Bioinformatics, Volume 34 export records of this page
first 1000 hits only:
see FAQ:
BHT key:
db/journals/bioinformatics/bioinformatics34.bht ask others
view this toc in
SPARQL queries Refine list refinements active!
zoomed in on?? of?? records
dismiss all constraints
view refined list in
dblp search
export refined list as
XML
JSON
JSONP
BibTeX
Volume 34, Number 1, January 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/Kaczor-Urbanowicz18 share record
persistent URL:
Karolina Elzbieta Kaczor-Urbanowicz ,Yong Kim ,Feng Li ,Timur Galeev ,Robert R. Kitchen ,Mark Gerstein ,Kikuye Koyano ,Sung-Hee Jeong ,Xiaoyan Wang ,David Elashoff ,So Young Kang ,Su Mi Kim ,Kyoung Kim ,Sung Kim ,David Chia ,Xinshu Xiao ,Joel S. Rozowsky ,David T. W. Wong :Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. 1-8 export record
dblp key:
journals/bioinformatics/ZhuAM18 share record
persistent URL:
Sha Joe Zhu ,Jacob Almagro-Garcia ,Gil McVean :Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. 9-15 export record
dblp key:
journals/bioinformatics/MendozaT18 share record
persistent URL:
Brian J. Mendoza ,Cong T. Trinh :Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms. 16-23 Sequence Analysis
export record
dblp key:
journals/bioinformatics/BaoSL18 share record
persistent URL:
Ergude Bao ,Chang-Jin Song ,Lingxiao Lan :ReMILO: reference assisted misassembly detection algorithm using short and long reads. 24-32 export record
dblp key:
journals/bioinformatics/LiuYHC18 share record
persistent URL:
Bin Liu ,Fan Yang ,De-Shuang Huang ,Kuo-Chen Chou :iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC. 33-40 Structural Bioinformatics
Gene expression
Systems Biology
Data and Text Mining
export record
dblp key:
journals/bioinformatics/MervinBKASFBEB18 share record
persistent URL:
Lewis H. Mervin ,Krishna C. Bulusu ,Leen Kalash ,Avid M. Afzal ,Fredrik Svensson ,Mike A. Firth ,Ian P. Barrett ,Ola Engkvist ,Andreas Bender :Orthologue chemical space and its influence on target prediction. 72-79 export record
dblp key:
journals/bioinformatics/WeiPFMHL18 share record
persistent URL:
Chih-Hsuan Wei ,Lon Phan ,Juliana Feltz ,Rama Maiti ,Tim Hefferon ,Zhiyong Lu :tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. 80-87 Bioimage Informatics
export record
dblp key:
journals/bioinformatics/BakkerSC18 share record
persistent URL:
Elco Bakker ,Peter S. Swain ,Matthew M. Crane :Morphologically constrained and data informed cell segmentation of budding yeast. 88-96 export record
dblp key:
journals/bioinformatics/BiffiMADWBSFMBC18 share record
persistent URL:
Carlo Biffi ,Antonio de Marvao ,Mark I Attard ,Timothy J. W. Dawes ,Nicola Whiffin ,Wenjia Bai ,Wenzhe Shi ,Catherine Francis ,Hannah Meyer ,Rachel J. Buchan ,Stuart A. Cook ,Daniel Rueckert ,Declan P. O'Regan :Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. 97-103 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/SeamanR18 share record
persistent URL:
Laura Seaman ,Indika Rajapakse :4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities. 104-106 export record
dblp key:
journals/bioinformatics/SingerRHTSTNPBC18 share record
persistent URL:
Jochen Singer ,Hans-Joachim Ruscheweyh ,Ariane L. Hofmann ,Thomas Thurnherr ,Franziska Singer ,Nora C. Toussaint ,Charlotte K. Y. Ng ,Salvatore Piscuoglio ,Christian Beisel ,Gerhard Christofori ,Reinhard Dummer ,Michael N. Hall ,Wilhelm Krek ,Mitchell P. Levesque ,Markus G. Manz ,Holger Moch ,Andreas Papassotiropoulos ,Daniel J. Stekhoven ,Peter Wild ,Thomas Wüst ,Bernd Rinn ,Niko Beerenwinkel :NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. 107-108 export record
dblp key:
journals/bioinformatics/ChenLHSSCL18 share record
persistent URL:
Kun-Tze Chen ,Chia-Liang Liu ,Shang-Hao Huang ,Hsin-Ting Shen ,Yi-Kung Shieh ,Hsien-Tai Chiu ,Chin Lung Lu :CSAR: a contig scaffolding tool using algebraic rearrangements. 109-111 export record
dblp key:
journals/bioinformatics/TernesRM18 share record
persistent URL:
Nils Ternès ,Federico Rotolo ,Stefan Michiels :biospear: an R package for biomarker selection in penalized Cox regression. 112-113 Sequence Analysis
Structural Bioinformatics
Systems Biology
Data and Text Mining
export record
dblp key:
journals/bioinformatics/RimonR18 share record
persistent URL:
Oded Rimon ,Dana Reichmann :Kfits: a software framework for fitting and cleaning outliers in kinetic measurements. 129-130 Databases and Ontologies
export record
dblp key:
journals/bioinformatics/Lopez-Massaguer18 share record
persistent URL:
Oriol López-Massaguer ,Ferran Sanz ,Manuel Pastor :An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. 131-133 Bioimage Informatics
export record
dblp key:
journals/bioinformatics/AriellyE18 share record
persistent URL:
Rani Arielly ,Yuval Ebenstein :Irys Extract. 134-136 export record
dblp key:
journals/bioinformatics/BernhemB18 share record
persistent URL:
Kristoffer Bernhem ,Hjalmar Brismar :SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy. 137-138 Special Issue:RECOMB-Seq/RECOMB-CCB/RECOMB-CG
Gene expression
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/Bansal18 share record
persistent URL:
Vikas Bansal :An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. 155-162 export record
dblp key:
journals/bioinformatics/SkumsZSGDKMRCJB18 share record
persistent URL:
Pavel Skums ,Alex Zelikovsky ,Rahul Singh ,Walker Gussler ,Zoya Dimitrova ,Sergey Knyazev ,Igor Mandric ,Sumathi Ramachandran ,David S. Campo ,Deeptanshu Jha ,Leonid Bunimovich ,Elizabeth Costenbader ,Connie Sexton ,Siobhán O'Connor ,Guo-liang Xia ,Yury Khudyakov :QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. 163-170 export record
dblp key:
journals/bioinformatics/LiuYLEQL18 share record
persistent URL:
Xinan Liu ,Ye Yu ,Jinpeng Liu ,Corrine F. Elliott ,Chen Qian ,Jinze Liu :A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures. 171-178 Corrigendum
Sequence Analysis
Erratum
Sequence Analysis
export record
dblp key:
journals/bioinformatics/YangG18 share record
persistent URL:
Zhi-Kai Yang ,Feng Gao :The systematic analysis of ultraconserved genomic regions in the budding yeast. 180 Volume 34, Number 2, January 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/KaleAT18 share record
persistent URL:
Gulce Kale ,Erman Ayday ,Öznur Tastan :A utility maximizing and privacy preserving approach for protecting kinship in genomic databases. 181-189 Sequence Analysis
export record
dblp key:
journals/bioinformatics/LinH18 share record
persistent URL:
Hsin-Nan Lin ,Wen-Lian Hsu :DART: a fast and accurate RNA-seq mapper with a partitioning strategy. 190-197 export record
dblp key:
journals/bioinformatics/DingLH18 share record
persistent URL:
Jun Ding ,Xiaoman Li ,Haiyan Hu :CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. 198-206 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/TibertiPFF18 share record
persistent URL:
Matteo Tiberti ,Alessandro Pandini ,Franca Fraternali ,Arianna Fornili :In silico identification of rescue sites by double force scanning. 207-214 export record
dblp key:
journals/bioinformatics/GuzenkoS18 share record
persistent URL:
Dmytro Guzenko ,Sergei V. Strelkov :CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments. 215-222 export record
dblp key:
journals/bioinformatics/NortheyBM18 share record
persistent URL:
Thomas C. Northey ,Anja Baresic ,Andrew C. R. Martin :IntPred: a structure-based predictor of protein-protein interaction sites. 223-229 export record
dblp key:
journals/bioinformatics/YangS18 share record
persistent URL:
Jing Yang ,Hong-Bin Shen :MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain. 230-238 Systems Biology
export record
dblp key:
journals/bioinformatics/XiaoLLCD18 share record
persistent URL:
Qiu Xiao ,Jiawei Luo ,Cheng Liang ,Jie Cai ,Pingjian Ding :A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations. 239-248 export record
dblp key:
journals/bioinformatics/KangLMB18 share record
persistent URL:
Yiming Kang ,Hien-Haw Liow ,Ezekiel J. Maier ,Michael R. Brent :NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources. 249-257 export record
dblp key:
journals/bioinformatics/GaoUGG18 share record
persistent URL:
Nan Papili Gao ,S. M. Minhaz Ud-Dean ,Olivier Gandrillon ,Rudiyanto Gunawan :SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. 258-266 Data and Text Mining
Bioimage Informatics
Applications Notes
Genome Analysis
Phylogenetics
Structural Bioinformatics
Gene expression
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/SeifertB18 share record
persistent URL:
Michael Seifert ,Andreas Beyer :regNet: an R package for network-based propagation of gene expression alterations. 308-311 export record
dblp key:
journals/bioinformatics/ChazalvielFPVMG18 share record
persistent URL:
Maxime Chazalviel ,Clément Frainay ,Nathalie Poupin ,Florence Vinson ,Benjamin Merlet ,Yoann Gloaguen ,Ludovic Cottret ,Fabien Jourdan :MetExploreViz: web component for interactive metabolic network visualization. 312-313 export record
dblp key:
journals/bioinformatics/ChuaBZ18 share record
persistent URL:
Huey-Eng Chua ,Sourav S. Bhowmick ,Jie Zheng :TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks. 314-316 Data and Text Mining
Databases and Ontologies
Letter to the Editor
Genome Analysis
export record
dblp key:
journals/bioinformatics/ForslundPCSAHMP18 share record
persistent URL:
Kristoffer Forslund ,Cécile Pereira ,Salvador Capella-Gutiérrez ,Alan W. Sousa da Silva ,Adrian M. Altenhoff ,Jaime Huerta-Cepas ,Matthieu Muffato ,Mateus Patricio ,Klaas Vandepoele ,Ingo Ebersberger ,Judith A. Blake ,Jesualdo Tomás Fernández-Breis ,Quest for Orthologs Consortium ,Brigitte Boeckmann ,Toni Gabaldón ,Erik L. L. Sonnhammer ,Christophe Dessimoz ,Suzanna Lewis :Gearing up to handle the mosaic nature of life in the quest for orthologs. 323-329 SPECIAL ISSUE:RECOMB-CCB2017
Genome Analysis
export record
dblp key:
journals/bioinformatics/HuangWP18 share record
persistent URL:
Xiaoqing Huang ,Damian Wójtowicz ,Teresa M. Przytycka :Detecting presence of mutational signatures in cancer with confidence. 330-337 export record
dblp key:
journals/bioinformatics/ChakrabortyA18 share record
persistent URL:
Abhijit Chakraborty ,Ferhat Ay :Identification of copy number variations and translocations in cancer cells from Hi-C data. 338-345 Sequence Analysis
Volume 34, Number 3, February 2018 Discovery Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/YangG18a share record
persistent URL:
Zhi-Kai Yang ,Feng Gao :The systematic analysis of ultraconserved genomic regions in the budding yeast. 361-366 Gene expression
Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/AijoMB18 share record
persistent URL:
Tarmo Äijö ,Christian L. Müller ,Richard Bonneau :Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. 372-380 export record
dblp key:
journals/bioinformatics/GuoZPZWN18 share record
persistent URL:
Weilong Guo ,Ping Zhu ,Matteo Pellegrini ,Michael Q. Zhang ,Xiangfeng Wang ,Zhongfu Ni :CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. 381-387 export record
dblp key:
journals/bioinformatics/KimCKBY18 share record
persistent URL:
Sun-Ah Kim ,Chang-Sung Cho ,Suh-Ryung Kim ,Shelley B. Bull ,Yun Joo Yoo :A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs. 388-397 export record
dblp key:
journals/bioinformatics/TangWYTZ18 share record
persistent URL:
Wei Tang ,Shixiang Wan ,Zhen Yang ,Andrew E. Teschendorff ,Quan Zou :Tumor origin detection with tissue-specific miRNA and DNA methylation markers. 398-406 Sequence Analysis
export record
dblp key:
journals/bioinformatics/BlischakKW18 share record
persistent URL:
Paul D. Blischak ,Laura Salter Kubatko ,Andrea D. Wolfe :SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. 407-415 export record
dblp key:
journals/bioinformatics/ChengWX18 share record
persistent URL:
Haoyu Cheng ,Ming Wu ,Yun Xu :FMtree: a fast locating algorithm of FM-indexes for genomic data. 416-424 export record
dblp key:
journals/bioinformatics/ParidaensWNL18 share record
persistent URL:
Tom Paridaens ,Glenn Van Wallendael ,Wesley De Neve ,Peter Lambert :AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality. 425-433 export record
dblp key:
journals/bioinformatics/OlekhnovichVUKT18 share record
persistent URL:
Evgenii I Olekhnovich ,Artem T. Vasilyev ,Vladimir Ulyantsev ,Elena S. Kostryukova ,Alexander V. Tyakht :MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. 434-444 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/NecciPDTT18 share record
persistent URL:
Marco Necci ,Damiano Piovesan ,Zsuzsanna Dosztányi ,Peter Tompa ,Silvio C. E. Tosatto :A comprehensive assessment of long intrinsic protein disorder from the DisProt database. 445-452 export record
dblp key:
journals/bioinformatics/YanH18 share record
persistent URL:
Yumeng Yan ,Sheng-You Huang :RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. 453-458 export record
dblp key:
journals/bioinformatics/NadalinC18 share record
persistent URL:
Francesca Nadalin ,Alessandra Carbone :Protein-protein interaction specificity is captured by contact preferences and interface composition. 459-468 export record
dblp key:
journals/bioinformatics/KyeongCK18 share record
persistent URL:
Hyun-Ho Kyeong ,Yoonjoo Choi ,Hak-Sung Kim :GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking. 469-476 export record
dblp key:
journals/bioinformatics/TaherzadehZLY18 share record
persistent URL:
Ghazaleh Taherzadeh ,Yaoqi Zhou ,Alan Wee-Chung Liew ,Yuedong Yang :Structure-based prediction of protein- peptide binding regions using Random Forest. 477-484 Gene expression
Systems Biology
export record
dblp key:
journals/bioinformatics/Angione18 share record
persistent URL:
Claudio Angione :Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism. 494-501 export record
dblp key:
journals/bioinformatics/XieZO18 share record
persistent URL:
Zhengwei Xie ,Tianyu Zhang ,Qi Ouyang :Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm. 502-510 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/RogersSMCGC18 share record
persistent URL:
Mark F. Rogers ,Hashem A. Shihab ,Matthew E. Mort ,David N. Cooper ,Tom R. Gaunt ,Colin Campbell :FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. 511-513 export record
dblp key:
journals/bioinformatics/MenegidioJON18 share record
persistent URL:
Fabiano B. Menegidio ,Daniela L. Jabes ,Regina Costa de Oliveira ,Luiz R. Nunes :Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses. 514-515 export record
dblp key:
journals/bioinformatics/IvakhnoRCTC18 share record
persistent URL:
Sergii Ivakhno ,Eric Roller ,Camilla Colombo ,Philip Tedder ,Anthony J. Cox :Canvas SPW: calling de novo copy number variants in pedigrees. 516-518 export record
dblp key:
journals/bioinformatics/JangL18 share record
persistent URL:
Ho Jang ,Hyunju Lee :Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data. 519-521 export record
dblp key:
journals/bioinformatics/Palarea-Albaladejo18 share record
persistent URL:
Javier Palarea-Albaladejo ,Kevin McLean ,Frank Wright ,David G. E. Smith :MALDIrppa: quality control and robust analysis for mass spectrometry data. 522-523 Gene expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Bioimage Informatics
Volume 34, Number 4, February 2018 Original Papers
Genome Analysis
Sequence Analysis
Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/Marin-LopezPABG18 share record
persistent URL:
Manuel Alejandro Marín-López ,Joan Planas-Iglesias ,Joaquim Aguirre-Plans ,Jaume Bonet ,Javier García-García ,Narcis Fernandez-Fuentes ,Baldo Oliva :On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. 592-598 export record
dblp key:
journals/bioinformatics/BondarevBZK18 share record
persistent URL:
Stanislav A. Bondarev ,Olga V. Bondareva ,Galina A. Zhouravleva ,Andrey V. Kajava :BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. 599-608 export record
dblp key:
journals/bioinformatics/CevostVM18 share record
persistent URL:
Jasmin Cevost ,Cédric Vaillant ,Sam Meyer :ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes. 609-616 Gene expression
Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/HuangERMYKBPH18 share record
persistent URL:
Xiayuan Huang ,Robert C. Elston ,Guilherme J. M. Rosa ,John Mayer ,Zhan Ye ,Terrie E. Kitchner ,Murray H. Brilliant ,David Page ,Scott J. Hebbring :Applying family analyses to electronic health records to facilitate genetic research. 635-642 export record
dblp key:
journals/bioinformatics/ChenKDWYGB18 share record
persistent URL:
Jun Chen ,Emily King ,Rebecca Deek ,Zhi Wei ,Yue Yu ,Diane E. Grill ,Karla V. Ballman :An omnibus test for differential distribution analysis of microbiome sequencing data. 643-651 Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/KulmanovKH18 share record
persistent URL:
Maxat Kulmanov ,Mohammad Asif Khan ,Robert Hoehndorf :DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. 660-668 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/ChanLRBNH18 share record
persistent URL:
Rachel C. W. Chan ,Maxwell W. Libbrecht ,Eric G. Roberts ,Jeffrey A. Bilmes ,William Stafford Noble ,Michael M. Hoffman :Segway 2.0: Gaussian mixture models and minibatch training. 669-671 export record
dblp key:
journals/bioinformatics/LareauA18 share record
persistent URL:
Caleb A. Lareau ,Martin J. Aryee :diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. 672-674 export record
dblp key:
journals/bioinformatics/AnilSAS18 share record
persistent URL:
Anandashankar Anil ,Rapolas Spalinskas ,Örjan Åkerborg ,Pelin Sahlén :HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications. 675-677 export record
dblp key:
journals/bioinformatics/MolnarHI18 share record
persistent URL:
Michael Molnar ,Ehsan Haghshenas ,Lucian Ilie :SAGE2: parallel human genome assembly. 678-680 export record
dblp key:
journals/bioinformatics/DuZLZY18 share record
persistent URL:
Lianming Du ,Chi Zhang ,Qin Liu ,Xiuyue Zhang ,Bisong Yue :Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. 681-683 Sequence Analysis
export record
dblp key:
journals/bioinformatics/SongLLMAHCWP18 share record
persistent URL:
Jiangning Song ,Fuyi Li ,André Leier ,Tatiana T. Marquez-Lago ,Tatsuya Akutsu ,Gholamreza Haffari ,Kuo-Chen Chou ,Geoffrey I. Webb ,Robert N. Pike :PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. 684-687 export record
dblp key:
journals/bioinformatics/PinsonPCAV18 share record
persistent URL:
Marie-Elisa Pinson ,Romain Pogorelcnik ,Franck Court ,Philippe Arnaud ,Catherine Vaurs-Barrière :CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data. 688-690 Gene expression
export record
dblp key:
journals/bioinformatics/SonesonR18 share record
persistent URL:
Charlotte Soneson ,Mark D. Robinson :Towards unified quality verification of synthetic count data with countsimQC. 691-692 Proteomics
export record
dblp key:
journals/bioinformatics/SaraeiSKE18 share record
persistent URL:
Sohrab Saraei ,Tomi Suomi ,Otto Kauko ,Laura L. Elo :Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics. 693-694 Systems Biology
export record
dblp key:
journals/bioinformatics/ShockleyVL18 share record
persistent URL:
Erin M. Shockley ,Jasper A. Vrugt ,Carlos F. Lopez :PyDREAM: high-dimensional parameter inference for biological models in python. 695-697 export record
dblp key:
journals/bioinformatics/SakuraiNSLIAK18 share record
persistent URL:
Nozomu Sakurai ,Takafumi Narise ,Joon-Soo Sim ,Chang-Muk Lee ,Chiaki Ikeda ,Nayumi Akimoto ,Shigehiko Kanaya :UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics. 698-700 export record
dblp key:
journals/bioinformatics/UppalMGJ18 share record
persistent URL:
Karan Uppal ,Chunyu Ma ,Young-Mi Go ,Dean P. Jones :xMWAS: a data-driven integration and differential network analysis tool. 701-702 export record
dblp key:
journals/bioinformatics/HoytKE18 share record
persistent URL:
Charles Tapley Hoyt ,Andrej Konotopez ,Christian Ebeling :PyBEL: a computational framework for Biological Expression Language. 703-704 export record
dblp key:
journals/bioinformatics/StaporWBHLFKHFH18 share record
persistent URL:
Paul Stapor ,Daniel Weindl ,Benjamin Ballnus ,Sabine Hug ,Carolin Loos ,Anna Fiedler ,Sabrina Krause ,Sabrina Hross ,Fabian Fröhlich ,Jan Hasenauer :PESTO: Parameter EStimation TOolbox. 705-707 Data and Text Mining
Databases and Ontologies
Bioimage Informatics
Volume 34, Number 5, March 2018 Discovery note
Sequence Analysis
export record
dblp key:
journals/bioinformatics/Sanchez-PulidoP18 share record
persistent URL:
Luis Sánchez-Pulido ,Chris P. Ponting :TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. 721-724 Original Papers
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/ZhaoLLW18 share record
persistent URL:
Lu Zhao ,Zhimin Liu ,Sasha F. Levy ,Song Wu :Bartender: a fast and accurate clustering algorithm to count barcode reads. 739-747 export record
dblp key:
journals/bioinformatics/KrizanovicERS18 share record
persistent URL:
Kresimir Krizanovic ,Amina Echchiki ,Julien Roux ,Mile Sikic :Evaluation of tools for long read RNA-seq splice-aware alignment. 748-754 export record
dblp key:
journals/bioinformatics/SchafferNCKKM18 share record
persistent URL:
Alejandro A. Schäffer ,Eric P. Nawrocki ,Yoon Choi ,Paul A. Kitts ,Ilene Karsch-Mizrachi ,Richard McVeigh :VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening. 755-759 export record
dblp key:
journals/bioinformatics/LiWUXFLG18 share record
persistent URL:
Yu Li ,Sheng Wang ,Ramzan Umarov ,Bingqing Xie ,Ming Fan ,Lihua Li ,Xin Gao :DEEPre: sequence-based enzyme EC number prediction by deep learning. 760-769 Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/GuoLYMETHP18 share record
persistent URL:
Xuan Guo ,Zhou Li ,Qiuming Yao ,Ryan S. Mueller ,Jimmy K. Eng ,David L. Tabb ,IV William Judson Hervey ,Chongle Pan :Sipros Ensemble improves database searching and filtering for complex metaproteomics. 795-802 export record
dblp key:
journals/bioinformatics/ThijssenDHW18 share record
persistent URL:
Bram Thijssen ,Tjeerd Dijkstra ,Tom Heskes ,Lodewyk F. A. Wessels :Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates. 803-811 export record
dblp key:
journals/bioinformatics/HuangCY18 share record
persistent URL:
Yu-An Huang ,Keith C. C. Chan ,Zhu-Hong You :Constructing prediction models from expression profiles for large scale lncRNA-miRNA interaction profiling. 812-819 Data and Text Mining
export record
dblp key:
journals/bioinformatics/NiuSCCWZZ18 share record
persistent URL:
Jinglong Niu ,Yan Shi ,Maolin Cai ,Zhixin Cao ,Dandan Wang ,Zhaozhi Zhang ,Xiaohua Douglas Zhang :Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques. 820-827 export record
dblp key:
journals/bioinformatics/ZhangZLWYD18 share record
persistent URL:
Yijia Zhang ,Wei Zheng ,Hongfei Lin ,Jian Wang ,Zhihao Yang ,Michel Dumontier :Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths. 828-835 export record
dblp key:
journals/bioinformatics/Diaz-Uriarte18 share record
persistent URL:
Ramón Díaz-Uriarte :Cancer progression models and fitness landscapes: a many-to-many relationship. 836-844 Bioimage Informatics
export record
dblp key:
journals/bioinformatics/RuszczyckiB18 share record
persistent URL:
Blazej Ruszczycki ,Tytus Bernas :Quality of biological images, reconstructed using localization microscopy data. 845-852 export record
dblp key:
journals/bioinformatics/HanZG18 share record
persistent URL:
Renmin Han ,Fa Zhang ,Xin Gao :A fast fiducial marker tracking model for fully automatic alignment in electron tomography. 853-863 Applications Notes
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/PinoCPT18 share record
persistent URL:
Sergio Díaz Del Pino ,Juan Falgueras Cano ,Esteban Pérez-Wohlfeil ,Oswaldo Trelles :mORCA: sailing bioinformatics world with mobile devices. 869-870 export record
dblp key:
journals/bioinformatics/BeccutiCAPADC18 share record
persistent URL:
Marco Beccuti ,Francesca Cordero ,Maddalena Arigoni ,Riccardo Panero ,Elvio Gilberto Amparore ,Susanna Donatelli ,Raffaele A. Calogero :SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. 871-872 export record
dblp key:
journals/bioinformatics/CaoGZC18 share record
persistent URL:
Minh Duc Cao ,Devika Ganesamoorthy ,Chenxi Zhou ,Lachlan J. M. Coin :Simulating the dynamics of targeted capture sequencing with CapSim. 873-874 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/GuanCYCJ18 share record
persistent URL:
Jinting Guan ,Moliang Chen ,Congting Ye ,James J. Cai ,Guoli Ji :AEGS: identifying aberrantly expressed gene sets for differential variability analysis. 881-883 export record
dblp key:
journals/bioinformatics/PolanskiGMBODW18 share record
persistent URL:
Krzysztof Polanski ,Bo Gao ,Sam A. Mason ,Paul Brown ,Sascha Ott ,Katherine J. Denby ,David L. Wild :Bringing numerous methods for expression and promoter analysis to a public cloud computing service. 884-886 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/MachielaC18 share record
persistent URL:
Mitchell J. Machiela ,Stephen J. Chanock :LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation. 887-889 Systems Biology
export record
dblp key:
journals/bioinformatics/Rodriguez-Martinez18 share record
persistent URL:
Andrea Rodriguez-Martinez ,Joram M. Posma ,Rafael Ayala ,Ana Luísa Neves ,Maryam Anwar ,Enrico Petretto ,Costanza Emanueli ,Dominique Gauguier ,Jeremy K. Nicholson ,Marc-Emmanuel Dumas :MWASTools: an R/bioconductor package for metabolome-wide association studies. 890-892 export record
dblp key:
journals/bioinformatics/PajaroOVA18 share record
persistent URL:
Manuel Pájaro ,Irene Otero-Muras ,Carlos Vázquez ,Antonio A. Alonso :SELANSI: a toolbox for simulation of stochastic gene regulatory networks. 893-895 Data and Text Mining
Bioimage Informatics
Volume 34, Number 6, March 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/TangSLZWQZSY18 share record
persistent URL:
Zaixiang Tang ,Yueping Shen ,Yan Li ,Xinyan Zhang ,Jia Wen ,Chen'ao Qian ,Wenzhuo Zhuang ,Xinghua Shi ,Nengjun Yi :Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information. 901-910 export record
dblp key:
journals/bioinformatics/RavanmehrKWM18 share record
persistent URL:
Vida Ravanmehr ,Minji Kim ,Zhiying Wang ,Olgica Milenkovic :ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data. 911-919 export record
dblp key:
journals/bioinformatics/SignalGDM18 share record
persistent URL:
Bethany Signal ,Brian S. Gloss ,Marcel E. Dinger ,Tim R. Mercer :Machine learning annotation of human branchpoints. 920-927 export record
dblp key:
journals/bioinformatics/MaaralaBDHB18 share record
persistent URL:
Altti Ilari Maarala ,Zurab Bzhalava ,Joakim Dillner ,Keijo Heljanko ,Davit Bzhalava :ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads. 928-935 export record
dblp key:
journals/bioinformatics/CarioW18 share record
persistent URL:
Clinton L. Cario ,John S. Witte :Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. 936-942 Sequence Analysis
Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/MarksSD18 share record
persistent URL:
Claire Marks ,Jiye Shi ,Charlotte M. Deane :Predicting loop conformational ensembles. 949-956 export record
dblp key:
journals/bioinformatics/KapaevT18 share record
persistent URL:
Roman R. Kapaev ,Philip V. Toukach :GRASS: semi-automated NMR-based structure elucidation of saccharides. 957-963 Gene expression
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/HanMBGSKAA18 share record
persistent URL:
Lichy Han ,Mateusz Maciejewski ,Christoph Brockel ,William Gordon ,Scott B. Snapper ,Joshua R. Korzenik ,Lovisa Afzelius ,Russ B. Altman :A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease. 985-993 export record
dblp key:
journals/bioinformatics/LuckenPCMRD18 share record
persistent URL:
Malte Lücken ,M. J. T. Page ,A. J. Crosby ,S. Mason ,Gesine Reinert ,Charlotte M. Deane :CommWalker: correctly evaluating modules in molecular networks in light of annotation bias. 994-1000 Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/Castillo-LaraA18 share record
persistent URL:
Sergio Castillo-Lara ,Josep F. Abril :PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. 1016-1023 Bioimage Informatics
Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/LochovskyZG18 share record
persistent URL:
Lucas Lochovsky ,Jing Zhang ,Mark Gerstein :MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. 1031-1033 export record
dblp key:
journals/bioinformatics/SendorekLYSBB18 share record
persistent URL:
Dorota H. Sendorek ,Emilie Lalonde ,Cindy Q. Yao ,Veronica Y. Sabelnykova ,Robert G. Bristow ,Paul C. Boutros :NanoStringNormCNV: pre-processing of NanoString CNV data. 1034-1036 export record
dblp key:
journals/bioinformatics/TanizawaFN18 share record
persistent URL:
Yasuhiro Tanizawa ,Takatomo Fujisawa ,Yasukazu Nakamura :DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. 1037-1039 export record
dblp key:
journals/bioinformatics/MoraesFAMLLASGM18 share record
persistent URL:
Lauro Ângelo Gonçalves de Moraes ,Érica Barbosa Felestrino ,Renata de Almeida Barbosa Assis ,Diogo Matos ,Joubert de Castro Lima ,Leandro de Araújo Lima ,Nalvo F. de Almeida Jr. ,João Carlos Setubal ,Camila Carrião Machado Garcia ,Leandro Márcio Moreira :TabPath: interactive tables for metabolic pathway analysis. 1040-1042 export record
dblp key:
journals/bioinformatics/Carvajal-Rodriguez18 share record
persistent URL:
Antonio Carvajal-Rodríguez :Myriads: P-value-based multiple testing correction. 1043-1045 export record
dblp key:
journals/bioinformatics/LiuW18 share record
persistent URL:
Tong Liu ,Zheng Wang :scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data. 1046-1047 Sequence Analysis
Phylogenetics
export record
dblp key:
journals/bioinformatics/PiccoloWCBCS18 share record
persistent URL:
Brian D. Piccolo ,Umesh D. Wankhade ,Sree V. Chintapalli ,Sudeepa Bhattacharyya ,Luo Chunqiao ,Kartik Shankar :Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data. 1050-1052 export record
dblp key:
journals/bioinformatics/LoucaD18 share record
persistent URL:
Stilianos Louca ,Michael Doebeli :Efficient comparative phylogenetics on large trees. 1053-1055 export record
dblp key:
journals/bioinformatics/BastkowskiMSWBM18 share record
persistent URL:
Sarah Bastkowski ,Daniel Mapleson ,Andreas Spillner ,Taoyang Wu ,Monika Balvociute ,Vincent Moulton :SPECTRE: a suite of phylogenetic tools for reticulate evolution. 1056-1057 Structural Bioinformatics
Gene expression
Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/CarverCVLHTWEA18 share record
persistent URL:
Tim Carver ,Alex P. Cunningham ,Chantal Babb de Villiers ,Andrew Lee ,Simon Hartley ,Marc Tischkowitz ,Fiona M. Walter ,Douglas F. Easton ,Antonis C. Antoniou :pedigreejs: a web-based graphical pedigree editor. 1069-1071 export record
dblp key:
journals/bioinformatics/AdamsSCCC18 share record
persistent URL:
Richard H. Adams ,Drew R. Schield ,Daren C. Card ,Andrew Corbin ,Todd A. Castoe :ThetaMater: Bayesian estimation of population size parameter θ from genomic data. 1072-1073 Databases and Ontologies
export record
dblp key:
journals/bioinformatics/PinedaCKKTLNHSC18 share record
persistent URL:
Sandy S. Pineda ,Pierre-Alain Chaumeil ,Anne Kunert ,Quentin Kaas ,Mike W. C. Thang ,Lien Le ,Michael Nuhn ,Volker Herzig ,Natalie J. Saez ,Ben Cristofori-Armstrong ,Raveendra Anangi ,Sebastian Senff ,Dominique Gorse ,Glenn F. King :ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins. 1074-1076 export record
dblp key:
journals/bioinformatics/ParkB18 share record
persistent URL:
Jeongbin Park ,Sangsu Bae :Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1. 1077-1079 Volume 34, Number 7, April 2018 Discovery note
Genome Analysis
export record
dblp key:
journals/bioinformatics/CechovaLBB18 share record
persistent URL:
Jana Cechová ,Jirí Lýsek ,Martin Bartas ,Václav Brázda :Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability. 1081-1085 Original Papers
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/RawiMKSKC18 share record
persistent URL:
Reda Rawi ,Raghvendra Mall ,Khalid Kunji ,Chen-Hsiang Shen ,Peter D. Kwong ,Gwo-Yu Chuang :PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine. 1092-1098 export record
dblp key:
journals/bioinformatics/GuoLHOSZ18 share record
persistent URL:
Rui Guo ,Yan-Ran Li ,Shan He ,Le Ou-Yang ,Yiwen Sun ,Zexuan Zhu :RepLong: de novo repeat identification using long read sequencing data. 1099-1107 export record
dblp key:
journals/bioinformatics/TsengCPCLZKLHLC18 share record
persistent URL:
Kuan-Chieh Tseng ,Yi-Fan Chiang-Hsieh ,Hsuan Pai ,Chi-Nga Chow ,Shu-Chuan Lee ,Han-Qin Zheng ,Po-Li Kuo ,Guan-Zhen Li ,Yu-Cheng Hung ,Na-Sheng Lin ,Wen-Chi Chang :microRPM: a microRNA prediction model based only on plant small RNA sequencing data. 1108-1115 export record
dblp key:
journals/bioinformatics/HoffmannFVMSA18 share record
persistent URL:
Anne Hoffmann ,Jörg Fallmann ,Elisa Vilardo ,Mario Mörl ,Peter F. Stadler ,Fabian Amman :Accurate mapping of tRNA reads. 1116-1124 export record
dblp key:
journals/bioinformatics/RangavittalHCTC18 share record
persistent URL:
Samarth Rangavittal ,Robert S. Harris ,Monika Cechova ,Marta Tomaszkiewicz ,Rayan Chikhi ,Kateryna D. Makova ,Paul Medvedev :RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. 1125-1131 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/YiRZAL18 share record
persistent URL:
Haidong Yi ,Ayush T. Raman ,Han Zhang ,Genevera I. Allen ,Zhandong Liu :Detecting hidden batch factors through data-adaptive adjustment for biological effects. 1141-1147 export record
dblp key:
journals/bioinformatics/NguyenB18 share record
persistent URL:
Phan Nguyen ,Rosemary Braun :Semi-supervised network inference using simulated gene expression dynamics. 1148-1156 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/LiaoSH18 share record
persistent URL:
Peizhou Liao ,Glen A. Satten ,Yi-Juan Hu :Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing. 1157-1163 Systems Biology
export record
dblp key:
journals/bioinformatics/OlayanAB18 share record
persistent URL:
Rawan S. Olayan ,Haitham Ashoor ,Vladimir B. Bajic :DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. 1164-1173 export record
dblp key:
journals/bioinformatics/RamirezM18 share record
persistent URL:
Carlos Ramírez ,Luis Mendoza :Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network. 1174-1182 export record
dblp key:
journals/bioinformatics/IvanovRRGMJDCMK18 share record
persistent URL:
Andrei A. Ivanov ,Brian Revennaugh ,Lauren Rusnak ,Valentina Gonzalez-Pecchi ,Xiulei Mo ,Margaret A. Johns ,Yuhong Du ,Lee A. D. Cooper ,Carlos Sanchez Moreno ,Fadlo R. Khuri ,Haian Fu :The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. 1183-1191 Data and Text Mining
Databases and Ontologies
Bioimage Informatics
Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/LindenbaumR18 share record
persistent URL:
Pierre Lindenbaum ,Richard Redon :bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. 1224-1225 export record
dblp key:
journals/bioinformatics/CokelaerCIMLSG18 share record
persistent URL:
Thomas Cokelaer ,Elisabeth Chen ,Francesco Iorio ,Michael P. Menden ,Howard Lightfoot ,Julio Saez-Rodriguez ,Mathew Garnett :GDSCTools for mining pharmacogenomic interactions in cancer. 1226-1228 export record
dblp key:
journals/bioinformatics/YuOY18 share record
persistent URL:
Yiming Yu ,Yidan Ouyang ,Wen Yao :shinyCircos: an R/Shiny application for interactive creation of Circos plot. 1229-1231 Sequence Analysis
export record
dblp key:
journals/bioinformatics/ShinLSPK18 share record
persistent URL:
Sunguk Shin ,Hanna Lee ,Hyeonju Son ,Soonmyung Paik ,Sangwoo Kim :AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing. 1232-1234 export record
dblp key:
journals/bioinformatics/McIverAFSMWSH18 share record
persistent URL:
Lauren J. McIver ,Galeb Abu-Ali ,Eric A. Franzosa ,Randall Schwager ,Xochitl C. Morgan ,Levi Waldron ,Nicola Segata ,Curtis Huttenhower :bioBakery: a meta'omic analysis environment. 1235-1237 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/HuangLX18 share record
persistent URL:
Yangyu Huang ,Haotian Li ,Yi Xiao :3dRPC: a web server for 3D RNA-protein structure prediction. 1238-1240 export record
dblp key:
journals/bioinformatics/NguyenCR18 share record
persistent URL:
Hai Nguyen ,David A. Case ,Alexander S. Rose :NGLview-interactive molecular graphics for Jupyter notebooks. 1241-1242 Gene expression
Systems Biology
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/NelsonSSLPHYOYB18 share record
persistent URL:
Justin Nelson ,Scott W. Simpkins ,Hamid Safizadeh ,Sheena C. Li ,Jeff S. Piotrowski ,Hiroyuki Hirano ,Yoko Yashiroda ,Hiroyuki Osada ,Minoru Yoshida ,Charles Boone ,Chad L. Myers :MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action. 1251-1252 Review
Systems Biology
export record
dblp key:
journals/bioinformatics/RubioloMS18 share record
persistent URL:
Mariano Rubiolo ,Diego H. Milone ,Georgina Stegmayer :Extreme learning machines for reverse engineering of gene regulatory networks from expression time series. 1253-1260 Volume 34, Number 8, April 2018 Original Papers
Sequence Analysis
export record
dblp key:
journals/bioinformatics/AvsecBCG18 share record
persistent URL:
Ziga Avsec ,Mohammadamin Barekatain ,Jun Cheng ,Julien Gagneur :Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. 1261-1269 export record
dblp key:
journals/bioinformatics/KeelDM18 share record
persistent URL:
Brittney N. Keel ,Bo Deng ,Etsuko N. Moriyama :MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks. 1270-1277 export record
dblp key:
journals/bioinformatics/GilF18 share record
persistent URL:
Nelson Gil ,András Fiser :Identifying functionally informative evolutionary sequence profiles. 1278-1286 export record
dblp key:
journals/bioinformatics/EscudieABMCVMHC18 share record
persistent URL:
Frédéric Escudié ,Lucas Auer ,Maria Bernard ,Mahendra Mariadassou ,Laurent Cauquil ,Katia Vidal ,Sarah Maman ,Guillermina Hernandez-Raquet ,Sylvie Combes ,Géraldine Pascal :FROGS: Find, Rapidly, OTUs with Galaxy Solution. 1287-1294 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/MiaoAPK18 share record
persistent URL:
Zong Miao ,Marcus Alvarez ,Päivi Pajukanta ,Arthur Ko :ASElux: an ultra-fast and accurate allelic reads counter. 1313-1320 export record
dblp key:
journals/bioinformatics/KimKHPT18 share record
persistent URL:
Sunghwan Kim ,Dongwan D. Kang ,Zhiguang Huo ,Yongseok Park ,George C. Tseng :Meta-analytic principal component analysis in integrative omics application. 1321-1328 export record
dblp key:
journals/bioinformatics/ZhouWZT18 share record
persistent URL:
Yan Zhou ,Xiang Wan ,Baoxue Zhang ,Tiejun Tong :Classifying next-generation sequencing data using a zero-inflated Poisson model. 1329-1335 export record
dblp key:
journals/bioinformatics/MayerRGP18 share record
persistent URL:
Joshua Mayer ,Raziur Rahman ,Souparno Ghosh ,Ranadip Pal :Sequential feature selection and inference using multi-variate random forests. 1336-1344 Systems Biology
export record
dblp key:
journals/bioinformatics/HayesM18 share record
persistent URL:
Wayne B. Hayes ,Nil Mamano :SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments. 1345-1352 export record
dblp key:
journals/bioinformatics/AliKWA18 share record
persistent URL:
Mehreen Ali ,Suleiman A. Khan ,Krister Wennerberg ,Tero Aittokallio :Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. 1353-1362 export record
dblp key:
journals/bioinformatics/SrinivasanCM18 share record
persistent URL:
Shyam Srinivasan ,William R. Cluett ,Radhakrishnan Mahadevan :Model-based design of bistable cell factories for metabolic engineering. 1363-1371 Data and Text Mining
export record
dblp key:
journals/bioinformatics/MelckenbeeckACP18 share record
persistent URL:
Ine Melckenbeeck ,Pieter Audenaert ,Didier Colle ,Mario Pickavet :Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations. 1372-1380 export record
dblp key:
journals/bioinformatics/LuoYYZWLW18 share record
persistent URL:
Ling Luo ,Zhihao Yang ,Pei Yang ,Yin Zhang ,Lei Wang ,Hongfei Lin ,Jian Wang :An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition. 1381-1388 export record
dblp key:
journals/bioinformatics/SotoZBA18 share record
persistent URL:
Axel J. Soto ,Chrysoula Zerva ,Riza Batista-Navarro ,Sophia Ananiadou :LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models. 1389-1397 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/Renaud18 share record
persistent URL:
Gabriel Renaud :glactools: a command-line toolset for the management of genotype likelihoods and allele counts. 1398-1400 export record
dblp key:
journals/bioinformatics/KoehorstDSSSS18 share record
persistent URL:
Jasper J. Koehorst ,Jesse C. J. van Dam ,Edoardo Saccenti ,Vítor A. P. Martins dos Santos ,María Suárez-Diez ,Peter J. Schaap :SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles. 1401-1403 export record
dblp key:
journals/bioinformatics/OrakovSSG18 share record
persistent URL:
Askarbek N. Orakov ,Nazgul Sakenova ,Anatoly A. Sorokin ,Igor Goryanin :ASAR: visual analysis of metagenomes in R. 1404-1405 export record
dblp key:
journals/bioinformatics/HarrisonCZ18 share record
persistent URL:
Katherine J. Harrison ,Valérie de Crécy-Lagard ,Rémi Zallot :Gene Graphics: a genomic neighborhood data visualization web application. 1406-1408 export record
dblp key:
journals/bioinformatics/TangLLZZ18 share record
persistent URL:
Bixia Tang ,Feifei Li ,Jing Li ,Wenming Zhao ,Zhihua Zhang :Delta: a new web-based 3D genome visualization and analysis platform. 1409-1410 Sequence Analysis
export record
dblp key:
journals/bioinformatics/WeberLDMQMOWKME18 share record
persistent URL:
Nick Weber ,David Liou ,Jennifer Dommer ,Philip MacMenamin ,Mariam Quiñones ,Ian Misner ,Andrew J. Oler ,Joe Wan ,Lewis Kim ,Meghan Coakley McCarthy ,Samuel Ezeji ,Karlynn Noble ,Darrell E. Hurt :Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. 1411-1413 export record
dblp key:
journals/bioinformatics/GranaLFPG18 share record
persistent URL:
Osvaldo Graña ,Hugo López-Fernández ,Florentino Fdez-Riverola ,David G. Pisano ,Daniel Glez-Peña :Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. 1414-1415 Gene expression
export record
dblp key:
journals/bioinformatics/ChiesaCP18 share record
persistent URL:
Mattia Chiesa ,Gualtiero I. Colombo ,Luca Piacentini :DaMiRseq - an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification. 1416-1418 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/Kofler18 share record
persistent URL:
Robert Kofler :SimulaTE: simulating complex landscapes of transposable elements of populations. 1419-1420 Systems Biology
export record
dblp key:
journals/bioinformatics/LigonFCBBH18 share record
persistent URL:
Thomas S. Ligon ,Fabian Fröhlich ,Oana Chis ,Julio R. Banga ,Eva Balsa-Canto ,Jan Hasenauer :GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. 1421-1423 export record
dblp key:
journals/bioinformatics/WarnkeHU18 share record
persistent URL:
Tom Warnke ,Tobias Helms ,Adelinde M. Uhrmacher :Reproducible and flexible simulation experiments with ML-Rules and SESSL. 1424-1427 export record
dblp key:
journals/bioinformatics/WuLWW18 share record
persistent URL:
Lin Wu ,Min Li ,Jianxin Wang ,Fang-Xiang Wu :CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis. 1428-1430 Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/ProbstR18 share record
persistent URL:
Daniel Probst ,Jean-Louis Reymond :FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web. 1433-1435 export record
dblp key:
journals/bioinformatics/PalmerPFA18 share record
persistent URL:
Andrew Palmer ,Prasad Phapale ,Dominik Fay ,Theodore Alexandrov :Curatr: a web application for creating, curating and sharing a mass spectral library. 1436-1438 Corrigendum
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/Kofler18a share record
persistent URL:
Robert Kofler :SimulaTE: simulating complex landscapes of transposable elements of populations. 1439 Erratum
Databases and Ontologies
Volume 34, Number 9, May 2018 Original Papers
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/ChengXC18 share record
persistent URL:
Xiang Cheng ,Xuan Xiao ,Kuo-Chen Chou :pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information. 1448-1456 export record
dblp key:
journals/bioinformatics/HuangKS18 share record
persistent URL:
Liren Huang ,Jan Krüger ,Alexander Sczyrba :Analyzing large scale genomic data on the cloud with Sparkhit. 1457-1465 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/NortonVLGB18 share record
persistent URL:
Scott S. Norton ,Jorge Vaquero-Garcia ,Nicholas F. Lahens ,Gregory R. Grant ,Yoseph Barash :Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. 1488-1497 export record
dblp key:
journals/bioinformatics/NapolitanoCMPSM18 share record
persistent URL:
Francesco Napolitano ,Diego Carrella ,Barbara Mandriani ,Sandra Pisonero-Vaquero ,Francesco Sirci ,Diego L. Medina ,Nicola Brunetti-Pierri ,Diego di Bernardo :gene2drug: a computational tool for pathway-based rational drug repositioning. 1498-1505 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/DerkachZC18 share record
persistent URL:
Andriy Derkach ,Haoyu Zhang ,Nilanjan Chatterjee :Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies. 1506-1513 Systems Biology
Data and Text Mining
export record
dblp key:
journals/bioinformatics/Fu0DY18 share record
persistent URL:
Guangyuan Fu ,Jun Wang ,Carlotta Domeniconi ,Guoxian Yu :Matrix factorization-based data fusion for the prediction of lncRNA-disease associations. 1529-1537 export record
dblp key:
journals/bioinformatics/PreuerLHBBK18 share record
persistent URL:
Kristina Preuer ,Richard P. I. Lewis ,Sepp Hochreiter ,Andreas Bender ,Krishna C. Bulusu ,Günter Klambauer :DeepSynergy: predicting anti-cancer drug synergy with Deep Learning. 1538-1546 export record
dblp key:
journals/bioinformatics/ZhuLCP18 share record
persistent URL:
Qile Zhu ,Xiaolin Li ,Ana Conesa ,Cécile Pereira :GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text. 1547-1554 export record
dblp key:
journals/bioinformatics/Jin0Y18 share record
persistent URL:
Zhuxuan Jin ,Jian Kang ,Tianwei Yu :Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations. 1555-1561 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/ClearyF18 share record
persistent URL:
Alan M. Cleary ,Andrew D. Farmer :Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny. 1562-1564 export record
dblp key:
journals/bioinformatics/LuberTCPK18 share record
persistent URL:
Jacob M. Luber ,Braden T. Tierney ,Evan M. Cofer ,Chirag J. Patel ,Aleksandar D. Kostic :Aether: leveraging linear programming for optimal cloud computing in genomics. 1565-1567 export record
dblp key:
journals/bioinformatics/ZhengZ18 share record
persistent URL:
Xiaobin Zheng ,Yixian Zheng :CscoreTool: fast Hi-C compartment analysis at high resolution. 1568-1570 export record
dblp key:
journals/bioinformatics/ZhangOYHY18 share record
persistent URL:
Xiao-Fei Zhang ,Le Ou-Yang ,Shuo Yang ,Xiaohua Hu ,Hong Yan :DiffGraph: an R package for identifying gene network rewiring using differential graphical models. 1571-1573 Sequence Analysis
export record
dblp key:
journals/bioinformatics/MaLGMCC18 share record
persistent URL:
Xuan Ma ,Chunyan Liu ,Lian-Feng Gu ,Beixin Mo ,Xiaofeng Cao ,Xuemei Chen :TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants. 1574-1576 export record
dblp key:
journals/bioinformatics/VuGSKR18 share record
persistent URL:
Duong Vu ,Sonja Georgievska ,Szaniszlo Szoke ,Arnold Kuzniar ,Vincent Robert :fMLC: fast multi-level clustering and visualization of large molecular datasets. 1577-1579 export record
dblp key:
journals/bioinformatics/GaoWZWCG18 share record
persistent URL:
Yubang Gao ,Huiyuan Wang ,Hangxiao Zhang ,Yongsheng Wang ,Jinfeng Chen ,Lian-Feng Gu :PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq. 1580-1582 export record
dblp key:
journals/bioinformatics/SuplatovKPVS18 share record
persistent URL:
Dmitry A. Suplatov ,Kirill E. Kopylov ,Nina N. Popova ,Vladimir V. Voevodin ,Vytas K. Svedas :Mustguseal: a server for multiple structure-guided sequence alignment of protein families. 1583-1585 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/LeeM18 share record
persistent URL:
Woonghee Lee ,John L. Markley :PINE-SPARKY.2 for automated NMR-based protein structure research. 1586-1588 Gene expression
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/KingFRMSP18 share record
persistent URL:
Brendan King ,Terry Farrah ,Matthew A. Richards ,Michael B. Mundy ,Evangelos Simeonidis ,Nathan D. Price :ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions. 1594-1596 export record
dblp key:
journals/bioinformatics/0007YW0W18 share record
persistent URL:
Min Li ,Jie Yang ,Fang-Xiang Wu ,Yi Pan ,Jianxin Wang :DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization. 1597-1599 Data and Text Mining
export record
dblp key:
journals/bioinformatics/GaliliOSS18 share record
persistent URL:
Tal Galili ,Alan O'Callaghan ,Jonathan Sidi ,Carson Sievert :heatmaply: an R package for creating interactive cluster heatmaps for online publishing. 1600-1602 export record
dblp key:
journals/bioinformatics/ZhouZSX18 share record
persistent URL:
Anbo Zhou ,Yeting Zhang ,Yazhou Sun ,Jinchuan Xing :PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool. 1603-1605 export record
dblp key:
journals/bioinformatics/TahsinWOMSG18 share record
persistent URL:
Tasnia Tahsin ,Davy Weissenbacher ,Karen O'Connor ,Arjun Magge ,Matthew Scotch ,Graciela Gonzalez-Hernandez :GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. 1606-1608 export record
dblp key:
journals/bioinformatics/ZhangZW18 share record
persistent URL:
Xiaohua Douglas Zhang ,Zhaozhi Zhang ,Dandan Wang :CGManalyzer: an R package for analyzing continuous glucose monitoring studies. 1609-1611 Databases and Ontologies
export record
dblp key:
journals/bioinformatics/KhanM18 share record
persistent URL:
Aziz Khan ,Anthony Mathelier :JASPAR RESTful API: accessing JASPAR data from any programming language. 1612-1614 export record
dblp key:
journals/bioinformatics/WeiJYXZJ18 share record
persistent URL:
Lin Wei ,Zhilin Jin ,Shengjie Yang ,Yanxun Xu ,Yitan Zhu ,Yuan Ji :TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data. 1615-1617 export record
dblp key:
journals/bioinformatics/FeiWLLZH18 share record
persistent URL:
Yuhan Fei ,Rui Wang ,Haoyuan Li ,Shu Liu ,Hongsheng Zhang ,Ji Huang :DPMIND: degradome-based plant miRNA-target interaction and network database. 1618-1620 Volume 34, Number 10, May 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/FehlmannBAFHKLR18 share record
persistent URL:
Tobias Fehlmann ,Christina Backes ,Julia Alles ,Ulrike Fischer ,Martin Hart ,Fabian Kern ,Hilde Langseth ,Trine Rounge ,Sinan Ugur Umu ,Mustafa Kahraman ,Thomas Laufer ,Jan Haas ,Cord Staehler ,Nicole Ludwig ,Matthias Hübenthal ,Benjamin Meder ,Andre Franke ,Hans-Peter Lenhof ,Eckart Meese ,Andreas Keller :A high-resolution map of the human small non-coding transcriptome. 1621-1628 export record
dblp key:
journals/bioinformatics/GaitatzesJSV18 share record
persistent URL:
Athanasios Gaitatzes ,Sarah H. Johnson ,James B. Smadbeck ,George Vasmatzis :Genome U-Plot: a whole genome visualization. 1629-1634 export record
dblp key:
journals/bioinformatics/DrubayGM18 share record
persistent URL:
Damien Drubay ,Daniel Gautheret ,Stefan Michiels :A benchmark study of scoring methods for non-coding mutations. 1635-1641 export record
dblp key:
journals/bioinformatics/BenelliRD18 share record
persistent URL:
Matteo Benelli ,Dario Romagnoli ,Francesca Demichelis :Tumor purity quantification by clonal DNA methylation signatures. 1642-1649 Sequence Analysis
export record
dblp key:
journals/bioinformatics/VogesOH18 share record
persistent URL:
Jan Voges ,Jörn Ostermann ,Mikel Hernaez :CALQ: compression of quality values of aligned sequencing data. 1650-1658 export record
dblp key:
journals/bioinformatics/AudanoRV18 share record
persistent URL:
Peter Audano ,Shashidhar Ravishankar ,Fredrik Vannberg :Mapping-free variant calling using haplotype reconstruction from k-mer frequencies. 1659-1665 export record
dblp key:
journals/bioinformatics/YangNWIWWPCSZC18 share record
persistent URL:
Yang Yang ,Katherine E. Niehaus ,Timothy M. Walker ,Zamin Iqbal ,A. Sarah Walker ,Daniel J. Wilson ,Tim E. A. Peto ,Derrick W. Crook ,E. Grace Smith ,Tingting Zhu ,David A. Clifton :Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data. 1666-1671 export record
dblp key:
journals/bioinformatics/LinGHLNSMMCRTS18 share record
persistent URL:
Yen-Yi Lin ,Alexander Gawronski ,Faraz Hach ,Sujun Li ,Ibrahim Numanagic ,Iman Sarrafi ,Swati Mishra ,Andrew W. McPherson ,Colin C. Collins ,Milan Radovich ,Haixu Tang ,Süleyman Cenk Sahinalp :Computational identification of micro-structural variations and their proteogenomic consequences in cancer. 1672-1681 export record
dblp key:
journals/bioinformatics/LinAJJ18 share record
persistent URL:
Jie Lin ,Donald A. Adjeroh ,Bing-Hua Jiang ,Yue Jiang :K2 and K 2 * : efficient alignment-free sequence similarity measurement based on Kendall statistics. 1682-1689 export record
dblp key:
journals/bioinformatics/SavojardoMFC18 share record
persistent URL:
Castrense Savojardo ,Pier Luigi Martelli ,Piero Fariselli ,Rita Casadio :DeepSig: deep learning improves signal peptide detection in proteins. 1690-1696 export record
dblp key:
journals/bioinformatics/KhanMVWCB18 share record
persistent URL:
Hamza Khan ,Hamid Mohamadi ,Benjamin P. Vandervalk ,René L. Warren ,Justin Chu ,Inanç Birol :ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. 1697-1704 export record
dblp key:
journals/bioinformatics/ZhangPW18 share record
persistent URL:
Juhua Zhang ,Wenbo Peng ,Lei Wang :LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks. 1705-1712 export record
dblp key:
journals/bioinformatics/MannakeeBWGK18 share record
persistent URL:
Brian K. Mannakee ,Uthra Balaji ,Agnieszka K. Witkiewicz ,Ryan N. Gutenkunst ,Erik S. Knudsen :Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors. 1713-1718 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/DongPZY18 share record
persistent URL:
Runze Dong ,Zhenling Peng ,Yang Zhang ,Jianyi Yang :mTM-align: an algorithm for fast and accurate multiple protein structure alignment. 1719-1725 Gene expression
export record
dblp key:
journals/bioinformatics/ImbertVGALGVV18 share record
persistent URL:
Alyssa Imbert ,Armand Valsesia ,Caroline Le Gall ,Claudia Armenise ,Gregory Lefebvre ,Pierre-Antoine Gourraud ,Nathalie Viguerie ,Nathalie Villa-Vialaneix :Multiple hot-deck imputation for network inference from RNA sequencing data. 1726-1732 export record
dblp key:
journals/bioinformatics/ChenGWJWHCX18 share record
persistent URL:
Xi Chen ,Jinghua Gu ,Xiao Wang ,Jin-Gyoung Jung ,Tian-Li Wang ,Leena Hilakivi-Clarke ,Robert Clarke ,Jianhua Xuan :CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data. 1733-1740 Genetics and Population Analysis
Systems Biology
Data and Text Mining
export record
dblp key:
journals/bioinformatics/GeorgescuW18 share record
persistent URL:
Constantin Georgescu ,Jonathan D. Wren :Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values. 1758-1766 Bioimage Informatics
Applications Notes
Genome Analysis
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/RamakerGC18 share record
persistent URL:
Ryne C. Ramaker ,Emily R. Gordon ,Sara J. Cooper :R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. 1789-1791 export record
dblp key:
journals/bioinformatics/LiWXMCJ18 share record
persistent URL:
Mengci Li ,Shouli Wang ,Guoxiang Xie ,Xiaohui Ma ,Tianlu Chen ,Wei Jia :polyPK: an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach. 1792-1794 export record
dblp key:
journals/bioinformatics/VijayanM18 share record
persistent URL:
Vipin Vijayan ,Tijana Milenkovic :Aligning dynamic networks with DynaWAVE. 1795-1798 Data and Text Mining
Volume 34, Number 11, June 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/NaLRS18 share record
persistent URL:
Joong Chae Na ,Jongchan Lee ,Je-Keun Rhee ,Soo-Yong Shin :PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling. 1801-1807 export record
dblp key:
journals/bioinformatics/DeveauDOBBCCLCB18 share record
persistent URL:
Paul Deveau ,Leo Colmet Daage ,Derek Oldridge ,Virginie Bernard ,Angela Bellini ,Mathieu Chicard ,Nathalie Clement ,Eve Lapouble ,Valerie Combaret ,Anne Boland ,Vincent Meyer ,Jean-Francois Deleuze ,Isabelle Janoueix-Lerosey ,Emmanuel Barillot ,Olivier Delattre ,John M. Maris ,Gudrun Schleiermacher ,Valentina Boeva :QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. 1808-1816 export record
dblp key:
journals/bioinformatics/NingWKMZXL18 share record
persistent URL:
Chao Ning ,Dan Wang ,Huimin Kang ,Raphael Mrode ,Lei Zhou ,Shizhong Xu ,Jianfeng Liu :A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values. 1817-1825 export record
dblp key:
journals/bioinformatics/PetrilloRCG18 share record
persistent URL:
Umberto Ferraro Petrillo ,Gianluca Roscigno ,Giuseppe Cattaneo ,Raffaele Giancarlo :Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms. 1826-1833 export record
dblp key:
journals/bioinformatics/DanekD18 share record
persistent URL:
Agnieszka Danek ,Sebastian Deorowicz :GTC: how to maintain huge genotype collections in a compressed form. 1834-1840 export record
dblp key:
journals/bioinformatics/YeLJLW18 share record
persistent URL:
Congting Ye ,Yuqi Long ,Guoli Ji ,Qingshun Quinn Li ,Xiaohui Wu :APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. 1841-1849 Sequence Analysis
Gene expression
export record
dblp key:
journals/bioinformatics/AfsariGCFKSKFZH18 share record
persistent URL:
Bahman Afsari ,Theresa Guo ,Michael Considine ,Liliana Florea ,Luciane T. Kagohara ,Genevieve L. Stein-O'Brien ,Dylan Kelley ,Emily Flam ,Kristina D. Zambo ,Patrick K. Ha ,Donald Geman ,Michael F. Ochs ,Joseph A. Califano ,Daria A. Gaykalova ,Alexander V. Favorov ,Elana J. Fertig :Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. 1859-1867 export record
dblp key:
journals/bioinformatics/FranksCW18 share record
persistent URL:
Jennifer M. Franks ,Guoshuai Cai ,Michael L. Whitfield :Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data. 1868-1874 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/ZhangWC18 share record
persistent URL:
Jie Zhang ,Zhi Wei ,Jun Chen :A distance-based approach for testing the mediation effect of the human microbiome. 1875-1883 Systems Biology
export record
dblp key:
journals/bioinformatics/ArmeanLTPH18 share record
persistent URL:
Irina M. Armean ,Kathryn S. Lilley ,Matthew W. B. Trotter ,Nicholas Charles Victor Pilkington ,Sean B. Holden :Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. 1884-1892 export record
dblp key:
journals/bioinformatics/GuoZLLSZTZC18 share record
persistent URL:
Weifeng Guo ,Shao-Wu Zhang ,Li-Li Liu ,Fei Liu ,Qianqian Shi ,Lei Zhang ,Ying Tang ,Tao Zeng ,Luonan Chen :Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. 1893-1903 export record
dblp key:
journals/bioinformatics/LuoLWLLW18 share record
persistent URL:
Huimin Luo ,Min Li ,Shaokai Wang ,Quan Liu ,Yaohang Li ,Jianxin Wang :Computational drug repositioning using low-rank matrix approximation and randomized algorithms. 1904-1912 export record
dblp key:
journals/bioinformatics/Kreutz18 share record
persistent URL:
Clemens Kreutz :An easy and efficient approach for testing identifiability. 1913-1921 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/JuliusdottirBRM18 share record
persistent URL:
Thorhildur Juliusdottir ,Karina Banasik ,Neil R. Robertson ,Richard Mott ,Mark I. McCarthy :Toppar: an interactive browser for viewing association study results. 1922-1924 export record
dblp key:
journals/bioinformatics/ChenZ18 share record
persistent URL:
Chunpeng James Chen ,Zhiwu Zhang :iPat: intelligent prediction and association tool for genomic research. 1925-1927 export record
dblp key:
journals/bioinformatics/WosteD18 share record
persistent URL:
Marius Wöste ,Martin Dugas :VIPER: a web application for rapid expert review of variant calls. 1928-1929 export record
dblp key:
journals/bioinformatics/PinelloFY18 share record
persistent URL:
Luca Pinello ,Rick Farouni ,Guo-Cheng Yuan :Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. 1930-1933 export record
dblp key:
journals/bioinformatics/Desvillechabrol18 share record
persistent URL:
Dimitri Desvillechabrol ,Rachel Legendre ,Claire Rioualen ,Christiane Bouchier ,Jacques van Helden ,Sean Kennedy ,Thomas Cokelaer :Sequanix: a dynamic graphical interface for Snakemake workflows. 1934-1936 Sequence Analysis
export record
dblp key:
journals/bioinformatics/KoressaarLKRAR18 share record
persistent URL:
Triinu Koressaar ,Maarja Lepamets ,Lauris Kaplinski ,Kairi Raime ,Reidar Andreson ,Maido Remm :Primer3_masker: integrating masking of template sequence with primer design software. 1937-1938 export record
dblp key:
journals/bioinformatics/TroshinPSBMB18 share record
persistent URL:
Peter V. Troshin ,James B. Procter ,Alexander Sherstnev ,Daniel L. Barton ,Fábio Madeira ,Geoffrey J. Barton :JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure. 1939-1940 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/KnappAZWMD18 share record
persistent URL:
Bernhard Knapp ,Marta Alcalá ,Hao Zhang ,Clare E. West ,P. Anton van der Merwe ,Charlotte M. Deane :pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions. 1941-1943 export record
dblp key:
journals/bioinformatics/PanjkovichS18 share record
persistent URL:
Alejandro Panjkovich ,Dmitri I. Svergun :CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data. 1944-1946 export record
dblp key:
journals/bioinformatics/FusaniWPC18 share record
persistent URL:
Lucia Fusani ,Ian D. Wall ,David Palmer ,Álvaro Cortés Cabrera :Optimal water networks in protein cavities with GAsol and 3D-RISM. 1947-1948 export record
dblp key:
journals/bioinformatics/WangSSSXG18 share record
persistent URL:
Juexin Wang ,Robert Sheridan ,Selçuk Onur Sümer ,Nikolaus Schultz ,Dong Xu ,Jianjiong Gao :G2S: a web-service for annotating genomic variants on 3D protein structures. 1949-1950 Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/ChengHSZJ18 share record
persistent URL:
Liang Cheng ,Yang Hu ,Jie Sun ,Meng Zhou ,Qinghua Jiang :DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function. 1953-1956 export record
dblp key:
journals/bioinformatics/DagleyM18 share record
persistent URL:
Michael J. Dagley ,Malcolm J. McConville :DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS. 1957-1958 export record
dblp key:
journals/bioinformatics/AmarVLS18 share record
persistent URL:
David Amar ,Amir Vizel ,Carmit Levy ,Ron Shamir :ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases. 1959-1961 Data and Text Mining
Bioimage Informatics
Review
Gene expression
Corrigendum
Gene expression
export record
dblp key:
journals/bioinformatics/VijayanM18a share record
persistent URL:
Vipin Vijayan ,Tijana Milenkovic :Aligning dynamic networks with DynaWAVE. 1980 Volume 34, Number 12, June 2018 Discovery note
Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/KaurS18 share record
persistent URL:
Gurmeet Kaur ,Srikrishna Subramanian :Evolutionary relationship between the cysteine and histidine rich domains (CHORDs) and Btk-type zinc fingers. 1981-1985 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/HaoYNAKBBP18 share record
persistent URL:
Yuhan Hao ,Liying Yang ,Antonio Galvao Neto ,Milan R. Amin ,Dervla Kelly ,Stuart M. Brown ,Ryan C. Branski ,Zhiheng Pei :HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA. 1986-1995 export record
dblp key:
journals/bioinformatics/XuFSWD18 share record
persistent URL:
Chao Xu ,Jian Fang ,Hui Shen ,Yu-Ping Wang ,Hong-Wen Deng :EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits. 1996-2003 export record
dblp key:
journals/bioinformatics/LuoFSH18 share record
persistent URL:
Zhihui Luo ,Xinping Fan ,Yao Su ,Yu S. Huang :Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. 2004-2011 export record
dblp key:
journals/bioinformatics/GuoWW18 share record
persistent URL:
Fei Guo ,Dan Wang ,Lusheng Wang :Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data. 2012-2018 Sequence Analysis
export record
dblp key:
journals/bioinformatics/WangWLL18 share record
persistent URL:
Anqi Wang ,Zhanyu Wang ,Zheng Li ,Lei M. Li :BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach. 2019-2028 export record
dblp key:
journals/bioinformatics/JiaZZ18 share record
persistent URL:
Cangzhi Jia ,Yun Zuo ,Quan Zou :O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique. 2029-2036 export record
dblp key:
journals/bioinformatics/Margelevicius18 share record
persistent URL:
Mindaugas Margelevicius :A low-complexity add-on score for protein remote homology search with COMER. 2037-2045 export record
dblp key:
journals/bioinformatics/ParkLKL18 share record
persistent URL:
Sung Yong Park ,Tanzy M. T. Love ,Shivankur Kapoor ,Ha Youn Lee :HIITE: HIV-1 incidence and infection time estimator. 2046-2052 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/ParkZ18 share record
persistent URL:
Seyoung Park ,Hongyu Zhao :Spectral clustering based on learning similarity matrix. 2069-2076 export record
dblp key:
journals/bioinformatics/JinMPN18 share record
persistent URL:
Suoqin Jin ,Adam L. Maclean ,Tao Peng ,Qing Nie :scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. 2077-2086 Systems Biology
Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/DardeGBLCSBCMJC18 share record
persistent URL:
Thomas A. Darde ,Pierre Gaudriault ,Rémi Beranger ,Clément Lancien ,Annaëlle Caillarec-Joly ,Olivier Sallou ,Nathalie Bonvallot ,Cécile Chevrier ,Séverine Mazaud-Guittot ,Bernard Jégou ,Olivier Collin ,Emmanuelle Becker ,Antoine D. Rolland ,Frédéric Chalmel :TOXsIgN: a cross-species repository for toxicogenomic signatures. 2116-2122 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/JiCYZYSPW18 share record
persistent URL:
Guoli Ji ,Moliang Chen ,Wenbin Ye ,Sheng Zhu ,Congting Ye ,Yaru Su ,Haonan Peng ,Xiaohui Wu :TSAPA: identification of tissue-specific alternative polyadenylation sites in plants. 2123-2125 export record
dblp key:
journals/bioinformatics/UrrutiaCZZJ18 share record
persistent URL:
Eugene Urrutia ,Hao Chen ,Zilu Zhou ,Nancy Ruonan Zhang ,Yuchao Jiang :Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. 2126-2128 export record
dblp key:
journals/bioinformatics/Wang18 share record
persistent URL:
Dapeng Wang :GCevobase: an evolution-based database for GC content in eukaryotic genomes. 2129-2131 Sequence Analysis
export record
dblp key:
journals/bioinformatics/PessiaC18 share record
persistent URL:
Alberto Pessia ,Jukka Corander :Kpax3: Bayesian bi-clustering of large sequence datasets. 2132-2133 export record
dblp key:
journals/bioinformatics/XuFLWW18 share record
persistent URL:
Clerk Nuo Xu ,Dongfang Fu ,Shiang Li ,Yuxuan Wang ,Aloysius Wong :GCPred: a web tool for guanylyl cyclase functional centre prediction from amino acid sequence. 2134-2135 Gene expression
Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/KimYLZC18 share record
persistent URL:
Hang J. Kim ,Zhenning Yu ,Andrew Lawson ,Hongyu Zhao ,Dongjun Chung :Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA. 2139-2141 export record
dblp key:
journals/bioinformatics/ItersonCHCH18 share record
persistent URL:
Maarten van Iterson ,Davy Cats ,Paul Hop ,BIOS Consortium ,Bastiaan T. Heijmans :omicsPrint: detection of data linkage errors in multiple omics studies. 2142-2143 export record
dblp key:
journals/bioinformatics/YanFC18 share record
persistent URL:
Qi Yan ,Zhou Fang ,Wei Chen :KMgene: a unified R package for gene-based association analysis for complex traits. 2144-2146 Systems Biology
export record
dblp key:
journals/bioinformatics/MondeelCB18 share record
persistent URL:
Thierry D. G. A. Mondeel ,Frédéric Crémazy ,Matteo Barberis :GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. 2147-2149 export record
dblp key:
journals/bioinformatics/WangLKM18 share record
persistent URL:
Zichen Wang ,Alexander Lachmann ,Alexandra B. Keenan ,Avi Ma'ayan :L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. 2150-2152 export record
dblp key:
journals/bioinformatics/CarbonellWSTTSK18 share record
persistent URL:
Pablo Carbonell ,Jerry Wong ,Neil Swainston ,Eriko Takano ,Nicholas J. Turner ,Nigel S. Scrutton ,Douglas B. Kell ,Rainer Breitling ,Jean-Loup Faulon :Selenzyme: enzyme selection tool for pathway design. 2153-2154 export record
dblp key:
journals/bioinformatics/MihBCCSKMZP18 share record
persistent URL:
Nathan Mih ,Elizabeth Brunk ,Ke Chen ,Edward Catoiu ,Anand Sastry ,Erol S. Kavvas ,Jonathan M. Monk ,Zhen Zhang ,Bernhard O. Palsson :ssbio: a Python framework for structural systems biology. 2155-2157 Databases and Ontologies
Volume 34, Number 13, July 2018 ISMB 2018 Proceedings July 6 to July 10, 2018, Chicago, IL, United States
Ismb 2018 - Intelligent Systems for molecular Biology Proceedings
Ismb 2018 Proceedings Papers Committee
export record
dblp key:
journals/bioinformatics/X18 share record
persistent URL:
ISMB 2018 PROCEEDINGS PAPERS COMMITTEE. i1 ISMB 2018 PROCEEDINGS
Bioinformatics Education
Bioinformatics of Microbes and Microbiomes
Comparative and Functional genomics
export record
dblp key:
journals/bioinformatics/PanWAJL18 share record
persistent URL:
Weihua Pan ,Steve Wanamaker ,Audrey M. V. Ah-Fong ,Howard S. Judelson ,Stefano Lonardi :Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. i43-i51 export record
dblp key:
journals/bioinformatics/SmailiGH18 share record
persistent URL:
Fatima Zohra Smaili ,Xin Gao ,Robert Hoehndorf :Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. i52-i60 export record
dblp key:
journals/bioinformatics/DadanehZQ18 share record
persistent URL:
Siamak Zamani Dadaneh ,Mingyuan Zhou ,Xiaoning Qian :Covariate-dependent negative binomial factor analysis of RNA sequencing data. i61-i69 export record
dblp key:
journals/bioinformatics/GlouzonO18 share record
persistent URL:
Jean-Pierre Séhi Glouzon ,Aïda Ouangraoua :aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences. i70-i78 export record
dblp key:
journals/bioinformatics/PouyanK18 share record
persistent URL:
Maziyar Baran Pouyan ,Dennis Kostka :Random forest based similarity learning for single cell RNA sequencing data. i79-i88 export record
dblp key:
journals/bioinformatics/HerW18 share record
persistent URL:
Hsuan-Lin Her ,Yu-Wei Wu :A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. i89-i95 export record
dblp key:
journals/bioinformatics/LiuLYN18 share record
persistent URL:
Jie Liu ,Dejun Lin ,Galip Gürkan Yardimci ,William Stafford Noble :Unsupervised embedding of single-cell Hi-C data. i96-i104 export record
dblp key:
journals/bioinformatics/GargRNGDM18 share record
persistent URL:
Shilpa Garg ,Mikko Rautiainen ,Adam M. Novak ,Erik Garrison ,Richard Durbin ,Tobias Marschall :A graph-based approach to diploid genome assembly. i105-i114 export record
dblp key:
journals/bioinformatics/GhareghaniPSMEK18 share record
persistent URL:
Maryam Ghareghani ,David Porubsky ,Ashley D. Sanders ,Sascha Meiers ,Evan E. Eichler ,Jan O. Korbel ,Tobias Marschall :Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. i115-i123 export record
dblp key:
journals/bioinformatics/MukherjeeZFSK18 share record
persistent URL:
Sumit Mukherjee ,Yue Zhang ,Joshua Fan ,Georg Seelig ,Sreeram Kannan :Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge. i124-i132 export record
dblp key:
journals/bioinformatics/ZhangWYZM18 share record
persistent URL:
Ruochi Zhang ,Yuchuan Wang ,Yang Yang ,Yang Zhang ,Jian Ma :Predicting CTCF-mediated chromatin loops using CTCF-MP. i133-i141 export record
dblp key:
journals/bioinformatics/MikheenkoPSAG18 share record
persistent URL:
Alla Mikheenko ,Andrey D. Prjibelski ,Vladislav Saveliev ,Dmitry Antipov ,Alexey A. Gurevich :Versatile genome assembly evaluation with QUAST-LG. i142-i150 General Computational Biology
export record
dblp key:
journals/bioinformatics/StaporFH18 share record
persistent URL:
Paul Stapor ,Fabian Fröhlich ,Jan Hasenauer :Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis. i151-i159 Genome Privacy and Security
Genomic variation Analysis
Macromolecular sequence, Structure, and function
export record
dblp key:
journals/bioinformatics/JurgesDE18 share record
persistent URL:
Christopher Jürges ,Lars Dölken ,Florian Erhard :Dissecting newly transcribed and old RNA using GRAND-SLAM. i218-i226 export record
dblp key:
journals/bioinformatics/ZhaoZGX18 share record
persistent URL:
Yixiu Zhao ,Xiangrui Zeng ,Qiang Guo ,Min Xu :An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification. i227-i236 export record
dblp key:
journals/bioinformatics/AokiS18 share record
persistent URL:
Genta Aoki ,Yasubumi Sakakibara :Convolutional neural networks for classification of alignments of non-coding RNA sequences. i237-i244 export record
dblp key:
journals/bioinformatics/ChoiFAGB18 share record
persistent URL:
Yoonjoo Choi ,Jacob M. Furlon ,Ryan B. Amos ,Karl E. Griswold ,Chris Bailey-Kellogg :DisruPPI: structure-based computational redesign algorithm for protein binding disruption. i245-i253 export record
dblp key:
journals/bioinformatics/SeoOPK18 share record
persistent URL:
Seokjun Seo ,Minsik Oh ,Youngjune Park ,Sun Kim :DeepFam: deep learning based alignment-free method for protein family modeling and prediction. i254-i262 export record
dblp key:
journals/bioinformatics/ZhuWBX18 share record
persistent URL:
Jianwei Zhu ,Sheng Wang ,Dongbo Bu ,Jinbo Xu :Protein threading using residue co-variation and deep learning. i263-i273 export record
dblp key:
journals/bioinformatics/JokinenHL18 share record
persistent URL:
Emmi Jokinen ,Markus Heinonen ,Harri Lähdesmäki :mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion. i274-i283 export record
dblp key:
journals/bioinformatics/LiXZXZFLGH18 share record
persistent URL:
Yu Li ,Fan Xu ,Fa Zhang ,Pingyong Xu ,Mingshu Zhang ,Ming Fan ,Lihua Li ,Xin Gao ,Renmin Han :DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. i284-i294 export record
dblp key:
journals/bioinformatics/OzturkOO18 share record
persistent URL:
Hakime Öztürk ,Elif Özkirimli Ölmez ,Arzucan Özgür :A novel methodology on distributed representations of proteins using their interacting ligands. i295-i303 export record
dblp key:
journals/bioinformatics/MahlichSRB18 share record
persistent URL:
Yannick Mahlich ,Martin Steinegger ,Burkhard Rost ,Yana Bromberg :HFSP: high speed homology-driven function annotation of proteins. i304-i312 export record
dblp key:
journals/bioinformatics/PengJR18 share record
persistent URL:
Yisu Peng ,Yuxiang Jiang ,Predrag Radivojac :Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. i313-i322 Mass spectrometry
export record
dblp key:
journals/bioinformatics/NguyenNM18 share record
persistent URL:
Dai Hai Nguyen ,Canh Hao Nguyen ,Hiroshi Mamitsuka :SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra. i323-i332 export record
dblp key:
journals/bioinformatics/LudwigDB18 share record
persistent URL:
Marcus Ludwig ,Kai Dührkop ,Sebastian Böcker :Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. i333-i340 Population genomics and molecular Evolution
export record
dblp key:
journals/bioinformatics/NouriK18 share record
persistent URL:
Nima Nouri ,Steven H. Kleinstein :A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. i341-i349 export record
dblp key:
journals/bioinformatics/Braun18 share record
persistent URL:
Edward L. Braun :An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins. i350-i356 export record
dblp key:
journals/bioinformatics/EatonWS18 share record
persistent URL:
Jesse Eaton ,Jingyi Wang ,Russell Schwartz :Deconvolution and phylogeny inference of structural variations in tumor genomic samples. i357-i365 export record
dblp key:
journals/bioinformatics/LafondMS18 share record
persistent URL:
Manuel Lafond ,Mona Meghdari Miardan ,David Sankoff :Accurate prediction of orthologs in the presence of divergence after duplication. i366-i375 export record
dblp key:
journals/bioinformatics/ZhuN18 share record
persistent URL:
Jiafan Zhu ,Luay Nakhleh :Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. i376-i385 Studies of phenotypes and Clinical Applications
export record
dblp key:
journals/bioinformatics/XingQYLZFXHP18 share record
persistent URL:
Wenhui Xing ,Junsheng Qi ,Xiaohui Yuan ,Lin Li ,Xiaoyu Zhang ,Yuhua Fu ,Shengwu Xiong ,Lun Hu ,Jing Peng :A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach. i386-i394 export record
dblp key:
journals/bioinformatics/SundinPMASMDHSH18 share record
persistent URL:
Iiris Sundin ,Tomi Peltola ,Luana Micallef ,Homayun Afrabandpey ,Marta Soare ,Muntasir Mamun Majumder ,Pedram Daee ,Chen He ,Baris Serim ,Aki S. Havulinna ,Caroline Heckman ,Giulio Jacucci ,Pekka Marttinen ,Samuel Kaski :Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge. i395-i403 export record
dblp key:
journals/bioinformatics/ZhangFZ18 share record
persistent URL:
Wensheng Zhang ,Erik K. Flemington ,Kun Zhang :Driver gene mutations based clustering of tumors: methods and applications. i404-i411 export record
dblp key:
journals/bioinformatics/RahimiG18 share record
persistent URL:
Arezou Rahimi ,Mehmet Gönen :Discriminating early- and late-stage cancers using multiple kernel learning on gene sets. i412-i421 export record
dblp key:
journals/bioinformatics/McCoyPVRGGYA18 share record
persistent URL:
Matthew J. McCoy ,Alexander J. Paul ,Matheus B. Victor ,Michelle Richner ,Harrison W. Gabel ,Haijun Gong ,Andrew S. Yoo ,Tae-Hyuk Ahn :LONGO: an R package for interactive gene length dependent analysis for neuronal identity. i422-i428 export record
dblp key:
journals/bioinformatics/BretschneiderGD18 share record
persistent URL:
Hannes Bretschneider ,Shreshth Gandhi ,Amit G. Deshwar ,Khalid Zuberi ,Brendan J. Frey :COSSMO: predicting competitive alternative splice site selection using deep learning. i429-i437 export record
dblp key:
journals/bioinformatics/BockGMRRB18 share record
persistent URL:
Christian Bock ,Thomas Gumbsch ,Michael Moor ,Bastian Rieck ,Damian Roqueiro ,Karsten M. Borgwardt :Association mapping in biomedical time series via statistically significant shapelet mining. i438-i446 export record
dblp key:
journals/bioinformatics/ZakeriSAEM18 share record
persistent URL:
Pooya Zakeri ,Jaak Simm ,Adam Arany ,Sarah ElShal ,Yves Moreau :Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information. i447-i456 export record
dblp key:
journals/bioinformatics/ZitnikAL18 share record
persistent URL:
Marinka Zitnik ,Monica Agrawal ,Jure Leskovec :Modeling polypharmacy side effects with graph convolutional networks. i457-i466 export record
dblp key:
journals/bioinformatics/GaiE18 share record
persistent URL:
Lisa Gai ,Eleazar Eskin :Finding associated variants in genome-wide association studies on multiple traits. i467-i474 export record
dblp key:
journals/bioinformatics/SauerwaldK18 share record
persistent URL:
Natalie Sauerwald ,Carl Kingsford :Quantifying the similarity of topological domains across normal and cancer human cell types. i475-i483 Systems Biology and Networks
export record
dblp key:
journals/bioinformatics/ZhangMI18 share record
persistent URL:
Wei Zhang ,Jianzhu Ma ,Trey Ideker :Classifying tumors by supervised network propagation. i484-i493 export record
dblp key:
journals/bioinformatics/BallnusSTH18 share record
persistent URL:
Benjamin Ballnus ,Steffen Schaper ,Fabian J. Theis ,Jan Hasenauer :Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. i494-i501 export record
dblp key:
journals/bioinformatics/PatkarS18 share record
persistent URL:
Sushant Patkar ,Roded Sharan :An optimization framework for network annotation. i502-i508 export record
dblp key:
journals/bioinformatics/CichonskaPSJAHA18 share record
persistent URL:
Anna Cichonska ,Tapio Pahikkala ,Sándor Szedmák ,Heli Julkunen ,Antti Airola ,Markus Heinonen ,Tero Aittokallio ,Juho Rousu :Learning with multiple pairwise kernels for drug bioactivity prediction. i509-i518 export record
dblp key:
journals/bioinformatics/SrivatsaKSEEDB18 share record
persistent URL:
Sumana Srivatsa ,Jack Kuipers ,Fabian Schmich ,Simone Eicher ,Mario Emmenlauer ,Christoph Dehio ,Niko Beerenwinkel :Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. i519-i527 export record
dblp key:
journals/bioinformatics/PetraliaWPYZW18 share record
persistent URL:
Francesca Petralia ,Li Wang ,Jie Peng ,Arthur Yan ,Jun Zhu ,Pei Wang :A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity. i528-i536 export record
dblp key:
journals/bioinformatics/KaleckyC18 share record
persistent URL:
Karel Kalecky ,Young-Rae Cho :PrimAlign: PageRank-inspired Markovian alignment for large biological networks. i537-i546 export record
dblp key:
journals/bioinformatics/XiaoBS18 share record
persistent URL:
Jinfeng Xiao ,Charles Blatti ,Saurabh Sinha :SigMat: a classification scheme for gene signature matching. i547-i554 export record
dblp key:
journals/bioinformatics/PowersGPTC18 share record
persistent URL:
Rani K. Powers ,Andrew Goodspeed ,Harrison Pielke-Lombardo ,Aik Choon Tan ,James C. Costello :GSEA-InContext: identifying novel and common patterns in expression experiments. i555-i564 Text Mining
Visualisation
export record
dblp key:
journals/bioinformatics/AbdellahHELAMS18 share record
persistent URL:
Marwan Abdellah ,Juan Hernando ,Stefan Eilemann ,Samuel Lapere ,Nicolas Antille ,Henry Markram ,Felix Schürmann :NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks. i574-i582 export record
dblp key:
journals/bioinformatics/BoutillierMLMKF18 share record
persistent URL:
Pierre Boutillier ,Mutaamba Maasha ,Xing Li ,Héctor F. Medina-Abarca ,Jean Krivine ,Jérôme Feret ,Ioana Cristescu ,Angus G. Forbes ,Walter Fontana :The Kappa platform for rule-based modeling. i583-i592 Author Index
export record
dblp key:
journals/bioinformatics/X18a share record
persistent URL:
Author Index. i593-i594 Original Papers
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/RaghupathyCVBSM18 share record
persistent URL:
Narayanan Raghupathy ,Kwangbom Choi ,Matthew J. Vincent ,Glen L. Beane ,Keith S. Sheppard ,Steven C. Munger ,Ron Korstanje ,Fernando Pardo-Manual de Villena ,Gary A. Churchill :Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. 2177-2184 export record
dblp key:
journals/bioinformatics/CaoPYHS18 share record
persistent URL:
Zhen Cao ,Xiaoyong Pan ,Yang Yang ,Yan Huang ,Hong-Bin Shen :The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. 2185-2194 Phylogenetics
Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/SantosFJGMM18 share record
persistent URL:
Ricardo N. dos Santos ,Allan J. R. Ferrari ,Hugo C. R. de Jesus ,Fábio C. Gozzo ,Faruck Morcos ,Leandro Martínez :Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. 2201-2208 export record
dblp key:
journals/bioinformatics/HuLYZ18 share record
persistent URL:
Jun Hu ,Zi Liu ,Dong-Jun Yu ,Yang Zhang :LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. 2209-2218 export record
dblp key:
journals/bioinformatics/OliveiraD18 share record
persistent URL:
Saulo Henrique Pires de Oliveira ,Charlotte M. Deane :Combining co-evolution and secondary structure prediction to improve fragment library generation. 2219-2227 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/YangCL18 share record
persistent URL:
Cheng-Hong Yang ,Li-Yeh Chuang ,Yu-Da Lin :Multiobjective multifactor dimensionality reduction to detect SNP-SNP interactions. 2228-2236 Systems Biology
export record
dblp key:
journals/bioinformatics/PratapaABFTPM18 share record
persistent URL:
Aditya Pratapa ,Neil Adames ,Pavel K. Brazhnik ,Nicholas Franzese ,John J. Tyson ,Jean Peccoud ,T. M. Murali :CrossPlan: systematic planning of genetic crosses to validate mathematical models. 2237-2244 export record
dblp key:
journals/bioinformatics/LuxBCLLAH18 share record
persistent URL:
Markus Lux ,Ryan Remy Brinkman ,Cédric Chauve ,Adam Laing ,Anna Lorenc ,Lucie Abeler-Dörner ,Barbara Hammer :flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry. 2245-2253 Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/YinJCLYCTZ18 share record
persistent URL:
Xiaole Yin ,Xiaotao Jiang ,Benli Chai ,Liguan Li ,Ying Yang ,James R. Cole ,James M. Tiedje ,Tong Zhang :ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. 2263-2270 export record
dblp key:
journals/bioinformatics/WuZWPHCKZ18 share record
persistent URL:
Jiansheng Wu ,Qiuming Zhang ,Weijian Wu ,Tao Pang ,Haifeng Hu ,Wallace K. B. Chan ,Xiaoyan Ke ,Yang Zhang :WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. 2271-2282 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/ShabalinHCCKAO18 share record
persistent URL:
Andrey A. Shabalin ,Mohammad W. Hattab ,Shaunna L. Clark ,Robin F. Chan ,Gaurav Kumar ,Karolina A. Åberg ,Edwin J. C. G. van den Oord :RaMWAS: fast methylome-wide association study pipeline for enrichment platforms. 2283-2285 export record
dblp key:
journals/bioinformatics/JessaK18 share record
persistent URL:
Selin Jessa ,Claudia L. Kleinman :chromswitch: a flexible method to detect chromatin state switches. 2286-2288 export record
dblp key:
journals/bioinformatics/CremonaPCMCV18 share record
persistent URL:
Marzia A. Cremona ,Alessia Pini ,Fabio Cumbo ,Kateryna D. Makova ,Francesca Chiaromonte ,Simone Vantini :IWTomics: testing high-resolution sequence-based 'Omics' data at multiple locations and scales. 2289-2291 Sequence Analysis
Phylogenetics
export record
dblp key:
journals/bioinformatics/MonitG18 share record
persistent URL:
Christopher Monit ,Richard A. Goldstein :SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny. 2297-2299 export record
dblp key:
journals/bioinformatics/DucheneDH18 share record
persistent URL:
David A. Duchêne ,Sebastián Duchêne ,Simon Y. W. Ho :PhyloMAd: efficient assessment of phylogenomic model adequacy. 2300-2301 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/NurminenH18 share record
persistent URL:
Anssi Nurminen ,Vesa P. Hytönen :StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data. 2302-2304 Gene expression
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/SellaVUAI18 share record
persistent URL:
Nadir Sella ,Louis Verny ,Guido Uguzzoni ,Séverine Affeldt ,Hervé Isambert :MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data. 2311-2313 export record
dblp key:
journals/bioinformatics/WandyNGDRH18 share record
persistent URL:
Joe Wandy ,Mu Niu ,Diana Giurghita ,Rónán Daly ,Simon Rogers ,Dirk Husmeier :ShinyKGode: an interactive application for ODE parameter inference using gradient matching. 2314-2315 export record
dblp key:
journals/bioinformatics/GundelHH18 share record
persistent URL:
Michaela Gündel ,Charles Tapley Hoyt ,Martin Hofmann-Apitius :BEL2ABM: agent-based simulation of static models in Biological Expression Language. 2316-2318 export record
dblp key:
journals/bioinformatics/CardosoZJSNH18 share record
persistent URL:
João G. R. Cardoso ,Ahmad A. Zeidan ,Kristian Jensen ,Nikolaus Sonnenschein ,Ana Rute Neves ,Markus J. Herrgård :MARSI: metabolite analogues for rational strain improvement. 2319-2321 Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/KulandaisamyPST18 share record
persistent URL:
A. Kulandaisamy ,S. Binny Priya ,R. Sakthivel ,Svetlana Tarnovskaya ,Ilya Bizin ,Peter Hönigschmid ,Dmitrij Frishman ,M. Michael Gromiha :MutHTP: mutations in human transmembrane proteins. 2325-2326 export record
dblp key:
journals/bioinformatics/SwainstonDJRCWF18 share record
persistent URL:
Neil Swainston ,Mark Dunstan ,Adrian J. Jervis ,Christopher J. Robinson ,Pablo Carbonell ,Alan R. Williams ,Jean-Loup Faulon ,Nigel S. Scrutton ,Douglas B. Kell :PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. 2327-2329 Message from the ISCB
Databases and Ontologies
Corrigenda
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/JaliliMMM18 share record
persistent URL:
Vahid Jalili ,Matteo Matteucci ,Marco Masseroli ,Marco J. Morelli :Using combined evidence from replicates to evaluate ChIP-seq peaks. 2338 export record
dblp key:
journals/bioinformatics/HoffmannFVMSA18a share record
persistent URL:
Anne Hoffmann ,Jörg Fallmann ,Elisa Vilardo ,Mario Mörl ,Peter F. Stadler ,Fabian Amman :Accurate mapping of tRNA reads. 2339 export record
dblp key:
journals/bioinformatics/ZhangZW18a share record
persistent URL:
Xiaohua Douglas Zhang ,Zhaozhi Zhang ,Dandan Wang :CGManalyzer: an R package for analyzing continuous glucose monitoring studies. 2340 Volume 34, Number 14, July 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/ZhuF18 share record
persistent URL:
Shijia Zhu ,Gang Fang :MatrixEpistasis: ultrafast, exhaustive epistasis scan for quantitative traits with covariate adjustment. 2341-2348 export record
dblp key:
journals/bioinformatics/ZhouWWZ18 share record
persistent URL:
Zilu Zhou ,Weixin Wang ,Li-San Wang ,Nancy Ruonan Zhang :Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. 2349-2355 export record
dblp key:
journals/bioinformatics/NakatoS18 share record
persistent URL:
Ryuichiro Nakato ,Katsuhiko Shirahige :Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile. 2356-2363 Sequence Analysis
Gene expression
export record
dblp key:
journals/bioinformatics/HuLHHWZRL18 share record
persistent URL:
Yu Hu ,Jennie Lin ,Jian Hu ,Gang Hu ,Kui Wang ,Hanrui Zhang ,Muredach P. Reilly ,Mingyao Li :PennDiff: detecting differential alternative splicing and transcription by RNA sequencing. 2384-2391 export record
dblp key:
journals/bioinformatics/VuWKNWPR18 share record
persistent URL:
Trung-Nghia Vu ,Quin F. Wills ,Krishna R. Kalari ,Nifang Niu ,Liewei Wang ,Yudi Pawitan ,Mattias Rantalainen :Isoform-level gene expression patterns in single-cell RNA-sequencing data. 2392-2400 export record
dblp key:
journals/bioinformatics/LeePHK18 share record
persistent URL:
Wanseon Lee ,Katharine Plant ,Peter Humburg ,Julian C. Knight :AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes. 2401-2408 Systems Biology
export record
dblp key:
journals/bioinformatics/BhadraBCR18 share record
persistent URL:
Sahely Bhadra ,Peter Blomberg ,Sandra Castillo ,Juho Rousu :Principal metabolic flux mode analysis. 2409-2417 export record
dblp key:
journals/bioinformatics/SampsonBMH18 share record
persistent URL:
Joshua N. Sampson ,Simina M. Boca ,Steven C. Moore ,Ruth Heller :FWER and FDR control when testing multiple mediators. 2418-2424 export record
dblp key:
journals/bioinformatics/ZengLLZ18 share record
persistent URL:
Xiangxiang Zeng ,Li Liu ,Linyuan Lü ,Quan Zou :Prediction of potential disease-associated microRNAs using structural perturbation method. 2425-2432 export record
dblp key:
journals/bioinformatics/TsiantisBB18 share record
persistent URL:
Nikolaos Tsiantis ,Eva Balsa-Canto ,Julio R. Banga :Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. 2433-2440 export record
dblp key:
journals/bioinformatics/Dimitrakopoulos18 share record
persistent URL:
Christos Dimitrakopoulos ,Sravanth Kumar Hindupur ,Luca Häfliger ,Jonas Behr ,Hesam Montazeri ,Michael N. Hall ,Niko Beerenwinkel :Network-based integration of multi-omics data for prioritizing cancer genes. 2441-2448 Data and Text Mining
export record
dblp key:
journals/bioinformatics/FabrisDPMF18 share record
persistent URL:
Fabio Fabris ,Aoife Doherty ,Daniel Palmer ,João Pedro de Magalhães ,Alex Alves Freitas :A new approach for interpreting Random Forest models and its application to the biology of ageing. 2449-2456 export record
dblp key:
journals/bioinformatics/BoomMSD18 share record
persistent URL:
Willem van den Boom ,Callie Mao ,Rebecca A. Schroeder ,David B. Dunson :Extrema-weighted feature extraction for functional data. 2457-2464 export record
dblp key:
journals/bioinformatics/YouZXSMZ18 share record
persistent URL:
Ronghui You ,Zihan Zhang ,Yi Xiong ,Fengzhu Sun ,Hiroshi Mamitsuka ,Shanfeng Zhu :GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. 2465-2473 export record
dblp key:
journals/bioinformatics/GaleaLV18 share record
persistent URL:
Dieter Galea ,Ivan Laponogov ,Kirill A. Veselkov :Exploiting and assessing multi-source data for supervised biomedical named entity recognition. 2474-2482 Applications Notes
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/SzalkaiG18 share record
persistent URL:
Balázs Szalkai ,Vince Grolmusz :SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification. 2487-2489 export record
dblp key:
journals/bioinformatics/NakamuraYTK18 share record
persistent URL:
Tsukasa Nakamura ,Kazunori D. Yamada ,Kentaro Tomii ,Kazutaka Katoh :Parallelization of MAFFT for large-scale multiple sequence alignments. 2490-2492 export record
dblp key:
journals/bioinformatics/Sun18 share record
persistent URL:
Yan-Bo Sun :FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data. 2493-2495 export record
dblp key:
journals/bioinformatics/LandererCZG18 share record
persistent URL:
Cedric Landerer ,Alexander Cope ,Russell L. Zaretzki ,Michael A. Gilchrist :AnaCoDa: analyzing codon data with Bayesian mixture models. 2496-2498 export record
dblp key:
journals/bioinformatics/ChenZLLMWWSDCS18 share record
persistent URL:
Zhen Chen ,Pei Zhao ,Fuyi Li ,André Leier ,Tatiana T. Marquez-Lago ,Yanan Wang ,Geoffrey I. Webb ,Alexander Ian Smith ,Roger J. Daly ,Kuo-Chen Chou ,Jiangning Song :iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. 2499-2502 export record
dblp key:
journals/bioinformatics/BerselliLT18 share record
persistent URL:
Michele Berselli ,Enrico Lavezzo ,Stefano Toppo :NeSSie: a tool for the identification of approximate DNA sequence symmetries. 2503-2505 Phylogenetics
export record
dblp key:
journals/bioinformatics/EscalonaRP18 share record
persistent URL:
Merly Escalona ,Sara Rocha ,David Posada :NGSphy: phylogenomic simulation of next-generation sequencing data. 2506-2507 Structural Bioinformatics
Gene expression
Data and Text Mining
export record
dblp key:
journals/bioinformatics/KostersLSSKZHLF18 share record
persistent URL:
M. Kösters ,Johannes Leufken ,Stefan Schulze ,K. Sugimoto ,Joshua Klein ,R. P. Zahedi ,Michael Hippler ,S. A Leidel ,Christian Fufezan :pymzML v2.0: introducing a highly compressed and seekable gzip format. 2513-2514 export record
dblp key:
journals/bioinformatics/LiQWWZMLZZJ18 share record
persistent URL:
Ruidong Li ,Han Qu ,Shibo Wang ,Julong Wei ,Le Zhang ,Renyuan Ma ,Jianming Lu ,Jianguo Zhu ,Wei-De Zhong ,Zhenyu Jia :GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. 2515-2517 Databases and Ontologies
Volume 34, Number 15, August 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/ArefeenLXJ18 share record
persistent URL:
Ashraful Arefeen ,Juntao Liu ,Xinshu Xiao ,Tao Jiang :TAPAS: tool for alternative polyadenylation site analysis. 2521-2529 export record
dblp key:
journals/bioinformatics/MandricKZ18 share record
persistent URL:
Igor Mandric ,Sergey Knyazev ,Alex Zelikovsky :Repeat-aware evaluation of scaffolding tools. 2530-2537 export record
dblp key:
journals/bioinformatics/GiambartolomeiL18 share record
persistent URL:
Claudia Giambartolomei ,Jimmy Zhenli Liu ,Wen Zhang ,Mads Hauberg ,Huwenbo Shi ,James Boocock ,Joe Pickrell ,Andrew E. Jaffe ,CommonMind Consortium ,Bogdan Pasaniuc ,Panos Roussos :A Bayesian framework for multiple trait colocalization from summary association statistics. 2538-2545 export record
dblp key:
journals/bioinformatics/WangYLMHRZACSSL18 share record
persistent URL:
Jiawei Wang ,Bingjiao Yang ,André Leier ,Tatiana T. Marquez-Lago ,Morihiro Hayashida ,Andrea Rocker ,Yanju Zhang ,Tatsuya Akutsu ,Kuo-Chen Chou ,Richard A. Strugnell ,Jiangning Song ,Trevor Lithgow :Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. 2546-2555 Sequence Analysis
export record
dblp key:
journals/bioinformatics/TurnerGIM18 share record
persistent URL:
Isaac Turner ,Kiran V. Garimella ,Zamin Iqbal ,Gil McVean :Integrating long-range connectivity information into de Bruijn graphs. 2556-2565 export record
dblp key:
journals/bioinformatics/MonteMGCB18 share record
persistent URL:
Matteo Lo Monte ,Candida Manelfi ,Marica Gemei ,Daniela Corda ,Andrea Rosario Beccari :ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors. 2566-2574 export record
dblp key:
journals/bioinformatics/LochelRFH18 share record
persistent URL:
Hannah F. Löchel ,Mona Riemenschneider ,Dmitrij Frishman ,Dominik Heider :SCOTCH: subtype A coreceptor tropism classification in HIV-1. 2575-2580 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/ViricelGSB18 share record
persistent URL:
Clément Viricel ,Simon de Givry ,Thomas Schiex ,Sophie Barbe :Cost function network-based design of protein-protein interactions: predicting changes in binding affinity. 2581-2589 export record
dblp key:
journals/bioinformatics/KlukowskiAZDGW18 share record
persistent URL:
Piotr Klukowski ,Michal Augoff ,Maciej Zieba ,Maciej Drwal ,Adam Gonczarek ,Michal J. Walczak :NMRNet: a deep learning approach to automated peak picking of protein NMR spectra. 2590-2597 export record
dblp key:
journals/bioinformatics/MengPY18 share record
persistent URL:
Qiaozhen Meng ,Zhenling Peng ,Jianyi Yang :CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction. 2598-2604 export record
dblp key:
journals/bioinformatics/KhuranaRKCBM18 share record
persistent URL:
Sameer Khurana ,Reda Rawi ,Khalid Kunji ,Gwo-Yu Chuang ,Halima Bensmail ,Raghvendra Mall :DeepSol: a deep learning framework for sequence-based protein solubility prediction. 2605-2613 Data and Text Mining
export record
dblp key:
journals/bioinformatics/PerchaA18 share record
persistent URL:
Bethany Percha ,Russ B. Altman :A global network of biomedical relationships derived from text. 2614-2624 export record
dblp key:
journals/bioinformatics/TarTBWCLGWO18 share record
persistent URL:
Paul D. Tar ,Neil A. Thacker ,M. Babur ,Yvonne Watson ,Sue Cheung ,R. A Little ,R. G. Gieling ,K. J. Williams ,J. P. B. O'Connor :A new method for the high-precision assessment of tumor changes in response to treatment. 2625-2633 export record
dblp key:
journals/bioinformatics/FeiZSY18 share record
persistent URL:
Teng Fei ,Tengjiao Zhang ,Weiyang Shi ,Tianwei Yu :Mitigating the adverse impact of batch effects in sample pattern detection. 2634-2641 export record
dblp key:
journals/bioinformatics/YangWBA18 share record
persistent URL:
Kevin K. Yang ,Zachary Wu ,Claire N. Bedbrook ,Frances H. Arnold :Learned protein embeddings for machine learning. 2642-2648 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/LawsonTBS18 share record
persistent URL:
John T. Lawson ,Eleni M. Tomazou ,Christoph Bock ,Nathan C. Sheffield :MIRA: an R package for DNA methylation-based inference of regulatory activity. 2649-2650 export record
dblp key:
journals/bioinformatics/NelsonHDGL18 share record
persistent URL:
Andrew D. L. Nelson ,Asher Haug-Baltzell ,Sean Davey ,Brian D. Gregory ,Eric Lyons :EPIC-CoGe: managing and analyzing genomic data. 2651-2653 export record
dblp key:
journals/bioinformatics/PengMO18 share record
persistent URL:
Jianhao Peng ,Olgica Milenkovic ,Idoia Ochoa :METHCOMP: a special purpose compression platform for DNA methylation data. 2654-2656 export record
dblp key:
journals/bioinformatics/XuZLHSLLDZJLJLZ18 share record
persistent URL:
Jing Xu ,Linna Zhao ,Di Liu ,Simeng Hu ,Xiuling Song ,Jin Li ,Hongchao Lv ,Lian Duan ,Mingming Zhang ,Qinghua Jiang ,Guiyou Liu ,Shuilin Jin ,Mingzhi Liao ,Meng Zhang ,Rennan Feng ,Fanwu Kong ,Liangde Xu ,Yongshuai Jiang :EWAS: epigenome-wide association study software 2.0. 2657-2658 export record
dblp key:
journals/bioinformatics/WinterWHAZC18 share record
persistent URL:
David J. Winter ,Steven H. Wu ,Abigail A. Howell ,Ricardo B. R. Azevedo ,Rebecca A. Zufall ,Reed A. Cartwright :accuMUlate: a mutation caller designed for mutation accumulation experiments. 2659-2660 export record
dblp key:
journals/bioinformatics/JungKJY18 share record
persistent URL:
Jaehee Jung ,Jong Im Kim ,Young-Sik Jeong ,Gangman Yi :AGORA: organellar genome annotation from the amino acid and nucleotide references. 2661-2663 Sequence Analysis
export record
dblp key:
journals/bioinformatics/WeiZFLW18 share record
persistent URL:
Zheng Wei ,Wei Zhang ,Huan Fang ,Yanda Li ,Xiaowo Wang :esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis. 2664-2665 export record
dblp key:
journals/bioinformatics/CosterDSCB18 share record
persistent URL:
Wouter De Coster ,Svenn D'Hert ,Darrin T. Schultz ,Marc Cruts ,Christine Van Broeckhoven :NanoPack: visualizing and processing long-read sequencing data. 2666-2669 export record
dblp key:
journals/bioinformatics/FletcherBMC18 share record
persistent URL:
Stephen J. Fletcher ,Mikael Bodén ,Neena Mitter ,Bernard J. Carroll :SCRAM: a pipeline for fast index-free small RNA read alignment and visualization. 2670-2672 export record
dblp key:
journals/bioinformatics/WiltonLFS18 share record
persistent URL:
Richard Wilton ,Xin Li ,Andrew P. Feinberg ,Alexander S. Szalay :Arioc: GPU-accelerated alignment of short bisulfite-treated reads. 2673-2675 Structural Bioinformatics
Gene expression
Systems Biology
export record
dblp key:
journals/bioinformatics/CalderoneC18 share record
persistent URL:
Alberto Calderone ,Gianni Cesareni :SPV: a JavaScript Signaling Pathway Visualizer. 2684-2686 Data and Text Mining
Databases and Ontologies
Bioimage Informatics
Letter to the Editor
Data and Text Mining
export record
dblp key:
journals/bioinformatics/MonsarratV18 share record
persistent URL:
Paul Monsarrat ,Jean-Noel Vergnes :Data mining of effect sizes from PubMed abstracts: a cross-study conceptual replication. 2698-2700 Volume 34, Number 16, August 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/UrsuBTWYNK18 share record
persistent URL:
Oana Ursu ,Nathan Boley ,Maryna Taranova ,Y. X. Rachel Wang ,Galip Gürkan Yardimci ,William Stafford Noble ,Anshul Kundaje :GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. 2701-2707 export record
dblp key:
journals/bioinformatics/DelehelleCALB18 share record
persistent URL:
Franklin Delehelle ,Sylvain Cussat-Blanc ,Jean-Marc Alliot ,Hervé Luga ,Patricia Balaresque :ASGART: fast and parallel genome scale segmental duplications mapping. 2708-2714 export record
dblp key:
journals/bioinformatics/SunHZCLLPCLWLL18 share record
persistent URL:
Xiwei Sun ,Yi Han ,Liyuan Zhou ,Enguo Chen ,Bingjian Lu ,Yong Liu ,Xiaoqing Pan ,Allen W. Cowley Jr. ,Mingyu Liang ,Qingbiao Wu ,Yan Lu ,Pengyuan Liu :A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data. 2715-2723 export record
dblp key:
journals/bioinformatics/ButkiewiczBLJMR18 share record
persistent URL:
Mariusz Butkiewicz ,Elizabeth E. Blue ,Yuk Yee Leung ,Xueqiu Jian ,Edoardo Marcora ,Alan E. Renton ,Amanda Kuzma ,Li-San Wang ,Daniel C. Koboldt ,Jonathan L. Haines ,William S. Bush :Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. 2724-2731 Sequence Analysis
export record
dblp key:
journals/bioinformatics/BrouwerHKBEKSI18 share record
persistent URL:
R. W. W. Brouwer ,M. C. G. N. van den Hout ,C. E. M. Kockx ,Erwin Brosens ,B. Eussen ,A. de Klein ,F. Sleutels ,Wilfred F. J. van IJcken :Nimbus: a design-driven analyses suite for amplicon-based NGS data. 2732-2739 export record
dblp key:
journals/bioinformatics/VeltriKS18 share record
persistent URL:
Daniel Veltri ,Uday Kamath ,Amarda Shehu :Deep learning improves antimicrobial peptide recognition. 2740-2747 export record
dblp key:
journals/bioinformatics/RoguskiOHD18 share record
persistent URL:
Lukasz Roguski ,Idoia Ochoa ,Mikel Hernaez ,Sebastian Deorowicz :FaStore: a space-saving solution for raw sequencing data. 2748-2756 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/LiuWSFGLFLLHZZW18 share record
persistent URL:
Wanlin Liu ,Lai Wei ,Jianan Sun ,Jinwen Feng ,Gaigai Guo ,Lizhu Liang ,Tianyi Fu ,Mingwei Liu ,Kai Li ,Yin Huang ,Weimin Zhu ,Bei Zhen ,Yi Wang ,Chen Ding ,Jun Qin :A reference peptide database for proteome quantification based on experimental mass spectrum response curves. 2766-2772 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/NielSDR18 share record
persistent URL:
Clément Niel ,Christine Sinoquet ,Christian Dina ,Ghislain Rocheleau :SMMB: a stochastic Markov blanket framework strategy for epistasis detection in GWAS. 2773-2780 export record
dblp key:
journals/bioinformatics/PriveAZB18 share record
persistent URL:
Florian Privé ,Hugues Aschard ,Andrey Ziyatdinov ,Michael G. B. Blum :Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr. 2781-2787 export record
dblp key:
journals/bioinformatics/MingDCWLY18 share record
persistent URL:
Jingsi Ming ,Mingwei Dai ,Mingxuan Cai ,Xiang Wan ,Jin Liu ,Can Yang :LSMM: a statistical approach to integrating functional annotations with genome-wide association studies. 2788-2796 export record
dblp key:
journals/bioinformatics/ZengHZ18 share record
persistent URL:
Ping Zeng ,Xingjie Hao ,Xiang Zhou :Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models. 2797-2807 Systems Biology
Data and Text Mining
export record
dblp key:
journals/bioinformatics/PoleksicX18 share record
persistent URL:
Aleksandar Poleksic ,Lei Xie :Predicting serious rare adverse reactions of novel chemicals. 2835-2842 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/BirminghamMMXF18 share record
persistent URL:
Amanda Birmingham ,Adam M. Mark ,Carlo Mazzaferro ,Guorong Xu ,Kathleen M. Fisch :Efficient population-scale variant analysis and prioritization with VAPr. 2843-2845 export record
dblp key:
journals/bioinformatics/RizzettoKSSRCLE18 share record
persistent URL:
Simone Rizzetto ,David N. P. Koppstein ,Jerome Samir ,Mandeep Singh ,Joanne H. Reed ,Curtis H. Cai ,Andrew R. Lloyd ,Auda A. Eltahla ,Christopher C. Goodnow ,Fabio Luciani :B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle. 2846-2847 Phylogenetics
Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/NeavesTM18 share record
persistent URL:
Samuel R. Neaves ,Sophia Tsoka ,Louise A. C. Millard :Reactome Pengine: a web-logic API to the Homo sapiens reactome. 2856-2858 export record
dblp key:
journals/bioinformatics/HuangJCI18 share record
persistent URL:
Justin K. Huang ,Tongqiu Jia ,Daniel E. Carlin ,Trey Ideker :pyNBS: a Python implementation for network-based stratification of tumor mutations. 2859-2861 export record
dblp key:
journals/bioinformatics/ToCWLCGCKCCY18 share record
persistent URL:
Andrew Ching-Yuet To ,David Ho-Ting Chu ,Angela Ruoning Wang ,Frances Cheuk-Yau Li ,Alan Wai-On Chiu ,Daisy Yuwei Gao ,Chung Hang Jonathan Choi ,Siu-Kai Kong ,Ting-Fung Chan ,King-Ming Chan ,Kevin Y. Yip :A comprehensive web tool for toehold switch design. 2862-2864 Data and Text Mining
Review
Gene expression
Corrigendum
Gene expression
Erratum
Gene expression
Volume 34, Number 17, September 2018 ECCB 2018:The 17th European Conference on Computational Biology
Genes
export record
dblp key:
journals/bioinformatics/WangDH18 share record
persistent URL:
Xiaoqian Wang ,Kamran Ghasedi Dizaji ,Heng Huang :Conditional generative adversarial network for gene expression inference. i603-i611 export record
dblp key:
journals/bioinformatics/VesztrocyDR18 share record
persistent URL:
Alex Warwick Vesztrocy ,Christophe Dessimoz ,Henning Redestig :Prioritising candidate genes causing QTL using hierarchical orthologous groups. i612-i619 export record
dblp key:
journals/bioinformatics/PlatonZBT18 share record
persistent URL:
Ludovic Platon ,Farida Zehraoui ,Abdelhafid Bendahmane ,Fariza Tahi :IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection. i620-i628 export record
dblp key:
journals/bioinformatics/GreensideSFK18 share record
persistent URL:
Peyton Greenside ,Tyler Shimko ,Polly Fordyce ,Anshul Kundaje :Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. i629-i637 export record
dblp key:
journals/bioinformatics/Ben-BassatCO18 share record
persistent URL:
Ilan Ben-Bassat ,Benny Chor ,Yaron Orenstein :A deep neural network approach for learning intrinsic protein-RNA binding preferences. i638-i646 export record
dblp key:
journals/bioinformatics/TiberiWCHF18 share record
persistent URL:
Simone Tiberi ,Mark Walsh ,Massimo Cavallaro ,Daniel Hebenstreit ,Bärbel Finkenstädt :Bayesian inference on stochastic gene transcription from flow cytometry data. i647-i655 export record
dblp key:
journals/bioinformatics/LinW18 share record
persistent URL:
Jiecong Lin ,Ka-Chun Wong :Off-target predictions in CRISPR-Cas9 gene editing using deep learning. i656-i663 export record
dblp key:
journals/bioinformatics/WangCY18 share record
persistent URL:
Zhezhen Wang ,John M. Cunningham ,Xinan Holly Yang :CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs. i664-i670 Genome
export record
dblp key:
journals/bioinformatics/El-Kebir18 share record
persistent URL:
Mohammed El-Kebir :SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. i671-i679 export record
dblp key:
journals/bioinformatics/YanGZ18 share record
persistent URL:
Hongwei Yan ,Andreas D. M. Gunawan ,Louxin Zhang :S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. i680-i686 export record
dblp key:
journals/bioinformatics/TogninalliRIB18 share record
persistent URL:
Matteo Togninalli ,Damian Roqueiro ,COPDGene Investigators ,Karsten M. Borgwardt :Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts. i687-i696 export record
dblp key:
journals/bioinformatics/WangN18 share record
persistent URL:
Yaxuan Wang ,Luay Nakhleh :Towards an accurate and efficient heuristic for species/gene tree co-estimation. i697-i705 export record
dblp key:
journals/bioinformatics/NumanagicGZBAH18 share record
persistent URL:
Ibrahim Numanagic ,Alim S. Gökkaya ,Lillian Zhang ,Bonnie Berger ,Can Alkan ,Faraz Hach :Fast characterization of segmental duplications in genome assemblies. i706-i714 export record
dblp key:
journals/bioinformatics/AndruschDKTKORN18 share record
persistent URL:
Andreas Andrusch ,Piotr Wojtek Dabrowski ,Jeanette Klenner ,Simon H. Tausch ,Claudia Kohl ,Abdalla Osman ,Bernhard Y. Renard ,Andreas Nitsche :PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples. i715-i721 export record
dblp key:
journals/bioinformatics/HanL0W18 share record
persistent URL:
Renmin Han ,Yu Li ,Xin Gao ,Sheng Wang :An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. i722-i731 export record
dblp key:
journals/bioinformatics/SalazarA18 share record
persistent URL:
Alex Salazar ,Thomas Abeel :Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations. i732-i742 export record
dblp key:
journals/bioinformatics/AyadPP18 share record
persistent URL:
Lorraine A. K. Ayad ,Solon P. Pissis ,Dimitris Polychronopoulos :CNEFinder: finding conserved non-coding elements in genomes. i743-i747 export record
dblp key:
journals/bioinformatics/JainKDPA18 share record
persistent URL:
Chirag Jain ,Sergey Koren ,Alexander T. Dilthey ,Adam M. Phillippy ,Srinivas Aluru :A fast adaptive algorithm for computing whole-genome homology maps. i748-i756 export record
dblp key:
journals/bioinformatics/PengZZLL18 share record
persistent URL:
Hui Peng ,Yi Zheng ,Zhixun Zhao ,Tao Liu ,Jinyan Li :Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions. i757-i765 export record
dblp key:
journals/bioinformatics/DadiSPASRR18 share record
persistent URL:
Temesgen Hailemariam Dadi ,Enrico Siragusa ,Vitor Piro ,Andreas Andrusch ,Enrico Seiler ,Bernhard Y. Renard ,Knut Reinert :DREAM-Yara: an exact read mapper for very large databases with short update time. i766-i772 Proteins
export record
dblp key:
journals/bioinformatics/LiuYWP18 share record
persistent URL:
Yang Liu ,Qing Ye ,Liwei Wang ,Jian Peng :Learning structural motif representations for efficient protein structure search. i773-i780 export record
dblp key:
journals/bioinformatics/LesgidouEGV18 share record
persistent URL:
Nastazia Lesgidou ,Elias Eliopoulos ,George N. Goulielmos ,Metaxia Vlassi :Insights on the alteration of functionality of a tyrosine kinase 2 variant: a molecular dynamics study. i781-i786 export record
dblp key:
journals/bioinformatics/MirabelloW18 share record
persistent URL:
Claudio Mirabello ,Björn Wallner :Topology independent structural matching discovers novel templates for protein interfaces. i787-i794 export record
dblp key:
journals/bioinformatics/OzdemirGK18 share record
persistent URL:
E. Sila Ozdemir ,Attila Gürsoy ,Ozlem Keskin :Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces. i795-i801 export record
dblp key:
journals/bioinformatics/HashemifarNKX18 share record
persistent URL:
Somaye Hashemifar ,Behnam Neyshabur ,Aly A. Khan ,Jinbo Xu :Predicting protein-protein interactions through sequence-based deep learning. i802-i810 export record
dblp key:
journals/bioinformatics/KarimiS18 share record
persistent URL:
Mostafa Karimi ,Yang Shen :iCFN: an efficient exact algorithm for multistate protein design. i811-i820 export record
dblp key:
journals/bioinformatics/OzturkOO18a share record
persistent URL:
Hakime Öztürk ,Arzucan Özgür ,Elif Özkirimli Ölmez :DeepDTA: deep drug-target binding affinity prediction. i821-i829 export record
dblp key:
journals/bioinformatics/ZhaoCTW18 share record
persistent URL:
Rundong Zhao ,Zixuan Cang ,Yiying Tong ,Guo-Wei Wei :Protein pocket detection via convex hull surface evolution and associated Reeb graph. i830-i837 Data
export record
dblp key:
journals/bioinformatics/JimenezRW18 share record
persistent URL:
Beatriz García Jiménez ,Tomás de la Rosa ,Mark D. Wilkinson :MDPbiome: microbiome engineering through prescriptive perturbations. i838-i847 export record
dblp key:
journals/bioinformatics/ManatakisRB18 share record
persistent URL:
Dimitris V. Manatakis ,Vineet K. Raghu ,Panayiotis V. Benos :piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks. i848-i856 export record
dblp key:
journals/bioinformatics/KulmanovSGH18 share record
persistent URL:
Maxat Kulmanov ,Paul N. Schofield ,Georgios V. Gkoutos ,Robert Hoehndorf :Ontology-based validation and identification of regulatory phenotypes. i857-i865 export record
dblp key:
journals/bioinformatics/WangCYNRS0H18 share record
persistent URL:
Xiaoqian Wang ,Hong Chen ,Jingwen Yan ,Kwangsik Nho ,Shannon L. Risacher ,Andrew J. Saykin ,Li Shen ,Heng Huang :Quantitative trait loci identification for brain endophenotypes via new additive model with random networks. i866-i874 export record
dblp key:
journals/bioinformatics/BachSBBR18 share record
persistent URL:
Eric Bach ,Sándor Szedmák ,Céline Brouard ,Sebastian Böcker ,Juho Rousu :Liquid-chromatography retention order prediction for metabolite identification. i875-i883 export record
dblp key:
journals/bioinformatics/ChenZCG18 share record
persistent URL:
Shifu Chen ,Yanqing Zhou ,Yaru Chen ,Jia Gu :fastp: an ultra-fast all-in-one FASTQ preprocessor. i884-i890 export record
dblp key:
journals/bioinformatics/SekhonSQ18 share record
persistent URL:
Arshdeep Sekhon ,Ritambhara Singh ,Yanjun Qi :DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications. i891-i900 export record
dblp key:
journals/bioinformatics/AlshahraniH18 share record
persistent URL:
Mona Alshahrani ,Robert Hoehndorf :Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. i901-i907 export record
dblp key:
journals/bioinformatics/0003LC0GS18 share record
persistent URL:
Florian Schmidt ,Markus List ,Engin Cukuroglu ,Sebastian Köhler ,Jonathan Göke ,Marcel H. Schulz :An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. i908-i916 export record
dblp key:
journals/bioinformatics/MiuraHBVGK18 share record
persistent URL:
Sayaka Miura ,Louise A. Huuki ,Tiffany Buturla ,Tracy Vu ,Karen Gomez ,Sudhir Kumar :Computational enhancement of single-cell sequences for inferring tumor evolution. i917-i926 Systems
export record
dblp key:
journals/bioinformatics/BarmanK18 share record
persistent URL:
Shohag Barman ,Yung-Keun Kwon :A Boolean network inference from time-series gene expression data using a genetic algorithm. i927-i933 export record
dblp key:
journals/bioinformatics/FriouxFTS18 share record
persistent URL:
Clémence Frioux ,Enora Fremy ,Camille Trottier ,Anne Siegel :Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. i934-i943 export record
dblp key:
journals/bioinformatics/GaudeletMP18 share record
persistent URL:
Thomas Gaudelet ,Noël Malod-Dognin ,Natasa Przulj :Higher-order molecular organization as a source of biological function. i944-i953 export record
dblp key:
journals/bioinformatics/JimenezGN18 share record
persistent URL:
Beatriz García Jiménez ,José Luis García lópez ,Juan Nogales :FLYCOP: metabolic modeling-based analysis and engineering microbial communities. i954-i963 export record
dblp key:
journals/bioinformatics/PirklB18 share record
persistent URL:
Martin Pirkl ,Niko Beerenwinkel :Single cell network analysis with a mixture of Nested Effects Models. i964-i971 export record
dblp key:
journals/bioinformatics/ReynaLR18 share record
persistent URL:
Matthew A. Reyna ,Mark D. M. Leiserson ,Benjamin J. Raphael :Hierarchical HotNet: identifying hierarchies of altered subnetworks. i972-i980 export record
dblp key:
journals/bioinformatics/SambamoorthyR18 share record
persistent URL:
Gayathri Sambamoorthy ,Karthik Raman :Understanding the evolution of functional redundancy in metabolic networks. i981-i987 export record
dblp key:
journals/bioinformatics/AbenWSKMSW18 share record
persistent URL:
Nanne Aben ,Johan A. Westerhuis ,Yipeng Song ,Henk A. L. Kiers ,Magali Michaut ,Age K. Smilde ,Lodewyk F. A. Wessels :iTOP: inferring the topology of omics data. i988-i996 export record
dblp key:
journals/bioinformatics/BosdrieszPKSBBB18 share record
persistent URL:
Evert Bosdriesz ,Anirudh Prahallad ,Bertram Klinger ,Anja Sieber ,Astrid Bosma ,René Bernards ,Nils Blüthgen ,Lodewyk F. A. Wessels :Comparative Network Reconstruction using mixed integer programming. i997-i1004 export record
dblp key:
journals/bioinformatics/PenfoldSRHWGGS18 share record
persistent URL:
Christopher A. Penfold ,Anastasiya Sybirna ,John E. Reid ,Yun Huang ,Lorenz Wernisch ,Zoubin Ghahramani ,Murray Grant ,M. Azim Surani :Branch-recombinant Gaussian processes for analysis of perturbations in biological time series. i1005-i1013 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/CickovskiN18 share record
persistent URL:
Trevor Cickovski ,Giri Narasimhan :Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA). 2881-2888 export record
dblp key:
journals/bioinformatics/LeungDF18 share record
persistent URL:
Michael K. K. Leung ,Andrew Delong ,Brendan J. Frey :Inference of the human polyadenylation code. 2889-2898 export record
dblp key:
journals/bioinformatics/LiHBLWG18 share record
persistent URL:
Yu Li ,Renmin Han ,Chongwei Bi ,Mo Li ,Sheng Wang ,Xin Gao :DeepSimulator: a deep simulator for Nanopore sequencing. 2899-2908 export record
dblp key:
journals/bioinformatics/GorenLWW18 share record
persistent URL:
Emily Goren ,Peng Liu ,Chao Wang ,Chong Wang :BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates. 2909-2917 Sequence Analysis
export record
dblp key:
journals/bioinformatics/VoP18 share record
persistent URL:
Nam S. Vo ,Vinhthuy Phan :Leveraging known genomic variants to improve detection of variants, especially close-by Indels. 2918-2926 export record
dblp key:
journals/bioinformatics/ChenZS18 share record
persistent URL:
Jiao Chen ,Yingchao Zhao ,Yanni Sun :De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding. 2927-2935 export record
dblp key:
journals/bioinformatics/WangXDHCZCX18 share record
persistent URL:
Dongwei Wang ,Chunling Xu ,Shanwen Ding ,Xin Huang ,Xi Cheng ,Chao Zhang ,Chun Chen ,Hui Xie :Identification and function of FAR protein family genes from a transcriptome analysis of Aphelenchoides besseyi. 2936-2943 export record
dblp key:
journals/bioinformatics/LiberisVSVL18 share record
persistent URL:
Edgar Liberis ,Petar Velickovic ,Pietro Sormanni ,Michele Vendruscolo ,Pietro Liò :Parapred: antibody paratope prediction using convolutional and recurrent neural networks. 2944-2950 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/MeyerB18 share record
persistent URL:
Hannah Verena Meyer ,Ewan Birney :PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships. 2951-2956 Systems Biology
export record
dblp key:
journals/bioinformatics/Frost18 share record
persistent URL:
H. Robert Frost :Computation and application of tissue-specific gene set weights. 2957-2964 export record
dblp key:
journals/bioinformatics/SchwammleJ18 share record
persistent URL:
Veit Schwämmle ,Ole Nørregaard Jensen :VSClust: feature-based variance-sensitive clustering of omics data. 2965-2972 Data and Text Mining
Databases and Ontologies
Bioimage Informatics
export record
dblp key:
journals/bioinformatics/AndronovMOOHVK18 share record
persistent URL:
Leonid Andronov ,Jonathan Michalon ,Khalid Ouararhni ,Igor Orlov ,Ali Hamiche ,Jean-Luc Vonesch ,Bruno P. Klaholz :3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. 3004-3012 export record
dblp key:
journals/bioinformatics/KartasaloLVVNR18 share record
persistent URL:
Kimmo Kartasalo ,Leena Latonen ,Jorma Vihinen ,Tapio Visakorpi ,Matti Nykter ,Pekka Ruusuvuori :Comparative analysis of tissue reconstruction algorithms for 3D histology. 3013-3021 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/GiordanoSMN18 share record
persistent URL:
Francesca Giordano ,Maximilian R. Stammnitz ,Elizabeth P. Murchison ,Zemin Ning :scanPAV: a pipeline for extracting presence-absence variations in genome pairs. 3022-3024 export record
dblp key:
journals/bioinformatics/ZhangXRCF18 share record
persistent URL:
Ji Zhang ,Yanwen Xiong ,Lynn Rogers ,Glen P. Carter ,Nigel French :Genome-by-genome approach for fast bacterial genealogical relationship evaluation. 3025-3027 export record
dblp key:
journals/bioinformatics/DallmanASJPSHMU18 share record
persistent URL:
Timothy Dallman ,Philip Ashton ,Ulf Schafer ,Aleksey Jironkin ,Anais Painset ,Sharif Shaaban ,Hassan Hartman ,Richard Myers ,Anthony Underwood ,Claire Jenkins ,Kathie Grant :SnapperDB: a database solution for routine sequencing analysis of bacterial isolates. 3028-3029 export record
dblp key:
journals/bioinformatics/AmiryousefiHP18 share record
persistent URL:
Ali Amiryousefi ,Jaakko Hyvönen ,Peter Poczai :IRscope: an online program to visualize the junction sites of chloroplast genomes. 3030-3031 export record
dblp key:
journals/bioinformatics/ClarkeBSF18 share record
persistent URL:
Thomas H. Clarke ,Lauren M. Brinkac ,Granger G. Sutton ,Derrick E. Fouts :GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models. 3032-3034 Sequence Analysis
export record
dblp key:
journals/bioinformatics/BudachM18 share record
persistent URL:
Stefan Budach ,Annalisa Marsico :pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks. 3035-3037 export record
dblp key:
journals/bioinformatics/RavasioRLG18 share record
persistent URL:
Viola Ravasio ,Marco Ritelli ,Andrea Legati ,Edoardo Giacopuzzi :GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS. 3038-3040 Phylogenetics
Gene expression
Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/YoshizoeTT18 share record
persistent URL:
Kazuki Yoshizoe ,Aika Terada ,Koji Tsuda :MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms. 3047-3049 Systems Biology
export record
dblp key:
journals/bioinformatics/HornakovaLVS18 share record
persistent URL:
Andrea Hornáková ,Markus List ,Jilles Vreeken ,Marcel H. Schulz :JAMI: fast computation of conditional mutual information for ceRNA network analysis. 3050-3051 export record
dblp key:
journals/bioinformatics/MoeinGMKPCdS18 share record
persistent URL:
Mahsa Moein ,Kamil Grzyb ,Teresa Gonçalves Martins ,Shinya Komoto ,Francesca Peri ,Alexander D. Crawford ,Aymeric Fouquier d'Hérouël ,Alexander Skupin :CaSiAn: a Calcium Signaling Analyzer tool. 3052-3054 Databases and Ontologies
Volume 34, Number 18, September 2018 Discovery note
Genome Analysis
export record
dblp key:
journals/bioinformatics/VervierM18 share record
persistent URL:
Kevin Vervier ,Jacob J. Michaelson :TiSAn: estimating tissue-specific effects of coding and non-coding variants. 3061-3068 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/PengZBTL18 share record
persistent URL:
Hui Peng ,Yi Zheng ,Michael Blumenstein ,Dacheng Tao ,Jinyan Li :CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling. 3069-3077 export record
dblp key:
journals/bioinformatics/HakkinenAFZKLCG18 share record
persistent URL:
Antti Häkkinen ,Amjad Alkodsi ,Chiara Facciotto ,Kaiyang Zhang ,Katja Kaipio ,Sirpa Leppä ,Olli Carpén ,Seija Grénman ,Johanna Hynninen ,Sakari Hietanen ,Rainer Lehtonen ,Sampsa Hautaniemi :Identifying differentially methylated sites in samples with varying tumor purity. 3078-3085 export record
dblp key:
journals/bioinformatics/LiuWHC18 share record
persistent URL:
Bin Liu ,Fan Weng ,De-Shuang Huang ,Kuo-Chen Chou :iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC. 3086-3093 Sequence Analysis
export record
dblp key:
journals/bioinformatics/Li18 share record
persistent URL:
Heng Li :Minimap2: pairwise alignment for nucleotide sequences. 3094-3100 export record
dblp key:
journals/bioinformatics/GawronskiUZLNRM18 share record
persistent URL:
Alexander Gawronski ,Michael Uhl ,Yajia Zhang ,Yen-Yi Lin ,Yashar S. Niknafs ,Varune R. Ramnarine ,Rohit Malik ,Felix Feng ,Arul M. Chinnaiyan ,Colin C. Collins ,Süleyman Cenk Sahinalp ,Rolf Backofen :MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. 3101-3110 export record
dblp key:
journals/bioinformatics/TajuNLKO18 share record
persistent URL:
Semmy Wellem Taju ,Trinh-Trung-Duong Nguyen ,Nguyen-Quoc-Khanh Le ,Rosdyana Mangir Irawan Kusuma ,Yu-Yen Ou :DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters. 3111-3117 export record
dblp key:
journals/bioinformatics/RaimondiOMV18 share record
persistent URL:
Daniele Raimondi ,Gabriele Orlando ,Yves Moreau ,Wim F. Vranken :Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping. 3118-3125 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/VargaT18 share record
persistent URL:
Julia Varga ,Gábor E. Tusnády :TMCrys: predict propensity of success for transmembrane protein crystallization. 3126-3130 export record
dblp key:
journals/bioinformatics/WangJWZZ18 share record
persistent URL:
Kaili Wang ,Yiren Jian ,Huiwen Wang ,Chen Zeng ,Yunjie Zhao :RBind: computational network method to predict RNA binding sites. 3131-3136 Gene expression
export record
dblp key:
journals/bioinformatics/PflugH18 share record
persistent URL:
Florian G. Pflug ,Arndt von Haeseler :TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers. 3137-3144 export record
dblp key:
journals/bioinformatics/YingLSL18 share record
persistent URL:
Dingge Ying ,Mulin Jun Li ,Pak Chung Sham ,Miao-Xin Li :A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues. 3145-3150 export record
dblp key:
journals/bioinformatics/ZhouWKIZ18 share record
persistent URL:
Xianxiao Zhou ,Minghui Wang ,Igor Katsyv ,Hanna Y. Irie ,Bin Zhang :EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. 3151-3159 Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/WangWLXLB18 share record
persistent URL:
Zi Wang ,Dali Wang ,Chengcheng Li ,Yichi Xu ,Husheng Li ,Zhirong Bao :Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis. 3169-3177 export record
dblp key:
journals/bioinformatics/ChenXWZYL18 share record
persistent URL:
Xing Chen ,Di Xie ,Lei Wang ,Qi Zhao ,Zhu-Hong You ,Hongsheng Liu :BNPMDA: Bipartite Network Projection for MiRNA-Disease Association prediction. 3178-3186 export record
dblp key:
journals/bioinformatics/BakirKGKS18 share record
persistent URL:
Mehmet Emin Bakir ,Savas Konur ,Marian Gheorghe ,Natalio Krasnogor ,Mike Stannett :Automatic selection of verification tools for efficient analysis of biochemical models. 3187-3195 Bioimage Informatics
export record
dblp key:
journals/bioinformatics/RobinsonC18 share record
persistent URL:
Sean Robinson ,Michael Courtney :Spatial quantification of the synaptic activity phenotype across large populations of neurons with Markov random fields. 3196-3204 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/PfeiferL18 share record
persistent URL:
Bastian Pfeifer ,Martin J. Lercher :BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation. 3205-3207 export record
dblp key:
journals/bioinformatics/PuigdevallC18 share record
persistent URL:
Pau Puigdevall ,Robert Castelo :GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. 3208-3210 export record
dblp key:
journals/bioinformatics/TongRZ18 share record
persistent URL:
Yin Tong ,Beibei Ru ,Jiangwen Zhang :miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer. 3211-3213 Phylogenetics
Gene expression
export record
dblp key:
journals/bioinformatics/MullerCLLD18 share record
persistent URL:
Sören Müller ,Ara Cho ,Siyuan J. Liu ,Daniel A. Lim ,Aaron Diaz :CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones. 3217-3219 export record
dblp key:
journals/bioinformatics/YanBGCW18 share record
persistent URL:
Aimin Yan ,Yuguang Ban ,Zhen Gao ,Xi Chen ,Lily Wang :PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data. 3220-3222 export record
dblp key:
journals/bioinformatics/MiaoDWZ18 share record
persistent URL:
Zhun Miao ,Ke Deng ,Xiaowo Wang ,Xuegong Zhang :DEsingle for detecting three types of differential expression in single-cell RNA-seq data. 3223-3224 Systems Biology
Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/ZhaoWARNSFPRC18 share record
persistent URL:
Sophie Zhao ,Ian Walsh ,Jodie L. Abrahams ,Louise Royle ,Terry Nguyen-Khuong ,Daniel Spencer ,Daryl L. Fernandes ,Nicolle H. Packer ,Pauline M. Rudd ,Matthew P. Campbell :GlycoStore: a database of retention properties for glycan analysis. 3231-3232 export record
dblp key:
journals/bioinformatics/NashSFASFR18 share record
persistent URL:
Anthony Nash ,Thomas Sewell ,Rhys A. Farrer ,Alireza Abdolrasouli ,Jennifer M. G. Shelton ,Matthew C. Fisher ,Johanna Rhodes :MARDy: Mycology Antifungal Resistance Database. 3233-3234 export record
dblp key:
journals/bioinformatics/Hernandez-Ferrer18 share record
persistent URL:
Carles Hernandez-Ferrer ,Juan R. González :CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies. 3235-3237 Bioimage Informatics
export record
dblp key:
journals/bioinformatics/WangYW18 share record
persistent URL:
Anliang Wang ,Xiaolong Yan ,Zhijun Wei :ImagePy: an open-source, Python-based and platform-independent software package for bioimage analysis. 3238-3240 Volume 34, Number 19, October 2018 Discovery note
Genome Analysis
export record
dblp key:
journals/bioinformatics/GozZT18 share record
persistent URL:
Eli Goz ,Zohar Zafrir ,Tamir Tuller :Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. 3241-3248 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/MaziarzPWG18 share record
persistent URL:
Marlena Maziarz ,Ruth M. Pfeiffer ,Yunhu Wan ,Mitchell H. Gail :Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation. 3249-3257 export record
dblp key:
journals/bioinformatics/Gotoh18 share record
persistent URL:
Osamu Gotoh :Modeling one thousand intron length distributions with fitild. 3258-3264 export record
dblp key:
journals/bioinformatics/MalikAP18 share record
persistent URL:
Laraib Malik ,Fatemeh Almodaresi ,Rob Patro :Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis. 3265-3272 Sequence Analysis
export record
dblp key:
journals/bioinformatics/DuraiS18 share record
persistent URL:
Dilip A. Durai ,Marcel H. Schulz :In silico read normalization using set multi-cover optimization. 3273-3280 export record
dblp key:
journals/bioinformatics/FilatovBK18 share record
persistent URL:
Gleb Filatov ,Bruno Bauwens ,Attila Kertész-Farkas :LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification. 3281-3288 export record
dblp key:
journals/bioinformatics/IqbalH18 share record
persistent URL:
Sumaiya Iqbal ,Md. Tamjidul Hoque :PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence. 3289-3299 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/JarmolinskaKDS18 share record
persistent URL:
Aleksandra I. Jarmolinska ,Michal Kadlof ,Pawel Dabrowski-Tumanski ,Joanna I. Sulkowska :GapRepairer: a server to model a structural gap and validate it using topological analysis. 3300-3307 export record
dblp key:
journals/bioinformatics/JonesK18 share record
persistent URL:
David T. Jones ,Shaun M. Kandathil :High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. 3308-3315 export record
dblp key:
journals/bioinformatics/HealBWTW18 share record
persistent URL:
Jack W. Heal ,Gail J. Bartlett ,Christopher W. Wood ,Andrew R. Thomson ,Derek N. Woolfson :Applying graph theory to protein structures: an Atlas of coiled coils. 3316-3323 export record
dblp key:
journals/bioinformatics/MinamiSOC18 share record
persistent URL:
Shintaro Minami ,Kengo Sawada ,Motonori Ota ,George Chikenji :MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers. 3324-3331 Gene expression
Systems Biology
Data and Text Mining
Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/ObregonSLCBAC18 share record
persistent URL:
Flavio Pazos Obregón ,Pablo Soto ,José Luis Lavín ,Ana Rosa Cortázar ,Rosa Barrio ,Ana María Aransay ,Rafael Cantera :Cluster Locator, online analysis and visualization of gene clustering. 3377-3379 export record
dblp key:
journals/bioinformatics/ShindeBIHLRZL18 share record
persistent URL:
Jayendra Shinde ,Quentin Bayard ,Sandrine Imbeaud ,Théo Z. Hirsch ,Feng Liu ,Victor Renault ,Jessica Zucman-Rossi ,Eric Letouzé :Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer. 3380-3381 Sequence Analysis
export record
dblp key:
journals/bioinformatics/StocksMBPMTDM18 share record
persistent URL:
Matthew B. Stocks ,Irina Mohorianu ,Matthew Beckers ,Claudia Paicu ,Simon Moxon ,Joshua Thody ,Tamas Dalmay ,Vincent Moulton :The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs. 3382-3384 export record
dblp key:
journals/bioinformatics/Marot-Lassauzaie18 share record
persistent URL:
Valérie Marot-Lassauzaie ,Michael Bernhofer ,Burkhard Rost :Correcting mistakes in predicting distributions. 3385-3386 export record
dblp key:
journals/bioinformatics/PedersenQ18a share record
persistent URL:
Brent S. Pedersen ,Aaron R. Quinlan :hts-nim: scripting high-performance genomic analyses. 3387-3389 export record
dblp key:
journals/bioinformatics/KressLPT18 share record
persistent URL:
Arnaud Kress ,Odile Lecompte ,Olivier Poch ,Julie Dawn Thompson :PROBE: analysis and visualization of protein block-level evolution. 3390-3392 export record
dblp key:
journals/bioinformatics/NursimuluXWKP18 share record
persistent URL:
Nirvana Nursimulu ,Leon L. Xu ,James D. Wasmuth ,Ivan Krukov ,John Parkinson :Improved enzyme annotation with EC-specific cutoffs using DETECT v2. 3393-3395 export record
dblp key:
journals/bioinformatics/KhanSLCTGDT18 share record
persistent URL:
Waqasuddin Khan ,Ganapathi Varma Saripella ,Thomas Ludwig ,Tania Cuppens ,Florian Thibord ,Emmanuelle Génin ,Jean-Francois Deleuze ,David-Alexandre Trégouët :MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data. 3396-3398 Phylogenetics
Structural Bioinformatics
Gene expression
Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/GorjancH18 share record
persistent URL:
Gregor Gorjanc ,John M. Hickey :AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs. 3408-3411 export record
dblp key:
journals/bioinformatics/LavilleBPZGWPRA18 share record
persistent URL:
Vincent Laville ,Amy R. Bentley ,Florian Privé ,Xiaofeng Zhu ,Jim Gauderman ,Thomas W. Winkler ,Michael A. Province ,D. C. Rao ,Hugues Aschard :VarExp: estimating variance explained by genome-wide GxE summary statistics. 3412-3414 Systems Biology
export record
dblp key:
journals/bioinformatics/ZhouHDYWS18 share record
persistent URL:
Jiajian Zhou ,Yile Huang ,Yingzhe Ding ,Jie Yuan ,Huating Wang ,Hao Sun :lncFunTK: a toolkit for functional annotation of long noncoding RNAs. 3415-3416 export record
dblp key:
journals/bioinformatics/MockWDBJH18 share record
persistent URL:
Andreas Mock ,Rolf Warta ,Steffen Dettling ,Benedikt Brors ,Dirk Jäger ,Christel Herold-Mende :MetaboDiff: an R package for differential metabolomic analysis. 3417-3418 export record
dblp key:
journals/bioinformatics/ZhangZN18 share record
persistent URL:
Baohong Zhang ,Shanrong Zhao ,Isaac Neuhaus :canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit. 3419-3420 Volume 34, Number 20, October 2018 Discovery note
Genome Analysis
Original Papers
Sequence Analysis
export record
dblp key:
journals/bioinformatics/PanS18 share record
persistent URL:
Xiaoyong Pan ,Hong-Bin Shen :Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. 3427-3436 export record
dblp key:
journals/bioinformatics/RahnBCEHR18 share record
persistent URL:
René Rahn ,Stefan Budach ,Pascal Costanza ,Marcel Ehrhardt ,Jonny Hancox ,Knut Reinert :Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. 3437-3445 export record
dblp key:
journals/bioinformatics/SalekinZH18 share record
persistent URL:
Sirajul Salekin ,Jianqiu (Michelle) Zhang ,Yufei Huang :Base-pair resolution detection of transcription factor binding site by deep deconvolutional network. 3446-3453 export record
dblp key:
journals/bioinformatics/GiancarloRU18 share record
persistent URL:
Raffaele Giancarlo ,Simona E. Rombo ,Filippo Utro :In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes. 3454-3460 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/DengZLZXW18 share record
persistent URL:
Wenping Deng ,Kui Zhang ,Sanzhen Liu ,Patrick X. Zhao ,Shizhong Xu ,Hairong Wei :JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions. 3470-3478 export record
dblp key:
journals/bioinformatics/MinLZ18 share record
persistent URL:
Wenwen Min ,Juan Liu ,Shihua Zhang :Edge-group sparse PCA for network-guided high dimensional data analysis. 3479-3487 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/KomarK18 share record
persistent URL:
Péter Kómár ,Deniz Kural :geck: trio-based comparative benchmarking of variant calls. 3488-3495 export record
dblp key:
journals/bioinformatics/BourkeGVJKSVASM18 share record
persistent URL:
Peter M. Bourke ,Geert van Geest ,Roeland E. Voorrips ,Johannes Jansen ,Twan Kranenburg ,Arwa Shahin ,Richard G. F. Visser ,Paul Arens ,Marinus J. M. Smulders ,Chris Maliepaard :polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. 3496-3502 Systems Biology
export record
dblp key:
journals/bioinformatics/KehlSKSWGLDSKTG18 share record
persistent URL:
Tim Kehl ,Lara Schneider ,Kathrin Kattler ,Daniel Stöckel ,Jenny Wegert ,Nico Gerstner ,Nicole Ludwig ,Ute Distler ,Markus Schick ,Ulrich Keller ,Stefan Tenzer ,Manfred Gessler ,Jörn Walter ,Andreas Keller ,Norbert M. Graf ,Eckart Meese ,Hans-Peter Lenhof :REGGAE: a novel approach for the identification of key transcriptional regulators. 3503-3510 export record
dblp key:
journals/bioinformatics/KleinCZ18 share record
persistent URL:
Joshua Klein ,Luis Carvalho ,Joseph Zaia :Application of network smoothing to glycan LC-MS profiling. 3511-3518 export record
dblp key:
journals/bioinformatics/ChengL18 share record
persistent URL:
Lixin Cheng ,Kwong-Sak Leung :Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome. 3519-3528 Data and Text Mining
Databases and Ontologies
export record
dblp key:
journals/bioinformatics/YangFQXS18 share record
persistent URL:
Yang Yang ,Xiaofeng Fu ,Wenhao Qu ,Yiqun Xiao ,Hong-Bin Shen :MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association. 3547-3556 export record
dblp key:
journals/bioinformatics/RazbanGDSDCPS18 share record
persistent URL:
Rostam M. Razban ,Amy I Gilson ,Niamh Durfee ,Hendrik Strobelt ,Kasper Dinkla ,Jeong-Mo Choi ,Hanspeter Pfister ,Eugene I. Shakhnovich :ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. 3557-3565 export record
dblp key:
journals/bioinformatics/BhowmickMB18 share record
persistent URL:
Pallab Bhowmick ,Yassene Mohammed ,Christoph H. Borchers :MRMAssayDB: an integrated resource for validated targeted proteomics assays. 3566-3571 Applications Notes
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/SeibtSH18 share record
persistent URL:
Kathrin M. Seibt ,Thomas Schmidt ,Tony Heitkam :FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses. 3575-3577 export record
dblp key:
journals/bioinformatics/QuangGP18 share record
persistent URL:
Daniel Quang ,Yuanfang Guan ,Stephen C. J. Parker :YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. 3578-3580 export record
dblp key:
journals/bioinformatics/LinGWKADFGACXO18 share record
persistent URL:
Jiaxing Lin ,Jeremy Gresham ,Tongrong Wang ,So Young Kim ,James Alvarez ,Jeffrey S. Damrauer ,Scott Floyd ,Joshua A. Granek ,Andrew S. Allen ,Cliburn Chan ,Jichun Xie ,Kouros Owzar :bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. 3581-3583 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/BullockTT18 share record
persistent URL:
Joshua M. A Bullock ,Konstantinos Thalassinos ,Maya Topf :Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry. 3584-3585 export record
dblp key:
journals/bioinformatics/JurcikBBMFDKBSS18 share record
persistent URL:
Adam Jurcík ,David Bednar ,Jan Byska ,Sérgio M. Marques ,Katarína Furmanová ,Lukas Daniel ,Piia Kokkonen ,Jan Brezovsky ,Ondrej Strnad ,Jan Stourac ,Antonín Pavelka ,Martin Manak ,Jirí Damborský ,Barbora Kozlíková :CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. 3586-3588 Systems Biology
export record
dblp key:
journals/bioinformatics/EdmandsHR18 share record
persistent URL:
William M. B. Edmands ,Josie Hayes ,Stephen M. Rappaport :SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis. 3589-3590 export record
dblp key:
journals/bioinformatics/KlingerRH18 share record
persistent URL:
Emmanuel Klinger ,Dennis Rickert ,Jan Hasenauer :pyABC: distributed, likelihood-free inference. 3591-3593 export record
dblp key:
journals/bioinformatics/ChangXGWYZHZ18 share record
persistent URL:
Cheng Chang ,Kaikun Xu ,Chaoping Guo ,Jinxia Wang ,Qi Yan ,Jian Zhang ,Fuchu He ,Yunping Zhu :PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data. 3594-3596 Data and Text Mining
Corrigendum
Data and Text Mining
export record
dblp key:
journals/bioinformatics/KosterR18 share record
persistent URL:
Johannes Köster ,Sven Rahmann :Snakemake - a scalable bioinformatics workflow engine. 3600 Volume 34, Number 21, November 2018 Original Papers
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/MajorosHCWYR18 share record
persistent URL:
William H. Majoros ,Carson Holt ,Michael Campbell ,Doreen Ware ,Mark Yandell ,Timothy E. Reddy :Predicting gene structure changes resulting from genetic variants via exon definition features. 3616-3623 export record
dblp key:
journals/bioinformatics/ZhangXZY18 share record
persistent URL:
Le Zhang ,Ming Xiao ,Jingsong Zhou ,Jun Yu :Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA). 3624-3630 export record
dblp key:
journals/bioinformatics/ShresthaYA18 share record
persistent URL:
Anish Man Singh Shrestha ,Naruki Yoshikawa ,Kiyoshi Asai :Combining probabilistic alignments with read pair information improves accuracy of split-alignments. 3631-3637 Phylogenetics
export record
dblp key:
journals/bioinformatics/ParagP18 share record
persistent URL:
Kris V. Parag ,Oliver G. Pybus :Exact Bayesian inference for phylogenetic birth-death models. 3638-3645 export record
dblp key:
journals/bioinformatics/DucheminGCABBBC18 share record
persistent URL:
Wandrille Duchemin ,Guillaume Gence ,Anne-Muriel Arigon Chifolleau ,Lars Arvestad ,Mukul S. Bansal ,Vincent Berry ,Bastien Boussau ,François Chevenet ,Nicolas Comte ,Adrián A. Davín ,Christophe Dessimoz ,David Dylus ,Damir Hasic ,Diego Mallo ,Rémi Planel ,David Posada ,Céline Scornavacca ,Gergely J. Szöllosi ,Louxin Zhang ,Eric Tannier ,Vincent Daubin :RecPhyloXML: a format for reconciled gene trees. 3646-3652 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/UsmanovaBBEGKLM18 share record
persistent URL:
Dinara R. Usmanova ,Natalya S. Bogatyreva ,Joan Ariño Bernad ,Aleksandra A. Eremina ,Anastasiya A. Gorshkova ,German M. Kanevskiy ,Lyubov R. Lonishin ,Alexander V. Meister ,Alisa G. Yakupova ,Fyodor A. Kondrashov ,Dmitry N. Ivankov :Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. 3653-3658 export record
dblp key:
journals/bioinformatics/PucciBKR18 share record
persistent URL:
Fabrizio Pucci ,Katrien V. Bernaerts ,Jean Marc Kwasigroch ,Marianne Rooman :Quantification of biases in predictions of protein stability changes upon mutations. 3659-3665 export record
dblp key:
journals/bioinformatics/Stepniewska-Dziubinska18 share record
persistent URL:
Marta M. Stepniewska-Dziubinska ,Piotr Zielenkiewicz ,Pawel Siedlecki :Development and evaluation of a deep learning model for protein-ligand binding affinity prediction. 3666-3674 export record
dblp key:
journals/bioinformatics/WozniakPSVK18 share record
persistent URL:
Pawel P. Wozniak ,J. Pelc ,M. Skrzypecki ,Gert Vriend ,Malgorzata Kotulska :Bio-knowledge-based filters improve residue-residue contact prediction accuracy. 3675-3683 Gene expression
export record
dblp key:
journals/bioinformatics/JiangSHC18 share record
persistent URL:
Hao Jiang ,Lydia L. Sohn ,Haiyan Huang ,Luonan Chen :Single cell clustering based on cell-pair differentiability correlation and variance analysis. 3684-3694 Genetics and Population Analysis
Systems Biology
Data and Text Mining
export record
dblp key:
journals/bioinformatics/NembriniKW18 share record
persistent URL:
Stefano Nembrini ,Inke R. König ,Marvin N. Wright :The revival of the Gini importance? 3711-3718 export record
dblp key:
journals/bioinformatics/OrzechowskiSHM18 share record
persistent URL:
Patryk Orzechowski ,Moshe Sipper ,Xiuzhen Huang ,Jason H. Moore :EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery. 3719-3726 export record
dblp key:
journals/bioinformatics/KongY18 share record
persistent URL:
Yunchuan Kong ,Tianwei Yu :A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data. 3727-3737 Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/BobayEO18 share record
persistent URL:
Louis-Marie Bobay ,Brian Shin-Hua Ellis ,Howard Ochman :ConSpeciFix: classifying prokaryotic species based on gene flow. 3738-3740 export record
dblp key:
journals/bioinformatics/TaeS18 share record
persistent URL:
Donghyun Tae ,Junhee Seok :mEBT: multiple-matching evidence-based translator of murine genomic responses for human immunity studies. 3741-3743 Sequence Analysis
export record
dblp key:
journals/bioinformatics/MaiZLLLWTL18 share record
persistent URL:
Huijun Mai ,Yifan Zhang ,Dinghua Li ,Henry Chi-Ming Leung ,Ruibang Luo ,Chi-Kwong Wong ,Hing-Fung Ting ,Tak Wah Lam :AC-DIAMOND v1: accelerating large-scale DNA-protein alignment. 3744-3746 export record
dblp key:
journals/bioinformatics/ZhaiSCTM18 share record
persistent URL:
Jingjing Zhai ,Jie Song ,Qian Cheng ,Yunjia Tang ,Chuang Ma :PEA: an integrated R toolkit for plant epitranscriptome analysis. 3747-3749 export record
dblp key:
journals/bioinformatics/TauschSALLNR18 share record
persistent URL:
Simon H. Tausch ,Benjamin Strauch ,Andreas Andrusch ,Tobias P. Loka ,Martin S. Lindner ,Andreas Nitsche ,Bernhard Y. Renard :LiveKraken--real-time metagenomic classification of illumina data. 3750-3752 export record
dblp key:
journals/bioinformatics/LerayHLM18 share record
persistent URL:
Matthieu Leray ,Shian-Lei Ho ,I-Jeng Lin ,Ryuji J. Machida :MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database. 3753-3754 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/RoseBVDPR18 share record
persistent URL:
Alexander S. Rose ,Anthony R. Bradley ,Yana Valasatava ,Jose M. Duarte ,Andreas Prlic ,Peter W. Rose :NGL viewer: web-based molecular graphics for large complexes. 3755-3758 export record
dblp key:
journals/bioinformatics/RossNGAAAB18 share record
persistent URL:
Caroline J. Ross ,Bilal Nizami ,Michael Glenister ,Olivier Sheik Amamuddy ,Ali Rana Atilgan ,Canan Atilgan ,Özlem Tastan Bishop :MODE-TASK: large-scale protein motion tools. 3759-3763 Systems Biology
export record
dblp key:
journals/bioinformatics/TanLNP18 share record
persistent URL:
Phit Ling Tan ,Yosvany López ,Kenta Nakai ,Ashwini Patil :TimeXNet Web: identifying cellular response networks from diverse omics time-course data. 3764-3765 export record
dblp key:
journals/bioinformatics/Yu18 share record
persistent URL:
Guangchuang Yu :Using meshes for MeSH term enrichment and semantic analyses. 3766-3767 Databases and Ontologies
export record
dblp key:
journals/bioinformatics/PengWMLWMCDW18 share record
persistent URL:
Bo Peng ,Gao Wang ,Jun Ma ,Man Chong Leong ,Chris Wakefield ,James M. Melott ,Yulun Chiu ,Di Du ,John N. Weinstein :SoS Notebook: an interactive multi-language data analysis environment. 3768-3770 export record
dblp key:
journals/bioinformatics/LiuHXHZG18 share record
persistent URL:
Chun-Jie Liu ,Fei-Fei Hu ,Meng-Xuan Xia ,Leng Han ,Qiong Zhang ,An-Yuan Guo :GSCALite: a web server for gene set cancer analysis. 3771-3772 export record
dblp key:
journals/bioinformatics/BorrelKF18 share record
persistent URL:
Alexandre Borrel ,Nicole C. Kleinstreuer ,Denis Fourches :Exploring drug space with ChemMaps.com. 3773-3775 Bioimage Informatics
Corrigenda
Bioimage Informatics
export record
dblp key:
journals/bioinformatics/OlayanAB18a share record
persistent URL:
Rawan S. Olayan ,Haitham Ashoor ,Vladimir B. Bajic :DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. 3779 export record
dblp key:
journals/bioinformatics/TsiantisBB18a share record
persistent URL:
Nikolaos Tsiantis ,Eva Balsa-Canto ,Julio R. Banga :Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. 3780 Volume 34, Number 22, November 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/WenCZLL18 share record
persistent URL:
Ming Wen ,Peisheng Cong ,Zhimin Zhang ,Hongmei Lu ,Tonghua Li :DeepMirTar: a deep-learning approach for predicting human miRNA targets. 3781-3787 export record
dblp key:
journals/bioinformatics/NavarroMFC18 share record
persistent URL:
Francisco Abad Navarro ,María Eugenia de la Morena-Barrio ,Jesualdo Tomás Fernández-Breis ,Javier Corral :Lost in translation: bioinformatic analysis of variations affecting the translation initiation codon in the human genome. 3788-3794 export record
dblp key:
journals/bioinformatics/TreepongGMCHV18 share record
persistent URL:
Panisa Treepong ,Christophe Guyeux ,Alexandre Meunier ,Charlotte Couchoud ,Didier Hocquet ,Benoit Valot :panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data. 3795-3800 export record
dblp key:
journals/bioinformatics/FangMTZYWCCT18 share record
persistent URL:
Zhou Fang ,Tianzhou Ma ,Gong Tang ,Li Zhu ,Qi Yan ,Ting Wang ,Juan C. Celedón ,Wei Chen ,George C. Tseng :Bayesian integrative model for multi-omics data with missingness. 3801-3808 Sequence Analysis
export record
dblp key:
journals/bioinformatics/CoelhoS18 share record
persistent URL:
Vitor L. Coelho ,Michael Sammeth :An automated method for detecting alternatively spliced protein domains. 3809-3816 export record
dblp key:
journals/bioinformatics/ErenM18 share record
persistent URL:
Kemal Eren ,Ben Murrell :RIFRAF: a frame-resolving consensus algorithm. 3817-3824 export record
dblp key:
journals/bioinformatics/YangYZXZWZ18 share record
persistent URL:
Cheng Yang ,Longshu Yang ,Man Zhou ,Haoling Xie ,Chengjiu Zhang ,May D. Wang ,Huaiqiu Zhu :LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning. 3825-3834 export record
dblp key:
journals/bioinformatics/LiuLHC18 share record
persistent URL:
Bin Liu ,Kai Li ,De-Shuang Huang ,Kuo-Chen Chou :iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach. 3835-3842 Phylogenetics
export record
dblp key:
journals/bioinformatics/MullerRS18 share record
persistent URL:
Nicola F. Müller ,David A. Rasmussen ,Tanja Stadler :MASCOT: parameter and state inference under the marginal structured coalescent approximation. 3843-3848 Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/JabbariWMW18 share record
persistent URL:
Hosna Jabbari ,Ian Wark ,Carlo Montemagno ,Sebastian Will :Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. 3849-3856 export record
dblp key:
journals/bioinformatics/Perez-BenitoHML18 share record
persistent URL:
Laura Pérez-Benito ,Andrew Henry ,Minos-Timotheos Matsoukas ,Laura Lopez ,Daniel Pulido ,Miriam Royo ,Arnau Cordomí ,Gary Tresadern ,Leonardo Pardo :The size matters? A computational tool to design bivalent ligands. 3857-3863 Genetics and Population Analysis
Systems Biology
export record
dblp key:
journals/bioinformatics/GligorijevicBB18 share record
persistent URL:
Vladimir Gligorijevic ,Meet Barot ,Richard Bonneau :deepNF: deep network fusion for protein function prediction. 3873-3881 export record
dblp key:
journals/bioinformatics/TianR18 share record
persistent URL:
Mingyuan Tian ,Jennifer L. Reed :Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis. 3882-3888 Data and Text Mining
export record
dblp key:
journals/bioinformatics/BaekLKY18 share record
persistent URL:
Junghwan Baek ,Byunghan Lee ,Sunyoung Kwon ,Sungroh Yoon :LncRNAnet: long non-coding RNA identification using deep learning. 3889-3897 export record
dblp key:
journals/bioinformatics/SchmokerDGVEB18 share record
persistent URL:
Anna M. Schmoker ,Heather E. Driscoll ,Stefanie R. Geiger ,James J. Vincent ,Alicia M. Ebert ,Bryan A. Ballif :An in silico proteomics screen to predict and prioritize protein-protein interactions dependent on post-translationally modified motifs. 3898-3906 export record
dblp key:
journals/bioinformatics/SuphavilaiBN18 share record
persistent URL:
Chayaporn Suphavilai ,Denis Bertrand ,Niranjan Nagarajan :Predicting Cancer Drug Response using a Recommender System. 3907-3914 Applications Notes
Genome Analysis
Sequence Analysis
export record
dblp key:
journals/bioinformatics/MurrayB18 share record
persistent URL:
Kevin D. Murray ,Justin O. Borevitz :Axe: rapid, competitive sequence read demultiplexing using a trie. 3924-3925 export record
dblp key:
journals/bioinformatics/Roberson18 share record
persistent URL:
Elisha D. Roberson :Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files. 3926-3928 export record
dblp key:
journals/bioinformatics/WhelanIB18 share record
persistent URL:
Simon Whelan ,Iker Irisarri ,Fabien Burki :PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. 3929-3930 export record
dblp key:
journals/bioinformatics/DhandaVHGPS18 share record
persistent URL:
Sandeep Kumar Dhanda ,Randi Vita ,Brendan Ha ,Alba Grifoni ,Bjoern Peters ,Alessandro Sette :ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins. 3931-3933 export record
dblp key:
journals/bioinformatics/KanaiMO18 share record
persistent URL:
Masahiro Kanai ,Yuichi Maeda ,Yukinori Okada :Grimon: graphical interface to visualize multi-omics networks. 3934-3936 export record
dblp key:
journals/bioinformatics/BordinD18 share record
persistent URL:
Nicola Bordin ,Damien P. Devos :ICBdocker: a Docker image for proteome annotation and visualization. 3937-3938 export record
dblp key:
journals/bioinformatics/CollinsW18 share record
persistent URL:
Kodi Collins ,Tandy J. Warnow :PASTA for proteins. 3939-3941 Structural Bioinformatics
Systems Biology
Data and Text Mining
Volume 34, Number 23, December 2018 Discovery note
Structural Bioinformatics
export record
dblp key:
journals/bioinformatics/PereiraL18 share record
persistent URL:
Joana Pereira ,Andrei N. Lupas :The ancestral KH peptide at the root of a domain family with three different folds. 3961-3965 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/ChenJRCHL18 share record
persistent URL:
Ping Chen ,Xinyun Jing ,Jian Ren ,Han Cao ,Pei Hao ,Xuan Li :Modelling BioNano optical data and simulation study of genome map assembly. 3966-3974 export record
dblp key:
journals/bioinformatics/GuanLZZO18 share record
persistent URL:
Yuanfang Guan ,Tingyang Li ,Hongjiu Zhang ,Fan Zhu ,Gilbert S. Omenn :Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile. 3975-3982 export record
dblp key:
journals/bioinformatics/MinHSRS18 share record
persistent URL:
Josine L. Min ,Gibran Hemani ,George Davey Smith ,Caroline Relton ,Matthew Suderman :Meffil: efficient normalization and analysis of very large DNA methylation datasets. 3983-3989 Sequence Analysis
export record
dblp key:
journals/bioinformatics/MunteanuMO18 share record
persistent URL:
Alina Munteanu ,Neelanjan Mukherjee ,Uwe Ohler :SSMART: sequence-structure motif identification for RNA-binding proteins. 3990-3998 export record
dblp key:
journals/bioinformatics/ChenCLWWS18 share record
persistent URL:
Guodong Chen ,Man Cao ,Kun Luo ,Lina Wang ,Pingping Wen ,Shaoping Shi :ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization. 3999-4006 export record
dblp key:
journals/bioinformatics/WeiZCSS18 share record
persistent URL:
Leyi Wei ,Chen Zhou ,Huangrong Chen ,Jiangning Song ,Ran Su :ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. 4007-4016 export record
dblp key:
journals/bioinformatics/MiuraGMHVBK18 share record
persistent URL:
Sayaka Miura ,Karen Gomez ,Oscar D. Murillo ,Louise A. Huuki ,Tracy Vu ,Tiffany Buturla ,Sudhir Kumar :Predicting clone genotypes from tumor bulk sequencing of multiple samples. 4017-4026 export record
dblp key:
journals/bioinformatics/Bengtsson-Palme18 share record
persistent URL:
Johan Bengtsson-Palme ,Rodney T. Richardson ,Marco Meola ,Christian Wurzbacher ,Émilie D. Tremblay ,Kaisa Thorell ,Kärt Kanger ,K. Martin Eriksson ,Guillaume J. Bilodeau ,Reed M. Johnson ,Martin Hartmann ,R. Henrik Nilsson :Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker. 4027-4033 Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/Erhard18 share record
persistent URL:
Florian Erhard :Estimating pseudocounts and fold changes for digital expression measurements. 4054-4063 export record
dblp key:
journals/bioinformatics/CorettoST18 share record
persistent URL:
Pietro Coretto ,Angela Serra ,Roberto Tagliaferri :Robust clustering of noisy high-dimensional gene expression data for patients subtyping. 4064-4072 Genetics and Population Analysis
Systems Biology
Data and Text Mining
Bioimage Informatics
Applications Notes
Genome Analysis
export record
dblp key:
journals/bioinformatics/NousiainenKRWLK18 share record
persistent URL:
Kari Nousiainen ,Kartiek Kanduri ,Isis Ricaño-Ponce ,Cisca Wijmenga ,Riitta Lahesmaa ,Vinod Kumar ,Harri Lähdesmäki :snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions. 4112-4114 export record
dblp key:
journals/bioinformatics/KedzierskaGCKRK18 share record
persistent URL:
Katarzyna Z. Kedzierska ,Livia Gerber ,Daniele Cagnazzi ,Michael Krützen ,Aakrosh Ratan ,Logan Kistler :SONiCS: PCR stutter noise correction in genome-scale microsatellites. 4115-4117 export record
dblp key:
journals/bioinformatics/TaboadaECM18 share record
persistent URL:
Blanca Taboada ,Karel Estrada ,Ricardo Ciria ,Enrique Merino :Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. 4118-4120 Phylogenetics
Structural Bioinformatics
Systems Biology
export record
dblp key:
journals/bioinformatics/SunWWS18 share record
persistent URL:
Kun Sun ,Jiguang Wang ,Huating Wang ,Hao Sun :GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies. 4129-4130 Data and Text Mining
export record
dblp key:
journals/bioinformatics/AghaeepourSKBSC18 share record
persistent URL:
Nima Aghaeepour ,Erin F. Simonds ,David J. H. F. Knapp ,Robert V. Bruggner ,Karen Sachs ,Anthony Culos ,Pier Federico Gherardini ,Nikolay Samusik ,Gabriela K. Fragiadakis ,Sean Bendall ,Brice Gaudilliere ,Martin S. Angst ,Connie J. Eaves ,William A. Weiss ,Wendy J. Fantl ,Garry P. Nolan :GateFinder: projection-based gating strategy optimization for flow and mass cytometry. 4131-4133 export record
dblp key:
journals/bioinformatics/Martinez-Vernon18 share record
persistent URL:
Andrea S. Martinez-Vernon ,Frederick Farrell ,Orkun S. Soyer :MetQy - an R package to query metabolic functions of genes and genomes. 4134-4137 Corrigenda
Data and Text Mining
Erratum
Data and Text Mining
Volume 34, Number 24, December 2018 Original Papers
Genome Analysis
export record
dblp key:
journals/bioinformatics/LinHCTSPEEKOBMG18 share record
persistent URL:
Hui-Yi Lin ,Po-Yu Huang ,Dung-Tsa Chen ,Heng-Yuan Tung ,Thomas A. Sellers ,Julio M. Pow-Sang ,Rosalind A. Eeles ,Doug Easton ,Zsofia Kote-Jarai ,Ali Amin Al Olama ,Sara Benlloch ,Kenneth Muir ,Graham G. Giles ,Fredrik Wiklund ,Henrik Gronberg ,Christopher A. Haiman ,Johanna Schleutker ,Børge G. Nordestgaard ,Ruth C. Travis ,Freddie Hamdy ,David E. Neal ,Nora Pashayan ,Kay-Tee Khaw ,Janet L. Stanford ,William J. Blot ,Stephen N. Thibodeau ,Christiane Maier ,Adam S. Kibel ,Cezary Cybulski ,Lisa A. Cannon-Albright ,Hermann Brenner ,Radka Kaneva ,Jyotsna Batra ,Manuel R. Teixeira ,Hardev Pandha ,Yong-Jie Lu ,PRACTICAL Consortium ,Jong Y. Park :AA9int: SNP interaction pattern search using non-hierarchical additive model set. 4141-4150 export record
dblp key:
journals/bioinformatics/LeeOS18 share record
persistent URL:
Jungwoo Lee ,Sejoon Oh ,Lee Sael :GIFT: Guided and Interpretable Factorization for Tensors with an application to large-scale multi-platform cancer analysis. 4151-4158 export record
dblp key:
journals/bioinformatics/AhmedWC18 share record
persistent URL:
Ibrahim Ahmed ,Peter J. Witbooi ,Alan Christoffels :Prediction of human-Bacillus anthracis protein-protein interactions using multi-layer neural network. 4159-4164 export record
dblp key:
journals/bioinformatics/Prufer18 share record
persistent URL:
Kay Prüfer :snpAD: an ancient DNA genotype caller. 4165-4171 export record
dblp key:
journals/bioinformatics/YuJWZL18 share record
persistent URL:
Guoxian Yu ,Yuan Jiang ,Jun Wang ,Hao Zhang ,Haiwei Luo :BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage. 4172-4179 Sequence Analysis
export record
dblp key:
journals/bioinformatics/ZuallaertGKSSN18 share record
persistent URL:
Jasper Zuallaert ,Fréderic Godin ,Mijung Kim ,Arne Soete ,Yvan Saeys ,Wesley De Neve :SpliceRover: interpretable convolutional neural networks for improved splice site prediction. 4180-4188 export record
dblp key:
journals/bioinformatics/CrawfordKBCG18 share record
persistent URL:
Victoria G. Crawford ,Alan Kuhnle ,Christina Boucher ,Rayan Chikhi ,Travis Gagie :Practical dynamic de Bruijn graphs. 4189-4195 export record
dblp key:
journals/bioinformatics/SuHZZWCCL18 share record
persistent URL:
Zhen-Dong Su ,Yan Huang ,Zhao-Yue Zhang ,Ya-Wei Zhao ,Dong Wang ,Wei Chen ,Kuo-Chen Chou ,Hao Lin :iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. 4196-4204 export record
dblp key:
journals/bioinformatics/SandmannKGRGVEW18 share record
persistent URL:
Sarah Sandmann ,Mohsen Karimi ,Aniek O. de Graaf ,Christian Rohde ,Stefanie Göllner ,Julian Varghese ,Jan Ernsting ,Gunilla Walldin ,Bert A. van der Reijden ,Carsten Müller-Tidow ,Luca Malcovati ,Eva Hellström-Lindberg ,Joop H. Jansen ,Martin Dugas :appreci8: a pipeline for precise variant calling integrating 8 tools. 4205-4212 export record
dblp key:
journals/bioinformatics/MorisseLL18 share record
persistent URL:
Pierre Morisse ,Thierry Lecroq ,Arnaud Lefebvre :Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph. 4213-4222 export record
dblp key:
journals/bioinformatics/LiLMLAPSLDSC18 share record
persistent URL:
Fuyi Li ,Chen Li ,Tatiana T. Marquez-Lago ,André Leier ,Tatsuya Akutsu ,Anthony W. Purcell ,Alexander Ian Smith ,Trevor Lithgow ,Roger J. Daly ,Jiangning Song ,Kuo-Chen Chou :Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. 4223-4231 Gene expression
export record
dblp key:
journals/bioinformatics/ZhangLLL18 share record
persistent URL:
Junpeng Zhang ,Lin Liu ,Jiuyong Li ,Thuc Duy Le :LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer. 4232-4240 Genetics and Population Analysis
Systems Biology
Data and Text Mining
Applications Notes
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene expression
export record
dblp key:
journals/bioinformatics/OrzechowskiPHM18 share record
persistent URL:
Patryk Orzechowski ,Artur Panszczyk ,Xiuzhen Huang ,Jason H. Moore :runibic: a Bioconductor package for parallel row-based biclustering of gene expression data. 4302-4304 export record
dblp key:
journals/bioinformatics/Patel18 share record
persistent URL:
Mitulkumar V. Patel :iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data. 4305-4306 Genetics and Population Analysis
export record
dblp key:
journals/bioinformatics/ZhangBRZCABI18 share record
persistent URL:
Peng Zhang ,Benedetta Bigio ,Franck Rapaport ,Shen-Ying Zhang ,Jean-Laurent Casanova ,Laurent Abel ,Bertrand Boisson ,Yuval Itan :PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations. 4307-4309 export record
dblp key:
journals/bioinformatics/LeesGBWC18 share record
persistent URL:
John A. Lees ,Marco Galardini ,Stephen D. Bentley ,Jeffrey N. Weiser ,Jukka Corander :pyseer: a comprehensive tool for microbial pangenome-wide association studies. 4310-4312 Systems Biology
export record
dblp key:
journals/bioinformatics/ChongX18 share record
persistent URL:
Jasmine Chong ,Jianguo Xia :MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data. 4313-4314 Databases and Ontologies
Bioimage Informatics
manage site settings
To protect your privacy, all features that rely on external API calls from your browser areturned off by default . You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more informationsee our F.A.Q.
Unpaywalled article links
Add open access links from to the list of external document links (if available).
load links from unpaywall.org
Privacy notice: By enabling the option above, your browser will contact the API ofunpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking theUnpaywall privacy policy .
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the of the Internet Archive (if available).
load content from archive.org
Privacy notice: By enabling the option above, your browser will contact the API ofarchive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking theInternet Archive privacy policy .
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API ofopencitations.net andsemanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking theOpenCitations privacy policy as well as theAI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from .
load data from openalex.org
Privacy notice: By enabling the option above, your browser will contact the API ofopenalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given byOpenAlex .
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by: