reproduction

Assessment of engineered cells using CellNet and RNA-seq.

2017-04-27

Patrick Cahan

Arthur H Radley
Remy M Schwab
Yuqi Tan
Jeesoo Kim
Emily K W Lo

Nature Protocols

Signal Transductions of BEAS-2B Cells in Response to Carcinogenic PM2.5 Exposure Based on a Microfluidic System.

2017-04-27

Jian Xu

Lulu Zheng
Sixiu Liu
Guoshun Zhuang
Qi Liu
Xinlian Zhang
Congrui Deng
Zhigang Guo
Wang Zhao
Tingna Liu
Yiqi Wang
Yuxiao Zhang
Jing Lin
Qiongzhen Wang
Guodong Sui

Analytical Chemistry

Altered nucleocytoplasmic proteome and transcriptome distributions in an in vitro model of amyotrophic lateral sclerosis

2017-04-28

Jong-Il Kim

Jee-Eun Kim
Yoon Ho Hong
Jin Young Kim
Gye Sun Jeon
Jung Hee Jung
Byung-Nam Yoon
Sung-Yeon Son
Kwang-Woo Lee
Jung-Joon Sung

PLOS ONE

The Distinct Transcriptional Response of the Midgut of Amblyomma sculptum and Amblyomma aureolatum Ticks to Rickettsia rickettsii Correlates to Their Differences in Susceptibility to Infection

2017-04-28

Andréa C Fogaça
Sirlei Daffre
Marcelo B. Labruna

Larissa A Martins
Maria F B de Melo Galletti
José M Ribeiro
André Fujita
Francisco B Costa

Frontiers in cellular and infection microbiology

The landscape of BRAF transcript and protein variants in human cancer.

2017-04-28

Letizia Pitto
Alberto Mercatanti
Simone Lubrano
Giovanni Signore
Monica Evangelista
Giorgio Cozza
Laura Poliseno

Andrea Marranci
Zhijie Jiang
Marianna Vitiello
Elena Guzzolino
Laura Comelli
Samanta Sarti
Cinzia Franchin
Ileabett Echevarría-Vargas
Andrea Tuccoli
Paolo Sportoletti
Ettore Luzi
Enrico Capobianco
Jessie Villanueva
Giorgio Arrigoni
Silvia Rocchiccioli
Nicholas Tsinoremas

Molecular Cancer

Gene length and detection bias in single cell RNA sequencing protocols.

2017-04-28

Alicia Oshlack
Luke Zappia
Belinda Phipson

F1000Research

Exercise-induced modification of the skeletal muscle transcriptome in Arabian horses.

2017-04-28

Katarzyna Ropka-Molik
Katarzyna Piórkowska

Monika Stefaniuk-Szmukier
Kacper Z Ukowski
Monika Bugno-Poniewierska

Physiological Genomics

550. Delineating Transcriptomic Profiles in PTSD: An RNAseq Investigation

2017-05

Sian Hemmings
Soraya Seedat

Laetitia Dicks
Mahjoubeh Jalali
Junaid Gamieldien
Leigh vd Heuvel

Biological Psychiatry

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.

2017-05-01

Tomaž Curk
Ina Huppertz
Miha Modic
Christian von Mering
Jernej Ule

Gregor Rot
Zhen Wang
Tina Lenče
Martina Hallegger
Nejc Haberman

Cell Reports

Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome

2017-05-01

Scott Ness

Roger B Brown
Nathaniel J Madrid
Hideaki Suzuki

PLOS ONE

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.

2017-05-01

Xiaohong Li
Guy Brock

Eric C Rouchka
Nigel G F Cooper
Dongfeng Wu
Timothy E O'Toole
Ryan S Gill
Abdallah M Eteleeb
Liz O'Brien
Shesh N Rai

PLOS ONE

Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells.

2017-05-01

Nissim Benvenisty

Shiran Bar
Maya Schachter
Talia Eldar-Geva

Cell Reports

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.

2017-05-01

Tom Maniatis
Raul Rabadan

Abbas H Rizvi
Pablo G Camara
Elena K Kandror
Thomas J Roberts
Ira Schieren

Nature Biotechnology

Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement.

2017-05-01

Yue-Ying Wang

Yu-Jun Dai
Jin-Yan Huang
Li Xia
Xiao-Dong Shi
Jie Xu
Jing Lu
Xian-Bin Su
Ying Yang
Wei-Na Zhang
Pan-Pan Wang
Song-Fang Wu
Ting Huang
Jian-Qing Mi
Ze-Guang Han
Zhu Chen
Sai-Juan Chen

Proceedings of the National Academy of Sciences of the United States of America

Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C- Cells.

2017-05-01

Achim Leutz
Franziska Paul
Alexander Mildner
Steffen Jung
Josef Priller

Jörg Schönheit
Amir Giladi
Eyal David
David Lara-Astiaso
Erika Lorenzo-Vivas
Louise Chappell-Maor
Ido Amit

Immunity

Integrating Results across Methodologies Is Essential for Producing Robust Neuronal Taxonomies.

2017-05-01

Mark S Cembrowski
Nelson Spruston

Neuron

HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development.

2017-05-01

Javier Lopez-Rios
Marco Osterwalder
Aimée Zuniga
Rolf Zeller

Frédéric Laurent
Ausra Girdziusaite
Julie Gamart
Iros Barozzi
Jennifer A Akiyama
Joy Lincoln

Cell Reports

Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism.

2017-05-02

Alison C Todd
Owen Dando
Roser Masgrau
Elena Galea
David J Wyllie
Giles E. Hardingham
Siddharthan Chandran
Abel Eraso-Pichot

Philip Hasel
Zoeb Jiwaji
Paul Baxter
Samuel Heron
Nóra M Márkus
Jamie McQueen
David W Hampton
Megan Torvell
Sachin S Tiwari
Sean McKay
Antonio Zorzano
T Ian Simpson

Nature Communications

Power analysis for RNA-Seq differential expression studies.

2017-05-03

Guy Brock

Lianbo Yu
Soledad Fernandez

BMC Bioinformatics

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

2017-05-03

Michael A Rieger
Oliver Stegle
Timm Schroeder
Andreas Trumpp

Nina Cabezas-Wallscheid
Florian Buettner
Pia Sommerkamp
Daniel Klimmeck
Luisa Ladel
Frederic B Thalheimer
Daniel Pastor-Flores
Leticia P Roma
Simon Renders
Petra Zeisberger
Adriana Przybylla
Katharina Schönberger
Roberta Scognamiglio
Sandro Altamura
Carolina M Florian
Malak Fawaz
Dominik Vonficht
Melania Tesio
Paul Collier
Dinko Pavlinic
Hartmut Geiger
Vladimir Benes
Tobias P Dick

Cell

Transcriptome-wide analysis of jasmonate-treated BY-2 cells reveals new transcriptional regulators associated with alkaloid formation in tobacco.

2017-05-04

Michael P. Timko

Yuping Yang
Pengcheng Yan
Che Yi
Wenzheng Li
Yuhui Chai
Lingling Fei
Ping Gao
Heping Zhao
Yingdian Wang
Bingwu Wang
Shengcheng Han

The Journal of Plant Physiology

Gene expression profiling in Pekin duck embryonic breast muscle.

2017-05-04

Kyle Schachtschneider

Tie-Shan Xu
Li-Hong Gu
Wei Huang
Wan-Liang Xia
Yun-Sheng Zhang
Ya-Ge Zhang
Guang Rong
Shui-Sheng Hou

PLOS ONE

Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice.

2017-05-04

Zhang Zhang

Lin Xia
Dong Zou
Jian Sang
Xingjian Xu
Hongyan Yin
Mengwei Li
Shuangyang Wu
Songnian Hu
Lili Hao

Journal of Genetics and Genomics

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts

2017-05-05

Wolfgang Kaisers

Petra Boukamp
Hans-Jürgen Stark
Holger Schwender
Julia Tigges
Jean Krutmann
Heiner Schaal

PLOS ONE

Connective Tissue Growth Factor Promotes Efficient Generation of Human Induced Pluripotent Stem Cell-Derived Choroidal Endothelium.

2017-05-05

Budd A. Tucker
Kristan S Worthington
Robert F. Mullins
Edwin M. Stone

Allison E Songstad
Kathleen R Chirco
Joseph C Giacalone
S Scott Whitmore
Kristin R Anfinson
Dalyz Ochoa
Cathryn M Cranston
Megan J Riker
Maurine Neiman

Stem Cells Translational Medicine

Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues

2017-05-08

Brent J Sinclair

Lauren E Des Marteaux
Alexander H McKinnon
Hiroko Udaka
Jantina Toxopeus

BMC Genomics

Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

2017-05-08

Sabeeha Merchant
Matteo Pellegrini
Sean D Gallaher
Melissa S Roth

Shawn J Cokus
Andreas Walter
David Lopez
Erika Erickson
Benjamin Endelman
Daniel Westcott
Carolyn A Larabell
Krishna K Niyogi

Proceedings of the National Academy of Sciences of the United States of America

Characterization of joining sites of a viral histone H4 on host insect chromosomes

2017-05-09

Yonggyun Kim

Sunil Kumar
Jin-Kyo Jung

PLOS ONE

iTRAQ and RNA-Seq Analyses Provide New Insights into Regulation Mechanism of Symbiotic Germination of Dendrobium officinale Seeds (Orchidaceae).

2017-05-10

Annegret Kohler

Juan Chen
Si Si Liu
Bo Yan
Hong Mei Luo
Xiao Mei Chen
Shun Xing Guo

Journal of Proteome Research

Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes.

2017-05-11

Roland Hartmann

Markus Gößringer
Marcus Lechner
Nadia Brillante
Christoph Weber
Walter Rossmanith

Nucleic Acids Research

Alternative TSSs are co-regulated in single cells in the mouse brain.

2017-05-11

Sten Linnarsson
Peter Lönnerberg

Kasper Karlsson

Molecular Systems Biology

The core transcriptome of mammalian placentas and the divergence of expression with placental shape.

2017-05-12

Eviatar Nevo
Don L Armstrong
Roberto Romero

Michael R McGowen
Amy Weckle
Priyadarshini Pantham
Jason Caravas
Dalen Agnew
Kurt Benirschke
Sue Savage-Rumbaugh
Chong J Kim
Günter P Wagner
Derek E Wildman

Placenta

RNA-seq analyses reveal that cervical spinal cords and anterior motor neurons from amyotrophic lateral sclerosis subjects show reduced expression of mitochondrial DNA-encoded respiratory genes, and rhTFAM may correct this respiratory deficiency.

2017-05-13

Nicholas J Tustison

Amy C Ladd
David G Brohawn
Ravindar R Thomas
Paula M Keeney
Stuart S Berr
Shaharyar M Khan
Francisco R Portell
Meiram Zh Shakenov
Patrick F Antkowiak
Bijoy Kundu
James P Bennett

Brain Research

Sexual Dimorphism and Retinal Mosaic Diversification Following the Evolution of a Violet Receptor in Butterflies.

2017-05-15

Adriana Briscoe
Peter Andolfatto

Kyle J McCulloch
Furong Yuan
Ying Zhen
Matthew L Aardema
Gilbert Smith
Jorge Llorente-Bousquets

Molecular Biology and Evolution

A computational approach for the functional classification of the epigenome.

2017-05-15

Anna Tramontano

Francesco Gandolfi

Epigenetics & Chromatin

Elevated PTTG and PBF predicts poor patient outcome and modulates DNA damage response genes in thyroid cancer.

2017-05-15

Martin L. Read

J C Fong
B Modasia
A Fletcher
W Imruetaicharoenchoke
R J Thompson
H Nieto
J J Reynolds
A Bacon
U Mallick
A Hackshaw
J C Watkinson
K Boelaert
A S Turnell
C J McCabe

Oncogene

Isolation of tissues and preservation of RNA from intact, germinated barley grain.

2017-05-16

Oliver Berkowitz
Natalie Betts
Ruijie Liu
Rachel A Burton
James Whelan

Helen M Collins
Birgitte Skadhauge
Christoph Dockter
Geoffrey B Fincher

The Plant Journal

Identification of human short introns.

2017-05-17

Syed H Ali

Emmanuel L Abebrese
Zachary R Arnold
Victoria M Andrews
Katharine Armstrong
Lindsay Burns
Hannah R Crowder
R Thomas Day
Daniel G Hsu
Katherine Jarrell
Grace Lee
Yi Luo
Daphine Mugayo
Zain Raza
Kyle Friend

PLOS ONE

A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

2017-05-17

Naoki Osada
Aya Takahashi

Yasuaki Takada
Ryutaro Miyagi
Toshinori Endo

Transcriptomics technologies.

2017-05-18

Thomas Shafee
Rohan Lowe
Mark Bleackley
Neil Shirley

Stephen Dolan

PLOS Computational Biology

Cell fixation and preservation for droplet-based single-cell transcriptomics.

2017-05-19

Nikolaus Rajewsky
Philipp Wahle
Salah Ayoub
Robert P Zinzen

Jonathan Alles
Nikos Karaiskos
Samantha D Praktiknjo
Stefanie Grosswendt
Pierre-Louis Ruffault
Luisa Schreyer
Anastasiya Boltengagen
Carmen Birchmeier
Christine Kocks

BMC Biology

An analysis of MyoD-dependent transcription using CRISPR/Cas9 gene targeting in Xenopus tropicalis embryos.

2017-05-20

Caitlin McQueen
Mary E. Pownall

Mechanisms of Development

The Atypical Response Regulator AtvR Is a New Player in Pseudomonas aeruginosa Response to Hypoxia and Virulence.

2017-05-22

Regina L Baldini

Gilberto Hideo Kaihami
Leandro Carvalho Dantas Breda
José Roberto Fogaça de Almeida
Thays de Oliveira Pereira
Gianlucca Gonçalves Nicastro
Ana Laura Boechat
Sandro Rogério de Almeida

Infection and Immunity

N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.

2017-05-24

Haiquan Li
Vincent Gardeux
Joanne Berghout
Yves A. Lussier
A. Grant Schissler

Qike Li
Ikbel Achour
Colleen Kenost
Hao Helen Zhang

BMC Medical Genomics

Krüppel-like factors compete for promoters and enhancers to fine-tune transcription.

2017-05-24

Timothy L. Bailey
Melissa D Ilsley
Stephen Huang
Kevin R Gillinder
Merlin Crossley
Andrew C Perkins

Graham W Magor

Nucleic Acids Research

scImpute: Accurate And Robust Imputation For Single Cell RNA-Seq Data

2017-05-24

Jingyi Jessica Li

Wei Vivian Li

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes

2017-05-25

Jens Nielsen
Bente Klarlund Pedersen
Mathias Uhlén
Leif Väremo
Camilla Scheele
Tora Henriksen

Christa Broholm
Maria Pedersen

Genome Medicine

ROTS: An R package for reproducibility-optimized statistical testing

2017-05-25

Laura L. Elo
Tomi Suomi

Fatemeh Seyednasrollah
Maria K Jaakkola
Thomas Faux

PLOS Computational Biology

The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data.

2017-05-25

Xuegong Zhang

Zhiyi Qin

PLOS ONE

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data.

2017-05-25

Gordon K Smyth

Aaron T L Lun
Gordon K Smyth

Statistical Applications in Genetics and Molecular Biology

Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease.

2017-05-25

Andrew R. Hesketh
Peter Henry St George-Hyslop

Paul M McKeever
TaeHyung Kim
Laura MacNair
Denise Miletic
Giorgio Favrin
Stephen G Oliver
Zhaolei Zhang
Janice Robertson

Neurobiology of Aging

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis.

2017-05-26

Tavi Nathanson
Eliza J Chang
Samuel Funt
Jacqueline L. Buros
Bülent Arman Aksoy

Alexandra Snyder
Arun Ahuja
Matthew D Hellmann
Hikmat Al-Ahmadie
Erik Yusko
Marissa Vignali
Sharon Benzeno
Mariel Boyd
Meredith Moran
Gopa Iyer
Harlan S Robins
Elaine R Mardis
Taha Merghoub
Jeff Hammerbacher
Jonathan E Rosenberg
Dean F Bajorin

PLOS Medicine

RNAseq Reveals Complex Response of Campylobacter jejuni to Ovine Bile and In vivo Gallbladder Environment.

2017-05-29

Qijing Zhang

Amanda J Kreuder
Jennifer A Schleining
Michael Yaeger
Paul J Plummer

Frontiers in Microbiology

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

2017-05-30

Paul Kellam
Nathan Lawless
Swee Hoe Ong

Irene Bassano
Thomas Whitehead
Mark Fife

BMC Genomics

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening

2017-05-30

Karen Schlauch
Richard L. Tillett
David Toubiana
Grant Cramer

Ryan Ghan
Juli Petereit
Aaron Fait

BMC Plant Biology

Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont

2017-05-30

Cecilia Wentrup

Lena König
Alexander Siegl
Thomas Penz
Susanne Haider
Julia Polzin
Evelyne Mann
Stephan Schmitz-Esser
Daryl Domman
Matthias Horn

mSystems

RNA-seq reveals conservation of function among the yolk sacs of human, mouse, and chicken.

2017-05-30

Sungsam Gong
Michael G Elliot

Tereza Cindrova-Davies
Eric Jauniaux
Graham J Burton
D Stephen Charnock-Jones

Proceedings of the National Academy of Sciences of the United States of America

Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish.

2017-05-30

Yuichiro Mishima

Yukihide Tomari

Genes to Cells

Reprint of: MicroRNA profiling of human intermediate monocytes.

2017-05-31

Loems Ziegler-Heitbrock

Adam M Zawada
Lu Zhang
Insa E Emrich
Kyrill S Rogacev
Nicolas Krezdorn
Björn Rotter
Danilo Fliser
Yvan Devaux
Loems Ziegler-Heitbrock
Gunnar H Heine

Immunobiology

Revealing allele-specific gene expression by single-cell transcriptomics.

2017-05-31

Qiaolin Deng

Julio Aguila Benitez
Shangli Cheng

International Journal of Biochemistry & Cell Biology

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex

2017-05-31

Ryuichiro Nakato
Katsuhiko Shirahige

Akiko Sakai
Yiwei Ling
Xubin Hou
Norikazu Hara
Tomoya Iijima
Yuchio Yanagawa
Ryozo Kuwano
Shujiro Okuda
Sayaka Sugiyama

Frontiers in Neuroscience

Large-scale genomic analyses of in vitro yeast-mycelium dimorphism in human, insect and plant pathogenic fungi: From ESTs to RNAseq experiments

2017-06

Louis Bernier

M. Nigg

Fungal Biology Reviews

Ly6Chi Monocytes and Their Macrophage Descendants Regulate Neutrophil Function and Clearance in Acetaminophen-Induced Liver Injury.

2017-06-01

Metsada Pasmanik-Chor
Steffen Jung

Nadine Graubardt
Milena Vugman
Odelia Mouhadeb
Gabriele Caliari
Metsada Pasmanik-Chor
Debby Reuveni
Ehud Zigmond
Eli Brazowski
Eyal David
Lousie Chappell-Maor
Chen Varol

Frontiers in Immunology

Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues.

2017-06-01

Isabel Molina

Meghan K Rains
Nayana Dilini Gardiyehewa de Silva

Tree Physiology

Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome

2017-06-01

Tariq Enver

Andrew E Teschendorff

Nature Communications

IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.

2017-06-01

Aviv Regev
Itay Tirosh
Olga Troyanskaya
Alex K. Shalek
Niroshana Anandasabapathy
Michelle A Lowes
Tae-Gyun Kim

Christopher J Nirschl
Mayte Suárez-Fariñas
Benjamin Izar
Sanjay Prakadan
Ruth Dannenfelser
Itay Tirosh
Yong Liu
Qian Zhu
K Sanjana P Devi
Shaina L Carroll
David Chau
Melika Rezaee
Ruiqi Huang
Judilyn Fuentes-Duculan
George X Song-Zhao
Nicholas Gulati
Sandra L King
Francisco J Quintana
Young-Suk Lee
James G Krueger
Kavita Y Sarin
Charles H Yoon
Levi Garraway

Cell

Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.

2017-06-01

Jie Qiao

Cell Stem Cell

Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma.

2017-06-02

Charmion I Cruickshank-Quinn
Thomas Danhorn

Mikaela A Miller
Sonia M Leach
Sean Jacobson
Matthew J Strand
Nichole A Reisdorph
Russell P Bowler
Irina Petrache
Katerina Kechris

PLOS ONE

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network.

2017-06-05

Ellen V. Rothenberg
Maile Romero-Wolf
Hiroyuki Hosokawa

William J R Longabaugh
Weihua Zeng
Jingli A Zhang
Camden S Jansen
Long Li
Pentao Liu
Hao Yuan Kueh
Ali Mortazavi

Proceedings of the National Academy of Sciences of the United States of America

lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets.

2017-06-05

Aristotelis Tsirigos

Yixiao Gong
Hsuan-Ting Huang
Yu Liang
Thomas Trimarchi
Iannis Aifantis

BMC Genomics

Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola.

2017-06-05

Humira Sonah
Rupesh K. Deshmukh

Caroline Labbé
Richard R Bélanger

Scientific Reports

The Landscape of Isoform Switches in Human Cancers.

2017-06-05

Kristoffer Vitting-Seerup
Albin Sandelin

Molecular Cancer Research

DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells.

2017-06-05

Mattia Pelizzola
Monica Mancini
Kamal Kishore
Nora Sahnane
Giorgio Giurato
Alessandro Weisz

C Pistore
E Giannoni
T Colangelo
F Rizzo
E Magnani
L Muccillo
S Rizzo
M Riccardi
V Del Vescovo
M Mandruzzato
F Macchi
M A Denti
D Furlan
V Colantuoni
P Chiarugi
I M Bonapace

Oncogene

Differential analysis of RNA-seq incorporating quantification uncertainty.

2017-06-05

Páll Melsted

Harold Pimentel
Nicolas L Bray
Suzette Puente
Lior Pachter

Nature Methods

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples

2017-06-06

Gunnar Dittmar

Petr V Nazarov
Arnaud Muller
Tony Kaoma
Nathalie Nicot
Cristina Maximo
Philippe Birembaut
Nhan L Tran
Laurent Vallar

BMC Genomics

RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism.

2017-06-06

Jacqueline Batley
Felipe Aguilera
David Edwards

David K Y Lim
Holger Schuhmann
Skye R Thomas-Hall
Kenneth C K Chan
Taylor J Wass
T Catalina Adarme-Vega
Cristiana G O Dal'Molin
Glen J Thorpe
Peer M Schenk

Bioresource Technology

A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.

2017-06-07

Hadas Keren-Shaul
Orit Matcovitch-Natan

Hadas Keren-Shaul
Amit Spinrad
Assaf Weiner
Orit Matcovitch-Natan
Raz Dvir-Szternfeld
Tyler K Ulland
Eyal David
Kuti Baruch
David Lara-Astaiso
Beata Toth
Shalev Itzkovitz
Marco Colonna
Michal Schwartz
Ido Amit

Cell

Dataset on transcriptional profiles and the developmental characteristics of PDGFRα expressing lung fibroblasts.

2017-06-07

Mehari Endale

Shawn Ahlfeld
Erik Bao
Xiaoting Chen
Jenna Green
Zach Bess
Matthew Weirauch
Yan Xu
Anne Karina Perl

Data in Brief

Immunoglobulin characteristics and RNAseq data of FcRL4+ B cells sorted from synovial fluid and tissue of patients with rheumatoid arthritis.

2017-06-07

Daniel Ramsköld
Caroline Grönwall
Vivianne Malmström

Khaled Amara
Elizabeth Clay
Lorraine Yeo
Julia Spengler
Natalie Sippl
James Cameron
Lena Israelsson
Philip J Titcombe
Ilfita Sahbudin
Andrew Filer
Karim Raza
Dagmar Scheel-Toellner

Data in Brief

Divergent roles of the Drosophila melanogaster globins.

2017-06-09

Thorsten Burmester

Agnes Wawrowski
Ines Diepenbruck
Katharina Schrick
Nina Seiwert
Fabian Ripp
Andreas Prothmann
Thomas Hankeln

Journal of Insect Physiology

A Novel In Vitro Human Granuloma Model of Sarcoidosis and Latent TB Infection.

2017-06-09

Peter White
Wolfgang Sadee

Elliott D Crouser
Evelyn Guirado Caceres
Mark W Julian
Audrey C Papp
Landon W Locke
Larry S Schlesinger

American Journal of Respiratory Cell and Molecular Biology

Use of Angiotensin System Inhibitors Is Associated with Immune Activation and Longer Survival in Nonmetastatic Pancreatic Ductal Adenocarcinoma.

2017-06-09

Kohei Shigeta
Kamila Naxerova
Ronald M. Evans

Hao Liu
Matthias Pinter
Joao Incio
Hang Lee
William W Ho
Jonathan A Crain
Alex Jacobson
Theodoros Michelakos
Daniella Dias-Santos
Andrea Zanconato
Theodore S Hong
Jeffrey W Clark
Janet E Murphy
David P Ryan
Vikram Deshpande
Keith D Lillemoe
Carlos Fernandez-Del Castillo
Michael Downes
James Michaelson
Cristina R Ferrone
Yves Boucher
Rakesh K Jain

Clinical Cancer Research

Gaining insights from RNA-Seq data using iDEP

2017-06-09

Steven Ge

Eun Wo Son

The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data

2017-06-12

Edward R. Dougherty

Eunji Kim
Ivan Ivanov
Jianping Hua
Johanna W Lampe
Meredith Aj Hullar
Robert S Chapkin

Cancer Informatics

Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors.

2017-06-13

Peter Deplazes
Adrian B. Hehl
Ramon M. Eichenberger

Chandra Ramakrishnan
Giancarlo Russo

Scientific Reports

Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq.

2017-06-13

James M Ward
Shannon Farris
Serena M. Dudek

Yu Wang

Frontiers in molecular neuroscience

Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries

2017-06-13

Stephen J Bush
David A Hume
Kim M Summers

Mary E B McCulloch
Emily L Clark

BMC Bioinformatics

The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells.

2017-06-13

Yohei Mikami
Han-Yu Shih
Toshinori Nakayama

Shigeru Iwata
Hong-Wei Sun
Stephen R Brooks
Dragana Jankovic
Kiyoshi Hirahara
Atsushi Onodera
Takeshi Kawabe
Kan Jiang
Alan Sher
John J O'Shea
Fred P Davis
Yuka Kanno

Immunity

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost.

2017-06-14

Susanne Bornelöv
Miriam Friedman-Einat

Susanne Bornelöv
Eyal Seroussi
Sara Yosefi
Ken Pendavis
Shane C Burgess
Manfred Grabherr
Leif Andersson

Genome Biology

Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections.

2017-06-14

Jonathan M. Palmer
Kenneth A Field

Sophia M Reeder
Jenni M Prokkola
Thomas M Lilley
DeeAnn M Reeder

Virulence

MicroRNAs control mRNA fate by compartmentalization based on 3' UTR length in male germ cells.

2017-06-15

Wei Yan
Chong Tang
Huili Zheng

Ying Zhang
Chong Tang
Tian Yu
Ruirui Zhang

Genome Biology

Insufficient antibody validation challenges oestrogen receptor beta research.

2017-06-15

Ola Söderberg

Sandra Andersson
Mårten Sundberg
Nusa Pristovsek
Ahmed Ibrahim
Philip Jonsson
Borbala Katona
Carl-Magnus Clausson
Agata Zieba
Margareta Ramström
Cecilia Williams
Anna Asplund

Nature Communications

Supplementation with small-extracellular vesicles from ovarian follicular fluid during in vitro production modulates bovine embryo development

2017-06-15

Rafael Vilar Sampaio
Felipe Perecin
Rinaldo Wellerson Pereira
Luiz L Coutinho

Juliano C da Silveira
Gabriella M Andrade
Maite Del Collado
Juliano R Sangalli
Luciano A Silva
Fábio V L Pinaffi
Izabelle B Jardim
Marcelo C Cesar
Marcelo F G Nogueira
Aline S M Cesar
Flávio V Meirelles

PLOS ONE

RNA-seq implicates deregulation of the immune system in the pathogenesis of diverticulitis.

2017-06-15

Kathleen M. Schieffer

Christine S Choi
Scott Emrich
Leonard Harris
Sue Deiling
Dipti M Karamchandani
Anna Salzberg
Yuka I Kawasawa
Gregory S Yochum
Walter A Koltun

American Journal of Physiology - Gastrointestinal and Liver Physiology

Transcriptomic Profiling in Human Decidua of Severe Preeclampsia Detected by RNA Sequencing.

2017-06-15

Zi-Jiang Chen

Jing Tong
Weixiu Zhao
Hong Lv
Wei-Ping Li
Cong Zhang

Journal of Cellular Biochemistry

Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids.

2017-06-16

Peter J. Myler
Franck Dumetz
Bart Cuypers
Manu Vanaerschot
Hideo Imamura
Pieter Meysman
Kris Laukens

Malgorzata A Domagalska
Géraldine de Muylder
Thomas Wolf Verdonckt
Gowthaman Ramasamy
Jean-Claude Dujardin

Scientific Reports

Characterization of slow cycling corneal limbal epithelial cells identifies putative stem cell markers.

2017-06-19

Chao Zhang

R Sartaj
P Wan
Z Pasha
V Guaiquil
A Liu
J Liu
Y Luo
E Fuchs
M I Rosenblatt

Scientific Reports

Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size.

2017-06-19

Robbie Waugh

Wenbin Guo
Cristiane P G Calixto
Nikoleta Tzioutziou
Ping Lin
John W S Brown
Runxuan Zhang

BMC Systems Biology

Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome.

2017-06-19

Timothy W Yu
Stefan Wiemann
Ganeshwaran H Mochida

Gilad D Evrony
Dwight R Cordero
Jun Shen
Jennifer N Partlow
Rachel E Rodin
R Sean Hill
Michael E Coulter
Anh-Thu N Lam
Divya Jayaraman
Dianne Gerrelli
Diana G Diaz
Chloe Santos
Victoria Morrison
Antonella Galli
Ulrich Tschulena
M Jocelyne Martel
Betty Spooner
Steven C Ryu
Princess C Elhosary
Jillian M Richardson
Danielle Tierney
Christopher A Robinson
Rajni Chibbar
Dana Diudea
Rebecca Folkerth
Sheldon Wiebe
A James Barkovich
James Irvine
Edmond G Lemire
Patricia Blakley
Christopher A Walsh

Genome Research

qSVA framework for RNA quality correction in differential expression analysis

2017-06-20

Daniel R. Weinberger
Andrew E Jaffe
Jeffrey T. Leek
Abhinav Nellore

Ran Tao
Alexis L Norris
Marc Kealhofer
Joo Heon Shin
Dewey Kim
Yankai Jia
Thomas M Hyde
Joel E Kleinman
Richard E Straub

Proceedings of the National Academy of Sciences of the United States of America

The RNA-seq analysis suggests a potential multi-component complement system in oyster Crassostrea gigas.

2017-06-20

Linsheng Song
Hao Wang

Lingling Wang
Huan Zhang
Leilei Wang
Daoxiang Zhang
Zhao Lv
Zhaoqun Liu
Weilin Wang
Zhi Zhou
Limei Qiu
Jun Li

Developmental and Comparative Immunology

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses.

2017-06-21

Rozaimi Razali
Mark Tester

Sandra M Schmöckel
Damien J Lightfoot
David E Jarvis

Frontiers in Plant Science

A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover.

2017-06-21

Roman A Romanov
Stefan Kubicek
Tomas Hökfelt
Fabiana Piscitelli
Rickard Sandberg

Katarzyna Malenczyk
Fatima Girach
Edit Szodorai
Petter Storm
Åsa Segerstolpe
Giuseppe Tortoriello
Robert Schnell
Jan Mulder
Erzsébet Borók
Vincenzo Di Marzo
Gábor Szabó
Gert Lubec
Ludwig Wagner
Leif Groop
Tibor Harkany

The EMBO Journal

A novel bZIP protein, Gsb1, is required for oxidative stress response, mating, and virulence in the human pathogen Cryptococcus neoformans.

2017-06-22

Yong-Sun Bahn

Seon Ah Cheon
Eun Jung Thak
Hyun Ah Kang

Scientific Reports

Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae).

2017-06-23

Pamela S. Soltis

Jacob B Landis
Douglas E Soltis

BMC Genomics

Identification of a novel fungus, Trichoderma asperellum GDFS1009, and comprehensive evaluation of its biocontrol efficacy.

2017-06-23

Mi Ni

Qiong Wu
Ruiyan Sun
Jia Yu
Yaqian Li
Chuanjin Yu
Kai Dou
Jianhong Ren
Jie Chen

PLOS ONE

The emerging role of circular RNAs in transcriptome regulation.

2017-06-24

Michael Janitz

S Huang
B Yang
B J Chen
N Bliim
U Ueberham
T Arendt

Genomics

Senescence-associated microRNAs target cell cycle regulatory genes in normal human lung fibroblasts.

2017-06-25

Georgios Markopoulos
Evangelos Kolettas
Maria Hatziapostolou

Eugenia Roupakia
Maria Tokamani
George Vartholomatos
Theodore Tzavaras
Frank O Fackelmayer
Raphael Sandaltzopoulos
Christos Polytarchou

Experimental Gerontology

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

2017-06-26

Jérôme Gouzy

Olivier Arnaiz
Erwin Van Dijk
Mireille Bétermier
Maoussi Lhuillier-Akakpo
Augustin de Vanssay
Sandra Duharcourt
Erika Sallet
Linda Sperling

BMC Genomics

WetA bridges cellular and chemical development in Aspergillus flavus.

2017-06-28

Jae-Hyuk Yu
Antonis Rokas

Ming-Yueh Wu
Matthew E Mead
Sun-Chang Kim

PLOS ONE

Hepatitis C Virus Strain-Dependent Usage of Apolipoprotein E Modulates Assembly Efficiency and Specific Infectivity of Secreted Virions.

2017-06-28

Daniel Todt

Romy Weller
Kathrin Hueging
Richard J P Brown
Sebastian Joecks
Florian W R Vondran
Thomas Pietschmann

Journal of Virology

RNA-Seq and CyTOF immuno-profiling of regenerating lacrimal glands identifies a novel subset of cells expressing muscle-related proteins

2017-06-29

Dillon R Hawley
Hema S Aluri

Jian Ding
Suharika Thotakura
Scott Haskett
Claire Kublin
Audrey Michel
Lisa Clapisson
Michael Mingueneau
Driss Zoukhri

PLOS ONE

Transcriptional consequences of XPA disruption in human cell lines.

2017-06-29

Yue Lu

Mandira Manandhar
Megan G Lowery
Karen S Boulware
Kevin H Lin

DNA Repair

Regulating cellular trace metal economy in algae.

2017-06-30

Sabeeha Merchant

Crysten E Blaby-Haas

Current Opinion in Plant Biology

zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications

2017-06-30

Koen Van den Berge
Charlotte Soneson
Mark D. Robinson

Michael I. Love
Lieven Clement

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.

2017-07-01

John C Marioni

Aaron T L Lun

Biostatistics

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-Seq data.

2017-07-01

Robert Petryszak
Alvis Brazma
Anja Füllgrabe
Maria C Keays

Laura Huerta
Y Amy Tang

Bioinformatics

Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut.

2017-07-01

Stephan Günther
David A. Matthews
Lisa Fong Poh Ng
Laurent Rénia
Bernadett Pályi
Antonino Di Caro
Armand Sprecher
Roman Wölfel
Fara Raymond Koundouno
Kilian Stoecker
Joseph Akoi Bore

Miles W Carroll
Sam Haldenby
Natasha Y Rickett
Isabel Garcia-Dorival
Xuan Liu
Gary Barker
E Diane Williamson
Thomas R Laws
Romy Kerber
Daouda Sissoko
Nóra Magyar
Mirella Biava
Tom E Fletcher
N'faly Magassouba
Julian A Hiscox

mSphere

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection.

2017-07-01

Hans-Joachim Mollenkopf
Martin Gengenbacher

Michael Zimmermann
Maria Kogadeeva
Gayle McEwen
Nicola Zamboni
Stefan Hugo Ernst Kaufmann
Uwe Sauer

mSystems

Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity.

2017-07-01

Linheng Li

Kelley S Yan
Olivier Gevaert
Grace X Y Zheng
Benedict Anchang
Christopher S Probert
Kathryn A Larkin
Paige S Davies
Zhuan-Fen Cheng
John S Kaddis
Arnold Han
Kelly Roelf
Ruben I Calderon
Esther Cynn
Xiaoyi Hu
Komal Mandleywala
Julie Wilhelmy
Sue M Grimes
David C Corney
Stéphane C Boutet
Jessica M Terry
Phillip Belgrader
Solongo B Ziraldo
Tarjei S Mikkelsen
Fengchao Wang
Richard J von Furstenberg
Nicholas R Smith
Parthasarathy Chandrakesan
Randal May
Mary Ann S Chrissy
Rajan Jain
Christine A Cartwright
Joyce C Niland
Young-Kwon Hong
Jill Carrington
David T Breault
Jonathan Epstein
Courtney W Houchen
John P Lynch
Martin G Martin
Sylvia K Plevritis
Christina Curtis
Hanlee P Ji
Susan J Henning
Melissa H Wong
Calvin J Kuo

Cell Stem Cell

Integrated gut/liver microphysiological systems elucidates inflammatory inter-tissue crosstalk.

2017-07-01

Douglas A Lauffenburger

Wen L K Chen
Collin Edington
Emily Suter
Jiajie Yu
Jeremy J Velazquez
Jason G Velazquez
Michael Shockley
Emma M Large
Raman Venkataramanan
David J Hughes
Cynthia L Stokes
David L Trumper
Rebecca L Carrier
Murat Cirit
Linda G Griffith

Biotechnology and Bioengineering

Progesterone Receptor Isoform Ratio: A Breast Cancer Prognostic and Predictive Factor for Antiprogestin Responsiveness.

2017-07-01

Charles M. Perou

Paola A Rojas
María May
Gonzalo R Sequeira
Andrés Elia
Michelle Alvarez
Paula Martínez
Pedro Gonzalez
Stephen Hewitt
Xiaping He
Alfredo Molinolo
Luz Gibbons
Martin C Abba
Hugo Gass
Claudia Lanari

Journal of the National Cancer Institute

Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.

2017-07-01

Isidore Rigoutsos

Rogan Magee
Phillipe Loher
Eric Londin

Bioinformatics

Identification of miRNAs involved in DRG neurite outgrowth and their putative targets.

2017-07-02

Vance P. Lemmon
Dario Motti

Jessica K Lerch
Matt C Danzi
Jared H Gans
Frank Kuo
Tatiana I Slepak
John L Bixby

FEBS Letters

Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae.

2017-07-03

Aimée M Dudley
Amy Sirr

Gareth A Cromie
Zhihao Tan
Michelle Hays
Eric W Jeffery

MassBlast: A workflow to accelerate RNA-seq and DNA database analysis

2017-07-03

Marie-France Sagot
Jean-Etienne Bassard
Susana Vinga

André Veríssimo
Alice Julien-Laferrière

Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia.

2017-07-04

Richard J Rodenburg
Angela Kaindl

Gudrun Schottmann
Sylvie Picker-Minh
Jana Marie Schwarz
Esther Gill
Werner Stenzel
Markus Schuelke

Mitochondrion

PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses.

2017-07-05

Cathrine Lillo

Amr R A Kataya
Maria T Creighton
Toga P Napitupulu
Christine Sætre
Behzad Heidari
Peter Ruoff

PLOS ONE

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.

2017-07-05

Robert Sebra
Mark Bender Gerstein

Sayed Mohammad Ebrahim Sahraeian
Marghoob Mohiyuddin
Hagen Tilgner
Pegah T Afshar
Kin Fai Au
Narges Bani Asadi
Wing Hung Wong
Michael P Snyder
Eric Schadt
Hugo Y K Lam

Nature Communications

Defects in dosage compensation impact global gene regulation in the mouse trophoblast.

2017-07-06

Takashi Sado
Koji Nagao

Yuka Sakata
Yuko Hoki
Hiroyuki Sasaki
Chikashi Obuse

Development

RNAseq-based transcriptome comparison of Saccharomyces cerevisiae strains isolated from diverse fermentative environments.

2017-07-06

Eladio Barrio

Clara Ibáñez
Roberto Pérez-Torrado
Miguel Morard
Christina Toft
Amparo Querol

International Journal of Food Microbiology

Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle.

2017-07-07

Peter J. Schaap
Mark Davids
Noora Ottman
Hauke Smidt
Maria Suarez-Diez

Sjef Boeren
Vitor A P Martins Dos Santos
Clara Belzer
Willem M de Vos

Applied and Environmental Microbiology

Single-cell transcriptomics of East-Asian pancreatic islets cells.

2017-07-10

Jianjun Liu

Rajkumar Dorajoo
Yusuf Ali
Vanessa S Y Tay
Jonathan Kang
Sudhagar Samydurai
Bernhard O Boehm

Scientific Reports

6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype.

2017-07-10

Roland Hartmann

Daria Elkina
Lennart Weber
Marcus Lechner
Olga Burenina
Andrea Weisert
Elena Kubareva
Gabriele Klug

RNA Biology

Neat1 is a p53-inducible lincRNA essential for transformation suppression.

2017-07-11

Stephano S. Mello
Tetsuro Hirose
John L. Rinn

Carolyn Sinow
Nitin Raj
Pawel K Mazur
Kathryn Bieging-Rolett
Daniela Kenzelmann Broz
Jamie F Conklin Imam
Hannes Vogel
Laura D Wood
Julien Sage
Shinichi Nakagawa
Laura D Attardi

Genes & Development

A Case of AML Characterized by a Novel t(4;15)(q31;q22) Translocation That Confers a Growth-Stimulatory Response to Retinoid-Based Therapy.

2017-07-11

Francisco Vega
Kevin Petrie

Justin M Watts
Aymee Perez
Lutecia Pereira
Yao-Shan Fan
Geoffrey Brown
Ronan T Swords
Arthur Zelent

International Journal of Molecular Sciences

Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans.

2017-07-12

Nils Joakim Færgeman
Richard R Sprenger
Susanne Mandrup

Eva Bang Harvald
Kathrine Brændgaard Dall
Christer S Ejsing
Ronni Nielsen
Alejandro Brenes Murillo
Mark Larance
Anton Gartner
Angus I Lamond

Cell systems

PLAG1 deficiency impairs spermatogenesis and sperm motility in mice.

2017-07-13

Stephen R. Doyle
Anne E O'Connor
Moira O'bryan
Daniel Barriga

Almas R Juma
Sylvia V H Grommen
D Jo Merriner
Nathan E Hall
Pauliina E Damdimopoulou
Adam H Hart
Wim J M Van de Ven
Bert De Groef

Scientific Reports

Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis.

2017-07-13

Aaron B Smith
Peter A Crisp
Diep R. Ganguly
Kevin D Murray
Ryan Lister
Justin O Borevitz
Barry J Pogson

Gonzalo M Estavillo
Iain R Searle
Ethan Ford
Ozren Bogdanović
Steven R Eichten

The Plant Cell

Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress

2017-07-14

Keywan Hassani-Pak
Robert C. King

Yongfang Wan
Rowan A C Mitchell
Malcolm J Hawkesford

Scientific Reports

Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses.

2017-07-15

Dengcai Liu

Yong Wang
Jingzhong Xie
Huaizhi Zhang
Bingmin Guo
Shunzong Ning
Yongxing Chen
Ping Lu
Qiuhong Wu
Miaomiao Li
Deyun Zhang
Guanghao Guo
Yan Zhang
Shaokui Zou
Jianwei Tang
Hong Zhao
Xicheng Wang
Jun Li
Wuyun Yang
Tingjie Cao
Guihong Yin
Zhiyong Liu

Theoretical and Applied Genetics

Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma

2017-07-17

Anne-Lise Børresen-Dale
Anshuman Panda
Surendra Kumar
Vessela Kristensen
Bjørn Naume

Sunniva Stordal Bjørklund
Michael Seiler
Doug Robinson
Jinesh Gheeya
Ming Yao
Grethe I Grenaker Alnæs
Deborah Toppmeyer
Margit Riis
Shridar Ganesan
Gyan Bhanot

Scientific Reports

Genome-wide RNA-Sequencing analysis identifies a distinct fibrosis gene signature in the conjunctiva after glaucoma surgery

2017-07-17

Christine Orengo
Jonathan Lees

Cynthia Yu-Wai-Man
Nicholas Owen
Aristides D Tagalakis
Stephen L Hart
Andrew R Webster
Peng T Khaw

Scientific Reports

Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium.

2017-07-18

Xuan Wang-Kan
Jonathan Betts
Barbara Chirullo
Vito Ricci
Roberto M La Ragione

Jessica M A Blair
Alasdair Ivens
Timothy J Opperman
Laura J V Piddock

mBio

Human iPSC Glial Mouse Chimeras Reveal Glial Contributions to Schizophrenia.

2017-07-18

Maiken Nedergaard
Steven A. Goldman
Paul J. Tesar

Martha S Windrem
Mikhail Osipovitch
Zhengshan Liu
Janna Bates
Devin Chandler-Militello
Lisa Zou
Jared Munir
Steven Schanz
Katherine McCoy
Robert H Miller
Su Wang
Robert L Findling
Steven A Goldman

Cell Stem Cell

RNA-Seq Identifies Circulating miR-125a-5p, miR-125b-5p, and miR-143-3p as Potential Biomarkers for Acute Ischemic Stroke.

2017-07-19

Martin Dichgans
Rainer Malik
Marco Duering

Steffen Tiedt
Matthias Prestel
Nicola Schieferdecker
Veronika Kautzky
Ivelina Stoycheva
Julia Böck
Bernd H Northoff
Matthias Klein
Franziska Dorn
Knut Krohn
Daniel Teupser
Arthur Liesz
Nikolaus Plesnila
Lesca Miriam Holdt

Circulation Research

Deletion of the celA gene in Aspergillus nidulans triggers overexpression of secondary metabolite biosynthetic genes.

2017-07-20

Frank Maixner
Joseph Strauss
Michael Sulyok

Gea Guerriero
Lucia Silvestrini
Sylvain Legay
Jean-Francois Hausman

Scientific Reports

Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli.

2017-07-20

Laura C Miller

Damarius S Fleming
Xiangdong Li
Darrell O Bayles
Frank Blecha
Yongming Sang

PLOS ONE

Gigaspora margarita with and without its endobacterium shows adaptive responses to oxidative stress.

2017-07-20

Paola Bonfante
Stefano Ghignone
Maria C de Pinto

Francesco Venice
Mara Novero
Alessandra Salvioli

Mycorrhiza

Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study.

2017-07-20

Thierry Balliau
Christophe Dunand
Elisabeth Jamet

Harold Duruflé
Vincent Hervé
Philippe Ranocha
Michel Zivy
Josiane Chourré
Hélène San Clemente
Vincent Burlat
Cécile Albenne
Sébastien Déjean

Plant Science

Direct targets of pSTAT5 signalling in erythropoiesis.

2017-07-21

Andrew C Perkins

Kevin R Gillinder
Hugh Tuckey
Charles C Bell
Graham W Magor
Stephen Huang
Melissa D Ilsley

PLOS ONE

Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors.

2017-07-25

Cathrine Lillo
Jodi Maple-Grødem

Maria T Creighton
Anna Kolton
Amr R A Kataya
Irina O Averkina
Behzad Heidari

Plant, Cell and Environment

Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

2017-07-26

Daria Gavriouchkina
Tatjana Sauka-Spengler
Vincenzo Cerundolo

Amy Kenyon
Jernej Zorman
Giorgio Napolitani

Scientific Reports

Dual RNA-Seq of Lysobacter capsici AZ78 - Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses.

2017-07-26

Paolo Sonego

Selena Tomada
Marco Moretto
Kristof Engelen
Ilaria Pertot
Michele Perazzolli
Gerardo Puopolo

Environmental Microbiology

Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.

2017-07-27

Eric Tycksen
Muhammad Farooq Rai

Linda J Sandell
Robert H Brophy

Journal of Orthopaedic Research

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes.

2017-07-28

Sean D McGrath

Jin Zhang
Malachi Griffith
Christopher A Miller
Obi L Griffith
David H Spencer
Jason R Walker
Vincent Magrini
Amy Ly
Nichole M Helton
Maria Trissal
Daniel C Link
Ha X Dang
David E Larson
Shashikant Kulkarni
Matthew G Cordes
Catrina C Fronick
Robert S Fulton
Jeffery M Klco
Elaine R Mardis
Timothy J Ley
Richard K Wilson
Christopher A Maher

Experimental Hematology

FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?

2017-07-29

Elisa V. Bandera
Christine Ambrosone

Allyson C Espinal
Matthew F Buas
Dan Wang
David Ting-Yuan Cheng
Lara Sucheston-Campbell
Qiang Hu
Li Yan
Rochelle Payne-Ondracek
Eduardo Cortes
Li Tang
Zhihong Gong
Gary Zirpoli
Thaer Khoury
Song Yao
Angela Omilian
Kitaw Demissie
Song Liu
Michael J Higgins

Breast Cancer Research and Treatment

Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements.

2017-07-31

Katrin Karbstein

Max B Ferretti
Homa Ghalei
Ethan A Ward
Elizabeth L Potts

Nature Structural & Molecular Biology

Simultaneous epitope and transcriptome measurement in single cells.

2017-07-31

Harold Swerdlow
Christoph Hafemeister
Marlon Stoeckius
Brian Houck-Loomis
Rahul Satija
Peter Smibert
William Stephenson
Pratip K. Chattopadhyay

Nature Methods

Copper homeostasis networks in the bacterium Pseudomonas aeruginosa.

2017-07-31

Lorena Novoa-Aponte
Julia Quintana

José M Argüello

Journal of Biological Chemistry

Comprehensive single-cell transcriptional profiling of a multicellular organism.

2017-08-01

Jay Shendure
Junyue Cao
Darren A Cusanovich
Scott Furlan

Jonathan S Packer
Vijay Ramani
Chau Huynh
Riza Daza
Xiaojie Qiu
Choli Lee
Frank J Steemers
Andrew Adey
Robert H Waterston
Cole Trapnell

Science

Impact of Alternative Splicing on the Human Proteome.

2017-08-01

John C Marioni
Vihandha O Wickramasinghe
Yansheng Liu
Alvis Brazma
Ruedi Aebersold

Mar Gonzàlez-Porta
Sergio Santos
Ashok R Venkitaraman

Cell Reports

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.

2017-08-01

Itoshi Nikaido

Hirotaka Matsumoto
Hisanori Kiryu
Chikara Furusawa
Minoru S H Ko
Shigeru B H Ko
Norio Gouda
Tetsutaro Hayashi

Bioinformatics

Cell-Type-Specific Translation Profiling Reveals a Novel Strategy for Treating Fragile X Syndrome.

2017-08-01

Caoimhe Kirby
Owen Dando
Peter C Kind
David J Wyllie
Giles E. Hardingham
Emily Osterweil

Sophie R Thomson
Sang S Seo
Stephanie A Barnes
Susana R Louros
Melania Muscas

Neuron

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

2017-08-01

Antonio Scialdone
John C Marioni
Carla Mulas
Iain C Macaulay
Jennifer Nichols
Wolf Reik

Hisham Mohammed
Irene Hernando-Herraez
Aurora Savino
Tamir Chandra
Thierry Voet
Wendy Dean

Cell Reports

Single-cell RNA-sequencing reveals a distinct population of proglucagon-expressing cells specific to the mouse upper small intestine.

2017-08-01

Berthold Göttgens
Leslie L Glass
Pierre Larraufie
Fernando J Calero-Nieto
Wajid Jawaid
Fiona M Gribble
Frank Reimann

Richard G Kay

Molecular Metabolism

TREM2 Maintains Microglial Metabolic Fitness in Alzheimer's Disease.

2017-08-01

Tyler K Ulland
Susan Gilfillan
Yingyue Zhou
Herbert W. "Skip" Virgin
David M. Holtzman

Wilbur M Song
Stanley Ching-Cheng Huang
Jason D Ulrich
Alexey Sergushichev
Wandy L Beatty
Alexander A Loboda
Nigel J Cairns
Amal Kambal
Ekaterina Loginicheva
Marina Cella
Emil R Unanue
Yaming Wang
Maxim N Artyomov
Marco Colonna

Cell

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells.

2017-08-01

Steven A. Sloan

Spyros Darmanis
Nina Huber
Themasap A Khan
Fikri Birey
Christine Caneda
Richard Reimer
Stephen R Quake
Ben A Barres
Sergiu P Paşca

Neuron

Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development.

2017-08-01

Jiwen Li
Arturo Alvarez-Buylla

Chunyang Wang
Zhuangzhi Zhang
Yan Wen
Lei An
Qifei Liang
Zhejun Xu
Song Wei
Weiwei Li
Teng Guo
Guoping Liu
Guangxu Tao
Yan You
Heng Du
Zhuoning Fu
Miao He
Bin Chen
Kenneth Campbell
John L Rubenstein
Zhengang Yang

Cerebral Cortex

Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas.

2017-08-04

Felix Sahm
Andreas von Deimling
Trevor J Pugh

Sameer Agnihotri
Suganth Suppiah
Peter D Tonge
Shahrzad Jalali
Arnavaz Danesh
Jeffery P Bruce
Yasin Mamatjan
George Klironomos
Lior Gonen
Karolyn Au
Sheila Mansouri
Sharin Karimi
Michael D Taylor
Normand J Laperriere
Kenneth D Aldape
Gelareh Zadeh

Nature Communications

A novel mutation of adenomatous polyposis coli (APC) gene results in the formation of supernumerary teeth.

2017-08-07

Wenping Cai

Fang Yu
Beizhan Jiang
Laijun Xu
Shangfeng Liu
Shouliang Zhao

Journal of Cellular and Molecular Medicine

Comparison of alternative approaches for analysing multi-level RNA-seq data.

2017-08-08

Tamas Dalmay

Irina Mohorianu
Amanda Bretman
Damian T Smith
Emily K Fowler
Tracey Chapman

PLOS ONE

Whole transcriptome profiling of taste bud cells.

2017-08-08

Alexander Bachmanov
Sunil K Sukumaran
Robert F. Margolskee

Brian C Lewandowski
Yumei Qin
Ramana Kotha

Scientific Reports

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.

2017-08-08

Nadav Ahituv

Ann H Ryu
Walter L Eckalbar
Anat Kreimer
Nir Yosef

Scientific Reports

Amiloride, An Old Diuretic Drug, Is a Potential Therapeutic Agent for Multiple Myeloma.

2017-08-08

Ramón García-Sanz
Irena Misiewicz-Krzeminska
Enrique M Ocio
Norma C. Gutiérrez

Elizabeta A Rojas
Luis Antonio Corchete
Laura San-Segundo
Juan F Martínez-Blanch
Francisco M Codoñer
Teresa Paíno
Noemí Puig
María Victoria Mateos

Clinical Cancer Research

Modeling Glaucoma: Retinal Ganglion Cells Generated from Induced Pluripotent Stem Cells of Patients with SIX6 Risk Allele Show Developmental Abnormalities.

2017-08-09

Pooja Teotia

Matthew J Van Hook
Christopher S Wichman
R Rand Allingham
Michael A Hauser
Iqbal Ahmad

Stem Cells

Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach.

2017-08-10

Pier Paolo Pandolfi

Kourosh Zarringhalam
Yvonne Tay
Prajna Kulkarni
Assaf C Bester
Rahul V Kulkarni

Scientific Reports

High Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

2017-08-11

Matteo Pellegrini
Manuel Rosa-Garrido
Yibin Wang

Douglas J Chapski
Anthony D Schmitt
Todd H Kimball
Elaheh Karbassi
Emma Monte
Enrique Balderas
Tsai-Ting Shih
Elizabeth Soehalim
Peipei Ping
Niels J Galjart
Shuxun Ren
Bing Ren
Thomas M Vondriska
David Liem

Circulation

Characterization of the human thyroid epigenome.

2017-08-14

Andrew Mungall
Steven Jones

Celia Siu
Sam Michael Wiseman
Sitanshu Gakkhar
Alireza Heravi-Moussavi
Misha Bilenky
Annaick Carles
Thomas Sierocinski
Angela Tam
Eric Yang Zhao
Katayoon Kasaian
Richard A Moore
Blair Walker
Thomas Thomson
Marco A Marra
Martin Hirst

Journal of Endocrinology

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression.

2017-08-14

Josef M Penninger
Christoph Bock
Quanah J Hudson
Tomasz Kuliński

Daniel Andergassen
Christoph P Dotter
Daniel Wenzel
Verena Sigl
Philipp C Bammer
Markus Muckenhuber
Daniela Mayer
Hans-Christian Theussl
Denise P Barlow
Florian M Pauler

eLife

Heart morphogenesis gene regulatory networks revealed by temporal expression analysis.

2017-08-14

Jonathon T Hill

Bradley Demarest
Megan Smith
Bushra Gorsi
H Joseph Yost

Development

Zygotic Genome Activation Occurs Shortly after Fertilization in Maize.

2017-08-16

Nicholas Putz

Junyi Chen
Nadia G Krohn
Philipp Cyprys
Stefanie Sprunck
Julia C Engelmann
Thomas Dresselhaus

The Plant Cell

Detection and removal of barcode swapping in single-cell RNA-seq data

2017-08-16

Aaron Lun

Jonathan A. Griffiths
Arianne C. Richard
Karsten Bach
John C. Marioni

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

2017-08-18

Tapio Lönnberg
Sarah Teichmann
Ashraful Haque

Jessica Engel

Genome Medicine

Itm2a silencing rescues lamin A mediated inhibition of 3T3-L1 adipocyte differentiation.

2017-08-18

Pavel V Baranov

Stephanie J Davies
James Ryan
Patrick B F O'Connor
Elaine Kenny
Derek Morris
Rosemary O'Connor
Tommie V McCarthy

Adipocyte

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers.

2017-08-21

Lisa Putral
Duncan Lambie
Lynlee L Lin
Tarl W. Prow
Ian Frazer

Van L T Hoang
Xiu-Cheng Quek
Jean-Marie Tan
Elizabeth J Payne
Sudipta Sinnya
Anthony P Raphael
Marcel E Dinger
H Peter Soyer

PeerJ

p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics.

2017-08-21

Jacob Stewart-Ornstein

Antonina Hafner
Jeremy E Purvis
William C Forrester
Martha L Bulyk
Galit Lahav

Nature Structural & Molecular Biology

Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network.

2017-08-21

Johanna Rhodes
Katherine J Denby
Richard Hickman
Lotte Caarls

Marcel C Van Verk
Anja J H Van Dijken
Marciel Pereira Mendes
Irene A Vroegop-Vos
Merel Steenbergen
Ivo Van der Nagel
Gert Jan Wesselink
Aleksey Jironkin
Adam Talbot
Michel De Vries
Robert C Schuurink
Corné M J Pieterse
Saskia C M Van Wees

The Plant Cell

Unmasking Transcriptional Heterogeneity in Senescent Cells.

2017-08-21

Victor Guryev

Alejandra Hernandez-Segura
Tristan V de Jong
Simon Melov
Judith Campisi
Marco Demaria

Current Biology

Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation

2017-08-23

Christian Bendixen
Frank Panitz

Andres Chana-Munoz
Agnieszka Jendroszek
Malene Sønnichsen
Rune Kristiansen
Jan K Jensen
Peter A Andreasen

PLOS ONE

Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection.

2017-08-23

Livia Kmetzsch
Patrícia Aline Gröhs Ferrareze
Augusto Schrank
Marilene H Vainstein

Rodrigo Silva Araujo Streit
Patricia Ribeiro Dos Santos
Francine Melise Dos Santos
Rita Maria Cunha de Almeida

Microorganisms

Regulation of a minimal transcriptome by repeat domain proteins.

2017-08-23

Aleksandra Filipovska

Nicola Ferreira
Oliver Rackham

Seminars in Cell & Developmental Biology

New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics.

2017-08-24

Itai Yanai

Maayan Baron

Genome Biology

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.

2017-08-24

Leonardo Collado-Torres
Andrew E Jaffe
Abhinav Nellore

F1000Research

RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines.

2017-08-24

Anna C. Berardi
Annalisa Radeghieri
M Gallorini
Igea D'Agnano
Paolo Bergese

Martina Berardocco
Sara Busatto
Chiara Raggi
Clarissa Gissi
Armando Felsani

Oncotarget

Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing.

2017-08-25

Sean C Daugherty

Anukul T Shenoy
Terry Brissac
Ryan P Gilley
Nikhil Kumar
Yong Wang
Norberto Gonzalez-Juarbe
Whitney S Hinkle
Amol C Shetty
Sandra Ott
Luke J Tallon
Jessy Deshane
Hervé Tettelin
Carlos J Orihuela

PLOS Pathogens

Massively parallel single-nucleus RNA-seq with DroNc-seq.

2017-08-28

Aviv Regev
Kristin Ardlie
Orit Rozenblatt-Rosen

Naomi Habib
Inbal Avraham-Davidi
Anindita Basu
Tyler Burks
Karthik Shekhar
Matan Hofree
Sourav R Choudhury
François Aguet
Ellen Gelfand
David A Weitz
Feng Zhang

Nature Methods

Hypoxia-inducible factor 2α (HIF-2α) promotes colon cancer growth by potentiating Yes-associated protein 1 (YAP1) activity.

2017-08-28

Xiaoya Ma

Huabing Zhang
Xiang Xue
Yatrik M Shah

Journal of Biological Chemistry

Single cell analysis of normal and leukemic hematopoiesis.

2017-08-29

Adam J Mead

Benjamin J Povinelli
Alba Rodriguez-Meira

Molecular Aspects of Medicine

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.

2017-08-30

Julia Ponomarenko
Javier Tapial
Ulrich Braunschweig
Antoni Hermoso
Miguel Manzanares

Kevin C H Ha
Timothy Sterne-Weiler
Andre Gohr
Mathieu Quesnel-Vallières
Jon Permanyer
Reza Sodaei
Yamile Marquez
Luca Cozzuto
Xinchen Wang
Melisa Gómez-Velázquez
Teresa Rayon
Benjamin Blencowe
Manuel Irimia

Genome Research

Functional analysis of a novel, thyroglobulin-embedded microRNA gene deregulated in papillary thyroid carcinoma.

2017-08-30

Krystian Jażdżewski
Barbara Górnicka

Monika Kolanowska
Anna Wójcicka
Anna Kubiak
Michał Świerniak
Marta Kotlarek
Monika Maciąg
Paweł Gaj
Łukasz Koperski

Scientific Reports

Cell-type- and tissue-specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense.

2017-08-30

Jörg Bohlmann

Jose M Celedon
Macaire M S Yuen
Angela Chiang
Hannah Henderson
Karen E Reid

The Plant Journal

Characterization and Genomic Localization of a SMAD4 Processed Pseudogene.

2017-08-31

Julian Weldon Adlard
David T. Bonthron
Ian M. Carr
Alexander Markham

Christopher M Watson
Nick Camm
Laura A Crinnion
Agne Antanaviciute
Ruth Charlton

The Journal of Molecular Diagnostics

Antitumor activity and expression profiles of genes induced by sulforaphane in human melanoma cells.

2017-09-01

Andrea Crisanti

Paola Arcidiacono
Francesco Ragonese
Anna Stabile
Alessandra Pistilli
Ekaterina Kuligina
Mario Rende
Ugo Bottoni
Stefano Calvieri
Roberta Spaccapelo

European Journal of Nutrition

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.

2017-09-01

Paul Klenerman

Shaked Afik
Kathleen B Yates
Kevin Bi
Samuel Darko
Jernej Godec
Ulrike Gerdemann
Leo Swadling
Daniel C Douek
Eleanor J Barnes
Arlene H Sharpe
W Nicholas Haining
Nir Yosef

Nucleic Acids Research

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures.

2017-09-01

Thalia E Chan

Thalia E Chan
Michael P H Stumpf
Ann C Babtie

Cell systems

Thyroid hormone receptor beta and NCOA4 regulate terminal erythrocyte differentiation.

2017-09-01

Harvey Lodish

Xiaofei Gao
Hsiang-Ying Lee
Wenbo Li
Randall Jeffrey Platt
M Inmaculada Barrasa
Qi Ma
Russell R Elmes
Michael G Rosenfeld

Proceedings of the National Academy of Sciences of the United States of America

Single-cell analyses to tailor treatments.

2017-09-01

Alex K. Shalek

Mikael Benson

Science Translational Medicine

Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses.

2017-09-05

Richard Lucius

Totta Ehret
Simone Spork
Christoph Dieterich
Richard Lucius
Emanuel Heitlinger

BMC Genomics

Effects of toxic Microcystis aeruginosa on the silver carp Hypophthalmichtys molitrix revealed by hepatic RNA-seq and miRNA-seq.

2017-09-05

Youji Wang

Menghong Hu
Xiancheng Qu
Lisha Pan
Chunxue Fu
Peixuan Jia
Qigen Liu
Youji Wang

Scientific Reports

Integrative analysis of DNA methylation and mRNA expression during differentiation of umbilical cord blood derived mononuclear cells to endothelial cells.

2017-09-05

Ja-Young Kwon

Yoonjeong Jeong
Yukyung Jun
Jihye Kim
Hyojin Park
Kyu-Sung Choi
Haiying Zhang
Jeong Ae Park
Young-Myeong Kim
Sanghyuk Lee
Young-Guen Kwon

Gene

A protein with an unusually short PPR domain, MEF8, affects editing at over 60 Arabidopsis mitochondrial C targets of RNA editing.

2017-09-05

Maureen R. Hanson

Michael F Diaz
Stephane Bentolila
Michael L Hayes
R Michael Mulligan

The Plant Journal

Assessing the activity of nonsense-mediated mRNA decay in lung cancer.

2017-09-06

Zhenguo Zhang

Meng Wang
Peiwei Zhang
Yufei Zhu
Xiangyin Kong
Landian Hu

BMC Medical Genomics

Toward the human cellular microRNAome.

2017-09-06

Valina L. Dawson
Avi Rosenberg
Marc K. Halushka
Arun H Patil
Min-Sik Kim
Ted M. Dawson

Matthew N McCall
Mohammed Adil
Yin Lu
Christopher J Mitchell
Pamela Leal-Rojas
Jinchong Xu
Manoj Kumar
Alexander S Baras
Dan E Arking
Kathleen H Burns
Akhilesh Pandey

Genome Research

Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.

2017-09-07

Steven Salzberg

Aparna Pallavajjala
Daehwan Kim
Tongbin Li
Gabriel Ghiaur
Richard J Jones
Kathleen H Burns
Yi Ning

Leukemia & Lymphoma

Discovery of Human-Similar Gene Fusions in Canine Cancers.

2017-09-07

Thomas Derrien

Ronan Ulvé
Mélanie Rault
Mathieu Bahin
Laetitia Lagoutte
Jérôme Abadie
Clotilde De Brito
Jean-Michel Coindre
Nadine Botherel
Audrey Rousseau
Valentin Wucher
Edouard Cadieu
Catherine Thieblemont
Christophe Hitte
Laurence Cornevin
Florian Cabillic
Laura Bachelot
David Gilot
Benoit Hennuy
Thierry Guillaudeux
Arnaud Le Goff
Benoît Hédan
Catherine André

Cancer Research

Identification of immunity-related genes in Plutella xylostella in response to fungal peptide destruxin A: RNA-Seq and DGE analysis.

2017-09-08

Muhammad Shakeel

Xiaoxia Xu
Jin Xu
Xun Zhu
Shuzhong Li
Xianqiang Zhou
Jialin Yu
Xiaojing Xu
Qiongbo Hu
Xiaoqiang Yu
Fengliang Jin

Scientific Reports

Genome-wide miRNA response to anacardic acid in breast cancer cells.

2017-09-08

Carolyn M. Klinge

David J Schultz
Penn Muluhngwi
Negin Alizadeh-Rad
Madelyn A Green
Eric C Rouchka
Sabine J Waigel

PLOS ONE

RALE051: a novel established cell line of sporadic Burkitt lymphoma.

2017-09-11

Anna Ferrari
Angelo Lonoce
Alberto L'Abbate
Clelia Tiziana Storlazzi
Elisa Ficarra
Giovanni Martinelli
Ilaria Iacobucci

Antonella Turchiano
Giulia Paciello
Federica Cattina
Enrica Imbrogno
Claudio Agostinelli
Pierluigi Zinzani
Enrico Derenzini

Leukemia & Lymphoma

MAJIQ-SPEL: Web-tool to interrogate classical and complex splicing variations from RNA-Seq data.

2017-09-11

Yoseph Barash

Christopher J Green
Matthew R Gazzara

Bioinformatics

Regulatory network changes between cell lines and their tissues of origin.

2017-09-12

John Quackenbush
Cho-Yi Chen
Abhijeet R Sonawane
Kimberly Glass
John Platig

Camila M Lopes-Ramos
Joseph N Paulson
Marieke L Kuijjer
Maud Fagny
Dawn L DeMeo

BMC Genomics

Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling.

2017-09-12

So Nakagawa

Toshihiro Sakurai
Hanako Bai
Rulan Bai
Kazuya Kusama
Atsushi Ideta
Yoshito Aoyagi
Kazuyuki Kaneko
Kosuke Iga
Jiro Yasuda
Takayuki Miyazawa
Kazuhiko Imakawa

Biochemical Journal

Splatter: simulation of single-cell RNA sequencing data.

2017-09-12

Alicia Oshlack
Luke Zappia
Belinda Phipson

Genome Biology

Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data.

2017-09-12

Qiang Gong
Raul Rabadan

Chao Wang
Weiwei Zhang
Javeed Iqbal
Yang Hu
Timothy C Greiner
Adam Cornish
Jo-Heon Kim
Francesco Abate
Xin Wang
Giorgio G Inghirami
Timothy W McKeithan
Wing C Chan

Scientific Reports

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing.

2017-09-13

Gary M Shaw

Wenying Pan
Thuy T M Ngo
Joan Camunas-Soler
Chun-Xiao Song
Mark Kowarsky
Yair J Blumenfeld
Ronald J Wong
David K Stevenson
Stephen R Quake

Clinical Chemistry

Analysis of the relationship between coexpression domains and chromatin 3D organization.

2017-09-13

José C Reyes

María E Soler-Oliva
José A Guerrero-Martínez
Valentina Bachetti

PLOS Computational Biology

Wounding Triggers Callus Formation via Dynamic Hormonal and Transcriptional Changes.

2017-09-13

Momoko Ikeuchi
Akira Iwase
Hitoshi Sakakibara
Bart Rymen
Shunsuke Watanabe

Alice Lambolez
Mikiko Kojima
Yumiko Takebayashi
Jefri Heyman
Mitsunori Seo
Lieven de Veylder
Keiko Sugimoto

Plant Physiology

Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation.

2017-09-13

Jihong Chen

Munerah Hamed
Saadia Khilji
Katherine Dixon
Alexandre Blais
Ilya Ioshikhes

Nucleic Acids Research

RNA-Seq reveals a central role for lectin, C1q and von Willebrand factor A domains in the defensive glue of a terrestrial slug.

2017-09-13

Christopher W Reid

Andrew M Smith
Cassandra Papaleo
Joseph M Bliss

Biofouling

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

2017-09-14

Alexander Lachmann
Avi Ma'ayan

Denis Torre
Alexandra B. Keenan
Kathleen M. Jagodnik
Hyojin J. Lee
Moshe C. Silverstein
Lily Wang

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

2017-09-15

Mick Watson
Emily L Clark
Chunlei Wu
Stephen J Bush
David A Hume
Alan Archibald
Kim M Summers

Mary E B McCulloch
Iseabail L Farquhar
Rachel Young
Lucas Lefevre
Clare Pridans
Hiu G Tsang
Cyrus Afrasiabi
C Bruce Whitelaw
Tom C Freeman

PLOS Genetics

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.

2017-09-15

Yoseph Barash

Mansi Y Shinde
Simone Sidoli
Katarzyna Kulej
Michael J Mallory
Caleb M Radens
Amanda L Reicherter
Rebecca L Myers
Kristen W Lynch
Benjamin A Garcia
Peter S Klein

Journal of Biological Chemistry

Small RNA-seq during acute maximal exercise reveal RNAs involved in vascular inflammation and cardiometabolic health: brief report.

2017-09-15

Olivia Ziegler

Ravi Shah
Ashish Yeri
Avash Das
Amanda Courtright-Lim
Ernest Gervino
Jeffrey Ocel
Pablo Quintero-Pinzon
Luke Wooster
Cole Shields Bailey
Kahraman Tanriverdi
Lea M Beaulieu
Jane E Freedman
Ionita Ghiran
Gregory D Lewis
Kendall Van Keuren-Jensen
Saumya Das

American Journal of Physiology - Heart and Circulatory Physiology

Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.

2017-09-18

Stuart A Ralph

Lee M Yeoh
Christopher D Goodman
Vanessa Mollard
Geoffrey I McFadden

BMC Genomics

Comparative analysis reveals genomic features of stress-induced transcriptional readthrough.

2017-09-19

Joan A. Steitz

Anna Vilborg
Niv Sabath
Yuval Wiesel
Jenny Nathans
Flonia Levy-Adam
Therese A Yario
Reut Shalgi

Proceedings of the National Academy of Sciences of the United States of America

RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis).

2017-09-20

Herman Silva

Víctor Aballai
Jorge E Aedo
Jonathan Maldonado
Macarena Bastias-Molina
Claudio Meneses
Sebastian Boltaña
Ariel Reyes
Alfredo Molina
Juan Antonio Valdés

Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics

Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists.

2017-09-21

David Roy Smith

Matheus Sanitá Lima

In-depth genetic analysis of sclerosing epithelioid fibrosarcoma reveals recurrent genomic alterations and potential treatment targets.

2017-09-22

Maria Debiec-Rychter
Raf Sciot
Fredrik Mertens

Elsa Arbajian
Florian Puls
Cristina R Antonescu
M Fernanda Amary
Vaiyapuri Sumathi
Marcus Järås
Linda Magnusson
Jenny Nilsson
Jakob Hofvander

Clinical Cancer Research

Two's company: studying interspecies relationships with dual RNA-seq.

2017-09-25

Sascha Brunke

Thomas Wolf
Philipp Kämmer
Jörg Linde

Current Opinion in Microbiology

Global and targeted approaches to single-cell transcriptome characterization.

2017-09-25

Tapio Lönnberg

Aleksandra A Kolodziejczyk

Briefings in functional genomics

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

2017-09-25

Anton J. Enright
Elissavet Kentepozidou
Matthew P Davis
Dimitrios M Vitsios

Leonor Quintais
Elia Benito-Gutiérrez
Stijn van Dongen

Nucleic Acids Research

Super-enhancers promote transcriptional dysregulation in nasopharyngeal carcinoma.

2017-09-26

Ling-Wen Ding

Jiang Yuan
Yan-Yi Jiang
Anand Mayakonda
Moli Huang
Han Lin
Fenggang Yu
Yanan Lu
Thomas Kwok Seng Loh
Marilynn Chow
Samantha L Savage
Jeffrey W Tyner
De-Chen Lin
H Phillip Koeffler

Cancer Research

The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli.

2017-09-27

Irene Wagner-Döbler
Jan P Meier-Kolthoff
Boyke Bunk
Jörg Overmann

Jannik Donner
Michael Reck
Michael Jarek
Constantin Benjamin App
Rolf Müller
Andreas Kirschning
Irene Wagner-Döbler

mSphere

HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data.

2017-09-27

Benjamin G Vincent

Martin L Buchkovich
Chad C Brown
Kimberly Robasky
Shengjie Chai
Sharon Westfall
Eric T Weimer
Jason G Powers

Genome Medicine

ENPP1 Mutation Causes Recessive Cole Disease by Altering Melanogenesis.

2017-09-27

Jianjun Liu

Marwa Chourabi
Mei Shan Liew
Shawn Lim
Dorra H'mida-Ben Brahim
Lobna Boussofara
Liang Dai
Pui Mun Wong
Jia Nee Foo
Badreddine Sriha
Kim Samirah Robinson
Simon Denil
John Ea Common
Ons Mamaï
Youcef Ben Khalifa
Mathieu Bollen
Mohamed Denguezli
Carine Bonnard
Ali Saad
Bruno Reversade

Journal of Investigative Dermatology

Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis.

2017-09-28

Hans Schöler
Juan M. Vaquerizas
Rocio Enriquez-Gasca
Ralf H Adams
Benjamín Hernández-Rodríguez

Hyun-Woo Jeong
JungMo Kim
Kee-Pyo Kim
Juyong Yoon
Susanne Adams

Nature Communications

Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling.

2017-09-29

Homa Rahnamoun
Shannon M Lauberth
Sascha H Duttke
Christopher K Glass

Hanbin Lu
Christopher Benner

Nature Communications

Hexokinases link DJ-1 to the PINK1/parkin pathway.

2017-09-29

David N Hauser
Wolfdieter Springer
Fabienne C. Fiesel
Mark R Cookson

Adamantios Mamais
Melissa M Conti
Christopher T Primiani
Ravindran Kumaran
Allissa A Dillman
Rebekah G Langston
Alexandra Beilina
Joseph H Garcia
Alberto Diaz-Ruiz
Michel Bernier
Xu Hou
Yan Li
Rafael de Cabo

Molecular Neurodegeneration

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation.

2017-09-29

Cristina Ivan
Yoseph Barash

Lauren K Brady
Hejia Wang
Caleb M Radens
Yue Bi
Milan Radovich
Amit Maity
Mircea Ivan
Constantinos Koumenis

PLOS Biology

ASAP: a Web-based platform for the analysis and interactive visualization of single-cell RNA-seq data.

2017-10-01

Vincent Gardeux

Fabrice P A David
Adrian Shajkofci
Petra C Schwalie
Bart Deplancke

Bioinformatics

Epithelial-Cell-Derived Phospholipase A2 Group 1B Is an Endogenous Anthelmintic.

2017-10-01

Lewis J Entwistle
Mariana Silva Dos Santos
Helena Helmby
Lucy Collinson

Victoria S Pelly
Stephanie M Coomes
Yashaswini Kannan
Jimena Perez-Lloret
Stephanie Czieso
James I MacRae
Abdul Sesay
Nikolay Nikolov
Amina Metidji
David Y Hui
Mark S Wilson

Cell Host & Microbe

Adenohypophysis placodal precursors exhibit distinctive features within the rostral preplacodal ectoderm.

2017-10-01

Paola Bovolenta

Luisa Sanchez-Arrones
África Sandonís
Marcos Julián Cardozo

Development

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.

2017-10-01

Anne Goriely
Jingtao Guo

Edward J Grow
Chongil Yi
Hana Mlcochova
Geoffrey J Maher
Cecilia Lindskog
Patrick J Murphy
Candice L Wike
Douglas T Carrell
James M Hotaling
Bradley R Cairns

Cell Stem Cell

Role of the Astroglial Glutamate Exchanger xCT in Ventral Hippocampus in Resilience to Stress.

2017-10-01

Paul Greengard

Carla Nasca
Benedetta Bigio
Danielle Zelli
Paolo de Angelis
Timothy Lau
Masahiro Okamoto
Hideyo Soya
Jason Ni
Lars Brichta
Rachael L Neve
Francis S Lee
Bruce S McEwen

Neuron

Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis.

2017-10-01

Ali Mortazavi

Marissa Macchietto
Dristi Angdembey
Negar Heidarpour
Lorrayne Serra
Bryan Rodriguez
Nicole El-Ali

Genome Biology and Evolution

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma.

2017-10-01

Derek Croote
Steven A. Sloan

Spyros Darmanis
Marco Mignardi
Sophia Chernikova
Peyman Samghababi
Ye Zhang
Norma Neff
Mark Kowarsky
Christine Caneda
Gordon Li
Steven D Chang
Ian David Connolly
Yingmei Li
Ben A Barres
Melanie Hayden Gephart
Stephen R Quake

Cell Reports

Antigen receptor repertoire profiling from RNA-seq data.

2017-10-01

Mikhail Shugay
Dmitriy M. Chudakov
Olga I Zolotareva

Dmitriy A Bolotin
Stanislav Poslavsky
Alexey N Davydov
Felix E Frenkel
Lorenzo Fanchi
Saskia Hemmers
Ekaterina V Putintseva
Anna S Obraztsova
Ravshan I Ataullakhanov
Alexander Y Rudensky
Ton N Schumacher

Nature Biotechnology

Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat.

2017-10-02

Agnelo Furtado
Robert Henry

Ravi C Nirmal
Parimalan Rangan

Scientific Reports

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

2017-10-03

Cho-Yi Chen
John Quackenbush
Abhijeet R Sonawane
Kimberly Glass
John Platig

Joseph N Paulson
Camila M Lopes-Ramos
Marieke L Kuijjer
Maud Fagny

BMC Bioinformatics

XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation.

2017-10-03

Wasim H. Chowdhury

Yuanhang Liu
Ping Wu
Jingqi Zhou
Teresa L Johnson-Pais
Zhao Lai
Ronald Rodriguez
Yidong Chen

BMC Bioinformatics

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.

2017-10-03

Zhandong Liu

Zhongming Zhao
Ken Chen
Yan Guo
Genevera I Allen
Jiajie Zhang
W Jim Zheng
Jianhua Ruan

BMC Genomics

Functional genomics of stromal cells in chronic inflammatory diseases.

2017-10-04

Kamil Slowikowski

Kevin Wei
Michael B Brenner
Soumya Raychaudhuri

Current Opinion in Rheumatology

CRISPR-mediated HDAC2 disruption identifies two distinct classes of target genes in human cells

2017-10-05

Paul S Knoepfler

Priyanka Somanath
Rachel Herndon Klein

PLOS ONE

Johne's disease in cattle: an in vitro model to study early response to infection of Mycobacterium avium subsp. paratuberculosis using RNA-seq.

2017-10-05

Francesco Strozzi
John L. Williams

Rosanna Marino
Rossana Capoferri
Simona Panelli
Giulietta Minozzi
Erminio Trevisi
Gustavo G M Snel
Paolo Ajmone-Marsan

Molecular Immunology

voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data.

2017-10-06

Dincer Goksuluk

Gokmen Zararsiz
Bernd Klaus
Selcuk Korkmaz
Vahap Eldem
Erdem Karabulut
Ahmet Ozturk

PeerJ

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.

2017-10-06

Alessandro Weisz
Luca Ricciardi
Giorgio Giurato
Roberta Tarallo

Giuseppina Bruno
Maria Ravo
Francesca Rizzo
Annamaria Salvati
Giovanna Marchese
Angela Cordella
Teresa Rocco
Valerio Gigantino
Biancamaria Pierri
Giovanni Cimmino
Luciano Milanesi
Concetta Ambrosino
Tuula A Nyman
Giovanni Nassa

Genome Biology

RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking.

2017-10-06

Alejandro Reyes

Margaret M Parker
Robert P Chase
Andrew Lamb
Aabida Saferali
Jeong H Yun
Blanca E Himes
Edwin K Silverman
Craig P Hersh
Peter J Castaldi

BMC Medical Genomics

Mouse embryonic stem cells can differentiate via multiple paths to the same state.

2017-10-09

James Alexander Briggs

Victor C Li
Seungkyu Lee
Clifford J Woolf
Allon Klein
Marc W Kirschner

eLife

Cardiovascular homeostasis dependence on MICU2, a regulatory subunit of the mitochondrial calcium uniporter.

2017-10-09

Kimberli J Kamer
Christine E. Seidman
Daniel M DeLaughter

Alexander G Bick
Hiroko Wakimoto
Yasemin Sancak
Olga Goldberger
Anna Axelsson
Daniel M DeLaughter
Joshua M Gorham
Vamsi K Mootha
J G Seidman

Proceedings of the National Academy of Sciences of the United States of America

SCENIC: single-cell regulatory network inference and clustering.

2017-10-09

Jean-Christophe Marine
J Wouters
Thomas Moerman
Carmen Bravo González-Blas
Gert Hulselmans
Sara Aibar
Jan Aerts

Vân Anh Huynh-Thu
Florian Rambow
Pierre Geurts
Joost van den Oord

Nature Methods

Alcohol feeding in mice promotes colonic hyperpermeability and changes in colonic organoid stem cell fate.

2017-10-09

Hemraj Dodiya
Faraz Bishehsari

Christopher B Forsyth
Maliha Shaikh
Garth Swanson
Robin M Voigt
Peter Wilkinson
Beata Samelco
Shiwen Song
Ali Keshavarzian

Alcoholism: Clinical and Experimental Research

Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages.

2017-10-09

Siyuan Zhan

Wei Zhao
Tianzeng Song
Yao Dong
Jiazhong Guo
Jiaxue Cao
Tao Zhong
Linjie Wang
Li Li
Hongping Zhang

Functional and Integrative Genomics

Identification of circular RNAs in human aortic valves.

2017-10-09

Jun Wang

Jianle Chen
Yun Jiang
Weidong Gu
Buqing Ni
Haoliang Sun
Wanjun Gu
Liang Chen
Yongfeng Shao

Gene

Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq.

2017-10-09

Gerrit Beemster
Bart Cuypers
Kris Laukens
Ronny Blust

Boris V Krivoshiev
Katrien Sprangers
Steven J Husson

Toxicology in Vitro

Molecular architecture underlying fluid absorption by the developing inner ear

2017-10-10

Michael Hoa

Keiji Honda
Sung Huhn Kim
Michael C Kelly
Joseph C Burns
Laura Constance
Xiangming Li
Fei Zhou
Matthew W Kelley
Philine Wangemann
Robert J Morell
Andrew J Griffith

eLife

Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus.

2017-10-10

Jan Strauss
Mark McMullan

Pirita Paajanen
Cock van Oosterhout
Matthew D Clark
Thomas Mock

Scientific Data

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples.

2017-10-10

Zhe-Xue Quan

Yong-Wei Yan
Bin Zou
Ting Zhu
Wael N Hozzein

PLOS ONE

Differential gene regulatory networks in development and disease.

2017-10-10

Arun J Singh
Chrissa Kioussi

Stephen A Ramsey
Theresa M Filtz

Cellular and Molecular Life Sciences

Broad role for YBX1 in defining the small noncoding RNA composition of exosomes.

2017-10-10

Randy Schekman
Matthew J Shurtleff

Jun Yao
Yidan Qin
Ryan M Nottingham
Morayma M Temoche-Diaz
Alan M Lambowitz

Proceedings of the National Academy of Sciences of the United States of America

RNASeq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus type 16 infection, including loss of epithelial barrier function.

2017-10-11

Derek Gatherer

T Klymenko
Q Gu
I Herbert
A Stevenson
V Iliev
G Watkins
C Pollock
R Bhatia
K Cuschieri
P Herzyk
S V Graham

Journal of Virology

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana.

2017-10-11

Xiao-Ning Zhang

Yifei Shi
Jordan J Powers
Nikhil B Gowda
Chong Zhang
Heba M M Ibrahim
Hannah B Ball
Samuel L Chen
Hua Lu
Stephen M Mount

BMC Genomics

Mitochondrial Cardiomyopathy Caused by Elevated Reactive Oxygen Species and Impaired Cardiomyocyte Proliferation.

2017-10-11

Zhiqiang Lin

Donghui Zhang
Yifei Li
Danielle A Heims-Waldron
Vassilios J Bezzerides
Silvia Guatimosim
Yuxuan Guo
Fei Gu
Pingzhu Zhou
Qing Ma
Jianming Liu
Da-Zhi Wang
William T Pu

Circulation Research

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens.

2017-10-12

Oana Ursu
Ernest Fraenkel

Sara J C Gosline
Neil Beeharry
Lauren Fink
Vikram Bhattacharjee
Shao-Shan Carol Huang
Yan Zhou
Tim Yen

PLOS ONE

Antifungal defense of probiotic Lactobacillus rhamnosus GG is mediated by blocking adhesion and nutrient depletion.

2017-10-12

Christina Braunsdorf
Jeanette Wagener

Daniela Mailänder-Sánchez
Christian Grumaz
Christoph Müller
Stefan Lorenz
Philip Stevens
Betty Hebecker
Bernhard Hube
Franz Bracher
Kai Sohn
Martin Schaller

PLOS ONE

Differential regulation of two FLNA transcripts explains some of the phenotypic heterogeneity in the loss-of-function filaminopathies.

2017-10-12

Zandra A Jenkins
Wenhua Wei
David Markie
Stephen Robertson

Alison Macharg
Cheng-Yee Chang
Margriet van Kogelenberg
Tim Morgan
Sophia Frentz
Jacek Pilch
Mark Hannibal
Nicola Foulds
George McGillivray
Richard J Leventer
Sixto García-Miñaúr
Stuart Sugito
Scott Nightingale
Tracy Dudding
Raj P Kapur

Human Mutation

Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis.

2017-10-13

Jinggui Fang

Muhammad Salman Haider
Cheng Zhang
Mahantesh M Kurjogi
Tariq Pervaiz
Ting Zheng
Chaobo Zhang
Chen Lide
Lingfie Shangguan

Scientific Reports

Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis.

2017-10-13

Laurence Florens
Myles Brown
Rosa Yoon
Reety Arora
Alexander J Federation
Peter M Howley

Jingwei Cheng
Donglim Esther Park
Christian Berrios
Elizabeth A White
Timothy Branigan
Tengfei Xiao
Thomas Westerling
Rhamy Zeid
Benjamin Strober
Selene K Swanson
James E Bradner
Megha Padi
Michael P Washburn
James A DeCaprio

PLOS Pathogens

Comparing two approaches of miR-34a target identification, biotinylated-miRNA pulldown vs miRNA overexpression.

2017-10-13

Ge Shan

Hassaan Mehboob Awan
Abdullah Shah
Farooq Rashid
Shuai Wei
Liang Chen

RNA Biology

Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells.

2017-10-13

Ning-Yi Shao

Mingtao Zhao
Shijun Hu
Ning Ma
Rajini Srinivasan
Fereshteh Jahanbani
Jaecheol Lee
Sophia L Zhang
Michael P Snyder
Joseph C Wu

Circulation Research

MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach.

2017-10-16

Chia-Lang Hsu
Hsuan-Cheng Huang
Hsueh-Fen Juan

Chantal Hoi Yin Cheung
Kai-Pu Chen
Siao-Ting Chong
Chang-Hsun Wu

Scientific Reports

A root-knot nematode small glycine and cysteine-rich secreted effector, MiSGCR1, is involved in plant parasitism.

2017-10-16

Bruno Favery

Chinh-Nghia Nguyen
Laetitia Perfus-Barbeoch
Michaël Quentin
Jianlong Zhao
Marc Magliano
Nathalie Marteu
Martine Da Rocha
Nicolas Nottet
Pierre Abad

New Phytologist

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.

2017-10-17

Dan Nettleton

Hung-Ying Lin
Qiang Liu
Xiao Li
Jinliang Yang
Sanzhen Liu
Yinlian Huang
Michael J Scanlon
Patrick S Schnable

Genome Biology

An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta

2017-10-17

Xiaolong Cao
Haobo Jiang

BMC Genomics

Characterization of amylolytic enzyme overproducing mutant of Aspergillus luchuensis obtained by ion beam mutagenesis.

2017-10-17

Taiki Futagami

Toshihiro Kojo
Chihiro Kadooka
Marisa Komohara
Shiori Onitsuka
Miya Tanimura
Yukiko Muroi
Shugo Kurazono
Yohei Shiraishi
Ken Oda
Kazuhiro Iwashita
Masahira Onoue
Kayu Okutsu
Yumiko Yoshizaki
Kazunori Takamine
Kazuki Mori
Hisanori Tamaki

The Journal of General and Applied Microbiology

Genome-Wide Analysis of the Transcription Start Sites and Promoter Motifs of Phytoplasmas.

2017-10-17

Yutaro Neriya

Takamichi Nijo
Hiroaki Koinuma
Nozomu Iwabuchi
Yugo Kitazawa
Kazuyuki Tanno
Yukari Okano
Kensaku Maejima
Yasuyuki Yamaji
Kenro Oshima
Shigetou Namba

DNA and Cell Biology

Simultaneous RNA-seq based transcriptional profiling of intracellular Brucella abortus and B. abortus-infected murine macrophages.

2017-10-17

Wongi Min

Huynh Tan Hop
Lauren Togonon Arayan
Alisha Wehdnesday Bernardo Reyes
Tran Xuan Ngoc Huy
Hu Jang Lee
Jee Soo Son
Suk Kim

Microbial Pathogenesis

The antibody repertoire of colorectal cancer.

2017-10-18

Seong Won Cha
Vineet Bafna

Stefano Bonissone
Seungjin Na
Pavel A Pevzner

Molecular & Cellular Proteomics

MicroRNA profiling of human primary macrophages exposed to dengue virus identifies miRNA-3614-5p as antiviral and regulator of ADAR1 expression.

2017-10-18

Mayra Diosa-Toro
Silvio Urcuqui-Inchima

Liliana Echavarría-Consuegra
Jacky Flipse
Geysson Javier Fernández
Joost Kluiver
Anke van den Berg
Jolanda M Smit

PLOS Neglected Tropical Diseases

Tomato CRY1a plays a critical role in the regulation of phytohormone homeostasis, plant development and carotenoid metabolism in fruits.

2017-10-18

Golam Jalal Ahammed

Chao-Chao Liu
Guo-Ting Wang
Chang-Jie Xu
Kun-Song Chen
Yan-Hong Zhou
Jing-Quan Yu

Plant, Cell and Environment

The Impacts of Genome-wide Analyses on our Understanding of Human Herpesvirus Diversity and Evolution.

2017-10-18
2018-01-01

Moriah L. Szpara

Daniel W Renner

Journal of Virology

Comparative transcriptome analysis reveals multiple functions for Mhy1p in lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica.

2017-10-18

Guangyuan Wang

Delong Li
Zhengang Miao
Shanshan Zhang
Wenxing Liang
Lin Liu

Biochimica et Biophysica Acta

Lipoprotein lipase reaches the capillary lumen in chickens despite an apparent absence of GPIHBP1.

2017-10-19

Haibo Jiang
André Bensadoun

Cuiwen He
Xuchen Hu
Rachel S Jung
Mikael Larsson
Yiping Tu
Sandra Duarte-Vogel
Paul Kim
Norma P Sandoval
Tara R Price
Christopher M Allan
Brian Raney
Rosemary L Walzem
Richard I Kuo
Anne P Beigneux
Loren G Fong
Stephen G Young

JCI insight

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium.

2017-10-19

Gina Chaput

Roberto Orellana
Lye Meng Markillie
Hugh Mitchell
Matt Gaffrey
Galya Orr
Kristen M DeAngelis

PLOS ONE

The type II transmembrane serine protease matriptase cleaves the amyloid precursor protein and reduces its processing to β amyloid.

2017-10-20

François Béliveau

Erwan Lanchec
Antoine Désilets
Anthony Flamier
Shaimaa Mahmoud
Gilbert Bernier
Denis Gris
Richard Leduc
Christine Lavoie

Journal of Biological Chemistry

Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease.

2017-10-23

Timothy J Vyse

Christopher A Odhams
Deborah S Cunninghame Graham

PLOS Genetics

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa).

2017-10-23

Aureliano Bombarely

José F Sánchez-Sevilla
José G Vallarino
Sonia Osorio
David Posé
Catharina Merchante
Miguel A Botella
Iraida Amaya
Victoriano Valpuesta

Scientific Reports

Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues.

2017-10-23

Andrew A Brown
Kerrin S. Small
Ana Viñuela

Olivier Delaneau
Tim D Spector
Emmanouil T Dermitzakis

Nature Genetics

Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research.

2017-10-23
2018-03-01

Wolfgang Sadee

Ana Caroline C Sá
Julie A Johnson

Clinical and Translational Science

Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle.

2017-10-24

Eduardo E. Zattara

Anna L M Macagno
Hannah A Busey
Armin P Moczek

Proceedings of the National Academy of Sciences of the United States of America

Neuromedin B expression defines the mouse retrotrapezoid nucleus.

2017-10-24

Suna Onengut-Gumuscu
Douglas A Bayliss
Patrice G Guyenet
Ruth L Stornetta

Yingtang Shi
Daniel S Stornetta
Emily A Farber
Stephen D Turner

Journal of Neuroscience

FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data.

2017-10-24

David P Leader

Sue A Krause
Aniruddha Pandit
Shireen A Davies
Julian A T Dow

Nucleic Acids Research

An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum.

2017-10-25

Xue Yan Yam
Mats Wahlgren

Rafael M Martins
Cameron R Macpherson
Aurélie Claes
Christine Scheidig-Benatar
Hiroshi Sakamoto
Peter Preiser
Suchi Goel
Odile Sismeiro
Jean-Yves Coppée
Artur Scherf

Scientific Reports

Efficient protein production by yeast requires global tuning of metabolism.

2017-10-25

Jens Nielsen
Jichen Bao

Mingtao Huang
Björn M Hallström
Dina Petranovic

Nature Communications

A review of genome-wide transcriptomics studies in Parkinson's disease.

2017-10-25

Soraya Seedat
Helena Kuivaniemi

Genevie Borrageiro
William Haylett
Soraya Bardien

European Journal of Neuroscience

Single-cell analysis identifies cellular markers of the HIV permissive cell.

2017-10-26

Sylvie Rato
Antonio Rausell
Angela Ciuffi

Miguel Muñoz
Amalio Telenti

PLOS Pathogens

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses.

2017-10-27

Joseph L Costello
Graham D. Pavitt

Christopher J Kershaw
Lydia M Castelli
David Talavera
William Rowe
Paul F G Sims
Mark P Ashe
Christopher M Grant
Simon J Hubbard

Genome Biology

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.

2017-10-27

Zhifu Sun

Asha Nair
Xianfeng Chen
Naresh Prodduturi
Junwen Wang
Jean-Pierre Kocher

Scientific Reports

Variant calling from RNA-seq data of the brain transcriptome of pigs and its application for allele-specific expression and imprinting analysis.

2017-10-27

Katarzyna Piórkowska
Maria Oczkowicz
Katarzyna Ropka-Molik

Tomasz Szmatoła

Gene

Bilin-dependent photoacclimation in Chlamydomonas reinhardtii.

2017-10-30

Sabeeha Merchant

Tyler M Wittkopp
Stefan Schmollinger
Shai I Saroussi
Wei Hu
Weiqing Zhang
Qiuling Fan
Sean D Gallaher
Michael T Leonard
Eric Soubeyrand
Gilles Basset
Arthur R Grossman
Deqiang Duanmu
J Clark Lagarias

The Plant Cell

Alterations in the host transcriptome in vitro following Rift Valley fever virus infection.

2017-10-30

Gustavo Palacios
Brett Beitzel
Aura Garrison

Chelsea Pinkham
Bibha Dahal
Cynthia L de la Fuente
Nicole Bracci
Michael Lindquist
Connie Schmaljohn
Aarthi Narayanan
Catherine E Campbell
Kylene Kehn-Hall

Scientific Reports

Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females.

2017-10-31

Simon J. Cockell

Louise I Pease
Peter D Clegg
Carole J Proctor
Daryl J Shanley
Mandy J Peffers

Scientific Reports

The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy.

2017-10-31

Brad R. Weeks

Canaan M Whitfield-Cargile
Kejun He
Ivan Ivanov
Jennifer S Goldsby
Ana Chamoun-Emanuelli
Laurie A Davidson
Robert S Chapkin

Scientific Reports

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

2017-11-01

Lennart Martens

Matthew C Chambers
Pratik D Jagtap
James E Johnson
Thomas McGowan
Praveen Kumar
Getiria Onsongo
Candace R Guerrero
Harald Barsnes
Marc Vaudel
Björn Grüning
Ira R Cooke
Mohammad Heydarian
Karen L Reddy
Timothy J Griffin

Cancer Research

MicroRNAs promote skeletal muscle differentiation of mesodermal iPSC-derived progenitors.

2017-11-01

Maurilio Sampaolesi
Hanne Grosemans

Giorgia Giacomazzi
Bryan Holvoet
Sander Trenson
Ellen Caluwé
Bojana Kravic
Álvaro Cortés-Calabuig
Christophe M Deroose
Stefan Janssens
Elizabeth McNally
Mattia Quattrocelli

Nature Communications

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.

2017-11-01

Aviv Regev
Nenad Sestan

Joseph R Ecker
Daniel H Geschwind
Arnold R Kriegstein
John Ngai
Pavel Osten
Damon Polioudakis
Nenad Sestan
Ian R Wickersham
Hongkui Zeng

Neuron

Guidelines for Genome-Scale Analysis of Biological Rhythms.

2017-11-01

Frédéric Gachon
Han Wang
Maria Olmedo
Pål O. Westermark
Dmitri A. Nusinow
Herman Wijnen
E Nagoshi
Charissa de Bekker
Debra J. Skene
Aziz Sancar
Eric E. Zhang
Paolo Sassone-Corsi
Francis J. Doyle III
Pierre Baldi
Kristin Eckel-Mahan
Martha Merrow

Michael E Hughes
Katherine C Abruzzi
Ravi Allada
Ron Anafi
Alaaddin Bulak Arpat
Gad Asher
Deborah Bell-Pedersen
Justin Blau
Steve Brown
M Fernanda Ceriani
Zheng Chen
Joanna C Chiu
Juergen Cox
Alexander M Crowell
Jason P DeBruyne
Luciano DiTacchio
Giles E Duffield
Jay C Dunlap
Karyn A Esser
Garret A FitzGerald
Daniel B Forger
Lauren J Francey
Ying-Hui Fu
Paul de Goede
Susan S Golden
Carla Green
John Harer
Stacey Harmer
Jeff Haspel
Michael H Hastings
Hanspeter Herzel
Erik D Herzog
Christy Hoffmann
Christian Hong
Jacob J Hughey
Jennifer M Hurley
Horacio O de la Iglesia
Carl Johnson
Steve A Kay
Nobuya Koike
Karl Kornacker
Achim Kramer
Katja Lamia
Tanya Leise
Scott A Lewis
Jiajia Li
Xiaodong Li
Andrew C Liu
Jennifer J Loros
Tami A Martino
Jerome S Menet
Andrew J Millar
Todd Mockler
Felix Naef
Michael N Nitabach
Louis J Ptáček
David Rand
Akhilesh B Reddy
Maria S Robles
Till Roenneberg
Michael Rosbash
Marc D Ruben
Samuel S C Rund
Amita Sehgal
Scott Sherrill-Mix
Kai-Florian Storch
Joseph S Takahashi
Hiroki R Ueda
Charles Weitz
Ying Xu
Gang Wu
Seung-Hee Yoo
Michael Young
Tomasz Zielinski
John B Hogenesch

Journal of Biological Rhythms

RNA-sequencing-based comparative analysis of human hepatic progenitor cells and their niche from alcoholic steatohepatitis livers.

2017-11-02

Matthias Van Haele
Olivier Govaere
Juan-Jose Ventura
Leo A van Grunsven

An Ceulemans
Stefaan Verhulst
Tania Roskams

Cell Death and Disease

RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole.

2017-11-03

Johan Höglund

Mihaela M Martis
Behdad Tarbiat
Eva Tydén
Désirée S Jansson

PLOS ONE

Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.

2017-11-03

Jörn Kalinowski

Luciana Fernandes Brito
Marta Irla
Volker F Wendisch

BMC Genomics

A survey of software tools for microRNA discovery and characterization using RNA-seq.

2017-11-06

Stefania Bortoluzzi
Enrico Gaffo

Michele Bortolomeazzi

Briefings in Bioinformatics

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature.

2017-11-06

Stephen P Cohen
Jan E Leach
Andy Pereira

Hongxia Liu
Cristiana T Argueso
Casiana Vera Cruz
Valerie Verdier

PLOS ONE

A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA-Seq.

2017-11-06

Andrew B. Barron

Xu-Jiang He
Wu-Jun Jiang
Mi Zhou
Zhi-Jiang Zeng

Insect Science

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

2017-11-07

Oliver Stegle
Davis J McCarthy
John C Marioni

Florian Buettner
Naruemon Pratanwanich

Genome Biology

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut.

2017-11-07

Ken S. Lau

Charles A Herring
Amrita Banerjee
Eliot T McKinley
Alan J Simmons
Jie Ping
Joseph T Roland
Jeffrey L Franklin
Qi Liu
Michael J Gerdes
Robert J Coffey

Cell systems

bcbioRNASeq: R package for bcbio RNA-seq analysis

2017-11-08

Michael J Steinbaugh

Lorena Pantano
Rory D. Kirchner
Victor Barrera
Brad A. Chapman
Mary E. Piper
Meeta Mistry
Radhika S. Khetani
Kayleigh D. Rutherford
Oliver Hofmann
John N. Hutchinson
Shannan Ho Sui

F1000Research

Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis.

2017-11-10

Deyou Zheng
Dejian Zhao

Mingyan Lin
Erika Pedrosa
Herbert M Lachman

BMC Genomics

A transcriptomic study of myogenic differentiation under the overexpression of PPARγ by RNA-Seq.

2017-11-10

Wen-Xing Li

Kan He
Guoying Wu
Daogang Guan
Wenwen Lv
Mengting Gong
Shoudong Ye
Aiping Lu

Scientific Reports

Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study.

2017-11-13

Tyler Alioto
Alberto Cuesta
Anna Esteve-Codina

Elena Chaves-Pozo
Yulema Valero
Jèssica Gómez-Garrido
Marc Dabad
José Meseguer
M Ángeles Esteban

Scientific Reports

Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence.

2017-11-14

Nadine Martin
Wolf Reik

Marieke Aarts
Athena Georgilis
Meryam Beniazza
Patrizia Beolchi
Ana Banito
Thomas Carroll
Marizela Kulisic
Daniel F Kaemena
Gopuraja Dharmalingam
Johannes Zuber
Keisuke Kaji
Tamir Chandra
Jesús Gil

Genes & Development

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

2017-11-14

Michael Han
Jens Keilwagen

Frank Hartung
Sven O. Twardziok
Jan Grau

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

2017-11-14

Fabian J. Theis

David S. Fischer
Anna K. Fiedler
Eric Kernfeld
Ryan M. J. Genga
Jan Hasenauer
Rene Maehr

The fractured landscape of RNA-seq alignment: The default in our STARs

2017-11-16

Sara Ballouz
Jesse Gillis

Alexander Dobin
Thomas R Gingeras

Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage.

2017-11-18

Felipe Klein Ricachenevsky
Janette Palma Fett
Rinaldo Pires Dos Santos

Raul Antonio Sperotto
Artur Teixeira de Araújo Junior
Janete Mariza Adamski
Denise Cargnelutti
Ben-Hur Neves de Oliveira
Renata Pereira da Cruz
Leila Picolli da Silva

Plant Cell Reports

RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum.

2017-11-21

Willem van Schaik
Tomasz K Prajsnar

Xinglin Zhang
Vincent de Maat
Ana M Guzmán Prieto
Jumamurat R Bayjanov
Mark de Been
Malbert R C Rogers
Marc J M Bonten
Stéphane Mesnage
Rob J L Willems

BMC Genomics

Oregano dietary supplementation modifies the liver transcriptome profile in broilers: RNASeq analysis.

2017-11-21

Camillo Pieramati
Stefano Capomaccio

Marcella Sabino
Katia Cappelli
Andrea Verini-Supplizi
Lorenzo Bomba
Paolo Ajmone-Marsan
Gabriella Cobellis
Oliviero Olivieri
Massimo Trabalza-Marinucci

Research in Veterinary Science

A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL.

2017-11-23

Meixue Zhou
Sergey Shabala

Ahsan Habib
Jonathan J Powell
Jiri Stiller
Miao Liu
Donald M Gardiner
Chunji Liu

Theoretical and Applied Genetics

Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation.

2017-11-24

Elie Maza
Nathalie Gonzalez
Chris Bowler

Julien Pirrello
Cynthia Deluche
Nathalie Frangne
Frédéric Gévaudant
Anis Djari
Mickaël Bourge
Jean-Pierre Renaudin
Spencer Brown
Mohamed Zouine
Christian Chevalier

The Plant Journal

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

2017-11-25

Antonio Scialdone
John C Marioni
Jonathan A Griffiths

BMC Genomics

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

2017-11-27

Ruolin Liu
Julie Dickerson

PLOS Computational Biology

STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.

2017-11-27

Jaromír Mikes
Peter Lönnerberg
Sten Linnarsson

Hannah Hochgerner
Rebecca Hodge
Abeer Heskol
Hermann Hubschle
Philip Lin
Simone Picelli
Gioele La Manno
Michael Ratz
Jude Dunne
Syed Husain
Ed Lein
Maithreyan Srinivasan
Amit Zeisel

Scientific Reports

Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri.

2017-11-28

Armin Hallmann

Benjamin Klein
Daniel Wibberg

BMC Biology

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model.

2017-11-28

Delphine Duprez
Sigmar Stricker
Marvin Martens

Mickael Orgeur
Stefan T Börno
Bernd Timmermann

Biology Open

Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq).

2017-12-01

Jan Oppelt

M Slany
L Cincarova

Applied and Environmental Microbiology

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population.

2017-12-05

Harm Nijveen
Wilco Ligterink

Elise A R Serin
L B Snoek
Leo A J Willems
Jose M Jiménez-Gómez
Henk W M Hilhorst

Frontiers in Genetics

A RNA-Seq Analysis of the Response of Photosynthetic System to Low Nitrogen Supply in Maize Leaf.

2017-12-05

Lixing Yuan

Xiaohuan Mu
Qinwu Chen
Fanjun Chen
Guohua Mi

International Journal of Molecular Sciences

Telomere heterogeneity linked to metabolism and pluripotency state revealed by simultaneous analysis of telomere length and RNA-seq in the same human embryonic stem cell.

2017-12-08

Yu Sun

Hua Wang
Kunshan Zhang
Yifei Liu
Yudong Fu
Shan Gao
Peng Gong
Haiying Wang
Zhongcheng Zhou
Ming Zeng
Zhenfeng Wu
Tong Chen
Siguang Li
Lin Liu

BMC Biology

Optimizing RNA-seq studies to investigate herbicide resistance.

2017-12-09

Patrick J. Tranel

Darci A Giacomini
Todd Gaines
Roland Beffa

Pest Management Science

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.

2017-12-11

Yoseph Barash

Scott Norton
Jorge Vaquero-Garcia
Nicholas F Lahens
Gregory R Grant

Bioinformatics

DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification.

2017-12-11

Luca Piacentini
Gualtiero I Colombo

Mattia Chiesa

Bioinformatics

netSmooth: Network-smoothing based imputation for single cell RNA-seq

2017-12-13

Altuna Akalin

Jonathan Ronen

The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis.

2017-12-15

Filip Van Nieuwerburgh
Dieter Deforce
Laurentijn Tilleman
Peter Vandamme

Diana A Aguilar-Ayala
Juan Carlos Palomino
Jorge A Gonzalez-Y-Merchand
Anandi Martin

Scientific Reports

Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.

2017-12-15

Xuhua Xia
Yulong Wei

Jordan R Silke

Scientific Reports

High-Throughput RNA-Seq Data Analysis of the Single Nucleotide Polymorphisms (SNPs) and Zygomorphic Flower Development in Pea (Pisum sativum L.).

2017-12-20

Shihao Su

Keyuan Jiao
Xin Li
Wuxiu Guo
Da Luo

International Journal of Molecular Sciences

RNA-Seq differential expression analysis: An extended review and a software tool.

2017-12-21

Fabrício M Lopes
Douglas Domingues

Juliana Costa-Silva

PLOS ONE

RNA-seq identifies a diminished differentiation gene signature in primary monolayer keratinocytes grown from lesional and uninvolved psoriatic skin.

2017-12-22

William R Swindell
Mrinal K. Sarkar

Yun Liang
Xianying Xing
Jaymie Baliwag
James T Elder
Andrew Johnston
Nicole L Ward
Johann E Gudjonsson

Scientific Reports

SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations

2017-12-24

Molly Hammell

Yu-Jui Ho
Naishitha Anaparthy
David Molik
Toby Aicher
Ami Patel
James Hicks

Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals multiple levels of regulation in phytoplasma-infected Ziziphus jujuba Mill.

2017-12-27

Jiancan Feng

Xia Ye
Huiyu Wang
Peng Chen
Bing Fu
Mengyang Zhang
Jidong Li
Xianbo Zheng
Bin Tan

Horticulture research

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

2017-12-28

Daniel Gautheret
Mélina Gallopin

Jérôme Audoux
Nicolas Philippe
Rayan Chikhi
Mikaël Salson
Mélina Gallopin
Marc Gabriel
Jérémy Le Coz
Emilie Drouineau
Thérèse Commes

Genome Biology

A systematic performance evaluation of clustering methods for single-cell RNA-seq data

2018

Charlotte Soneson
Mark D. Robinson

Angelo Duò

F1000Research

Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) inferred from RNA-Seq data

2018

Kazuo Ishii
Tomoko Matsuda

Toshinori Kozaki
Tetsuo Gotoh

PLOS ONE

Transcriptomics and RNA-Seq Data Analysis

2018

Xuhua Xia

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses () and Cattle ()

2018

Carolina N Correia
Stephen V. Gordon

Kirsten E McLoughlin
Nicolas C Nalpas
David A Magee
John A Browne
Kevin Rue-Albrecht
David E MacHugh

Frontiers in Genetics

Using Supervised Learning Methods for Gene Selection in RNA-Seq Case-Control Studies

2018

Stephane Wenric

Ruhollah Shemirani

Frontiers in Genetics

Clinical significance and effect of MTDH/AEG-1 in bladder urothelial cancer: a study based on immunohistochemistry, RNA-seq, and in vitro verification

2018

Gang Chen

Yu Zhang
Li-Jie Zhang
Yi-Wu Dang
Sheng-Hua Li
Hai-Biao Yan

Cancer Management and Research

Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase ( )

2018

Christophe D Chabbert
Tanja Eberhart
Werner J Kovacs

Ilaria Guccini
Wilhelm Krek

F1000Research

Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.

2018-01-01

Ben Langmead
Abhinav Nellore

Christopher Wilks
Phani Gaddipati

Bioinformatics

Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap.

2018-01-01

Aristeidis G Telonis
Isidore Rigoutsos

Phillipe Loher

Methods in Molecular Biology

Brachypodium distachyon Long Noncoding RNAs: Genome-Wide Identification and Expression Analysis.

2018-01-01

Edoardo Bertolini

Concetta De Quattro
Erica Mica
Mario Enrico Pè

Methods in Molecular Biology

Preparing cDNA Libraries from Lytic Phage-Infected Cells for Whole Transcriptome Analysis by RNA-Seq.

2018-01-01

Bob G Blasdel

Pieter-Jan Ceyssens
Rob Lavigne

Methods in Molecular Biology

A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond.

2018-01-01

Benjamin J Lang

Kristina M Holton
Jianlin Gong
Stuart K Calderwood

Methods in Molecular Biology

Application of RNA-seq and Bioimaging Methods to Study Microbe-Microbe Interactions and Their Effects on Biofilm Formation and Gene Expression.

2018-01-01

Lars Jelsbak
Claus Sternberg

Cristina Isabel Amador

Methods in Molecular Biology

Laser Capture Microdissection-Based RNA-Seq of Barley Grain Tissues.

2018-01-01

Martin Mascher

Ronny Brandt
Johannes Thiel

Methods in Molecular Biology

Genome-Wide circRNA Profiling from RNA-seq Data.

2018-01-01

Pedro Miura

Daphne A Cooper
Mariela Cortés-López

Methods in Molecular Biology

RNA-Seq Analysis of the Transcriptome of Leaf Senescence in Tobacco.

2018-01-01

Yongfeng Guo

Wei Li

Methods in Molecular Biology

netSmooth: Network-smoothing based imputation for single cell RNA-seq.

2018-01-03

Altuna Akalin

Jonathan Ronen

F1000Research

RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.

2018-01-06

Tino Polen
Björn Usadel
Michael Bott
Jörn Kalinowski

Angela Kranz
Tobias Busche
Alexander Vogel

BMC Genomics

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs.

2018-01-11

Yuliaxis Ramayo-Caldas
Klaus Wimmers
David Torrallardona

Maria Ballester
Juan Pablo Sánchez
Olga González-Rodríguez
Manuel Revilla
Henry Reyer
Raquel Quintanilla

Scientific Reports

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review.

2018-01-15

Gokhlesh Kumar

Arun Sudhagar
Mansour El-Matbouli

International Journal of Molecular Sciences

A general and flexible method for signal extraction from single-cell RNA-seq data.

2018-01-18

Jean-Philippe Vert

Davide Risso
Fanny Perraudeau
Svetlana Gribkova
Sandrine Dudoit

Nature Communications

Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications

2018-01-18

Charlotte Soneson
Michael I Love
Mark D. Robinson
Jean-Philippe Vert

Koen Van den Berge
Fanny Perraudeau
Davide Risso
Sandrine Dudoit
Lieven Clement

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii.

2018-01-23

Wangzhen Guo

Guozhong Zhu
Weixi Li
Feng Zhang

BMC Genomics

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq.

2018-01-25

Xiaonan Wang

Fabienne Lescroart
Xionghui Lin
Benjamin Swedlund
Souhir Gargouri
Adriana Sànchez-Dànes
Victoria Moignard
Christine Dubois
Catherine Paulissen
Sarah Kinston
Cédric Blanpain

Science

Identification and visualisation of differential isoform expression in RNA-seq time series.

2018-02-01

Cristina Martí

María José Nueda
Jordi Martorell-Marugan
Sonia Tarazona
Ana Conesa

Bioinformatics

RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment.

2018-02-08

Hung-Pin Tu

Kuo-Hua Lin
Ming-Yii Huang
Wei-Chung Cheng
Shu-Chi Wang
Shih-Hua Fang
Chia-Cheng Su
Yung-Li Hung
Po-Len Liu
Chi-Shuo Chen
Yu-Ting Wang
Chia-Yang Li

Scientific Reports

RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites.

2018-02-09

Christoph Lippuner
Walter Basso
Nicholas C Smith
Peter Deplazes

Chandra Ramakrishnan
Marc W Schmid
Michal Okoniewski
Michael Hässig
Adrian B Hehl

International Journal for Parasitology

De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq.

2018-02-09

Min Du

Na Li
Baozhen Niu
Yanhong Liu
Dongjing You
Defu Jiang
Congquan Ruan
Zhengquan Qin
Taowen Song
Wentao Wang

PLOS ONE

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data.

2018-02-14

Qian Zhou

Xiaoquan Su
Gongchao Jing
Songlin Chen
Kang Ning

BMC Genomics

Oasis 2: improved online analysis of small RNA-seq data.

2018-02-14

Stefan Bonn

Raza-Ur Rahman
Abhivyakti Gautam
Jörn Bethune
Abdul Sattar
Maksims Fiosins
Daniel Sumner Magruder
Vincenzo Capece
Orr Shomroni

BMC Bioinformatics

RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer.

2018-02-14

Zonggao Shi

Chunyan Li
Laura Tarwater
Jun Li
Yang Li
William Kaliney
Darshan S Chandrashekar
M Sharon Stack

Journal of oncology

Mixed-species RNAseq analysis of human lymphoma cells adhering to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of mantle cell lymphoma and chronic lymphocytic leukemia patien

2018-02-15

Johan Henriksson

Gustav Arvidsson
Birgitta Sander
Anthony P Wright

Haematologica

Machine learning integration of rheumatoid arthritis synovial histology and RNAseq data identifies three disease subtypes.

2018-02-22

Dana E Orange

Phaedra Agius
Edward F DiCarlo
Nicolas Robine
Heather Geiger
Jackie Szymonifka
Michael McNamara
Ryan Cummings
Kathleen M Andersen
Serene Mirza
Mark Figgie
Lionel Ivashkiv
Alessandra B Pernis
Caroline Jiang
Mayu Frank
Robert Darnell
Nithya Lingampali
Robinson William
Ellen Gravallese
Vivian P Bykerk
Susan M Goodman
Laura T Donlin
Accelerating Medicine Partnership: RA/SLE Network

Arthritis & Rheumatology

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data

2018-02-22

Lukas Simon
Fabian J. Theis

Sebastian Karg
Alexander J Westermann
Marion Engel
Ali HA Elbehery
Burkhard Hense
Matthias Heinig
Li Deng

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.

2018-02-23

Harold Swerdlow
Andrew Butler
Lionel B Ivashkiv
William Stephenson

Laura T Donlin
Cristina Rozo
Bernadette Bracken
Ali Rashidfarrokhi
Susan M Goodman
Vivian P Bykerk
Dana E Orange
Robert B Darnell
Rahul Satija

Nature Communications

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

2018-02-26

Koen Van den Berge

Fanny Perraudeau
Charlotte Soneson
Michael I Love
Davide Risso
Jean-Philippe Vert
Mark D Robinson
Sandrine Dudoit
Lieven Clement

Genome Biology

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

2018-03-01

Raffaele A. Calogero
Marco Beccuti

Francesca Cordero
Maddalena Arigoni
Riccardo Panero
Elvio G Amparore
Susanna Donatelli

Bioinformatics

First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data.

2018-03-01

Christian R. Voolstra
Jan D Brüwer

PeerJ

Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease.

2018-03-01

A Jennifer Morton

Paul W Hook
Sarah A McClymont
Gabrielle H Cannon
William D Law
Loyal A Goff
Andrew S McCallion

American Journal of Human Genetics

Exponential scaling of single-cell RNA-seq in the past decade

2018-03-01

Valentine Svensson
Sarah Teichmann

Roser Vento-Tormo

Nature Protocols

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients.

2018-03-06

Marta Seco-Cervera
José Luis García-giménez

Dayme González-Rodríguez
José Santiago Ibáñez-Cabellos
Lorena Peiró-Chova
Federico V Pallardó

Scientific Data

An accurate and robust imputation method scImpute for single-cell RNA-seq data.

2018-03-08

Jingyi Jessica Li
Wei Vivian Li

Nature Communications

Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq.

2018-03-09

Aviv Regev

Shristi Pandey
Karthik Shekhar
Alexander F Schier

Current Biology

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis.

2018-03-15

Ehsan Vafadarnejad
Panagiota Arampatzi
Antoine-Emmanuel Saliba
Dennis Wolf
Alma Zernecke

Clément Cochain
Pelisek Jaroslav
Holger Winkels
Klaus Ley

Circulation Research

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.

2018-03-20

Jens Wrammert
Colin Havenar-Daughton

Amit A Upadhyay
Robert C Kauffman
Amber N Wolabaugh
Alice Cho
Nirav B Patel
Samantha M Reiss
Reem A Dawoud
Gregory K Tharp
Iñaki Sanz
Bali Pulendran
Shane Crotty
F Eun-Hyung Lee
Steven E Bosinger

Genome Medicine

Author Correction: UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.

2018-03-20

Zhifu Sun

Asha Nair
Xianfeng Chen
Naresh Prodduturi
Junwen Wang
Jean-Pierre Kocher

Scientific Reports

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

2018-03-27

Oliver Billker
Matthew Berriman
Ana Rita Gomes

Adam J Reid
Arthur M Talman
Hayley M Bennett
Mandy J Sanders
Christopher J R Illingworth
Mara Kn Lawniczak

eLife

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.

2018-03-28

Quaid D Morris

Kevin C H Ha
Benjamin J Blencowe

Genome Biology

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.

2018-04-01

Volker Hovestadt
Christian Dorfer
Angel M. Carcaboso
Maria Martinez-Lage
Mark W. Kieran
Orit Rozenblatt-Rosen
Aviv Regev
Mariella G Filbin
Christopher W Mount
Nathan D Mathewson
Michelle Monje
Gad Getz

Itay Tirosh
McKenzie L Shaw
Leah E Escalante
Cyril Neftel
Nelli Frank
Kristine Pelton
Christine M Hebert
Christine Haberler
Keren Yizhak
Johannes Gojo
Kristof Egervari
Peter van Galen
Dennis M Bonal
Quang-De Nguyen
Alexander Beck
Claire Sinai
Thomas Czech
Liliana Goumnerova
Cinzia Lavarino
Jaume Mora
Ravindra Mylvaganam
Christina C Luo
Andreas Peyrl
Mara Popović
Amedeo Azizi
Tracy T Batchelor
Matthew P Frosch
Pratiti Bandopadhayay
Rameen Beroukhim
Gerhard Fritsch
Kai W Wucherpfennig
David N Louis
Irene Slavc
Keith L Ligon
Todd R Golub
Bradley E Bernstein
Mario L Suvà

Science

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.

2018-04-01

Angela Ciuffi
Matthias Cavassini

Monica Golumbeanu
Sara Cristinelli
Sylvie Rato
Miguel Munoz
Niko Beerenwinkel

Cell Reports

Identification of Hub Genes and Pathways in Zika Virus Infection Using RNA-Seq Data: A Network-Based Computational Approach.

2018-04-02

Sanathoi Gurumayum
Rahul Brahma
Mathavan Muthaiyan

Leimarembi Devi Naorem
Jeyakodi Gopal
Amouda Venkatesan

Viral Immunology

RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages.

2018-04-02

Isabel Roditi

Arunasalam Naguleswaran
Nicholas Doiron

BMC Genomics

RNA sequencing (RNA-seq) reveals extremely low levels of reticulocyte-derived globin gene transcripts in peripheral blood from horses (Equus caballus) and cattle (Bos taurus)

2018-04-04

Kévin Rue-Albrecht
David E. MacHugh

Carolina N Correia
Kirsten E McLoughlin
Nicolas C Nalpas
David A Magee
John A Browne
Stephen V. Gordon

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

2018-04-05

Stephen J Bush
Mark P Stevens

Lucy Freem
Amanda J MacCallum
Jenny O'Dell
Chunlei Wu
Cyrus Afrasiabi
Androniki Psifidi
Jacqueline Smith
Kim M Summers
David A Hume

A Beginner's Guide to Analysis of RNA-seq Data.

2018-04-06

Elizabeth T. Bartom

Clarissa M Koch
Stephen F Chiu
Mahzad Akbarpour
Ankit Bharat
Karen M Ridge
Deborah R Winter

American Journal of Respiratory Cell and Molecular Biology

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.

2018-04-09

Cindy R Eide
Jakub Tolar

Huanan Zhang
Catherine A A Lee
Zhuliu Li
John R Garbe
Raphael Petegrosso
Rui Kuang

PLOS Computational Biology

Massive mining of publicly available RNA-seq data from human and mouse.

2018-04-10

Avi Ma'ayan
Moshe C Silverstein
Alexander Lachmann

Denis Torre
Alexandra B Keenan
Kathleen M Jagodnik
Hoyjin J Lee
Lily Wang

Nature Communications

Approximate inference of gene regulatory network models from RNA-Seq time series data.

2018-04-11

Thomas Thorne

BMC Bioinformatics

Sialome diversity of ticks revealed by RNAseq of single tick salivary glands.

2018-04-13

José M. Ribeiro
Jan Perner

Sára Kropáčková
Petr Kopáček

PLOS Neglected Tropical Diseases

Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations

2018-04-14

Raffaele A. Calogero
Alessandro Weisz

Riccardo Panero
Maddalena Arigoni
Martina Olivero
Francesca Cordero
Marco Beccuti
Maria Flavia Direnzo

RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomas.

2018-04-16

Marcos Malumbres

Pilar López-Nieva
Pablo Fernández-Navarro
Concepción Vaquero-Lorenzo
María Villa-Morales
Osvaldo Graña-Castro
María Ángeles Cobos-Fernández
José Luis López-Lorenzo
Pilar Llamas
Laura González-Sanchez
Isabel Sastre
Marina Pollan
Javier Santos
José Fernández-Piqueras

BMC Cancer

The Physcomitrella patens gene atlas project: large scale RNA-seq based expression data.

2018-04-22

Alessandro Alboresi
Manuel Hiss
Inés Ponce de León
Daniel Lang
Kerrie Barry

Pierre-François Perroud
Fabian B Haas
Kristian K Ullrich
Mojgan Amirebrahimi
Roberto Bassi
Sandrine Bonhomme
Haodong Chen
Juliet Coates
Tomomichi Fujita
Anouchka Guyon-Debast
Junyan Lin
Anna Lipzen
Fabien Nogué
Melvin J Oliver
Ralph S Quatrano
Catherine Rameau
Bernd Reiss
Ralf Reski
Mariana Ricca
Younousse Saidi
Ning Sun
Peter Szövényi
Avinash Sreedasyam
Jane Grimwood
Gary Stacey
Jeremy Schmutz
Stefan A Rensing

The Plant Journal

A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.

2018-04-26

Joan E Rodríguez-Gil
Alex Clop
Marta Gòdia

Fabiana Quoos Mayer
Julieta Nafissi
Anna Castelló
Armand Sánchez

Systems Biology in Reproductive Medicine

Biomarker Identification from RNA-Seq Data using a Robust Statistical Approach.

2018-04-30

Munirul Alam

Zobaer Akond
Md Nurul Haque Mollah

Bioinformation

Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity

2018-05

Haja N. Kadarmideen

Ruta Skinkyte-Juskiene
Lisette J A Kogelman

Current Genomics

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

2018-05

Arnau Sebé-Pedrós
François Spitz

Baptiste Saudemont
Elad Chomsky
Flora Plessier
Marie-Pierre Mailhé
Justine Renno
Yann Loe-Mie
Aviezer Lifshitz
Zohar Mukamel
Sandrine Schmutz
Sophie Novault
Patrick R.H. Steinmetz
Amos Tanay
Heather Marlow

Cell

RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments.

2018-05-01

Ernesto Picardi

Federico Zambelli
Francesca Mastropasqua
Anna Maria D'Erchia
Graziano Pesole
Giulio Pavesi

Nucleic Acids Research

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

2018-05-01

Alicia Oshlack
Nadia M Davidson

GigaScience

Improving the value of public RNA-seq expression data by phenotype prediction.

2018-05-01

Shannon Ellis
Leonardo Collado-Torres
Andrew E Jaffe
Jeffrey T. Leek

Nucleic Acids Research

Evaluation of commercially available small RNASeq library preparation kits using low input RNA.

2018-05-05

Olivia Ziegler
Elizabeth D Hutchins

Ashish Yeri
Amanda Courtright
Kirsty Danielson
Eric Alsop
Elizabeth Carlson
Michael Hsieh
Avash Das
Ravi V Shah
Joel Rozowsky
Saumya Das
Kendall Van Keuren-Jensen

BMC Genomics

Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis.

2018-05-15

Thomas D Kocher
Deshou Wang

Wenjing Tao
Jinlin Chen
Dejie Tan
Jing Yang
Lina Sun
Jing Wei
Matthew A Conte

BMC Genomics

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.

2018-05-16

Tim Beißbarth

Alexander Wolff
Michaela Bayerlová
Jochen Gaedcke
Dieter Kube

PLOS ONE

The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development

2018-05-16

Vanika Garg

Himabindu Kudapa
Annapurna Chitikineni
Rajeev K. Varshney

Plant, Cell and Environment

Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy.

2018-05-24

Meredith D McNeil

Shamsul A Bhuiyan
Paul J Berkman
Barry J Croft
Karen S Aitken

PLOS ONE

Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data.

2018-05-29

Atsushi J. Nagano

Akinori Awazu
Takahiro Tanabe
Mari Kamitani
Ayumi Tezuka

Scientific Reports

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi.

2018-05-30

Michael Han
Jens Keilwagen

Frank Hartung
Sven O Twardziok
Jan Grau

BMC Bioinformatics

Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq.

2018-05-30

Kristyna Kupkova
Karel Sedlar

Pavlina Koscova
Maryna Vasylkivska
Barbora Branska
Jan Kolek
Petra Patakova
Ivo Provaznik

BMC Genomics

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

2018-06

Luke Zappia
Belinda Phipson
Alicia Oshlack

PLOS Computational Biology

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

2018-06-01

Lukas Simon
Fabian J. Theis

S Karg
A J Westermann
M Engel
A H A Elbehery
B Hense
M Heinig
L Deng

GigaScience

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis.

2018-06-04

Jie Qiao

Xiaoying Fan
Ji Dong
Suijuan Zhong
Yuan Wei
Qian Wu
Liying Yan
Jun Yong
Le Sun
Xiaoye Wang
Yangyu Zhao
Wei Wang
Jie Yan
Xiaoqun Wang
Fuchou Tang

Cell Research

RNA-Seq reveals large quantitative differences between the transcriptomes of outbreak and non-outbreak locusts.

2018-06-15

Mohammed Bakkali

R Martín-Blázquez

Scientific Reports

RNAseq analysis of hippocampal microglia after kainic acid-induced seizures.

2018-06-20

Long-Jun Wu
Ukpong B Eyo
Jason R. Richardson

Dale B Bosco
Jiaying Zheng
Zhiyan Xu
Jiyun Peng
Ke Tang
Cheng Yan
Jun Huang
Lijie Feng
Gongxiong Wu
Hui Wang

Molecular Brain

BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud

2018-06-20

Avi Ma'ayan

Denis Torre
Alexander Lachmann

bcbioRNASeq: R package for bcbio RNA-seq analysis

2018-06-20

Michael J Steinbaugh
Víctor Barrera

Lorena Pantano
Rory D. Kirchner
Brad A. Chapman
Mary E. Piper
Meeta Mistry
Radhika S. Khetani
Kayleigh D. Rutherford
Oliver Hofmann
John N. Hutchinson
Shannan Ho Sui

F1000Research

RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.).

2018-06-28

Rajeev Kumar Varshney
Mahendar Thudi
Vanika Garg

Keyvan Mahdavi Mashaki
Ali Asghar Nasrollahnezhad Ghomi
Himabindu Kudapa
Annapurna Chitikineni
Khalil Zaynali Nezhad
Ahad Yamchi
Hasan Soltanloo

PLOS ONE

Predicting essential proteins based on RNA-Seq, subcellular localization and GO annotation datasets

2018-07

Hamido Fujita
Aidong Zhang

Xiujuan Lei
Jie Zhao

Knowledge-Based Systems

Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research

2018-07

Tae Hoon Kim

Pradipta Ray
Andrew Torck
Lilyana Quigley
Andi Wangzhou
Matthew Neiman
Chandranshu Rao
Tiffany Lam
Ji-Young Kim
Michael Q Zhang
Gregory Dussor
Theodore J Price

Pain

SPAR: small RNA-seq portal for analysis of sequencing experiments.

2018-07-01

Alexandre Amlie-Wolf

Pavel P Kuksa
Živadin Katanic
Otto Valladares
Li-San Wang
Yuk Yee Leung

Nucleic Acids Research

Clinker: visualizing fusion genes detected in RNA-seq data

2018-07-01

Alicia Oshlack
Paul G Ekert
Nadia M Davidson
Ian J Majewski

Breon M Schmidt
Anthony D K Hawkins
Ray Bartolo

GigaScience

Limitations of alignment-free tools in total RNA-seq quantification

2018-07-03

Claus O. Wilke
Douglas C Wu

Jun Yao
Kevin S Ho
Alan M Lambowitz

BMC Genomics

Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species

2018-07-03

Guiomar Rotllant

Tuan Viet Nguyen
Hyungtaek Jung
David Hurwood
Peter Mather
Tomer Ventura

Hydrobiologia

An Online Compendium of CHO RNA-Seq Data Allows Identification of CHO Cell Line-Specific Transcriptomic Signatures

2018-07-05

Helene Faustrup Kildegaard
Mikael Rørdam Andersen

Ankita Singh

Biotechnology Journal

Detection and removal of barcode swapping in single-cell RNA-seq data

2018-07-10

Jonathan A Griffiths
John C Marioni

Arianne C Richard
Karsten Bach
Aaron T L Lun

Nature Communications

RNASeq analysis of Aedes albopictus mosquitoes during chikungunya virus infection

2018-07-11

Prasad N Paradkar
Ravikiran Vedururu

Matthew J Neave
Mary Tachedjian
Paul R Gorry
Jean-Bernard Duchemin

RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas

2018-07-11

Paola Zigrino
Janet Kelso
Anja Bosserhoff

Manfred Kunz
Henry Löffler-Wirth
Michael Dannemann
Edith Willscher
Gero Doose
Tina Kottek
Birgit Nickel
Lydia Hopp
Jenny Landsberg
Steve Hoffmann
Thomas Tüting
Cornelia Mauch
Jochen Utikal
Mirjana Ziemer
Hans-Joachim Schulze
Michael Hölzel
Alexander Roesch
Susanne Kneitz
Svenja Meierjohann
Hans Binder
Manfred Schartl

Oncogene

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting

2018-07-11

Stefan L Ameres
Eric A Miska
Wayo Matsushima

Veronika A Herzog
Tobias Neumann
Katharina Gapp
Johannes Zuber

Development

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes

2018-07-15

Julian C Knight
Peter Humburg

Wanseon Lee
Katharine Plant

Bioinformatics

Blue light induces a neuroprotective gene expression program in Drosophila photoreceptors

2018-07-20

Vikki M. Weake

Hana Hall
Jingqun Ma
Sudhanshu Shekhar
Walter D Leon-Salas

BMC Neuroscience

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

2018-07-31

Sarah Teichmann

Ida Lindeman
Guy Emerton
Lira Mamanova
Omri Snir
Krzysztof Polanski
Shuo-Wang Qiao
Ludvig M. Sollid
Michael J. T. Stubbington

Nature Methods

RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol

2018-08

Xiaokang Zhang
Eileen Marie Hanna
Fekadu Yadetie
Nello Blaser
Anders Goksøyr

Libe Aranguren-Abadía
Marta Eide
Morten Brun
Inge Jonassen
Odd André Karlsen

Aquatic Toxicology

Elysium: RNA-seq Alignment in the Cloud

2018-08-02

Alexander Lachmann
Avi Ma'ayan

Zhuorui Xie

Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites

2018-08-07

Rickard Sandberg
Mats Wahlgren

Mtakai Ngara
Mia Palmkvist
Sven Sagasser
Daisy Hjelmqvist
Åsa K Björklund
Johan Ankarklev

Experimental Cell Research

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

2018-08-07

Stephen J Bush
Mark P Stevens
Kim M Summers

Lucy Freem
Amanda J MacCallum
Jenny O'Dell
Chunlei Wu
Cyrus Afrasiabi
Androniki Psifidi
Jacqueline Smith
David A Hume

BMC Genomics

DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq

2018-08-08

R Shalgi

Yuval Wiesel
Niv Sabath

BMC Genomics

RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants

2018-08-09

Mikhail I. Schelkunov

Aleksey A Penin
Maria D Logacheva

BMC Genomics

Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads

2018-08-13

Jean Thierry-Mieg

Grzegorz M Boratyn
Danielle Thierry-Mieg
Ben Busby
Thomas L Madden

Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection

2018-08-20

Zhao Zhang

Xintong Liu
Xiaoqian Cao
Shaochuan Shi
Na Zhao
Dandan Li
Peihong Fang
Xi Chen
Weicong Qi

BMC Genetics

RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease

2018-08-27

Kirill Tsyganov
Andrew J. Perry

Stuart Kenneth Archer
David Powell

Journal of Open Source Software

RNA-seq coupled to proteomic analysis reveals high sperm proteome variation between two closely related marine mussel species

2018-09

Mónica Carrera
Andrés Pérez-Figueroa

Mónica R. Romero
Willie J. Swanson
David O.F. Skibinski
Angel P. Diz

Journal of Proteomics

Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations

2018-09

Molly Hammell

Yu-Jui Ho
Naishitha Anaparthy
David Molik
Grinu Mathew
Toby Aicher
Ami Patel
James Hicks

Genome Research

ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes

2018-09-01

Sung-Huan Yu
Konrad Förstner

Jörg Vogel

GigaScience

RNA-seq analysis reveals different gene ontologies and pathways in rheumatoid arthritis and Kashin-Beck disease

2018-09-05

Xiong Guo
Duan Chen

Fangfang Yu
Xiaodong Zhang
Dandan Yao
Gangquan Si
Ying Gao
Zongqiang Gao
Farooq Umer

International Journal of Rheumatic Diseases

Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

2018-09-05

Vadim V Yuzhakov

Lyudmila V Dergunova
Ivan B Filippenkov
Vasily V Stavchansky
Alina E Denisova
Sergey A Mozerov
Leonid V Gubsky
Svetlana A Limborska

BMC Genomics

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

2018-09-06

Matthew Chung
Silvia Libro
Amol C Shetty
Claire M. Fraser

Laura Teigen
Hong Liu
Nikhil Kumar
Xuechu Zhao
Robin E Bromley
Luke J Tallon
Lisa Sadzewicz
David A Rasko
Scott G Filler
Jeremy M Foster
Michelle L Michalski
Vincent M Bruno
Julie C Dunning Hotopp

Scientific Reports

SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data

2018-09-08

Michael I Love

Yuchen Yang
Ruth Huh
Houston W Culpepper
Yuan Lin
Yun Li

Bioinformatics

AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

2018-09-19

Kathryn Unsworth
Mathew G Lewsey
James Whelan

Andrew J Robinson
Muluneh Tamiru
Rachel Salby
Clayton Bolitho
Andrew Williams
Simon Huggard
Eva Fisch

BMC Plant Biology

scClustViz – Single-cell RNAseq cluster assessment and visualization

2018-09-21

Brendan T. Innes

Gary D. Bader

F1000Research

RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

2018-09-21

Guy Smagghe

Er-Hu Chen
Qiu-Li Hou
Wei Dou
Dan-Dan Wei
Yong Yue
Rui-Lin Yang
Shuai-Feng Yu
Kristof De Schutter
Jin-Jun Wang

BMC Genomics

Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription

2018-09-24

Owen Dando

Jing Qiu
Paul S. Baxter
Philip Hasel
Samuel Heron
T. Ian Simpson
Giles E. Hardingham

Nature Protocols

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

2018-09-25

Angel Rubio

Juan P Romero
María Ortiz-Estévez
Ander Muniategui
Soraya Carrancio
Fernando J de Miguel
Fernando Carazo
Luis M Montuenga
Remco Loos
Rubén Pío
Matthew W B Trotter

BMC Genomics

Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA

2018-09-26

Kimon Froussios
Gordon G Simpson
Nicholas Schurch
Geoffrey J. Barton

Kira Mourao
Radoslaw Lukoszek
Katarzyna MacKinnon
Celine Duc

MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

2018-09-30

Lukas Simon
Fabian J. Theis

George Tsitsiridis
Philipp Angerer

Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data

2018-10

Kacper Żukowski
Katarzyna Piórkowska
Maria Oczkowicz
Katarzyna Ropka-Molik

Anna Bereta
Mirosław Tyra
Grzegorz Żak

Asian-Australasian Journal of Animal Sciences

Evaluation of the Expression of Genes Associated with Inflammation and Apoptosis in Androgenetic Alopecia by Targeted RNA-Seq

2018-10

Augusto Rojas-Martinez

Lizeth Martinez-Jacobo
Claudia I Ancer-Arellano
Rocio Ortiz-Lopez
Mauricio Salinas-Santander
Cesar Daniel Villarreal-Villarreal
Jesus Ancer-Rodriguez
Bianka Camacho-Zamora
Viviana Zomosa-Signoret
Carlos E Medina-De la Garza
Jorge Ocampo-Candiani

Skin appendage disorders

Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures

2018-10

Alexandre Favereaux

Anaïs Soula
Mélissa Valere
María-José López-González
Vicky Ury-Thiery
Alexis Groppi
Marc Landry
Macha Nikolski

RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment

2018-10-02

Ladislav Merta
Daniel Rösel

Vladimír Čermák
Aneta Gandalovičová
Jitka Fučíková
Radek Špíšek
Jan Brábek

Scientific Data

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq

2018-10-05

Nenad Sestan
Mark Bender Gerstein

Becky C Carlyle
Robert R Kitchen
Jing Zhang
Rashaun S Wilson
Tukiet T Lam
Joel S Rozowsky
Kenneth R Williams
Nenad Sestan
Angus C Nairn

Journal of Proteome Research

Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics datasets

2018-10-06

Siqi Liu
Zhe Ren

Da Qi
Pugh Nina
Kai Li
Bo Wen
Ruo Zhou
Shaohang Xu
Andrew R. Jones

Molecular & Cellular Proteomics

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps

2018-10-09

Ali Mortazavi
Matthias Merkenschlager
Jesper Tegnér
David Gomez-Cabrero

Camden Jansen
Ricardo Ramirez
Nicole El-Ali
Ana Conesa

Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by 71 Using RNA-Seq

2018-10-11

Yuefei Jin

Ying Li
Chao Zhang
Luwei Qin
Dong Li
Guangyuan Zhou
Dejian Dang
Shuaiyin Chen
Tiantian Sun
Rongguang Zhang
Weidong Wu
Yuanlin Xi
Guangcai Duan

Viruses

Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands

2018-10-15

Barbara Braden
Richard Peter Owen
Benjamin Schuster-Böckler
Chris Ponting
David T Severson
Adam Bailey

Michael Joseph White
Robert Goldin
Lai Mun Wang
Carlos Ruiz-Puig
Nicholas David Maynard
Angie Green
Paolo Piazza
David Buck
Mark Ross Middleton
Xin Lu

Nature Communications

Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions

2018-10-22

Mark F Sabbagh
Amir Rattner
Jeremy Nathans
Philip M Smallwood

Xi Peng
Francesco Emiliani
Hong Lei

eLife

Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63

2018-10-26

Nobuyuki Tanaka
Kaneyasu Nishimura
Juha Kere

Shintaro Katayama
Aparna Reddy
Naoya Niwa
Hiroshi Hongo
Koichiro Ogihara
Takeo Kosaka
Ryuichi Mizuno
Eiji Kikuchi
Shuji Mikami
Ayako Miyakawa
Ernest Arenas
Mototsugu Oya
Per Uhlén

Cancer Medicine

Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling

2018-10-26

Paola Vittorioso
Anna Tramontano

Riccardo Lorrai
Francesco Gandolfi
Alessandra Boccaccini
Veronica Ruta
Marco Possenti
Paolo Costantino
Rosalba Lepore

Scientific Reports

RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ

2018-10-31

Jose M Vidal-taboada
Alfonso Gerardo Garcia Diaz Barriga
Carme Solà
Josep Saura

Marta Pulido-Salgado

Scientific Reports

Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq

2018-10-31

Dai Fei Elmer Ker

Dan Wang
Rashmi Sharma
Bin Zhang
Ben Passarelli
Norma Neff
Chunyi Li
William Maloney
Stephen Quake
Yunzhi Peter Yang

Stem Cell Research & Therapy

A semi-supervised deep learning method based on stacked sparse auto-encoder for cancer prediction using RNA-seq data

2018-11

Zongli Lin

Yawen Xiao
Jun Wu
Xiaodong Zhao

Computer Methods and Programs in Biomedicine

Response of cell-wall composition and RNA-seq transcriptome to methyl-jasmonate in Brachypodium distachyon callus

2018-11

Louise V. Michaelson
Jackie Freeman

Lucy S Hyde
Till K Pellny
Rachael Simister
Simon J McQueen-Mason
Rowan A C Mitchell

Planta

Comparing RNA-Seq and microarray gene expression data in two zones of the root apex relevant to spaceflight

2018-11

Anna-Lisa Paul

Aparna Krishnamurthy
Robert J Ferl

Applications in Plant Sciences

Species-complex diversification and host-plant associations in Bemisia tabaci: A plant-defence, detoxification perspective revealed by RNA-Seq analyses

2018-11

Habibu Mugerwa
Sharon van Brunschot
Paul Visendi

Osnat Malka
Diego Santos-Garcia
Ester Feldmesser
Elad Sharon
Renate Krause-Sakate
Hélène Delatte
Mitulkumar Patel
Susan Seal
John Colvin
Shai Morin

Molecular Ecology

A fast detection of fusion genes from paired-end RNA-seq data

2018-11-01

Trung N. Vu

Wenjiang Deng
Quang Thinh Trac
Stefano Calza
Woochang Hwang
Yudi Pawitan

BMC Genomics

Salt stress in the renal tubules is linked to TAL-specific expression of uromodulin and an upregulation of heat shock genes

2018-11-01

Alisha Aman
Anna Dominiczak

Lesley A Graham
Desmond D Campbell
Julian Augley
Delyth Graham
Martin W McBride
Niall J Fraser
Nicholas R Ferreri
Sandosh Padmanabhan

Physiological Genomics

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

2018-11-06

Douglas A Lauffenburger

Manu P Kumar
Jinyan Du
Georgia Lagoudas
Yang Jiao
Andrew Sawyer
Daryl C Drummond
Andreas Raue

Cell Reports

Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq

2018-11-08

Miyako Kodama
Henrik Brinch-Pedersen
M Thomas P Gilbert

Shrikant Sharma
Inger Bæksted Holme
Bjarne Joernsgaard
Tsaneta Dzhanfezova
Daniel Buchvaldt Amby
Filipe Garrett Vieira
Shanlin Liu

BMC Genomics

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

2018-11-08

Shigeo Takumi

Moeko Okada
Kentaro Yoshida
Ryo Nishijima
Asami Michikawa
Yuka Motoi
Kazuhiro Sato

BMC Plant Biology

Evaluation of immune repertoire inference methods from RNA-seq data

2018-11-09

Xiaole Shirley Liu

Xihao Hu
Jian Zhang
Jun S Liu
Bo Li

Nature Biotechnology

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance

2018-11-14

Charles C. Kim

Alyssa Baccarella
Claire R Williams
Jay Z Parrish

BMC Bioinformatics

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

2018-11-19

Jens Preussner
Sarah Teichmann
Xi Chen
Mario Looso
Michail Yekelchyk
Thomas Braun

Guangshuai Jia
Stefan Guenther
Xuejun Yuan
Carsten Kuenne
Yonggang Zhou

Nature Communications

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities

2018-11-21

Heiner Schaal
Wolfgang Kaisers

Holger Schwender

International Journal of Molecular Sciences

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women

2018-11-23

Signe Altmäe

Kadri Rekker
Marina Suhorutshenko
Maire Peters
Juan F Martinez-Blanch
Francisco M Codoñer
Felipe Vilella
Carlos Simón
Andres Salumets
Agne Velthut-Meikas

Genes

Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq

2018-11-27

Francisco Perfectti

Carolina Osuna-Mascaró
Rafael Rubio de Casas

Scientific Reports

A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference

2018-11-27

Paul Visendi
Nedeljka N. Rosic
Chon-Kit Kenneth Chan
Jacqueline Batley

Michał T. Lorenc
Meng Lin
Paulina Kaniewska
Brett J. Ferguson
Peter M. Gresshoff
David Edwards

Functional and Integrative Genomics

RNA-seq data from mature male gonads of marine mussels Mytilus edulis and M. galloprovincialis

2018-12

Andrés Pérez-Figueroa

Angel P. Diz
Mónica R. Romero
Willie J. Swanson
David O.F. Skibinski

Data in Brief

Quantitative RNAseq analysis of Ugandan KS tumors reveals KSHV gene expression dominated by transcription from the LTd downstream latency promoter

2018-12

Timothy M Rose

A Gregory Bruce
Serge Barcy
Matt Fitzgibbon
Lisa R Matsumoto
Minako Ikoma
Corey Casper
Jackson Orem
Warren Phipps

PLOS Pathogens

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species

2018-12-01

Margaret Staton

Miriam Payá-Milans
James W Olmstead
Gerardo Nunez
Timothy A Rinehart

GigaScience

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

2018-12-01

Gemy Kaithakottil
Luca Venturini
David Swarbreck

Daniel Mapleson

GigaScience

Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra

2018-12-12

Vincent Segura
Odile Rogier

Aurélien Chateigner
Souhila Amanzougarene
Marie-Claude Lesage-Descauses
Sandrine Balzergue
Véronique Brunaud
José Caius
Ludivine Soubigou-Taconnat
Véronique Jorge

BMC Genomics

Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

2018-12-17

Philip J Ebert

Hong Wang
Yupeng Li
John W Ryder
Justin T Hole
David C Airey
Hui-Rong Qian
Benjamin Logsdon
Alice Fisher
Zeshan Ahmed
Tracey K Murray
Annalisa Cavallini
Suchira Bose
Brian J Eastwood
David A Collier
Jeffrey L Dage
Bradley B Miller
Kalpana M Merchant
Michael J O'Neill
Ronald B Demattos

Molecular Neurodegeneration

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

2018-12-19

Steven Ge

Eun Wo Son
Runan Yao

BMC Bioinformatics

A test metric for assessing single-cell RNA-seq batch correction

2018-12-20

Maren Büttner
F. Alexander Wolf
Fabian J. Theis
Zhichao Miao
Sarah Teichmann

Nature Methods

Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

2018-12-20

Gursharn Singh Randhawa

Omika Thakur

BMC Genomics

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data

2018-12-24

Angelo Di Leo

Dario Romagnoli
Giulia Boccalini
Martina Bonechi
Chiara Biagioni
Paola Fassan
Roberto Bertorelli
Veronica De Sanctis
Ilenia Migliaccio
Luca Malorni
Matteo Benelli

BMC Genomics

Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

2018-12-29

Boas Pucker

Samuel F Brockington

BMC Genomics

Androgen and Oestrogen Affect the Expression of Long Non-Coding RNAs During Phallus Development in a Marsupial

2018-12-30

Yu Chen
Marilyn Renfree

Yoko Kuroki
Geoff Shaw
Andrew J Pask
Hongshi Yu
Atsushi Toyoda
Asao Fujiyama

Non-coding RNA

Screening human cell lines for viral infections applying RNA-Seq data analysis

2019

Hans Guenter Drexler
Claudia Pommerenke

Cord C Uphoff
Sabine A Denkmann

PLOS ONE

LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics

2019

Daniel Hebenstreit

Nigel P Dyer
Vahid Shahrezaei

PeerJ

Comparative STAT3-Regulated Gene Expression Profile in Renal Cell Carcinoma Subtypes

2019

Ashok Sharma

Rebekah L Robinson
Shan Bai
Saleh Heneidi
Tae Jin Lee
Sai Karthik Kodeboyina
Nikhil Patel
Shruti Sharma

Frontiers in Oncology

Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo

2019

Xiaoya Ma

Tingxian Deng
Aixin Liang
Shasha Liang
Xingrong Lu
Anqin Duan
Chunying Pang
Guohua Hua
Shenhe Liu
Giuseppe Campanile
Angela Salzano
Bianca Gasparrini
Gianluca Neglia
Xianwei Liang
Liguo Yang

Frontiers in Genetics

Fast and accurate differential transcript usage by testing equivalence class counts

2019

Marek Cmero
Nadia M Davidson
Alicia Oshlack

F1000Research

High-Depth RNA-Seq Data Sets for Studying Gene Expression Changes Mediated by Phase-Variable DNA Methyltransferases in Nontypeable Haemophilus influenzae

2019-01

Lauren O Bakaletz

John M Atack
Michael P Jennings

Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses

2019-01

Moritz Bömer
Paul Visendi

Ajith I. Rathnayake
Steven O. Sewe
Juan Paolo A. Sicat
Gonçalo Silva
P. Lava Kumar
Susan E. Seal

Physiological and Molecular Plant Pathology

Transcriptional and epigenetic profiling of nutrient-deprived cells to identify novel regulators of autophagy

2019-01

Mario Mauthe
Michal Mokry

J G C Peeters
L W Picavet
S G J M Coenen
S J Vervoort
E Mocholi
C de Heus
J Klumperman
S J Vastert
F Reggiori
P J Coffer
J van Loosdregt

Autophagy

Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells

2019-01-02

Caroline H Johnson
Gary Siuzdak

Benedikt Warth
Amelia Palermo
Nicholas J W Rattray
Nathan V Lee
Zhou Zhu
Linh T Hoang
Yuping Cai
Anthony Mazurek
Stephen Dann
Todd VanArsdale
Valeria R Fantin
David Shields

Metabolites

Molecular signatures of multiple myeloma progression through single cell RNA-Seq

2019-01-03

Andre J van Wijnen

Jin Sung Jang
Ying Li
Amit Kumar Mitra
Lintao Bi
Alexej Abyzov
Linda B Baughn
Brian Van Ness
Vincent Rajkumar
Shaji Kumar
Jin Jen

Blood Cancer Journal

Differential expression feature extraction (DEFE) and its application in RNA-seq data analysis

2019-01-03

Youlian Pan

Yifeng Li
Ziying Liu
Anuradha Surendra
Lipu Wang
Nora A. Foroud
Ravinder K. Goyal
Therese Ouellet
Pierre R. Fobert

A Hybrid Deep Clustering Approach for Robust Cell Type Profiling Using Single-cell RNA-seq Data: Supplementary Figures and Tables

2019-01-04

Dmitry Korkin
Suhas Srinivasan

Nathan T Johnson

RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed

2019-01-07

Christian Diot

Frédéric Hérault
Magalie Houée-Bigot
Elisabeth Baéza
Olivier Bouchez
Diane Esquerré
Christophe Klopp

BMC Genomics

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

2019-01-09

Yuri Motorin
Mark Helm

Genes

Stability of methods for differential expression analysis of RNA-seq data

2019-01-11

Zhen Pang

Bingqing Lin

BMC Genomics

Dynamics of transcriptional regulation from total RNA-seq experiments: Supplemental Figures and Methods

2019-01-14

Mattia Pelizzola

Mattia Furlan
Stefano de Pretis
Eugenia Galeota
Michele Caselle

Expression analysis of lung miRNAs responding to ovine VM virus infection by RNA-seq

2019-01-18

Martin Bilbao-Arribas

Naiara Abendaño
Endika Varela-Martínez
Ramsés Reina
Damián de Andrés
Begoña M Jugo

BMC Genomics

Single-cell RNA-seq denoising using a deep count autoencoder

2019-01-23

Maria Mircea
Lukas Simon
Fabian J. Theis

Gökcen Eraslan
Nikola S Mueller

Nature Communications

RNA-seq of HaHV-1-infected abalones reveals a common transcriptional signature of Malacoherpesviruses

2019-01-30

Umberto Rosani

Chang-Ming Bai
Ya-Nan Li
Shu-Min Zhang
Lu-Sheng Xin
Chong-Ming Wang

Scientific Reports

O157:H7 transcriptome datasets for comparison of RNA-seq and microarray platforms

2019-02

Nicola Holden

Ewa Grabowiecka
David Martin
Louise Crozier

Data in Brief

Key role of SMN/SYNCRIP and RNA-Motif 7 in spinal muscular atrophy: RNA-Seq and motif analysis of human motor neurons

2019-02-01

Nereo Bresolin
Andreina Bordoni

Federica Rizzo
Monica Nizzardo
Shikha Vashisht
Erika Molteni
Valentina Melzi
Michela Taiana
Sabrina Salani
Pamela Santonicola
Elia Di Schiavi
Monica Bucchia
Irene Faravelli
Giacomo Pietro Comi
Uberto Pozzoli
Stefania Corti

Brain

Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

2019-02-11

Guoping Zhang

Xiaoyan Quan
Jianbin Zeng
Guang Chen

BMC Plant Biology

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma

2019-02-13

Franco Locatelli

Domenico Alessandro Silvestris
Ernesto Picardi
Valeriana Cesarini
Bruno Fosso
Nicolò Mangraviti
Luca Massimi
Maurizio Martini
Graziano Pesole
Angela Gallo

Genome Biology

Loss of Function in Escherichia coli Exposed to Environmentally Relevant Concentrations of Benzalkonium Chloride

2019-02-15

Gavin Humphreys
Hitesh B Mistry
Andrew J. McBain

Sarah Forbes
Nicola Morgan
Alejandro Amézquita

Applied and Environmental Microbiology

gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization

2019-02-22

David M. Blei

Hanna Mendes Levitin
Jinzhou Yuan
Yim Ling Cheng
Francisco Jr Ruiz
Erin C Bush
Jeffrey N Bruce
Peter Canoll
Antonio Iavarone
Anna Lasorella
Peter A Sims

Molecular Systems Biology

The role of the GATA transcription factor AreB in regulation of nitrogen and carbon metabolism in Aspergillus nidulans

2019-03-01

Piotr Węgleński

Patrycja Chudzicka-Ormaniec
Maria Macios
Michał Koper
Gareth D Weedall
Mark X Caddick
Agnieszka Dzikowska

FEMS Microbiology Letters

Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells

2019-03-06

Emanuela Mazzon
Placido Bramanti
Oriana Trubiani

Luigi Chiricosta
Francesca Diomede

Cells

Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression

2019-03-29

Mogens Sandø Lund

Zexi Cai
Bernt Guldbrandtsen
Goutam Sahana

BMC Genomics

Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage

2019-04

Timothy E. Hardingham

B Ajekigbe
K Cheung
Y Xu
A J Skelton
A Panagiotopoulos
J Soul
D J Deehan
M J Barter
D A Young

Osteoarthritis and Cartilage

Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer

2019-04-02

Nicolas Wentzensen

Jessica Kaufmann
Titus J Brinker
Niels Grabe

Oncotarget

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

2019-04-02

Kimberly Glass

Jarrett D Morrow
Robert P Chase
Margaret M Parker
Minseok Seo
Miguel Divo
Caroline A Owen
Peter Castaldi
Dawn L DeMeo
Edwin K Silverman
Craig P Hersh

Respiratory Research

Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain

2019-04-12

Ken Sugino
Erin Clark
Anton Schulmann
Yasuyuki Shima
Lihua Wang
David L Hunt
Bryan M Hooks
Tränkner D
Jayaram Chandrashekar
Serge Picard
Andrew L. Lemire
Nelson Spruston
Adam W. Hantman
Sacha B. Nelson

eLife

Ryūtō: network-flow based transcriptome reconstruction

2019-04-16

Peter F. Stadler

Thomas Gatter

BMC Bioinformatics

Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids

2019-04-23

Jacintha Ellers

Mark Lammers
Ken Kraaijeveld
Janine Mariën

BMC Genomics

Leukodystrophy-associated mutations down-regulate the RNA polymerase III transcript and important regulatory RNA

2019-05-03

Benoit Coulombe

Karine Choquet
Diane Forget
Elisabeth Meloche
Marie-Josée Dicaire
Geneviève Bernard
Adeline Vanderver
Raphael Schiffmann
Marc R Fabian
Martin Teichmann
Bernard Brais
Claudia L Kleinman

Journal of Biological Chemistry

Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions

2019-05-03

William R Blevins

Lucas B Carey
M Mar Albà

BMC Research Notes

Model-Based Methods for Transcript Expression-Level Quantification in RNA-Seq

Zhaohui Steve Qin

Zhaonan Sun
Han Wu
Yu Zhu

Movatterモバイル変換

Wikidata:WikiCite/Wikidata lists/Items about RNA-Seq

scientific article