Bioinformatics, Volume 35

Volume 35, Number 1, January 2019

Original Papers
Genome Analysis

• 
  Nilotpal Sanyal,Min-Tzu Lo,Karolina Kauppi,Srdjan Djurovic,Ole A. Andreassen,Valen E. Johnson,Chi-Hua Chen:
  GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies.1-11

Sequence Analysis

• 
  Nelson Gil,András Fiser:
  The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.12-19
• 
  Ehsan Haghshenas,Süleyman Cenk Sahinalp,Faraz Hach:
  lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.20-27

Gene expression

• 
  Kieran R. Campbell,Christopher Yau:
  A descriptive marker gene approach to single-cell pseudotime inference.28-35
• 
  Eleonora Lusito,Barbara Felice,Giovanni D'Ario,Alessandro Ogier,Francesca Montani,Pier Paolo Di Fiore,Fabrizio Bianchi:
  Unraveling the role of low-frequency mutated genes in breast cancer.36-46
• 
  Sumon Ahmed,Magnus Rattray,Alexis Boukouvalas:
  GrandPrix: scaling up the Bayesian GPLVM for single-cell data.47-54
• 
  Marjan Farahbod,Paul Pavlidis:
  Differential coexpression in human tissues and the confounding effect of mean expression levels.55-61
• 
  Andrea Rau,Michael Flister,Hallgeir Rui,Paul L. Auer:
  Exploring drivers of gene expression in the Cancer Genome Atlas.62-68

Genetics and Population Analysis

• 
  Christian X. Weichenberger,Johannes Rainer,Cristian Pattaro,Peter P. Pramstaller,Francisco S. Domingues:
  Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees.69-76

Systems Biology

• 
  Lei Han,Lei Li,Feng Wen,Lei Zhong,Tong Zhang,Xiu-Feng Wan:
  Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus.77-87
• 
  Barnali Das,Abhijeet Rajendra Patil,Pralay Mitra:
  A network-based zoning for parallel whole-cell simulation.88-94
• 
  Mohammad Sajjad Ghaemi,Daniel B. DiGiulio,Kévin Contrepois,Benjamin J. Callahan,Thuy T. M. Ngo,Brittany Lee-McMullen,Benoit Lehallier,Anna Robaczewska,David Mcilwain,Yael Rosenberg-Hasson,Ronald J. Wong,Cecele Quaintance,Anthony Culos,Natalie Stanley,Athena Tanada,Amy Tsai,Dyani Gaudilliere,Edward Ganio,Xiaoyuan Han,Kazuo Ando,Leslie McNeil,Martha Tingle,Paul H. Wise,Ivana Maric,Marina Sirota,Tony Wyss-Coray,Virginia D. Winn,Maurice L. Druzin,Ronald Gibbs,Gary L. Darmstadt,David B. Lewis,Vahid Partovi Nia,Bruno Agard,Robert Tibshirani,Garry P. Nolan,Michael P. Snyder,David A. Relman,Stephen R. Quake,Gary M. Shaw,David K. Stevenson,Martin S. Angst,Brice Gaudilliere,Nima Aghaeepour:
  Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.95-103
• 
  Fangping Wan,Lixiang Hong,An Xiao,Tao Jiang,Jianyang Zeng:
  NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions.104-111

Data and Text Mining

• 
  Jianwen Fang:
  Tightly integrated genomic and epigenomic data mining using tensor decomposition.112-118

Applications Notes
Genome Analysis

• 
  Jerome Kelleher,Mike Lin,Carl H. Albach,Ewan Birney,Robert Davies,Marina Gourtovaia,David Glazer,Cristina Y. González,David K. Jackson,Aaron Kemp,John Marshall,Andrew Nowak,Alexander Senf,Jaime M. Tovar-Corona,Alexander Vikhorev,Thomas M. Keane,GA4GH Streaming Task Team:
  htsget: a protocol for securely streaming genomic data.119-121
• 
  Velimir Gayevskiy,Tony Roscioli,Marcel E. Dinger,Mark J. Cowley:
  Seave: a comprehensive web platform for storing and interrogating human genomic variation.122-125
• 
  Zhaohui Gu,Charles Mullighan:
  ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations.126-129
• 
  André Gohr,Manuel Irimia:
  Matt: Unix tools for alternative splicing analysis.130-132
• 
  Sebastian Deorowicz,Adam Gudys,Maciej Dlugosz,Marek Kokot,Agnieszka Danek:
  Kmer-db: instant evolutionary distance estimation.133-136
• 
  Patrick K. Kimes,Alejandro Reyes:
  Reproducible and replicable comparisons using SummarizedBenchmark.137-139
• 
  Marc Chakiachvili,Sylvain Milanesi,Anne-Muriel Arigon Chifolleau,Vincent Lefort:
  WAVES: a web application for versatile enhanced bioinformatic services.140-142

Sequence Analysis

• 
  Levent Albayrak,Kamil Khanipov,George Golovko,Yuriy Fofanov:
  Broom: application for non-redundant storage of high throughput sequencing data.143-145
• 
  Seyed Morteza Hosseini,Diogo Pratas,Armando J. Pinho:
  Cryfa: a secure encryption tool for genomic data.146-148

Phylogenetics

• 
  Salvatore Cosentino,Wataru Iwasaki:
  SonicParanoid: fast, accurate and easy orthology inference.149-151

Structural Bioinformatics

• 
  Maciej Antczak,Marcin Zablocki,Tomasz Zok,Agnieszka Rybarczyk,Jacek Blazewicz,Marta Szachniuk:
  RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs.152-155

Gene expression

• 
  Jamil Najafov,Ayaz Najafov:
  GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution.156-159

Genetics and Population Analysis

• 
  Shijia Zhu,Tongqi Qian,Yujin Hoshida,Yuan Shen,Jing Yu,Ke Hao:
  GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data.160-163
• 
  Corbin Quick,Christian Fuchsberger,Daniel Taliun,Gonçalo R. Abecasis,Michael Boehnke,Hyun Min Kang:
  emeraLD: rapid linkage disequilibrium estimation with massive datasets.164-166

Systems Biology

• 
  Pierre Salvy,Georgios Fengos,Meriç Ataman,Thomas Pathier,Keng C. Soh,Vassily Hatzimanikatis:
  pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis.167-169

Data and Text Mining

• 
  Jean-Michel Claverie,Thi Ngan Ta:
  ACDtool: a web-server for the generic analysis of large data sets of counts.170-171

Databases and Ontologies

• 
  Chuan Jiao,Pengpeng Yan,Cuihua Xia,Zhaoming Shen,Zexi Tan,Yanyan Tan,Kangli Wang,Yi Jiang,Lingling Huang,Rujia Dai,Yu Wei,Yan Xia,Qingtuan Meng,Yanmei Ouyang,Liu Yi,Fangyuan Duan,Jiacheng Dai,Shunan Zhao,Chunyu Liu,Chao Chen:
  BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains.172-174
• 
  Zeyu Wen,Jiahua He,Huanyu Tao,Sheng-You Huang:
  PepBDB: a comprehensive structural database of biological peptide-protein interactions.175-177

Bioimage Informatics

• 
  Paolo Inglese,Gonçalo D. S. Correia,Zoltan Takats,Jeremy K. Nicholson,Robert C. Glen:
  SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data.178-180

Volume 35, Number 2, January 2019

Original Papers
Genome Analysis

• 
  Joeri J. Meijsen,Alexandros Rammos,Archie Campbell,Caroline Hayward,David J. Porteous,Ian J. Deary,Riccardo E. Marioni,Kristin K. Nicodemus:
  Using tree-based methods for detection of gene-gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study.181-188
• 
  Malene Juul,Tobias Madsen,Qianyun Guo,Johanna Bertl,Asger Hobolth,Manolis Kellis,Jakob Skou Pedersen:
  ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.189-199
• 
  Bianca Dumitrascu,Gregory Darnell,Julien Ayroles,Barbara E. Engelhardt:
  Statistical tests for detecting variance effects in quantitative trait studies.200-210
• 
  Chris-André Leimeister,Thomas Dencker,Burkhard Morgenstern:
  Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.211-218
• 
  Yunan Luo,Yun William Yu,Jianyang Zeng,Bonnie Berger,Jian Peng:
  Metagenomic binning through low-density hashing.219-226

Sequence Analysis

• 
  Sebastian Deorowicz,Joanna Walczyszyn,Agnieszka Debudaj-Grabysz:
  CoMSA: compression of protein multiple sequence alignment files.227-234

Structural Bioinformatics

• 
  Yu-Chen Lo,Tianyun Liu,Kari M. Morrissey,Satoko Kakiuchi-Kiyota,Adam R. Johnson,Fabio Broccatelli,Yu Zhong,Amita Joshi,Russ B. Altman:
  Computational analysis of kinase inhibitor selectivity using structural knowledge.235-242
• 
  Miha Skalic,Alejandro Varela-Rial,José Jiménez,Gerard Martínez-Rosell,Gianni De Fabritiis:
  LigVoxel: inpainting binding pockets using 3D-convolutional neural networks.243-250

Gene expression

• 
  Jiaan Dai,Wei Jiang,Fengchao Yu,Weichuan Yu:
  Xolik: finding cross-linked peptides with maximum paired scores in linear time.251-257
• 
  Emmanuel Curis,Cindie Courtin,Pierre Alexis Geoffroy,Jean-Louis Laplanche,Bruno Saubaméa,Cynthia Marie-Claire:
  Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios.258-265

Systems Biology

• 
  Matthias P. Gerstl,Stefan Müller,Georg Regensburger,Jürgen Zanghellini:
  Flux tope analysis: studying the coordination of reaction directions in metabolic networks.266-273
• 
  Clément Frainay,Sandrine Aros,Maxime Chazalviel,Thomas Garcia,Florence Vinson,Nicolas Weiss,Benoit Colsch,Frédéric Sedel,Dominique Thabut,Christophe Junot,Fabien Jourdan:
  MetaboRank: network-based recommendation system to interpret and enrich metabolomics results.274-283
• 
  Olivia Eriksson,Alexandra Jauhiainen,Sara Maad Sasane,Andrei Kramer,Anu G. Nair,Carolina Sartorius,Jeanette Hellgren Kotaleski:
  Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models.284-292

Data and Text Mining

• 
  Piotr Klukowski,Mario Schubert:
  Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.293-300
• 
  Etienne Becht,Yannick Simoni,Elaine Coustan-Smith,Maximilien Evrard,Yang Cheng,Lai Guan Ng,Dario Campana,Evan W. Newell:
  Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting.301-308
• 
  Masashi Tsubaki,Kentaro Tomii,Jun Sese:
  Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences.309-318

Bioimage Informatics

• 
  Renmin Han,Xiaohua Wan,Lun Li,Albert F. Lawrence,Peng Yang,Yu Li,Sheng Wang,Fei Sun,Zhiyong Liu,Xin Gao,Fa Zhang:
  AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.319-328

Applications Notes
Genome Analysis

• 
  Pierre Simon Garcia,Frédéric Jauffrit,Christophe Grangeasse,Céline Brochier-Armanet:
  GeneSpy, a user-friendly and flexible genomic context visualizer.329-331

Sequence Analysis

• 
  David Jakubec,Jirí Vondrásek,Robert D. Finn:
  3DPatch: fast 3D structure visualization with residue conservation.332-334
• 
  Sebastian Uhrig,Holger Klein:
  PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data.335-336
• 
  James K. Bonfield,Shane A. McCarthy,Richard Durbin:
  Crumble: reference free lossy compression of sequence quality values.337-339

Gene expression

• 
  Dana Wyman,Ali Mortazavi:
  TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts.340-342
• 
  Sara B. Linker,Jonathan Y. Hsu,Adela Pfaff,Debha Amatya,Shu-Meng Ko,Sarah Voter,Quinn Wong,Fred H. Gage:
  BrainImageR: spatiotemporal gene set analysis referencing the human brain.343-345

Systems Biology

• 
  Soumita Ghosh,Abhik Datta,Kaisen Tan,Hyungwon Choi:
  SLIDE - a web-based tool for interactive visualization of large-scale - omics data.346-348

Databases and Ontologies

• 
  David R. Damerell,Claire Strain-Damerell,Sefa Garsot,Stephen P. Joyce,Paul Barrett,Brian D. Marsden:
  SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications.349-351

Review
Databases and Ontologies

• 
  Hojjat Naderi-Meshkin,Xin Lai,Raheleh Amirkhah,Julio Vera,John E. J. Rasko,Ulf Schmitz:
  Exosomal lncRNAs and cancer: connecting the missing links.352-360

Volume 35, Number 3, February 2019

Discovery note
Systems Biology

• 
  Hua Yu,Lu Lu,Bingke Jiao,Chengzhi Liang:
  Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples.361-364

Original Papers
Genome Analysis

• 
  Nora von Thenen,Erman Ayday,A. Ercüment Çiçek:
  Re-identification of individuals in genomic data-sharing beacons via allele inference.365-371

Sequence Analysis

• 
  Luca Parca,Bruno Ariano,Andrea Cabibbo,Marco Paoletti,Annalaura Tamburrini,Antonio Palmeri,Gabriele Ausiello,Manuela Helmer-Citterich:
  Kinome-wide identification of phosphorylation networks in eukaryotic proteomes.372-379
• 
  Wei Zheng,Qi Mao,Robert J. Genco,Jean Wactawski-Wende,Michael Buck,Yunpeng Cai,Yijun Sun:
  A parallel computational framework for ultra-large-scale sequence clustering analysis.380-388
• 
  Xinguo Lu,Xin Qian,Xing Li,Qiumai Miao,Shaoliang Peng:
  DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters.389-397
• 
  Xiang Cheng,Wei-Zhong Lin,Xuan Xiao,Kuo-Chen Chou:
  pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC.398-406
• 
  Harun Mustafa,Ingo Schilken,Mikhail Karasikov,Carsten Eickhoff,Gunnar Rätsch,André Kahles:
  Dynamic compression schemes for graph coloring.407-414
• 
  Chen Sun,Paul Medvedev:
  Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.415-420
• 
  Ben Langmead,Christopher Wilks,Valentin Antonescu,Rone Charles:
  Scaling read aligners to hundreds of threads on general-purpose processors.421-432
• 
  Avdesh Mishra,Pujan Pokhrel,Md. Tamjidul Hoque:
  StackDPPred: a stacking based prediction of DNA-binding protein from sequence.433-441
• 
  Jeffrey M. Yunes,Patricia C. Babbitt:
  Effusion: prediction of protein function from sequence similarity networks.442-451

Structural Bioinformatics

• 
  Marcin Kowiel,Dariusz Brzezinski,Przemyslaw J. Porebski,Ivan G. Shabalin,Mariusz Jaskolski,Wladek Minor:
  Automatic recognition of ligands in electron density by machine learning.452-461
• 
  Justina Jankauskaite,Brian Jiménez-García,Justas Dapkunas,Juan Fernández-Recio,Iain H. Moal:
  SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.462-469
• 
  Rubén Sánchez García,Carlos Oscar Sánchez Sorzano,José María Carazo,Joan Segura:
  BIPSPI: a method for the prediction of partner-specific protein-protein interfaces.470-477

Gene expression

• 
  Rasmus Henningsson,Magnus Fontes:
  SMSSVD: SubMatrix Selection Singular Value Decomposition.478-486
• 
  Shiquan Sun,Jiaqiang Zhu,Sahar Mozaffari,Carole Ober,Mengjie Chen,Xiang Zhou:
  Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies.487-496

Systems Biology

• 
  Alberto Valdeolivas,Laurent Tichit,Claire Navarro,Sophie Perrin,Gaëlle Odelin,Nicolas Levy,Pierre Cau,Elisabeth Remy,Anaïs Baudot:
  Random walk with restart on multiplex and heterogeneous biological networks.497-505

Bioimage Informatics

• 
  Bruce A. Corliss,H. Clifton Ray,James T. Patrie,Jennifer Mansour,Sam Kesting,Janice H. Park,Gustavo K. Rohde,Paul A. Yates,Kevin A. Janes,Shayn M. Peirce:
  CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures.506-514

Applications Notes
Genome Analysis

• 
  Caralyn Reisle,Karen L. Mungall,Caleb Choo,Daniel Paulino,Dustin W. Bleile,Amir Muhammadzadeh,Andrew J. Mungall,Richard A. Moore,Inna Shlafman,Robin Coope,Stephen Pleasance,Yussanne Ma,Steven J. M. Jones:
  MAVIS: merging, annotation, validation, and illustration of structural variants.515-517
• 
  Haiming Tang,Robert D. Finn,Paul D. Thomas:
  TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.518-520

Sequence Analysis

• 
  Hadrien Gourlé,Oskar Karlsson-Lindsjö,Juliette Hayer,Erik Bongcam-Rudloff:
  Simulating Illumina metagenomic data with InSilicoSeq.521-522
• 
  Robert Lanfear,Miriam Schalamun,David Kainer,Weiwen Wang,Benjamin Schwessinger:
  MinIONQC: fast and simple quality control for MinION sequencing data.523-525

Phylogenetics

• 
  Emmanuel Paradis,Klaus Schliep:
  ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.526-528

Genetics and Population Analysis

• 
  Zongxiao He,Lu Wang,Andrew Thomas DeWan,Suzanne M. Leal:
  MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data.529-531

Systems Biology

• 
  Kieu Trinh Do,David J. N. P. Rasp,Gabi Kastenmüller,Karsten Suhre,Jan Krumsiek:
  MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions.532-534
• 
  Iñigo Apaolaza,Luis Vitores Valcarcel,Francisco J. Planes:
  gMCS: fast computation of genetic minimal cut sets in large networks.535-537

Data and Text Mining

• 
  Zainab Noor,Jemma X. Wu,Dana Pascovici,Abidali Mohamedali,Mark P. Molloy,Mark S. Baker,Shoba Ranganathan:
  iSwathX: an interactive web-based application for extension of DIA peptide reference libraries.538-539

Corrigendum
Data and Text Mining

• 
  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.540

Volume 35, Number 4, February 2019

Discovery note
Sequence Analysis

• 
  Reuben J. Pengelly,Andrew Collins:
  Linkage disequilibrium maps to guide contig ordering for genome assembly.541-545

Original Papers
Genome Analysis

• 
  Justin Miller,Brandon D. Pickett,Perry G. Ridge:
  JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.546-552
• 
  Zi Yang,George Michailidis:
  Quantifying heterogeneity of expression data based on principal components.553-559
• 
  Timothy J. Peters,Hugh J. French,Stephen T. Bradford,Ruth Pidsley,Clare Stirzaker,Hilal Varinli,Shalima Nair,Wenjia Qu,Jenny Song,Katherine A. Giles,Aaron L. Statham,Helen Speirs,Terence P. Speed,Susan J. Clark:
  Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.560-570
• 
  Jack M. Fu,Elizabeth J. Leslie,Alan F. Scott,Jeffrey C. Murray,Mary L. Marazita,Terri H. Beaty,Robert B. Scharpf,Ingo Ruczinski:
  Detection of de novo copy number deletions from targeted sequencing of trios.571-578
• 
  Markus Fricke,Ruman Gerst,Bashar Ibrahim,Michael Niepmann,Manja Marz:
  Global importance of RNA secondary structures in protein-coding sequences.579-583

Sequence Analysis

• 
  Bansho Masutani,Shinichi Morishita:
  A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer.584-592
• 
  Wenying He,Cangzhi Jia,Quan Zou:
  4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction.593-601

Gene expression

• 
  Jiazhou Chen,Hong Peng,Guoqiang Han,Hongmin Cai,Jiulun Cai:
  HOGMMNC: a higher order graph matching with multiple network constraints model for gene-drug regulatory modules identification.602-610
• 
  Magdalena E. Strauß,John E. Reid,Lorenz Wernisch:
  GPseudoRank: a permutation sampler for single cell orderings.611-618
• 
  Sungwon Jung:
  KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein-protein interactions.619-627

Genetics and Population Analysis

• 
  Miao-Xin Li,Lin Jiang,Timothy Shin Heng Mak,Johnny S. H. Kwan,Chao Xue,Peikai Chen,Henry Chi-Ming Leung,Liqian Cui,Tao Li,Pak Chung Sham:
  A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia.628-635

Systems Biology

• 
  Beibei Ru,Yin Tong,Jiangwen Zhang:
  MR4Cancer: a web server prioritizing master regulators for cancer.636-642
• 
  Eunji Kim,Ivan Ivanov,Edward R. Dougherty:
  Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective.643-649

Data and Text Mining

• 
  Tatiana Radchenko,Fabien Fontaine,Luca Morettoni,Ismael Zamora:
  WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source.650-655

Databases and Ontologies

• 
  Magnus Palmblad,Anna-Lena Lamprecht,Jon C. Ison,Veit Schwämmle:
  Automated workflow composition in mass spectrometry-based proteomics.656-664
• 
  Richard Wilton,Sarah J. Wheelan,Alexander S. Szalay,Steven L. Salzberg:
  The Terabase Search Engine: a large-scale relational database of short-read sequences.665-670

Applications Notes
Genome Analysis

• 
  Xiaofei Zhao:
  BinDash, software for fast genome distance estimation on a typical personal laptop.671-673
• 
  Jonathan Laperle,Simon Hébert-Deschamps,Joanny Raby,David A. de Lima Morais,Michel Barrette,David Bujold,Charlotte Bastin,Marc-Antoine Robert,Jean-François Nadeau,Marie Harel,Alexei Nordell-Markovits,Alain Veilleux,Guillaume Bourque,Pierre-Étienne Jacques:
  The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets.674-676

Sequence Analysis

• 
  Szymon Grabowski,Wojciech Bieniecki:
  copMEM: finding maximal exact matches via sampling both genomes.677-678
• 
  Marie Locard-Paulet,Julien Parra,Renaud Albigot,Emmanuelle Mouton-Barbosa,Laurent Bardi,Odile Burlet-Schiltz,Julien Marcoux:
  VisioProt-MS: interactive 2D maps from intact protein mass spectrometry.679-681
• 
  Matthew Higgins,Matt Ravenhall,Daniel Ward,Jody Phelan,Amy Ibrahim,Matthew S. Forrest,Taane G. Clark,Susana G. Campino:
  PrimedRPA: primer design for recombinase polymerase amplification assays.682-684

Structural Bioinformatics

• 
  Eoin Fahy,Jorge Álvarez-Jarreta,Christopher J. Brasher,An Nguyen,Jade I Hawksworth,Patricia Rodrigues,Sven Meckelmann,Stuart M. Allen,Valerie B. O'Donnell:
  LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics.685-687
• 
  Ian Walsh,Terry Nguyen-Khuong,Katherine Wongtrakul-Kish,Shi Jie Tay,Daniel Chew,Tasha José,Christopher H. Taron,Pauline M. Rudd:
  GlycanAnalyzer: software for automated interpretation of N-glycan profiles after exoglycosidase digestions.688-690
• 
  Sheng Wang,Shiyang Fei,Zongan Wang,Yu Li,Jinbo Xu,Feng Zhao,Xin Gao:
  PredMP: a web server for de novo prediction and visualization of membrane proteins.691-693
• 
  Mateusz Kurcinski,Tymoteusz Oleniecki,Maciej Pawel Ciemny,Aleksander Kuriata,Andrzej Kolinski,Sebastian Kmiecik:
  CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.694-695

Systems Biology

• 
  Gwendolien Sergeant,Lennart Martens,Marleen Van Troys,Paola Masuzzo:
  DoRes within CellMissy: dose-response analysis on cell migration and related data.696-697
• 
  Zhiwei Zhou,Xiaotao Shen,Xi Chen,Jia Tu,Xin Xiong,Zheng-Jiang Zhu:
  LipidIMMS Analyzer: integrating multi-dimensional information to support lipid identification in ion mobility - mass spectrometry based lipidomics.698-700
• 
  Shaoli Das,Xiang Deng,Kevin Camphausen,Uma T. Shankavaram:
  DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers.701-702

Databases and Ontologies

• 
  Rocío Nieto-Arellano,Héctor Sánchez-Iranzo:
  zfRegeneration: a database for gene expression profiling during regeneration.703-705

Bioimage Informatics

• 
  Hengyang Lu,Jiabing Li,Melisa A. Martinez-Paniagua,Irfan N. Bandey,Amit Amritkar,Harjeet Singh,David Mayerich,Navin Varadarajan,Badrinath Roysam:
  TIMING 2.0: high-throughput single-cell profiling of dynamic cell-cell interactions by time-lapse imaging microscopy in nanowell grids.706-708

Letter to the Editor
Databases and Ontologies

• 
  Bo Peng,Man Chong Leong,Huann-Sheng Chen,Melissa Rotunno,Katy R. Brignole,John Clarke,Leah E. Mechanic:
  Genetic Simulation Resources and the GSR Certification Program.709-710

Review
Systems Biology

• 
  Florian Schmidt,Marcel H. Schulz:
  On the problem of confounders in modeling gene expression.711-719

Erratum
Systems Biology

• 
  Bruce A. Corliss,H. Clifton Ray,James T. Patrie,Jennifer Mansour,Sam Kesting,Janice H. Park,Gustavo K. Rohde,Paul A. Yates,Kevin A. Janes,Shayn M. Peirce:
  CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures.720-721

Volume 35, Number 5, March 2019

Discovery note
Data and Text Mining

• 
  Zheng Zhang,Zhaozhong Zhu,Wenjun Chen,Zena Cai,Beibei Xu,Zhiying Tan,Aiping Wu,Xingyi Ge,Xinhong Guo,Zhongyang Tan,Zanxian Xia,Haizhen Zhu,Taijiao Jiang,Yousong Peng:
  Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors.723-728

Original Papers
Genome Analysis

• 
  Marco Masseroli,Arif Canakoglu,Pietro Pinoli,Abdulrahman Kaitoua,Andrea Gulino,Olha Horlova,Luca Nanni,Anna Bernasconi,Stefano Perna,Eirini Stamoulakatou,Stefano Ceri:
  Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data.729-736

Sequence Analysis

• 
  Angelika Merkel,Marcos Fernández-Callejo,Eloi Casals,Santiago Marco-Sola,Ronald P. Schuyler,Ivo Glynne Gut,Simon C. Heath:
  gemBS: high throughput processing for DNA methylation data from bisulfite sequencing.737-742
• 
  Thomas Shafee,Marilyn A. Anderson:
  A quantitative map of protein sequence space for the cis-defensin superfamily.743-752
• 
  Aashish Jain,Daisuke Kihara:
  Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.753-759
• 
  Lizhen Shi,Xiandong Meng,Elizabeth Tseng,Michael Mascagni,Zhong Wang:
  SpaRC: scalable sequence clustering using Apache Spark.760-768

Phylogenetics

• 
  Edin Husic,Xinyue Li,Ademir Hujdurovic,Miika Mehine,Romeo Rizzi,Veli Mäkinen,Martin Milanic,Alexandru I. Tomescu:
  MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP.769-777

Gene expression

• 
  Darlene Lu,Yorghos Tripodis,Louis C. Gerstenfeld,Serkalem Demissie:
  Clustering of temporal gene expression data with mixtures of mixed effects models with a penalized likelihood.778-786
• 
  Yuanyuan Bian,Chong He,Jie Hou,Jianlin Cheng,Jing Qiu:
  PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects.787-797

Genetics and Population Analysis

• 
  Gerton Lunter:
  Haplotype matching in large cohorts using the Li and Stephens model.798-806
• 
  Zhenwei Dai,Sunny Hei Wong,Jun Yu,Yingying Wei:
  Batch effects correction for microbiome data with Dirichlet-multinomial regression.807-814

Systems Biology

• 
  Z. S. Wallace,Sara Brin Rosenthal,Kathleen M. Fisch,Trey Ideker,Roman Sásik:
  On entropy and information in gene interaction networks.815-822
• 
  Shila Ghazanfar,Dario Strbenac,John T. Ormerod,Jean Yee Hwa Yang,Ellis Patrick:
  DCARS: differential correlation across ranked samples.823-829
• 
  Alejandro Fernández Villaverde,Fabian Fröhlich,Daniel Weindl,Jan Hasenauer,Julio R. Banga:
  Benchmarking optimization methods for parameter estimation in large kinetic models.830-838

Data and Text Mining

• 
  Jon Ander Novella,Payam Emami Khoonsari,Stephanie Herman,Daniel Whitenack,Marco Capuccini,Joachim Burman,Kim Kultima,Ola Spjuth:
  Container-based bioinformatics with Pachyderm.839-846

Databases and Ontologies

• 
  Jie Yuan,Jiajian Zhou,Huating Wang,Hao Sun:
  SKmDB: an integrated database of next generation sequencing information in skeletal muscle.847-855
• 
  Víctor H. Tierrafría,Citlalli Mejía-Almonte,J. M. Camacho-Zaragoza,Heladia Salgado,K. Alquicira,Chu Ishida,Socorro Gama-Castro,Julio Collado-Vides:
  MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.856-864

Applications Notes
Genome Analysis

• 
  Adam D. Scott,Kuan-Lin Huang,Amila Weerasinghe,R. Jay Mashl,Qingsong Gao,Fernanda Martins Rodrigues,Matthew A. Wyczalkowski,Li Ding:
  CharGer: clinical Characterization of Germline variants.865-867
• 
  Niko Popitsch:
  VARAN-GIE: curation of genomic interval sets.868-870

Sequence Analysis

• 
  Michael Vilsker,Yumna Moosa,Sam Nooij,Vagner Fonseca,Yoika Ghysens,Korneel Dumon,Raf Pauwels,Luiz Carlos Alcantara,Ewout Vanden Eynden,Anne-Mieke Vandamme,Koen Deforche,Tulio de Oliveira:
  Genome Detective: an automated system for virus identification from high-throughput sequencing data.871-873

Structural Bioinformatics

• 
  Agnes Meyder,Stefanie Kampen,Jochen Sieg,Rainer Fährrolfes,Nils-Ole Friedrich,Florian Flachsenberg,Matthias Rarey:
  StructureProfiler: an all-in-one tool for 3D protein structure profiling.874-876

Gene expression

• 
  Tahmid Mehdi,Swneke D. Bailey,Paul Guilhamon,Mathieu Lupien:
  C3D: a tool to predict 3D genomic interactions between cis-regulatory elements.877-879
• 
  Daniel Toro-Domínguez,Jordi Martorell-Marugan,Raúl López-Domínguez,Adrián García-Moreno,Víctor González-Rumayor,Marta E. Alarcón-Riquelme,Pedro Carmona-Saez:
  ImaGEO: integrative gene expression meta-analysis from GEO database.880-882

Genetics and Population Analysis

• 
  Yan Zhao,Li Ma,Sukun Jiang,George D. Song,Shaohua He,Hong Li,Qing Song:
  AncestryView: data-driven visualization of whole-genome local-ancestry.883-885
• 
  Samuel Neuenschwander,Frédéric Michaud,Jérôme Goudet:
  QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time.886-888

Systems Biology

• 
  George Minadakis,Margarita Zachariou,Anastasis Oulas,George M. Spyrou:
  PathwayConnector: finding complementary pathways to enhance functional analysis.889-891
• 
  Jennifer Hannig,Heiko Giese,Börje Schweizer,Leonie Amstein,Jörg Ackermann,Ina Koch:
  isiKnock: in silico knockouts in signaling pathways.892-894
• 
  Andrew Keller,Juan D. Chavez,James E. Bruce:
  Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.895-897
• 
  Cheng Chang,Mansheng Li,Chaoping Guo,Yuqing Ding,Kaikun Xu,Mingfei Han,Fuchu He,Yunping Zhu:
  PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis.898-900

Data and Text Mining

• 
  Hugo Varet,Jean-Yves Coppée:
  checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes.901-902

Volume 35, Number 6, March 2019

Original Papers
Genome Analysis

• 
  Naomi Yamada,William K. M. Lai,Nina Farrell,B. Franklin Pugh,Shaun Mahony:
  Characterizing protein-DNA binding event subtypes in ChIP-exo data.903-913
• 
  Loredana M. Genovese,Marco M. Mosca,Marco Pellegrini,Filippo Geraci:
  Dot2dot: accurate whole-genome tandem repeats discovery.914-922

Structural Bioinformatics

• 
  Simone Marini,Francesca Vitali,Sara Rampazzi,Andrea Demartini,Tatsuya Akutsu:
  Protease target prediction via matrix factorization.923-929
• 
  Hong Su,Mengchen Liu,Saisai Sun,Zhenling Peng,Jianyi Yang:
  Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods.930-936
• 
  Kliment Olechnovic,Bohdan Monastyrskyy,Andriy Kryshtafovych,Ceslovas Venclovas:
  Comparative analysis of methods for evaluation of protein models against native structures.937-944
• 
  Kai-Chun Chang,Emmanuel Oluwatobi Salawu,Yuan-Yu Chang,Jin-Der Wen,Lee-Wei Yang:
  Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting.945-952

Gene expression

• 
  Tiehang Duan,José P. Pinto,Xiaohui Xie:
  Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures.953-961
• 
  Itamar Kanter,Piero Dalerba,Tomer Kalisky:
  A cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors.962-971
• 
  Lin Shi,Johan A. Westerhuis,Johan Rosén,Rikard Landberg,Carl Brunius:
  Variable selection and validation in multivariate modelling.972-980
• 
  Tyler J. Gorrie-Stone,Melissa C. Smart,Ayden Saffari,Karim Malki,Eilis J. Hannon,Joe Burrage,Jonathan Mill,Meena Kumari,Leonard C. Schalkwyk:
  Bigmelon: tools for analysing large DNA methylation datasets.981-986
• 
  Nurgazy Sulaimanov,Sunil Kumar,Frédéric Burdet,Mark Ibberson,Marco Pagni,Heinz Koeppl:
  Inferring gene expression networks with hubs using a degree weighted Lasso approach.987-994
• 
  Johannes Köster,Myles Brown,Xiaole Shirley Liu:
  A Bayesian model for single cell transcript expression analysis on MERFISH data.995-1001

Genetics and Population Analysis

• 
  Brent Kirkpatrick,Shufei Ge,Liangliang Wang:
  Efficient computation of the kinship coefficients.1002-1008

Systems Biology

• 
  Mahsa Ghanbari,Julia Lasserre,Martin Vingron:
  The Distance Precision Matrix: computing networks from non-linear relationships.1009-1017
• 
  Eun Jeong Min,Sandra E. Safo,Qi Long:
  Penalized co-inertia analysis with applications to -omics data.1018-1025
• 
  Daniel Morgan,Andreas Tjärnberg,Torbjörn E. M. Nordling,Erik L. L. Sonnhammer:
  A generalized framework for controlling FDR in gene regulatory network inference.1026-1032

Databases and Ontologies

• 
  Pavel P. Kuksa,Alexandre Amlie-Wolf,Zivadin Katanic,Otto Valladares,Li-San Wang,Yuk Yee Leung:
  DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.1033-1039
• 
  Qichao Tu,Lu Lin,Lei Cheng,Ye Deng,Zhili He:
  NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes.1040-1048

Applications Notes
Genome Analysis

• 
  Jason M. Inman,Granger G. Sutton,Erin Beck,Lauren M. Brinkac,Thomas H. Clarke,Derrick E. Fouts:
  Large-scale comparative analysis of microbial pan-genomes using PanOCT.1049-1050
• 
  Wai Yee Wong,Oleg Simakov:
  RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation.1051-1052

Sequence Analysis

• 
  Fei Song,Chunmei Cui,Lin Gao,Qinghua Cui:
  miES: predicting the essentiality of miRNAs with machine learning and sequence features.1053-1054

Gene expression

• 
  Hendrik Schultheis,Carsten Kuenne,Jens Preussner,Rene Wiegandt,Annika Fust,Mette Bentsen,Mario Looso:
  WIlsON: Web-based Interactive Omics VisualizatioN.1055-1057
• 
  José Fernández Navarro,Joakim Lundeberg,Patrik L. Ståhl:
  ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets.1058-1060

Genetics and Population Analysis

• 
  Biao Zeng,Greg Gibson:
  PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness.1061-1063
• 
  Stephen C. Watts,Scott C. Ritchie,Michael Inouye,Kathryn E. Holt:
  FastSpar: rapid and scalable correlation estimation for compositional data.1064-1066

Data and Text Mining

• 
  Hongbin Yang,Chaofeng Lou,Lixia Sun,Jie Li,Yingchun Cai,Zhuang Wang,Weihua Li,Guixia Liu,Yun Tang:
  admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties.1067-1069
• 
  Anamaria Crisan,Tamara Munzner,Jennifer L. Gardy:
  Adjutant: an R-based tool to support topic discovery for systematic and literature reviews.1070-1072

Databases and Ontologies

• 
  Thomas R. Sibley,Evan J. Silberman,James I. Mullins:
  ISDB: a database toolkit for storing and analyzing viral integration site data.1073-1075
• 
  K. Joeri van der Velde,Floris Imhann,Bart Charbon,Chao Pang,David van Enckevort,Mariska Slofstra,Ruggero Barbieri,Rudi Alberts,Dennis Hendriksen,Fleur D. L. Kelpin,Mark de Haan,Tommy de Boer,Sido Haakma,Connor Stroomberg,Salome Scholtens,Gert-Jan van de Geijn,Eleonora A. M. Festen,Rinse K. Weersma,Morris A. Swertz:
  MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.1076-1078
• 
  Pablo Mier,Miguel A. Andrade-Navarro:
  Traitpedia: a collaborative effort to gather species traits.1079-1081

Corrigendum
Databases and Ontologies

• 
  Ehsaneddin Asgari,Kiavash Garakani,Alice C. McHardy,Mohammad R. K. Mofrad:
  MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.1082

Volume 35, Number 7, April 2019

Original Papers
Genome Analysis

• 
  Pariya Behrouzi,Ernst C. Wit:
  De novo construction of polyploid linkage maps using discrete graphical models.1083-1093
• 
  Changchun Xie,Yuet-Kin Leung,Aimin Chen,Ding-Xin Long,Catherine Hoyo,Shuk-Mei Ho:
  Differential methylation values in differential methylation analysis.1094-1097

Sequence Analysis

• 
  Emilio Fenoy,José M. G. Izarzugaza,Vanessa Isabell Jurtz,Søren Brunak,Morten Nielsen:
  A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction.1098-1107
• 
  Shixiong Zhang,Xiangtao Li,Qiuzhen Lin,Ka-Chun Wong:
  Synergizing CRISPR/Cas9 off-target predictions for ensemble insights and practical applications.1108-1115
• 
  Stavros Makrodimitris,Roeland C. H. J. van Ham,Marcel J. T. Reinders:
  Improving protein function prediction using protein sequence and GO-term similarities.1116-1124
• 
  Manal Kalkatawi,Arturo Magana-Mora,Boris R. Jankovic,Vladimir B. Bajic:
  DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions.1125-1132
• 
  Chun-Chi Chen,Xiaoning Qian,Byung-Jun Yoon:
  RNAdetect: efficient computational detection of novel non-coding RNAs.1133-1141
• 
  Min Li,Li Tang,Fang-Xiang Wu,Yi Pan,Jianxin Wang:
  SCOP: a novel scaffolding algorithm based on contig classification and optimization.1142-1150

Phylogenetics

• 
  Lucas Czech,Pierre Barbera,Alexandros Stamatakis:
  Methods for automatic reference trees and multilevel phylogenetic placement.1151-1158
• 
  Ivana Pilizota,Clément-Marie Train,Adrian M. Altenhoff,Henning Redestig,Christophe Dessimoz:
  Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.1159-1166

Gene expression

• 
  Jinmyung Jung,Yeeok Kang,Hyojung Paik,Mijin Kwon,Hasun Yu,Doheon Lee:
  Deconvoluting essential gene signatures for cancer growth from genomic expression in compound-treated cells.1167-1173

Genetics and Population Analysis

• 
  Anwoy Kumar Mohanty,Dana Vuzman,Laurent C. Francioli,Christopher Cassa,Ágnes Tóth-Petróczy,Shamil R. Sunyaev:
  novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data.1174-1180
• 
  Haohan Wang,Benjamin J. Lengerich,Bryon Aragam,Eric P. Xing:
  Precision Lasso: accounting for correlations and linear dependencies in high-dimensional genomic data.1181-1187

Systems Biology

• 
  Gaëlle Letort,Arnau Montagud,Gautier Stoll,Randy W. Heiland,Emmanuel Barillot,Paul Macklin,Andrei Yu. Zinovyev,Laurence Calzone:
  PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.1188-1196
• 
  Zicheng Hu,Benjamin S. Glicksberg,Atul J. Butte:
  Robust prediction of clinical outcomes using cytometry data.1197-1203
• 
  Andrew J. Sedgewick,Kristina Buschur,Ivy Shi,Joseph D. Ramsey,Vineet K. Raghu,Dimitris V. Manatakis,Yingze Zhang,Jessica Bon,Divay Chandra,Chad Karoleski,Frank C. Sciurba,Peter Spirtes,Clark Glymour,Panayiotis V. Benos:
  Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis.1204-1212

Data and Text Mining

• 
  Erin Oerton,Ian Roberts,Patrick S. H. Lewis,Tim Guilliams,Andreas Bender:
  Understanding and predicting disease relationships through similarity fusion.1213-1220

Bioimage Informatics

• 
  Axel Theorell,Johannes Seiffarth,Alexander Grünberger,Katharina Nöh:
  When a single lineage is not enough: Uncertainty-Aware Tracking for spatio-temporal live-cell image analysis.1221-1228

Applications Notes
Phylogenetics

• 
  Joseph T. Miller,Rebecca Pirzl,Dan Rosauer,Garry Jolley-Rogers,Temi Varghese:
  Phylolink: phylogenetically-based profiling, visualisations and metrics for biodiversity.1229-1230

Structural Bioinformatics

• 
  Jan Jelínek,Josef Pánek:
  cpPredictor: a web server for template-based prediction of RNA secondary structure.1231-1233
• 
  Yi He,Suhani Nagpal,Mourad Sadqi,Eva de Alba,Victor F. Muñoz:
  Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts.1234-1236
• 
  Miha Skalic,Gerard Martínez-Rosell,José Jiménez,Gianni De Fabritiis:
  PlayMolecule BindScope: large scale CNN-based virtual screening on the web.1237-1238
• 
  Sabri Hamad,Gianluca Adornetto,J. Jesús Naveja,Aakash Chavan Ravindranath,Johannes Raffler,Mónica Campillos:
  HitPickV2: a web server to predict targets of chemical compounds.1239-1240
• 
  Sergio Decherchi,Andrea Spitaleri,John E. Stone,Walter Rocchia:
  NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.1241-1243

Genetics and Population Analysis

• 
  Jiangshan J. Shen,Chao Yang,Yong-Fei Wang,Ting-You Wang,Mengbiao Guo,Yu-Lung Lau,Xuejun Zhang,Yujun Sheng,Wanling Yang:
  HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels.1244-1246

Systems Biology

• 
  Zichen Wang,Edward He,Kevin Sani,Kathleen M. Jagodnik,Moshe C. Silverstein,Avi Ma'ayan:
  Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.1247-1248

Data and Text Mining

• 
  Kai Li,Marc Vaudel,Bing Zhang,Yan Ren,Bo Wen:
  PDV: an integrative proteomics data viewer.1249-1251
• 
  Graham M. Hughes,Emma C. Teeling:
  AGILE: an assembled genome mining pipeline.1252-1254
• 
  Matthieu Marbac,Mohammed Sedki:
  VarSelLCM: an R/C++ package for variable selection in model-based clustering of mixed-data with missing values.1255-1257

Databases and Ontologies

• 
  Gabriele Sales,Enrica Calura,Chiara Romualdi:
  metaGraphite-a new layer of pathway annotation to get metabolite networks.1258-1260

Bioimage Informatics

• 
  Nathan Heath Patterson,Ethan Yang,Elizabeth-Ann Kranjec,Pierre Chaurand:
  Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes.1261-1262

Volume 35, Number 8, April 2019

Discovery note
Genome Analysis

• 
  Roozbeh Dehghannasiri,Linda Szabo,Julia Salzman:
  Ambiguous splice sites distinguish circRNA and linear splicing in the human genome.1263-1268

Original Papers
Genome Analysis

• 
  Yuchen Yang,Ruth Huh,Houston W. Culpepper,Yuan Lin,Michael I. Love,Yun Li:
  SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data.1269-1277
• 
  Xuesi Dong,Lijuan Lin,Ruyang Zhang,Yang Zhao,David C. Christiani,Yongyue Wei,Feng Chen:
  TOBMI: trans-omics block missing data imputation using a k-nearest neighbor weighted approach.1278-1283
• 
  Jaroslav Budis,Juraj Gazdarica,Ján Radvánszky,Gábor Szücs,Marcel Kucharík,Lucia Strieskova,Iveta Gazdaricova,Maria Harsanyova,Frantisek Duris,Gabriel Minarik,Martina Sekelska,Bálint Nagy,Ján Turna,Tomás Szemes:
  Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing.1284-1291

Sequence Analysis

• 
  Hussein Al-Asadi,Kushal K. Dey,John Novembre,Matthew Stephens:
  Inference and visualization of DNA damage patterns using a grade of membership model.1292-1298
• 
  Chang Xu,Xiujing Gu,Raghavendra Padmanabhan,Zhong Wu,Quan Peng,John DiCarlo,Yexun Wang:
  smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.1299-1309
• 
  Jaroslav Budis,Marcel Kucharík,Frantisek Duris,Juraj Gazdarica,Michaela Zrubcová,Andrej Ficek,Tomás Szemes,Brona Brejová,Ján Radvánszky:
  Dante: genotyping of known complex and expanded short tandem repeats.1310-1317
• 
  Patrick V. Holec,Joseph Berleant,Mark Bathe,Michael E. Birnbaum:
  A Bayesian framework for high-throughput T cell receptor pairing.1318-1325
• 
  Leyi Wei,Shasha Luan,Luis Augusto Eijy Nagai,Ran Su,Quan Zou:
  Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species.1326-1333

Structural Bioinformatics

• 
  Maciej Wójcikowski,Michal Kukielka,Marta M. Stepniewska-Dziubinska,Pawel Siedlecki:
  Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.1334-1341
• 
  Daniel Wiegreffe,Daniel Alexander,Peter F. Stadler,Dirk Zeckzer:
  RNApuzzler: efficient outerplanar drawing of RNA-secondary structures.1342-1349

Gene expression

• 
  Kevin Y. X. Wang,Alexander M. Menzies,Ines P. Silva,James S. Wilmott,Yibing Yan,Matthew Wongchenko,Richard F. Kefford,Richard A. Scolyer,Georgina V. Long,Garth Tarr,Samuel Müller,Jean Yee Hwa Yang:
  bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays.1350-1357
• 
  Trang T. Le,Ryan J. Urbanowicz,Jason H. Moore,Brett A. McKinney:
  STatistical Inference Relief (STIR) feature selection.1358-1365

Genetics and Population Analysis

• 
  Bin Guo,Baolin Wu:
  Powerful and efficient SNP-set association tests across multiple phenotypes using GWAS summary data.1366-1372
• 
  Qiuying Sha,Zhenchuan Wang,Xiao Zhang,Shuanglin Zhang:
  A clustering linear combination approach to jointly analyze multiple phenotypes for GWAS.1373-1379

Systems Biology

• 
  Silvia Calderazzo,Marco Brancaccio,Bärbel Finkenstädt:
  Filtering and inference for stochastic oscillators with distributed delays.1380-1387
• 
  Ishita K. Khan,Aashish Jain,Reda Rawi,Halima Bensmail,Daisuke Kihara:
  Prediction of protein group function by iterative classification on functional relevance network.1388-1394

Data and Text Mining

• 
  Yuan Luo,Chengsheng Mao,Yiben Yang,Fei Wang,Faraz S. Ahmad,Donna Arnett,Marguerite R. Irvin,Sanjiv J. Shah:
  Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization.1395-1403

Databases and Ontologies

• 
  Albert Casanovas,Óscar Gallardo,Montserrat Carrascal,Joaquin Abian:
  TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells.1404-1413

Applications Notes
Genome Analysis

• 
  Cheng-Kai Shiau,Jia-Hsin Huang,Huai-Kuang Tsai:
  CATANA: a tool for generating comprehensive annotations of alternative transcript events.1414-1415
• 
  Tuan Trieu,Oluwatosin Oluwadare,Julia Wopata,Jianlin Cheng:
  GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure.1416-1418
• 
  Nengjun Yi,Zaixiang Tang,Xinyan Zhang,Boyi Guo:
  BhGLM: Bayesian hierarchical GLMs and survival models, with applications to genomics and epidemiology.1419-1421
• 
  Evgeny Anatskiy,Devon Patrick Ryan,Björn A. Grüning,Laura Arrigoni,Thomas Manke,Ulrike Bönisch:
  Parkour LIMS: high-quality sample preparation in next generation sequencing.1422-1424

Sequence Analysis

• 
  Benjamin D. Lee:
  Squiggle: a user-friendly two-dimensional DNA sequence visualization tool.1425-1426

Gene expression

• 
  Oana M. Enache,David L. Lahr,Ted E. Natoli,Lev Litichevskiy,David Wadden,Corey Flynn,Joshua Gould,Jacob K. Asiedu,Rajiv Narayan,Aravind Subramanian:
  The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices.1427-1429
• 
  Xian Liu,Mingfei Han,Chen Zhao,Cheng Chang,Yunping Zhu,Changhui Ge,Ronghua Yin,Yiqun Zhan,Changyan Li,Miao Yu,Fuchu He,Xiaoming Yang:
  KeggExp: a web server for visual integration of KEGG pathways and expression profile data.1430-1432

Genetics and Population Analysis

• 
  Junfang Chen,Dietmar Lippold,Josef Frank,William Rayner,Andreas Meyer-Lindenberg,Emanuel Schwarz:
  Gimpute: an efficient genetic data imputation pipeline.1433-1435

Systems Biology

• 
  Minoo Ashtiani,Mehdi Mirzaie,Mohieddin Jafari:
  CINNA: an R/CRAN package to decipher Central Informative Nodes in Network Analysis.1436-1437

Databases and Ontologies

• 
  Yi Zhang,Mohith Manjunath,Yeonsung Kim,Joerg Heintz,Jun S. Song:
  SequencEnG: an interactive knowledge base of sequencing techniques.1438-1440
• 
  Alejandro Brenes,Angus I. Lamond:
  The Encyclopedia of Proteome Dynamics: the KinoViewer.1441-1442

Erratum
Databases and Ontologies

• 
  Bansho Masutani,Shinichi Morishita:
  A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer.1443

Volume 35, Number 9, May 2019

Retracted
Genome Analysis

• 
  (Withdrawn)RETRACTED: LFQC: a lossless compression algorithm for FASTQ files.e1-e7

Original Papers
Genome Analysis

• 
  Chen Cao,Lauren Mak,Guangxu Jin,Paul Gordon,Kai Ye,Quan Long:
  PRESM: personalized reference editor for somatic mutation discovery in cancer genomics.1445-1452
• 
  Hai Yang,Rui Chen,Quan Wang,Qiang Wei,Ying Ji,Guangze Zheng,Xue Zhong,Nancy J. Cox,Bingshan Li:
  De novo pattern discovery enables robust assessment of functional consequences of non-coding variants.1453-1460

Sequence Analysis

• 
  Pieter Meysman,Nicolas De Neuter,Sofie Gielis,Danh Bui Thi,Benson Ogunjimi,Kris Laukens:
  On the viability of unsupervised T-cell receptor sequence clustering for epitope preference.1461-1468
• 
  Chao-Qin Feng,Zhao-Yue Zhang,Xiao-Juan Zhu,Yan Lin,Wei Chen,Hua Tang,Hao Lin:
  iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators.1469-1477
• 
  Néli José da Fonseca Jr.,Marcelo Querino Lima Afonso,Lucas Carrijo de Oliveira,Lucas Bleicher:
  A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection.1478-1485
• 
  Dengke Zhao,William D. Baez,Kurt Fredrick,Ralf Bundschuh:
  RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling.1486-1493
• 
  Xiaoyong Pan,Lars Juhl Jensen,Jan Gorodkin:
  Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.1494-1502

Structural Bioinformatics

• 
  Wen Torng,Russ B. Altman:
  High precision protein functional site detection using 3D convolutional neural networks.1503-1512
• 
  Ludovica Montanucci,Pier Luigi Martelli,Nir Ben-Tal,Piero Fariselli:
  A natural upper bound to the accuracy of predicting protein stability changes upon mutations.1513-1517

Systems Biology

• 
  Alexander M. Crowell,Casey S. Greene,Jennifer J. Loros,Jay C. Dunlap:
  Learning and Imputation for Mass-spec Bias Reduction (LIMBR).1518-1526
• 
  Jianghong Yang,Ao Li,Yongqiang Li,Xiangqian Guo,Minghui Wang:
  A novel approach for drug response prediction in cancer cell lines via network representation learning.1527-1535
• 
  Chih-Hsu Lin,Daniel M. Konecki,Meng Liu,Stephen J. Wilson,Huda Nassar,Angela D. Wilkins,David F. Gleich,Olivier Lichtarge:
  Multimodal network diffusion predicts future disease-gene-chemical associations.1536-1543

Data and Text Mining

• 
  Florian Plaza Oñate,Emmanuelle Le Chatelier,Mathieu Almeida,Alessandra C. L. Cervino,Franck Gauthier,Frédéric Magoulès,S. Dusko Ehrlich,Matthieu Pichaud:
  MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data.1544-1552
• 
  Sampo Pyysalo,Simon Baker,Imran Ali,Stefan Haselwimmer,Tejas Shah,Andrew Young,Yufan Guo,Johan Högberg,Ulla Stenius,Masashi Narita,Anna Korhonen:
  LION LBD: a literature-based discovery system for cancer biology.1553-1561

Databases and Ontologies

• 
  Adriano Barbosa-Silva,Dorina Bratfalean,Wei Gu,Venkata P. Satagopam,Paul Houston,Lauren B. Becnel,Serge Eifes,Fabien Richard,Andreas Tielmann,Sascha Herzinger,Kavita Rege,Rudi Balling,Paul Peeters:
  Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART.1562-1565
• 
  Shengsong Xie,Qin Zhu,Wubin Qu,Zhong Xu,Xiangdong Liu,Xinyun Li,Shijun Li,Wubin Ma,Yiliang Miao,Lisheng Zhang,Xiaoyong Du,Wuzi Dong,Haiwei Li,Changzhi Zhao,Yunlong Wang,Yaping Fang,Shuhong Zhao:
  sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs.1566-1572

Applications Notes
Genome Analysis

• 
  Li Chen,Ye Wang,Bing Yao,Amit Mitra,Xu Wang,Xiao Qin:
  TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction.1573-1575

Sequence Analysis

• 
  Xavier Bofill-De Ros,Kevin Chen,Susanna Chen,Nikola Tesic,Dusan Randjelovic,Nikola Skundric,Svetozar Nesic,Vojislav Varjacic,Elizabeth H. Williams,Raunaq Malhotra,Minjie Jiang,Shuo Gu:
  QuagmiR: a cloud-based application for isomiR big data analytics.1576-1578
• 
  Tamsen Dunn,Gwenn Berry,Dorothea Emig-Agius,Yu Jiang,Serena Lei,Anita Iyer,Nitin Udar,Han-Yu Chuang,Jeff Hegarty,Michael Dickover,Brandy Klotzle,Justin Robbins,Marina Bibikova,Marc Peeters,Michael Strömberg:
  Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data.1579-1581
• 
  Thomas A. Hopf,Anna G. Green,Benjamin Schubert,Sophia Mersmann,Charlotta Schärfe,John Ingraham,Ágnes Tóth-Petróczy,Kelly Brock,Adam J. Riesselman,Perry Palmedo,Chan Kang,Robert P. Sheridan,Eli J. Draizen,Christian Dallago,Chris Sander,Debora S. Marks:
  The EVcouplings Python framework for coevolutionary sequence analysis.1582-1584

Structural Bioinformatics

• 
  Anna Vangone,Jörg Schaarschmidt,Panagiotis I. Koukos,Cunliang Geng,Nevia Citro,Mikael E. Trellet,Li C. Xue,Alexandre M. J. J. Bonvin:
  Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.1585-1587
• 
  Sebastian Stolzenberg:
  PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles.1588-1590
• 
  Gideon Lapidoth,Jake Parker,Jaime Prilusky,Sarel Jacob Fleishman:
  AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains.1591-1593

Gene expression

• 
  Marco Trevisan-Herraz,Navratan Bagwan,Fernando García-Marqués,José Manuel Rodriguez,Inmaculada Jorge,Iakes Ezkurdia,Elena Bonzon-Kulichenko,Jesús Vázquez:
  SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.1594-1596
• 
  Tianzhou Ma,Zhiguang Huo,Anche Kuo,Li Zhu,Zhou Fang,Xiangrui Zeng,Chien-Wei Lin,Silvia Liu,Lin Wang,Peng Liu,Tanbin Rahman,Lun-Ching Chang,Sunghwan Kim,Jia Li,Yongseok Park,Chi Song,Steffi Oesterreich,Etienne Sibille,George C. Tseng:
  MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis.1597-1599

Systems Biology

• 
  Maxwell Lewis Neal,Christopher T. Thompson,Karam G. Kim,Ryan C. James,Daniel L. Cook,Brian E. Carlson,John H. Gennari:
  SemGen: a tool for semantics-based annotation and composition of biosimulation models.1600-1602
• 
  Le Yuan,Yu Tian,Shaozhen Ding,Yanfang Liu,Fu Chen,Tong Zhang,Weizhong Tu,Junni Chen,Qian-Nan Hu:
  PrecursorFinder: a customized biosynthetic precursor explorer.1603-1604
• 
  Maria Suprun,Mayte Suárez-Fariñas:
  PlateDesigner: a web-based application for the design of microplate experiments.1605-1607
• 
  Florian Schmidt,Fabian Kern,Peter Ebert,Nina Baumgarten,Marcel H. Schulz:
  TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis.1608-1609

Bioimage Informatics

• 
  Marcus A. Badgeley,Manway Liu,Benjamin S. Glicksberg,Mark M. Shervey,John R. Zech,Khader Shameer,Joseph Lehar,Eric K. Oermann,Michael V. McConnell,Thomas M. Snyder,Joel T. Dudley:
  CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis.1610-1612

Letter to the Editor
Sequence Analysis

• 
  Nidhi Shah,Michael G. Nute,Tandy J. Warnow,Mihai Pop:
  Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.1613-1614

Review
Genome Analysis

• 
  Chakravarthi Kanduri,Christoph Bock,Sveinung Gundersen,Eivind Hovig,Geir Kjetil Sandve:
  Colocalization analyses of genomic elements: approaches, recommendations and challenges.1615-1624

Volume 35, Number 10, May 2019

Original Papers
Genome Analysis

• 
  Hadi Fanaee-T,Magne Thoresen:
  Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization.1625-1633
• 
  Dina Svetlitsky,Tal Dagan,Vered Chalifa-Caspi,Michal Ziv-Ukelson:
  CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes.1634-1643
• 
  Can Yang,Xiang Wan,Xinyi Lin,Mengjie Chen,Xiang Zhou,Jin Liu:
  CoMM: a collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information.1644-1652
• 
  Hao Ding,Michael F. Sharpnack,Chao Wang,Kun Huang,Raghu Machiraju:
  Integrative cancer patient stratification via subspace merging.1653-1659

Sequence Analysis

• 
  Hailin Hu,An Xiao,Sai Zhang,Yangyang Li,Xuanling Shi,Tao Jiang,Linqi Zhang,Lei Zhang,Jianyang Zeng:
  DeepHINT: understanding HIV-1 integration via deep learning with attention.1660-1667

Phylogenetics

• 
  Anamaria Crisan,Jennifer L. Gardy,Tamara Munzner:
  A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT.1668-1676
• 
  Ki-Hok Liao,Wing-Kai Hon,Chuan Yi Tang,Wen-Ping Hsieh:
  MetaSMC: a coalescent-based shotgun sequence simulator for evolving microbial populations.1677-1685

Structural Bioinformatics

• 
  Saisai Sun,Qi Wu,Zhenling Peng,Jianyi Yang:
  Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles.1686-1691
• 
  Gang Hu,Zhonghua Wu,Christopher J. Oldfield,Chen Wang,Lukasz A. Kurgan:
  Quality assessment for the putative intrinsic disorder in proteins.1692-1700

Gene expression

• 
  Divya Niveditha,Sudeshna Mukherjee,Syamantak Majumder,Rajdeep Chowdhury,Shibasish Chowdhury:
  A global transcriptomic pipeline decoding core network of genes involved in stages leading to acquisition of drug-resistance to cisplatin in osteosarcoma cells.1701-1711
• 
  Hui-Zeng Sun,Ke Zhao,Mi Zhou,Yanhong Chen,Le Luo Guan:
  Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle.1712-1719

Genetics and Population Analysis

• 
  Louis Raynal,Jean-Michel Marin,Pierre Pudlo,Mathieu Ribatet,Christian P. Robert,Arnaud Estoup:
  ABC random forests for Bayesian parameter inference.1720-1728
• 
  Mingwei Dai,Xiang Wan,Hao Peng,Yao Wang,Yue Liu,Jin Liu,Zongben Xu,Can Yang:
  Joint analysis of individual-level and summary-level GWAS data by leveraging pleiotropy.1729-1736

Data and Text Mining

• 
  Da Chen Emily Koo,Richard Bonneau:
  Towards region-specific propagation of protein functions.1737-1744
• 
  Xuan Wang,Yu Zhang,Xiang Ren,Yuhao Zhang,Marinka Zitnik,Jingbo Shang,Curtis P. Langlotz,Jiawei Han:
  Cross-type biomedical named entity recognition with deep multi-task learning.1745-1752

Databases and Ontologies

• 
  Shayoni Ray,Samrawit Gebre,Homer Fogle,Daniel C. Berrios,Peter B. Tran,Jonathan M. Galazka,Sylvain V. Costes:
  GeneLab: Omics database for spaceflight experiments.1753-1759

Applications Notes
Genome Analysis

• 
  Weihua Pan,Stefano Lonardi:
  Accurate detection of chimeric contigs via Bionano optical maps.1760-1762
• 
  Pieter J. K. Libin,Koen Deforche,Ana B. Abecasis,Kristof Theys:
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes.1763-1765

Sequence Analysis

• 
  Tony E. Lewis,Ian Sillitoe,Jonathan G. Lees:
  cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.1766-1767
• 
  Yuk Yee Leung,Otto Valladares,Yi-Fan Chou,Han-Jen Lin,Amanda Kuzma,Laura Cantwell,Liming Qu,William J. Salerno,Gerard D. Schellenberg,Li-San Wang:
  VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.1768-1770

Phylogenetics

• 
  Benoit Morel,Alexey M. Kozlov,Alexandros Stamatakis:
  ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.1771-1773

Structural Bioinformatics

• 
  Wing Ki Wong,Guy Georges,Francesca Ros,Sebastian Kelm,Alan P. Lewis,Bruck Taddese,Jinwoo Leem,Charlotte M. Deane:
  SCALOP: sequence-based antibody canonical loop structure annotation.1774-1776
• 
  Zhe Wang,Xuwen Wang,Youyong Li,Tailong Lei,Ercheng Wang,Dan Li,Yu Kang,Feng Zhu,Tingjun Hou:
  farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.1777-1779

Gene expression

• 
  Jason R. Phillips,Daniel L. Svoboda,Arpit Tandon,Shyam Patel,Alex Sedykh,Deepak Mav,Byron Kuo,Carole L. Yauk,Longlong Yang,Russell S. Thomas,Jeff S. Gift,J. Allen Davis,Louis Olszyk,B. Alex Merrick,Richard S. Paules,Fred Parham,Trey Saddler,Ruchir R. Shah,Scott S. Auerbach:
  BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.1780-1782

Genetics and Population Analysis

• 
  Arthur T. O. Melo,Iago Hale:
  Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP.1783-1785
• 
  Chi Zhang,Shan-Shan Dong,Jun-Yang Xu,Weiming He,Tie-Lin Yang:
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.1786-1788

Systems Biology

• 
  Chongyang Tan,Wei Cui,Xinping Cui,Kang Ning:
  Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling.1789-1791
• 
  Minzhe Zhang,Sangin Lee,Bo Yao,Guanghua Xiao,Lin Xu,Yang Xie:
  DIGREM: an integrated web-based platform for detecting effective multi-drug combinations.1792-1794
• 
  Yann Beauxis,Grégory Genta-Jouve:
  MetWork: a web server for natural products anticipation.1795-1796

Data and Text Mining

• 
  Han Cao,Jiayu Zhou,Emanuel Schwarz:
  RMTL: an R library for multi-task learning.1797-1798
• 
  Axel J. Soto,Piotr Przybyla,Sophia Ananiadou:
  Thalia: semantic search engine for biomedical abstracts.1799-1801

Bioimage Informatics

• 
  Georges Hattab,Tim W. Nattkemper:
  SeeVis - 3D space-time cube rendering for visualization of microfluidics image data.1802-1804

Volume 35, Number 11, June 2019

Original Papers
Genome Analysis

• 
  Beibei Ru,Jianlong Sun,Qingzheng Kang,Yin Tong,Jiangwen Zhang:
  A framework for identifying dysregulated chromatin regulators as master regulators in human cancer.1805-1812
• 
  Anton Pirogov,Peter Pfaffelhuber,Angelika Börsch-Haubold,Bernhard Haubold:
  High-complexity regions in mammalian genomes are enriched for developmental genes.1813-1819

Sequence Analysis

• 
  Wei Zheng,Le Yang,Robert J. Genco,Jean Wactawski-Wende,Michael Buck,Yijun Sun:
  SENSE: Siamese neural network for sequence embedding and alignment-free comparison.1820-1828
• 
  Baraa Orabi,Emre Erhan,Brian McConeghy,Stanislav V. Volik,Stephane Le Bihan,Robert Bell,Colin C. Collins,Cédric Chauve,Faraz Hach:
  Alignment-free clustering of UMI tagged DNA molecules.1829-1836
• 
  Zhen Cao,Shihua Zhang:
  Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction.1837-1843
• 
  Loris Nanni,Sheryl Brahnam:
  Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins.1844-1851

Phylogenetics

• 
  Niema Moshiri,Manon Ragonnet-Cronin,Joel O. Wertheim,Siavash Mirarab:
  FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.1852-1861
• 
  Rui Borges,João Paulo Machado,Cidália Gomes,Ana Paula Rocha,Agostinho Antunes:
  Measuring phylogenetic signal between categorical traits and phylogenies.1862-1869

Structural Bioinformatics

• 
  Sebastian Daberdaku,Carlo Ferrari:
  Antibody interface prediction with 3D Zernike descriptors and SVM.1870-1876

Gene expression

• 
  Yumi Kawamura,Shinsuke Koyama,Ryo Yoshida:
  Statistical inference of the rate of RNA polymerase II elongation by total RNA sequencing.1877-1884
• 
  Anna Papiez,Michal Marczyk,Joanna Polanska,Andrzej Polanski:
  BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm.1885-1892
• 
  Ruiqing Zheng,Min Li,Xiang Chen,Fang-Xiang Wu,Yi Pan,Jianxin Wang:
  BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks.1893-1900

Genetics and Population Analysis

• 
  Mary D. Fortune,Chris Wallace:
  simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics.1901-1906
• 
  Tzipi Braun,Antonio V. Bordería,Cyril Barbezange,Marco Vignuzzi,Yoram Louzoun:
  Long-term context-dependent genetic adaptation of the viral genetic cloud.1907-1915

Systems Biology

• 
  Andrea Rodriguez-Martinez,Rafael Ayala,Joram M. Posma,Nikita Harvey,Beatriz Jiménez,Kazuhiro Sonomura,Taka-Aki Sato,Fumihiko Matsuda,Pierre A. Zalloua,Dominique Gauguier,Jeremy K. Nicholson,Marc-Emmanuel Dumas:
  pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra.1916-1922
• 
  Yonghyun Nam,Jong Ho Jhee,Junhee Cho,Ji-Hyun Lee,Hyunjung Shin:
  Disease gene identification based on generic and disease-specific genome networks.1923-1930

Data and Text Mining

• 
  Milton Pividori,Andres Cernadas,Luis A. de Haro,Fernando Carrari,Georgina Stegmayer,Diego H. Milone:
  Clustermatch: discovering hidden relations in highly diverse kinds of qualitative and quantitative data without standardization.1931-1939

Bioimage Informatics

• 
  Johannes Leuschner,Maximilian Schmidt,Pascal Fernsel,Delf Lachmund,Tobias Boskamp,Peter Maass:
  Supervised non-negative matrix factorization methods for MALDI imaging applications.1940-1947
• 
  Meiling Wang,Xiaoke Hao,Jiashuang Huang,Wei Shao,Daoqiang Zhang:
  Discovering network phenotype between genetic risk factors and disease status via diagnosis-aligned multi-modality regression method in Alzheimer's disease.1948-1957

Applications Notes
Genome Analysis

• 
  Xu Ren,Pei Fen Kuan:
  methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.1958-1959
• 
  Roberto Vera Alvarez,Lorinc Sándor Pongor,Leonardo Mariño-Ramírez,David Landsman:
  TPMCalculator: one-step software to quantify mRNA abundance of genomic features.1960-1962
• 
  Rebecca Rose,Olga Golosova,Dmitrii Sukhomlinov,Aleksey Tiunov,Mattia Prosperi:
  Flexible design of multiple metagenomics classification pipelines with UGENE.1963-1965

Gene expression

• 
  Ashish Jain,Geetu Tuteja:
  TissueEnrich: Tissue-specific gene enrichment analysis.1966-1967

Genetics and Population Analysis

• 
  Abbas A. Rizvi,Ezgi Karaesmen,Martin Morgan,Leah Preus,Junke Wang,Michael Sovic,Theresa Hahn,Lara E. Sucheston-Campbell:
  gwasurvivr: an R package for genome-wide survival analysis.1968-1970
• 
  Milton Pividori,Hae Kyung Im:
  ukbREST: efficient and streamlined data access for reproducible research in large biobanks.1971-1973

Systems Biology

• 
  Tiago Chedraoui Silva,Simon G. Coetzee,Nicole Gull,Lijing Yao,Dennis J. Hazelett,Houtan Noushmehr,De-Chen Lin,Benjamin P. Berman:
  ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.1974-1977

Databases and Ontologies

• 
  Christos Kopanos,Vasilis Tsiolkas,Alexandros Kouris,Charles E. Chapple,Monica Albarca Aguilera,Richard Meyer,Andreas Massouras:
  VarSome: the human genomic variant search engine.1978-1980
• 
  Matthew C. Canver,Daniel E. Bauer,Takahiro Maeda,Luca Pinello:
  DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens.1981-1984

Corrigendum
Databases and Ontologies

• 
  Yuk Yee Leung,Otto Valladares,Yi-Fan Chou,Han-Jen Lin,Amanda Kuzma,Laura Cantwell,Liming Qu,Prabhakaran Gangadharan,William J. Salerno,Gerard D. Schellenberg,Li-San Wang:
  VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.1985

Volume 35, Number 12, June 2019

Discovery note
Genome analysis

• 
  Zhi-Kai Yang,Hao Luo,Yanming Zhang,Baijing Wang,Feng Gao:
  Pan-genomic analysis provides novel insights into the association of E.coli with human host and its minimal genome.1987-1991

Original Papers
Genome analysis

• 
  Eva-Maria Huessler,Martin Schäfer,Holger Schwender,Pablo Landgraf:
  BayMAP: a Bayesian hierarchical model for the analysis of PAR-CLIP data.1992-2000
• 
  Eran Barash,Neta Sal-Man,Sivan Sabato,Michal Ziv-Ukelson:
  BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM.2001-2008
• 
  Md-Nafiz Hamid,Iddo Friedberg:
  Identifying antimicrobial peptides using word embedding with deep recurrent neural networks.2009-2016

Sequence analysis

• 
  Jiawei Wang,Jiahui Li,Bingjiao Yang,Ruopeng Xie,Tatiana T. Marquez-Lago,André Leier,Morihiro Hayashida,Tatsuya Akutsu,Yanju Zhang,Kuo-Chen Chou,Joel Selkrig,Tieli Zhou,Jiangning Song,Trevor Lithgow:
  Bastion3: a two-layer ensemble predictor of type III secreted effectors.2017-2028
• 
  Mark Howison,Mia Coetzer,Rami Kantor:
  Measurement error and variant-calling in deep Illumina sequencing of HIV.2029-2035
• 
  Miguel Correa Marrero,Richard G. H. Immink,Dick de Ridder,Aalt D. J. van Dijk:
  Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis.2036-2042
• 
  Sebastian Deorowicz,Agnieszka Debudaj-Grabysz,Adam Gudys,Szymon Grabowski:
  Whisper: read sorting allows robust mapping of DNA sequencing data.2043-2050
• 
  Li Xue,Bin Tang,Wei Chen,Jiesi Luo:
  DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence.2051-2057
• 
  Wei Shi,Jianhua Chen,Mao Luo,Min Chen:
  High efficiency referential genome compression algorithm.2058-2065
• 
  Yuansheng Liu,Zu-Guo Yu,Marcel E. Dinger,Jinyan Li:
  Index suffix-prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression.2066-2074
• 
  Fu-Ying Dao,Hao Lv,Fang Wang,Chao-Qin Feng,Hui Ding,Wei Chen,Hao Lin:
  Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique.2075-2083

Gene expression

• 
  Anqi Zhu,Joseph G. Ibrahim,Michael I. Love:
  Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences.2084-2092
• 
  Gregory J. Hunt,Saskia Freytag,Melanie Bahlo,Johann Gagnon-Bartsch:
  dtangle: accurate and robust cell type deconvolution.2093-2099

Systems biology

• 
  Mengshi Zhou,Yang Chen,Rong Xu:
  A Drug-Side Effect Context-Sensitive Network approach for drug target prediction.2100-2107
• 
  Mahdi Shafiee Kamalabad,Alexander Martin Heberle,Kathrin Thedieck,Marco Grzegorczyk:
  Partially non-homogeneous dynamic Bayesian networks based on Bayesian regression models with partitioned design matrices.2108-2117
• 
  Jacob D. Davis,Eberhard O. Voit:
  Metrics for regulated biochemical pathway systems.2118-2124

Data and text mining

• 
  João C. Marques,Michael B. Orger:
  Clusterdv: a simple density-based clustering method that is robust, general and automatic.2125-2132

Databases and ontologies

• 
  Fatima Zohra Smaili,Xin Gao,Robert Hoehndorf:
  OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.2133-2140

Bioimage informatics

• 
  Hao Yuan,Lei Cai,Zhengyang Wang,Xia Hu,Shaoting Zhang,Shuiwang Ji:
  Computational modeling of cellular structures using conditional deep generative networks.2141-2149

Applications Notes
Genome analysis

• 
  Robert D. Stewart,Marc D. Auffret,Timothy J. Snelling,Rainer Roehe,Mick Watson:
  MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).2150-2152
• 
  Arthur Zwaenepoel,Yves Van de Peer:
  wgd - simple command line tools for the analysis of ancient whole-genome duplications.2153-2155
• 
  Marek S. Wiewiórka,Anna Lesniewska,Agnieszka Szmurlo,Kacper Stepien,Mateusz Borowiak,Michal J. Okoniewski,Tomasz Gambin:
  SeQuiLa: an elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals.2156-2158

Gene expression

• 
  Thomas Moerman,Sara Aibar Santos,Carmen Bravo González-Blas,Jaak Simm,Yves Moreau,Jan Aerts,Stein Aerts:
  GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks.2159-2161

Genetics and population analysis

• 
  Regev Schweiger,Yaniv Erlich,Shai Carmi:
  FactorialHMM: fast and exact inference in factorial hidden Markov models.2162-2164

Systems biology

• 
  Alireza Khatamian,Evan O. Paull,Andrea Califano,Jiyang Yu:
  SJARACNe: a scalable software tool for gene network reverse engineering from big data.2165-2166

Retracted Article
Systems biology

• 
  (Withdrawn)RETRACTED: Analysis and prediction of β-turn types using multinomial logistic regression and artificial neural network.e8-e15

Volume 35, Number 13, July 2019

Original Papers
Genome Analysis

• 
  Axel Poulet,Ben Li,Tristan Dubos,Juan Carlos Rivera-Mulia,David M. Gilbert,Zhaohui S. Qin:
  RT States: systematic annotation of the human genome using cell type-specific replication timing programs.2167-2176
• 
  Richard C. Brown,Gerton Lunter:
  An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs.2177-2184
• 
  Rodrigo Santamaría,Roberto Therón,Laura Durán,Alicia García-Holgado,Sara González,Mar Sánchez,Francisco Antequera:
  Genome-wide search of nucleosome patterns using visual analytics.2185-2192

Sequence Analysis

• 
  Alexander Payne,Nadine Holmes,Vardhman K. Rakyan,Matthew Loose:
  BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.2193-2198
• 
  Carine Rey,Philippe Veber,Bastien Boussau,Marie Sémon:
  CAARS: comparative assembly and annotation of RNA-Seq data.2199-2207
• 
  Ioannis A. Tamposis,Konstantinos D. Tsirigos,Margarita C. Theodoropoulou,Panagiota I. Kontou,Pantelis G. Bagos:
  Semi-supervised learning of Hidden Markov Models for biological sequence analysis.2208-2215
• 
  Abdurrahman Elbasir,Balasubramanian Moovarkumudalvan,Khalid Kunji,Prasanna R. Kolatkar,Raghvendra Mall,Halima Bensmail:
  DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction.2216-2225

Gene expression

• 
  Ameen Eetemadi,Ilias Tagkopoulos:
  Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships.2226-2234
• 
  Jun Li,Alicia T. Lamere:
  DiPhiSeq: robust comparison of expression levels on RNA-Seq data with large sample sizes.2235-2242

Genetics and Population Analysis

• 
  Eran Elhaik,Desmond M. Ryan:
  Pair Matcher (PaM): fast model-based optimization of treatment/case-control matches.2243-2250
• 
  Bin Guo,Baolin Wu:
  Integrate multiple traits to detect novel trait-gene association using GWAS summary data with an adaptive test approach.2251-2257

Systems Biology

• 
  T. Van Du Tran,Sébastien Moretti,Alix T. Coste,Sara Amorim-Vaz,Dominique Sanglard,Marco Pagni:
  Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.2258-2266
• 
  Fiorenza Gianì,Giulia Russo,Marzio Pennisi,Laura Sciacca,Francesco Frasca,Francesco Pappalardo:
  Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells.2267-2275

Data and Text Mining

• 
  Samaneh Kouchaki,Yang Yang,Timothy M. Walker,A. Sarah Walker,Daniel J. Wilson,Timothy E. A Peto,Derrick W. Crook,CRyPTIC Consortium,David A. Clifton:
  Application of machine learning techniques to tuberculosis drug resistance analysis.2276-2282

Databases and Ontologies

• 
  Jamie Soul,Tim E. Hardingham,Ray P. Boot-Handford,Jean-Marc Schwartz:
  SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data.2283-2290

Bioimage Informatics

• 
  Henrik Failmezger,Ezgi Dursun,Sebastian Dümcke,Max Endele,Don Poron,Timm Schroeder,Anne Krug,Achim Tresch:
  Clustering of samples with a tree-shaped dependence structure, with an application to microscopic time lapse imaging.2291-2299

Applications Notes
Genome Analysis

• 
  Yasminka A Jakubek,F. Anthony San Lucas,Paul Scheet:
  Directional allelic imbalance profiling and visualization from multi-sample data with RECUR.2300-2302
• 
  Olga Kunyavskaya,Andrey D. Prjibelski:
  SGTK: a toolkit for visualization and assessment of scaffold graphs.2303-2305
• 
  Jikai Zhang,Haidong Lan,Yuandong Chan,Yuan Shang,Bertil Schmidt,Weiguo Liu:
  BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures.2306-2308
• 
  Moritz Schaefer,Djork-Arné Clevert,Bertram Weiss,Andreas Steffen:
  PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations.2309-2310
• 
  Laurent Lacroix:
  G4HunterApps.2311-2312
• 
  Gang Peng,Rashaun Wilson,Yishuo Tang,TuKiet T. Lam,Angus C. Nairn,Kenneth R. Williams,Hongyu Zhao:
  ProteomicsBrowser: MS/proteomics data visualization and investigation.2313-2314
• 
  Jannah Shamsani,Stephen H. Kazakoff,Irina M. Armean,Will McLaren,Michael T. Parsons,Bryony A Thompson,Tracy A. O'Mara,Sarah E. Hunt,Nicola Waddell,Amanda B. Spurdle:
  A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity.2315-2317
• 
  Matthew D. Czajkowski,Daniel P. Vance,Steven A. Frese,Giorgio Casaburi:
  GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets.2318-2319

Phylogenetics

• 
  Ritika Ramani,Katie Krumholz,Yi-Fei Huang,Adam C. Siepel:
  PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP.2320-2322

Structural Bioinformatics

• 
  Jacob D. Durrant:
  BlendMol: advanced macromolecular visualization in Blender.2323-2325

Gene expression

• 
  Tobias Jakobi,Alexey Uvarovskii,Christoph Dieterich:
  circtools - a one-stop software solution for circular RNA research.2326-2328
• 
  Saeid Parvandeh,Brett A. McKinney:
  EpistasisRank and EpistasisKatz: interaction network centrality methods that integrate prior knowledge networks.2329-2331

Systems Biology

• 
  Federico Baldini,Almut Heinken,Laurent Heirendt,Stefanía Magnúsdóttir,Ronan M. T. Fleming,Ines Thiele:
  The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.2332-2334
• 
  Bob Chen,Charles A. Herring,Ken S. Lau:
  pyNVR: investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction.2335-2337
• 
  Hongyang Li,Shuai Hu,Nouri Neamati,Yuanfang Guan:
  TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction.2338-2339

Bioimage Informatics

• 
  Taras Sych,Thomas Schubert,Romain Vauchelles,Josef Madl,Ramin Omidvar,Roland Thuenauer,Ludovic Richert,Yves Mély,Winfried Römer:
  GUV-AP: multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles.2340-2342

Letter to the Editor
Data and Text Mining

• 
  Stefano Nembrini:
  Bias in the intervention in prediction measure in random forests: illustrations and recommendations.2343-2345

Corrigenda
Data and Text Mining

• 
  Siamak Zamani Dadaneh,Mingyuan Zhou,Xiaoning Qian:
  Bayesian negative binomial regression for differential expression with confounding factors.2346
• 
  Johannes Köster,Myles Brown,Xiaole Shirley Liu:
  A Bayesian model for single cell transcript expression analysis on MERFISH data.2347
• 
  Zhenwei Dai,Sunny Hei Wong,Jun Yu,Yingying Wei:
  Batch effects correction for microbiome data with Dirichlet-multinomial regression.2348

Volume 35, Number 14, July 2019

Discovery note
Sequence Analysis

• 
  Vikram Alva,Andrei N. Lupas:
  Histones predate the split between bacteria and archaea.2349-2353

Original Papers
Genome Analysis

• 
  Alexander J. Nash,Boris Lenhard:
  A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates.2354-2361
• 
  Catharina Lippmann,Alfred Ultsch,Jörn Lötsch:
  Computational functional genomics-based reduction of disease-related gene sets to their key components.2362-2370
• 
  Zhihao Xia,Yu Li,Bin Zhang,Zhongxiao Li,Yuhui Hu,Wei Chen,Xin Gao:
  DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.2371-2379

Sequence Analysis

• 
  Chang Sik Kim,Sumitra Mohan,Mahmood Ayub,Dominic G. Rothwell,Caroline Dive,Ged Brady,Crispin J. Miller:
  In silico error correction improves cfDNA mutation calling.2380-2385
• 
  Duolin Wang,Yanchun Liang,Dong Xu:
  Capsule network for protein post-translational modification site prediction.2386-2394
• 
  Xiaoying Wang,Bin Yu,Anjun Ma,Cheng Chen,Bingqiang Liu,Qin Ma:
  Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique.2395-2402

Structural Bioinformatics

• 
  Jack Hanson,Kuldip K. Paliwal,Thomas Litfin,Yuedong Yang,Yaoqi Zhou:
  Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.2403-2410
• 
  Seung Hwan Hong,Keehyoung Joo,Jooyoung Lee:
  ConDo: protein domain boundary prediction using coevolutionary information.2411-2417
• 
  David Simoncini,Kam Y. J. Zhang,Thomas Schiex,Sophie Barbe:
  A structural homology approach for computational protein design with flexible backbone.2418-2426
• 
  Amaya Jiménez,Slavica Jonic,Tomás Majtner,Joaquín Otón,Jose Luis Vilas,David Maluenda,Javier Mota,Erney Ramírez-Aportela,Marta Martínez,Yaiza Rancel,Joan Segura,Rubén Sánchez García,Roberto Melero,Laura del Cano,Pablo Conesa,Lars Skjaerven,Roberto Marabini,José María Carazo,Carlos Oscar Sánchez Sorzano:
  Validation of electron microscopy initial models via small angle X-ray scattering curves.2427-2433
• 
  Shinichiro Tsuchiya,Issaku Yamada,Kiyoko F. Aoki-Kinoshita:
  GlycanFormatConverter: a conversion tool for translating the complexities of glycans.2434-2440

Gene expression

• 
  Yang Shi,Mengqiao Wang,Weiping Shi,Ji-Hyun Lee,Huining Kang,Hui Jiang:
  Accurate and efficient estimation of small P-values with the cross-entropy method: applications in genomic data analysis.2441-2448

Systems Biology

• 
  Andrew Parton,Victoria McGilligan,Melody Chemaly,Maurice O'Kane,Steven Watterson:
  New models of atherosclerosis and multi-drug therapeutic interventions.2449-2457

Data and Text Mining

• 
  Johanna Schwarz,Dominik Heider:
  GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making.2458-2465

Databases and Ontologies

• 
  Jimmy Ka Ho Chiu,Rick Twee-Hee Ong:
  ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases.2466-2474

Bioimage Informatics

• 
  Xiongtao Ruan,Robert F. Murphy:
  Evaluation of methods for generative modeling of cell and nuclear shape.2475-2485

Applications Notes
Genome Analysis

• 
  Hong-Dong Li,Tianjian Bai,Erin Sandford,Margit Burmeister,Yuanfang Guan:
  BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets.2486-2488
• 
  Tobias Rausch,Markus Hsi-Yang Fritz,Jan O. Korbel,Vladimir Benes:
  Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.2489-2491
• 
  Tania Cuppens,Thomas E. Ludwig,Pascal Trouvé,Emmanuelle Génin:
  GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype.2492-2494
• 
  Gregory McInnes,Yosuke Tanigawa,Chris DeBoever,Adam Lavertu,Julia Eve Olivieri,Matthew Aguirre,Manuel A. Rivas:
  Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics.2495-2497

Sequence Analysis

• 
  Ehsaneddin Asgari,Philipp C. Münch,Till R. Lesker,Alice C. McHardy,Mohammad R. K. Mofrad:
  DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.2498-2500
• 
  Jiamin Sun,Hao Liu,Jianxiao Liu,Shikun Cheng,Yong Peng,Qinghua Zhang,Jianbing Yan,Haijun Liu,Ling-Ling Chen:
  CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes.2501-2503

Phylogenetics

• 
  Clément-Marie Train,Miguel Pignatelli,Adrian M. Altenhoff,Christophe Dessimoz:
  iHam and pyHam: visualizing and processing hierarchical orthologous groups.2504-2506

Structural Bioinformatics

• 
  Aleix Lafita,Pengfei Tian,Robert B. Best,Alex Bateman:
  TADOSS: computational estimation of tandem domain swap stability.2507-2508

Genetics and Population Analysis

• 
  Thomas Sherman,Jack M. Fu,Robert B. Scharpf,Alexandre Bureau,Ingo Ruczinski:
  Detection of rare disease variants in extended pedigrees using RVS.2509-2511
• 
  Bongsong Kim,Xinbin Dai,Wenchao Zhang,Zhaohong Zhuang,Darlene L. Sanchez,Thomas Lübberstedt,Yun Kang,Michael K. Udvardi,William D. Beavis,Shizhong Xu,Patrick X. Zhao:
  GWASpro: a high-performance genome-wide association analysis server.2512-2514

Systems Biology

• 
  Héléna A. Gaspar,Christopher Hübel,Gerome Breen:
  Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes.2515-2517

Data and Text Mining

• 
  Adrián Bazaga,Alfonso Valencia,María-José Rementeria:
  BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications.2518-2520
• 
  Zheng Kuang,Ying Wang,Lei Li,Xiaozeng Yang:
  miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.2521-2522
• 
  Sergio Castillo-Lara,Josep F. Abril:
  PPaxe: easy extraction of protein occurrence and interactions from the scientific literature.2523-2524

Letter to the Editor
Structural Bioinformatics

• 
  Ludovica Montanucci,Castrense Savojardo,Pier Luigi Martelli,Rita Casadio,Piero Fariselli:
  On the biases in predictions of protein stability changes upon variations: the INPS test case.2525-2527

Corrigendum
Structural Bioinformatics

• 
  Wei Zhang,Jianzhu Ma,Trey Ideker:
  Classifying tumors by supervised network propagation.2528

Ismb/ECCB 2019 Conference Proceedings
ISMB/ECCB 2019 PROCEEDINGS

• 
  Yana Bromberg,Nadia El-Mabrouk,Predrag Radivojac:
  ISMB/ECCB 2019 Proceedings.i1-i2

Ismb/ECCB 2019 Proceedings Papers Committee

• 
  ISMB/ECCB 2019 PROCEEDINGS PAPERS COMMITTEE.i3

Bioinformatics Education

• 
  Martin Strazar,Lan Zagar,Jaka Kokosar,Vesna Tanko,Ales Erjavec,Pavlin G. Policar,Anze Staric,Janez Demsar,Gad Shaulsky,Vilas Menon,Andrew Lemire,Anup Parikh,Blaz Zupan:
  scOrange - a tool for hands-on training of concepts from single-cell data analytics.i4-i12

Bioinformatics of Microbes and Microbiomes

• 
  Camilo Valdes,Vitalii Stebliankin,Giri Narasimhan:
  Large scale microbiome profiling in the cloud.i13-i22
• 
  Sahar Tavakoli,Shibu Yooseph:
  Learning a mixture of microbial networks using minorization-maximization.i23-i30
• 
  Erfan Sayyari,Ban Kawas,Siavash Mirarab:
  TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification.i31-i40

Comparative and Functional genomics

• 
  Wei Vivian Li,Jingyi Jessica Li:
  A statistical simulator scDesign for rational scRNA-seq experimental design.i41-i50
• 
  Martin D. Muggli,Bahar Alipanahi,Christina Boucher:
  Building large updatable colored de Bruijn graphs via merging.i51-i60
• 
  Ivan Tolstoganov,Anton Bankevich,Zhoutao Chen,Pavel A. Pevzner:
  cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.i61-i70
• 
  André Hennig,Kay Nieselt:
  Efficient merging of genome profile alignments.i71-i80
• 
  Ali Ghaffaari,Tobias Marschall:
  Fully-sensitive seed finding in sequence graphs using a hybrid index.i81-i89
• 
  Song-Yao Zhang,Shao-Wu Zhang,Xiao-Nan Fan,Teng Zhang,Jia Meng,Yufei Huang:
  FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes.i90-i98
• 
  Qiao Liu,Hairong Lv,Rui Jiang:
  hicGAN infers super resolution Hi-C data with generative adversarial networks.i99-i107
• 
  Surag Nair,Daniel S. Kim,Jacob Perricone,Anshul Kundaje:
  Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.i108-i116
• 
  Krister M. Swenson,Mathieu Blanchette:
  Large-scale mammalian genome rearrangements coincide with chromatin interactions.i117-i126
• 
  Guillaume Marçais,Dan F. DeBlasio,Prashant Pandey,Carl Kingsford:
  Locality-sensitive hashing for the edit distance.i127-i135
• 
  Hirak Sarkar,Avi Srivastava,Rob Patro:
  Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level.i136-i144
• 
  Abbas Roayaei Ardakany,Ferhat Ay,Stefano Lonardi:
  Selfish: discovery of differential chromatin interactions via a self-similarity measure.i145-i153
• 
  Lisa Handl,Adrin Jalali,Michael Scherer,Ralf Eggeling,Nico Pfeifer:
  Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data.i154-i163

General Computational Biology

• 
  Dai Hai Nguyen,Canh Hao Nguyen,Hiroshi Mamitsuka:
  ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra.i164-i172
• 
  Avanti Shrikumar,Eva Prakash,Anshul Kundaje:
  GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs.i173-i182
• 
  Hao Yang,Hao Chi,Wen-Feng Zeng,Wen-Jing Zhou,Si-Min He:
  pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework.i183-i190
• 
  Michio Iwata,Longhao Yuan,Qibin Zhao,Yasuo Tabei,Francois Berenger,Ryusuke Sawada,Sayaka Akiyoshi,Momoko Hamano,Yoshihiro Yamanishi:
  Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm.i191-i199
• 
  Yan Gao,Bo Liu,Yadong Wang,Yi Xing:
  TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain.i200-i207
• 
  Dan Guo,Kylie A. Bemis,Catherine Rawlins,Jeffrey N. Agar,Olga Vitek:
  Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues.i208-i217

Genome Privacy and Security

• 
  Teppo Mikael Niinimäki,Mikko A. Heikkilä,Antti Honkela,Samuel Kaski:
  Representation transfer for differentially private drug sensitivity prediction.i218-i224

Genomic variation Analysis

• 
  Xiao Yang,Yasushi Saito,Arjun A. Rao,Hyunsung John Kim,Pranav Singh,Eric Scott,Matthew Larson,Wenying Pan,Mohini Desai,Earl Hubbell:
  Alignment-free filtering for cfNA fusion fragments.i225-i232
• 
  Ardalan Naseri,Erwin Holzhauser,Degui Zhi,Shaojie Zhang:
  Efficient haplotype matching between a query and a panel for genealogical search.i233-i241
• 
  Vikas Bansal:
  Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes.i242-i248

Macromolecular sequence, Structure, and function

• 
  Renmin Han,Zhipeng Bao,Xiangrui Zeng,Tongxin Niu,Fa Zhang,Min Xu,Xin Gao:
  A joint method for marker-free alignment of tilt series in electron tomography.i249-i259
• 
  Ruogu Lin,Xiangrui Zeng,Kris Kitani,Min Xu:
  Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms.i260-i268
• 
  Ameni Trabelsi,Mohamed Chaabane,Asa Ben-Hur:
  Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities.i269-i277
• 
  Haoyang Zeng,David K. Gifford:
  DeepLigand: accurate prediction of MHC class I ligands using peptide embedding.i278-i283
• 
  Hao Chen,Dipan Shaw,Jianyang Zeng,Dongbo Bu,Tao Jiang:
  DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning.i284-i294
• 
  Liang Huang,He Zhang,Dezhong Deng,Kai Zhao,Kaibo Liu,David A. Hendrix,David H. Mathews:
  LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.i295-i304
• 
  Muhao Chen,Chelsea J.-T. Ju,Guangyu Zhou,Xuelu Chen,Tianran Zhang,Kai-Wei Chang,Carlo Zaniolo,Wei Wang:
  Multifaceted protein-protein interaction prediction based on Siamese residual RCNN.i305-i314
• 
  Azat M. Tagirdzhanov,Alexander Shlemov,Alexey A. Gurevich:
  NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches.i315-i323
• 
  Jiansheng Wu,Ben Liu,Wallace K. B. Chan,Weijian Wu,Tao Pang,Haifeng Hu,Shancheng Yan,Xiaoyan Ke,Yang Zhang:
  Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors.i324-i332
• 
  Zichao Yan,Eric Lécuyer,Mathieu Blanchette:
  Prediction of mRNA subcellular localization using deep recurrent neural networks.i333-i342
• 
  Jian Zhang,Lukasz A. Kurgan:
  SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences.i343-i353
• 
  Stefan Mautner,Soheila Montaseri,Milad Miladi,Martin Raden,Fabrizio Costa,Rolf Backofen:
  ShaKer: RNA SHAPE prediction using graph kernel.i354-i359
• 
  Dinithi Sumanaweera,Lloyd Allison,Arun Siddharth Konagurthu:
  Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors.i360-i369

Population genomics and molecular Evolution

• 
  Jiafan Zhu,Xinhao Liu,Huw A. Ogilvie,Luay Nakhleh:
  A divide-and-conquer method for scalable phylogenetic network inference from multilocus data.i370-i378
• 
  Sahand Khakabimamaghani,Salem Malikic,Jeffrey Tang,Dujian Ding,Ryan D. Morin,Leonid Chindelevitch,Martin Ester:
  Collaborative intra-tumor heterogeneity detection.i379-i388
• 
  Sayed-Rzgar Hosseini,Ramón Díaz-Uriarte,Florian Markowetz,Niko Beerenwinkel:
  Estimating the predictability of cancer evolution.i389-i397
• 
  Pavel Skums,Viachaslau Tsyvina,Alex Zelikovsky:
  Inference of clonal selection in cancer populations using single-cell sequencing data.i398-i407
• 
  Nuraini Aguse,Yuanyuan Qi,Mohammed El-Kebir:
  Summarizing the solution space in tumor phylogeny inference by multiple consensus trees.i408-i416
• 
  Erin K. Molloy,Tandy J. Warnow:
  TreeMerge: a new method for improving the scalability of species tree estimation methods.i417-i426

Studies of phenotypes and Clinical Applications

• 
  Héctor Climente-González,Chloé-Agathe Azencott,Samuel Kaski,Makoto Yamada:
  Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data.i427-i435
• 
  Gregor Sturm,Francesca Finotello,Florent Petitprez,Jitao David Zhang,Jan Baumbach,Wolf-Herman Fridman,Markus List,Tatsiana Aneichyk:
  Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.i436-i445
• 
  Anika Cheerla,Olivier Gevaert:
  Deep learning with multimodal representation for pancancer prognosis prediction.i446-i454
• 
  Mengyun Yang,Huimin Luo,Yaohang Li,Jianxin Wang:
  Drug repositioning based on bounded nuclear norm regularization.i455-i463
• 
  Caroline Labelle,Anne Marinier,Sébastien Lemieux:
  Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose-response experiments.i464-i473
• 
  Lei Du,Kefei Liu,Lei Zhu,Xiaohui Yao,Shannon L. Risacher,Lei Guo,Andrew J. Saykin,Li Shen:
  Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis: a longitudinal study of the ADNI cohort.i474-i483
• 
  Jakob Richter,Katrin Madjar,Jörg Rahnenführer:
  Model-based optimization of subgroup weights for survival analysis.i484-i491
• 
  Welles Robinson,Roded Sharan,Mark D. M. Leiserson:
  Modeling clinical and molecular covariates of mutational process activity in cancer.i492-i500
• 
  Hossein Sharifi-Noghabi,Olga I. Zolotareva,Colin C. Collins,Martin Ester:
  MOLI: multi-omics late integration with deep neural networks for drug response prediction.i501-i509
• 
  Soufiane Mourragui,Marco Loog,Mark A. van de Wiel,Marcel J. T. Reinders,Lodewyk F. A. Wessels:
  PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors.i510-i519
• 
  Do-Hoon Lee,Sangseon Lee,Sun Kim:
  PRISM: methylation pattern-based, reference-free inference of subclonal makeup.i520-i529
• 
  Benjamin Chidester,Tianming Zhou,Minh N. Do,Jian Ma:
  Rotation equivariant and invariant neural networks for microscopy image analysis.i530-i537
• 
  Bojian Yin,Marleen Balvert,Rick A. A. van der Spek,Bas E. Dutilh,Sander M. Bohté,Jan Veldink,Alexander Schönhuth:
  Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype.i538-i547

Systems Biology and Networks

• 
  Markus Heinonen,Maria Osmala,Henrik Mannerström,Janne Wallenius,Samuel Kaski,Juho Rousu,Harri Lähdesmäki:
  Bayesian metabolic flux analysis reveals intracellular flux couplings.i548-i557
• 
  Alexis Baudin,Soumya Paul,Cui Su,Jun Pang:
  Controlling large Boolean networks with single-step perturbations.i558-i567
• 
  Sumit Mukherjee,Thanneer M. Perumal,Kenneth Daily,Solveig K. Sieberts,Larsson Omberg,Christoph Preuss,Gregory W. Carter,Lara M. Mangravite,Benjamin A. Logsdon:
  Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation.i568-i576
• 
  Mathias Cardner,Nathalie Meyer-Schaller,Gerhard Christofori,Niko Beerenwinkel:
  Inferring signalling dynamics by integrating interventional with observational data.i577-i585
• 
  Aline Marguet,Marc Lavielle,Eugenio Cinquemani:
  Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data.i586-i595
• 
  Markus List,Azim Dehghani Amirabad,Dennis Kostka,Marcel H. Schulz:
  Large-scale inference of competing endogenous RNA networks with sparse partial correlation.i596-i604
• 
  Jerzy Tiuryn,Ewa Szczurek:
  Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.i605-i614
• 
  Reza Miraskarshahi,Hooman Zabeti,Tamon Stephen,Leonid Chindelevitch:
  MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks.i615-i623
• 
  Mitchell J. Wagner,Aditya Pratapa,T. M. Murali:
  Reconstructing signaling pathways using regular language constrained paths.i624-i633
• 
  Torsten Gross,Matthew Wongchenko,Yibing Yan,Nils Blüthgen:
  Robust network inference using response logic.i634-i642

Author Index

• 
  Author Index.i643-i644

Volume 35, Number 15, August 2019

Discovery note
Genome Analysis

• 
  Sarah N. Mapelli,Sara Napoli,Giuseppina Pisignano,Ramon Garcia-Escudero,Giuseppina M. Carbone,Carlo V. Catapano:
  Deciphering the complexity of human non-coding promoter-proximal transcriptome.2529-2534

Original Papers
Genome Analysis

• 
  Dipan Shaw,Hao Chen,Tao Jiang:
  DeepIsoFun: a deep domain adaptation approach to predict isoform functions.2535-2544

Sequence Analysis

• 
  Joseph Mingrone,Edward Susko,Joseph P. Bielawski:
  ModL: exploring and restoring regularity when testing for positive selection.2545-2554
• 
  Arthur Gilly,Lorraine Southam,Daniel Suveges,Karoline Kuchenbaecker,Rachel Moore,Giorgio E. M. Melloni,Konstantinos Hatzikotoulas,Aliki-Eleni Farmaki,Graham Ritchie,Jeremy Schwartzentruber,Petr Danecek,Britt Kilian,Martin O. Pollard,Xiangyu Ge,Emmanouil Tsafantakis,George V. Dedoussis,Eleftheria Zeggini:
  Very low-depth whole-genome sequencing in complex trait association studies.2555-2561

Phylogenetics

• 
  Asher Moshe,Tal Pupko:
  Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices.2562-2568

Structural Bioinformatics

• 
  Mattia Miotto,Pier Paolo Olimpieri,Lorenzo Di Rienzo,Francesco Ambrosetti,Pietro Corsi,Rosalba Lepore,Gian Gaetano Tartaglia,Edoardo Milanetti:
  Insights on protein thermal stability: a graph representation of molecular interactions.2569-2577
• 
  Eduardo Mayol,Mercedes Campillo,Arnau Cordomí,Mireia Olivella:
  Inter-residue interactions in alpha-helical transmembrane proteins.2578-2584
• 
  Claire Marks,Charlotte M. Deane:
  Increasing the accuracy of protein loop structure prediction with evolutionary constraints.2585-2592

Gene expression

• 
  Ziwei Chen,Shaokun An,Xiangqi Bai,Fuzhou Gong,Liang Ma,Lin Wan:
  DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data.2593-2601
• 
  Jie Hao,Wei Cao,Jian Huang,Xin Zou,Zeguang Han:
  Optimal Gene Filtering for Single-Cell data (OGFSC) - a gene filtering algorithm for single-cell RNA-seq data.2602-2609

Genetics and Population Analysis

• 
  Wenqiang Shi,Oriol Fornes,Wyeth W. Wasserman:
  Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants.2610-2617

Systems Biology

• 
  Annika Röhl,Tanguy Riou,Alexander Bockmayr:
  Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection.2618-2625
• 
  Rongting Huang,Yuanhua Huang,Yubin Guo,Shangwei Ji,Ming Lu,Tingting Li:
  Systematic characterization and prediction of post-translational modification cross-talk between proteins.2626-2633
• 
  Meshari Alazmi,Hiroyuki Kuwahara,Othman Soufan,Lizhong Ding,Xin Gao:
  Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions.2634-2643

Bioimage Informatics

• 
  Topaz Gilad,José Reyes,Jia-Yun Chen,Galit Lahav,Tammy Riklin Raviv:
  Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy.2644-2653

Applications Notes
Genome Analysis

• 
  Guoli Ji,Wenbin Ye,Yaru Su,Moliang Chen,Guangzao Huang,Xiaohui Wu:
  AStrap: identification of alternative splicing from transcript sequences without a reference genome.2654-2656
• 
  Sunyoung Shin,Rebecca Hudson,Christopher Harrison,Mark Craven,Sündüz Keles:
  atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding.2657-2659
• 
  Lucian P. Smith,Jon A Yamato,Mary K. Kuhner:
  CNValidator: validating somatic copy-number inference.2660-2662

Sequence Analysis

• 
  Carlos de Lannoy,Judith Risse,Dick de Ridder:
  poreTally: run and publish de novo nanopore assembler benchmarks.2663-2664
• 
  Christopher M. Gibb,Robert Jackson,Sabah Mohammed,Jinan Fiaidhi,Ingeborg Zehbe:
  Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data.2665-2667
• 
  Swaine L. Chen:
  Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets.2668-2670
• 
  Josephine Burgin,Corentin Molitor,Fady R. Mohareb:
  MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment.2671-2673
• 
  Shubham Chandak,Kedar Tatwawadi,Idoia Ochoa,Mikel Hernaez,Tsachy Weissman:
  SPRING: a next-generation compressor for FASTQ data.2674-2676

Structural Bioinformatics

• 
  Mirco Michel,David Menéndez Hurtado,Arne Elofsson:
  PconsC4: fast, accurate and hassle-free contact predictions.2677-2679

Genetics and Population Analysis

• 
  Felipe Llinares-López,Laetitia Papaxanthos,Damian Roqueiro,Dean A. Bodenham,Karsten M. Borgwardt:
  CASMAP: detection of statistically significant combinations of SNPs in association mapping.2680-2682
• 
  Ehsan Ullah,Michaël Aupetit,Arun Das,Abhishek Patil,Nooral Al Muftah,Reda Rawi,Mohamad Saad,Halima Bensmail:
  KinVis: a visualization tool to detect cryptic relatedness in genetic datasets.2683-2685

Systems Biology

• 
  Asa Thibodeau,Dong-Guk Shin:
  TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators.2686-2689

Data and Text Mining

• 
  Céline Trébeau,Jacques Boutet de Monvel,Fabienne Wong Jun Tai,Christine Petit,Raphaël Etournay:
  DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments.2690-2691

Letters to the Editor
Genome Analysis

• 
  Boris Vishnepolsky,Malak Pirtskhalava:
  Comment on: 'Empirical comparison of web-based antimicrobial peptide prediction tools'.2692-2694
• 
  Musa Nur Gabere,William Stafford Noble:
  Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'.2695-2696

Sequence Analysis

• 
  Raúl A González-Pech,Timothy G. Stephens,Cheong Xin Chan:
  Commonly misunderstood parameters of NCBI BLAST and important considerations for users.2697-2698
• 
  Thomas L. Madden,Ben Busby,Jian Ye:
  Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows.2699-2700

Data and Text Mining

• 
  Stefano Nembrini:
  On what to permute in test-based approaches for variable importance measures in Random Forests.2701-2705

Volume 35, Number 16, August 2019

Discovery note
Sequence Analysis

• 
  Justin R. Klesmith,Benjamin J. Hackel:
  Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit.2707-2712
• 
  Igor E. Eliseev,Ivan N. Terterov,Anna N. Yudenko,Olga V. Shamova:
  Linking sequence patterns and functionality of alpha-helical antimicrobial peptides.2713-2717

Systems Biology

• 
  Tamir Tuller,Alon Diament,Avital Yahalom,Assaf Zemach,Shimshi Atar,Daniel A. Chamovitz:
  The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana.2718-2723

Original Papers
Genome Analysis

• 
  Leopold Carron,Jean Baptiste Morlot,Vincent Matthys,Annick Lesne,Julien Mozziconacci:
  Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps.2724-2729
• 
  Ramzan Umarov,Hiroyuki Kuwahara,Yu Li,Xin Gao,Victor V. Solovyev:
  Promoter analysis and prediction in the human genome using sequence-based deep learning models.2730-2737

Sequence Analysis

• 
  Blake Hewelt,Haiqing Li,Mohit Kumar Jolly,Prakash Kulkarni,Isa Mambetsariev,Ravi Salgia:
  The DNA walk and its demonstration of deterministic chaos - relevance to genomic alterations in lung cancer.2738-2748
• 
  Jialin Yu,Shaoping Shi,Fang Zhang,Guodong Chen,Man Cao:
  PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization.2749-2756
• 
  Balachandran Manavalan,Shaherin Basith,Tae Hwan Shin,Leyi Wei,Gwang Lee:
  mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation.2757-2765
• 
  Fenglin Luo,Minghui Wang,Yu Liu,Xing-Ming Zhao,Ao Li:
  DeepPhos: prediction of protein phosphorylation sites with deep learning.2766-2773
• 
  Alice Cheng,Charles E. Grant,William S. Noble,Timothy L. Bailey:
  MoMo: discovery of statistically significant post-translational modification motifs.2774-2782
• 
  Houxiang Zhu,Chun Liang:
  CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity.2783-2789
• 
  Jan Ludwiczak,Aleksander Winski,Krzysztof Szczepaniak,Vikram Alva,Stanislaw Dunin-Horkawicz:
  DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences.2790-2795
• 
  Wei Chen,Hao Lv,Fulei Nie,Hao Lin:
  i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome.2796-2800

Structural Bioinformatics

• 
  Mikhail Karasikov,Guillaume Pagès,Sergei Grudinin:
  Smooth orientation-dependent scoring function for coarse-grained protein quality assessment.2801-2808

Gene expression

• 
  Xiangtao Li,Shixiong Zhang,Ka-Chun Wong:
  Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning.2809-2817
• 
  Jinyan Chan,Xuan Wang,Jacob A. Turner,Nicole E. Baldwin,Jinghua Gu:
  Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing.2818-2826

Data and Text Mining

• 
  Yinsheng Zhou,Han Zhang,Yaning Yang:
  CSHAP: efficient haplotype frequency estimation based on sparse representation.2827-2833

Bioimage Informatics

• 
  Yang Yang,Mingyu Zhou,Qingwei Fang,Hong-Bin Shen:
  AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model.2834-2842

Applications Notes
Genome Analysis

• 
  Hung Nguyen,Sangam Shrestha,Sorin Draghici,Tin Nguyen:
  PINSPlus: a tool for tumor subtype discovery in integrated genomic data.2843-2846
• 
  Jos B. Poell,Matias Mendeville,Daoud Sie,Arjen Brink,Ruud H. Brakenhoff,Bauke Ylstra:
  ACE: absolute copy number estimation from low-coverage whole-genome sequencing data.2847-2849
• 
  Georgette Tanner,David R. Westhead,Alastair P. Droop,Lucy F. Stead:
  Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing.2850-2852

Sequence Analysis

• 
  Giorgio Gonnella,Niklas Niehus,Stefan Kurtz:
  GfaViz: flexible and interactive visualization of GFA sequence graphs.2853-2855
• 
  Milot Mirdita,Martin Steinegger,Johannes Söding:
  MMseqs2 desktop and local web server app for fast, interactive sequence searches.2856-2858
• 
  Linfang Jin,Jinhuo Lai,Yang Zhang,Ying Fu,Shuhang Wang,Heng Dai,Bingding Huang:
  BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads.2859-2861

Structural Bioinformatics

• 
  Milad Miladi,Soheila Montaseri,Rolf Backofen,Martin Raden:
  Integration of accessibility data from structure probing into RNA-RNA interaction prediction.2862-2864

Gene expression

• 
  Tallulah S. Andrews,Martin Hemberg:
  M3Drop: dropout-based feature selection for scRNASeq.2865-2867

Genetics and Population Analysis

• 
  Paula Tataru,Thomas Bataillon:
  polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species.2868-2869

Systems Biology

• 
  Xiaotao Shen,Zheng-Jiang Zhu:
  MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery.2870-2872
• 
  Hoon Hong,Alexey Ovchinnikov,Gleb Pogudin,Chee Yap:
  SIAN: software for structural identifiability analysis of ODE models.2873-2874
• 
  Diego A. A. Morais,Rita M. C. Almeida,Rodrigo J. S. Dalmolin:
  Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction.2875-2876

Data and Text Mining

• 
  Samir Kanaan-Izquierdo,Andrey Ziyatdinov,Maria Araceli Burgueño,Alexandre Perera-Lluna:
  Multiview: a software package for multiview pattern recognition methods.2877-2879
• 
  Dries Vaneechoutte,Klaas Vandepoele:
  Curse: building expression atlases and co-expression networks from public RNA-Seq data.2880-2881

Databases and Ontologies

• 
  Lihua Liu,David R. Damerell,Leonidas Koukouflis,Yufeng Tong,Brian D. Marsden,Matthieu Schapira:
  UbiHub: a data hub for the explorers of ubiquitination pathways.2882-2884

Corrigendum
Databases and Ontologies

• 
  Yuan Luo,Chengsheng Mao,Yiben Yang,Fei Wang,Faraz S. Ahmad,Donna Arnett,Marguerite R. Irvin,Sanjiv J. Shah:
  Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization.2885

Volume 35, Number 17, September 2019

Discovery note
Genome Analysis

• 
  Bandana Kumari,Ravindra Kumar,Manish Kumar:
  Identifying residues that determine palmitoylation using association rule mining.2887-2890

Original Papers
Genome Analysis

• 
  Feifei Xiao,Xizhi Luo,Ning Hao,Yue Niu,Xiangjun Xiao,Guoshuai Cai,Christopher I. Amos,Heping Zhang:
  An accurate and powerful method for copy number variation detection.2891-2898
• 
  Zhong Zhuang,Xiaotong Shen,Wei Pan:
  A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data.2899-2906
• 
  David Heller,Martin Vingron:
  SVIM: structural variant identification using mapped long reads.2907-2915
• 
  John C. Stansfield,Kellen Garrison Cresswell,Mikhail G. Dozmorov:
  multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments.2916-2923
• 
  Mark R. Zucker,Lynne V. Abruzzo,Carmen D. Herling,Lynn L. Barron,Michael J. Keating,Zachary B. Abrams,Nyla A. Heerema,Kevin R. Coombes:
  Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.2924-2931

Sequence Analysis

• 
  Subrata Saha,Jethro Johnson,Soumitra Pal,George M. Weinstock,Sanguthevar Rajasekaran:
  MSC: a metagenomic sequence classification algorithm.2932-2940
• 
  Chun-Chi Chen,Hyundoo Jeong,Xiaoning Qian,Byung-Jun Yoon:
  TOPAS: network-based structural alignment of RNA sequences.2941-2948
• 
  Guangyu Wang,Hongyan Yin,Boyang Li,Chunlei Yu,Fan Wang,Xingjian Xu,Jiabao Cao,Yiming Bao,Liguo Wang,Amir Ali Abbasi,Vladimir B. Bajic,Lina Ma,Zhang Zhang:
  Characterization and identification of long non-coding RNAs based on feature relationship.2949-2956
• 
  Meng Zhang,Fuyi Li,Tatiana T. Marquez-Lago,André Leier,Cunshuo Fan,Chee Keong Kwoh,Kuo-Chen Chou,Jiangning Song,Cangzhi Jia:
  MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters.2957-2965
• 
  Lisle E. Mose,Charles M. Perou,Joel S. Parker:
  Improved indel detection in DNA and RNA via realignment with ABRA2.2966-2973
• 
  Zachary Sethna,Yuval Elhanati,Curtis G. Callan Jr.,Aleksandra M. Walczak,Thierry Mora:
  OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs.2974-2981
• 
  Ke Yan,Xiaozhao Fang,Yong Xu,Bin Liu:
  Protein fold recognition based on multi-view modeling.2982-2990
• 
  Yaojun Wang,Dongbo Bu,Chuncui Huang,Hui Wang,Jinyu Zhou,Junchuan Dong,Weiyi Pan,Jingwei Zhang,Qi Zhang,Yan Li,Shiwei Sun:
  Best-first search guided multistage mass spectrometry-based glycan identification.2991-2997

Phylogenetics

• 
  Huy N. Nguyen,Ashish Jain,Oliver Eulenstein,Iddo Friedberg:
  Tracing the ancestry of operons in bacteria.2998-3004

Structural Bioinformatics

• 
  Allan J. R. Ferrari,Fábio C. Gozzo,Leandro Martínez:
  Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints.3005-3012
• 
  José Ramón López-Blanco,Pablo Chacón:
  KORP: knowledge-based 6D potential for fast protein and loop modeling.3013-3019
• 
  Sebastian Maurer-Stroh,Nora L. Krutz,Petra S. Kern,Vithiagaran Gunalan,Minh N. Nguyen,Vachiranee Limviphuvadh,Frank Eisenhaber,G. Frank Gerberick:
  AllerCatPro - prediction of protein allergenicity potential from the protein sequence.3020-3027

Gene expression

• 
  Eyal Simonovsky,Ronen Schuster,Esti Yeger Lotem:
  Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety.3028-3037
• 
  Xin Gao,Deqing Hu,Madelaine Gogol,Hua Li:
  ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions.3038-3045

Genetics and Population Analysis

• 
  Anastasia Gurinovich,Harold Bae,John J. Farrell,Stacy Andersen,Stefano Monti,Annibale Puca,Gil Atzmon,Nir Barzilai,Thomas T. Perls,Paola Sebastiani:
  PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects.3046-3054

Systems Biology

• 
  Amrit Singh,Casey P. Shannon,Benoît Gautier,Florian Rohart,Michaël Vacher,Scott J. Tebbutt,Kim-Anh Lê Cao:
  DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays.3055-3062
• 
  Philipp Schneider,Steffen Klamt:
  Characterizing and ranking computed metabolic engineering strategies.3063-3072
• 
  Helge Hass,Carolin Loos,Elba Raimúndez-Álvarez,Jens Timmer,Jan Hasenauer,Clemens Kreutz:
  Benchmark problems for dynamic modeling of intracellular processes.3073-3082
• 
  Joeri van Strien,Sergio Guerrero-Castillo,Iliana A Chatzispyrou,Riekelt H. Houtkooper,Ulrich Brandt,Martijn A. Huynen:
  COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome.3083-3091
• 
  Hideko Kawakubo,Yusuke Matsui,Itaru Kushima,Norio Ozaki,Teppei Shimamura:
  A network of networks approach for modeling interconnected brain tissue-specific networks.3092-3101
• 
  Yuezhe Li,Tiffany Jann,Paola Vera-Licona:
  Benchmarking time-series data discretization on inference methods.3102-3109

Data and Text Mining

• 
  Angela Noufaily,Roger A. Morbey,Felipe J. Colón-González,Alex J. Elliot,Gillian E. Smith,Iain R. Lake,Noel D. McCarthy:
  Comparison of statistical algorithms for daily syndromic surveillance aberration detection.3110-3118

Databases and Ontologies

• 
  Huiyuan Wang,Huihui Wang,Hangxiao Zhang,Sheng Liu,Yongsheng Wang,Yubang Gao,Feihu Xi,Liangzhen Zhao,Bo Liu,Anireddy S. N. Reddy,Chentao Lin,Lian-Feng Gu:
  The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species.3119-3126
• 
  Jianrong Li,Chun-Yip Tong,Tsai-Jung Sung,Ting-Yu Kang,Xianghong Jasmine Zhou,Chun-Chi Liu:
  CMEP: a database for circulating microRNA expression profiling.3127-3132
• 
  Thomas A. Darde,Estelle Lecluze,Aurélie Lardenois,Isabelle Stévant,Nathan Alary,Frank Tüttelmann,Olivier Collin,Serge Nef,Bernard Jégou,Antoine D. Rolland,Frédéric Chalmel:
  The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community.3133-3139

Applications Notes
Genome Analysis

• 
  Marc Streit,Samuel Gratzl,Holger Stitz,Andreas Wernitznig,Thomas Zichner,Christian Haslinger:
  Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.3140-3142
• 
  Kevin Matlock,Raziur Rahman,Souparno Ghosh,Ranadip Pal:
  Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features.3143-3145
• 
  Adrien L. S. Jacquin,Duncan T. Odom,Margus Lukk:
  Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.3146-3147
• 
  He-Chuan Yang,Bingxin Lu,Lan Huong Lai,Abner Herbert Lim,Jacob Josiah Santiago Alvarez,Weiwei Zhai:
  PSiTE: a Phylogeny guided Simulator for Tumor Evolution.3148-3150
• 
  Johannes Rainer,Laurent Gatto,Christian X. Weichenberger:
  ensembldb: an R package to create and use Ensembl-based annotation resources.3151-3153
• 
  Oskari Timonen,Mikko Särkkä,Tibor Fülöp,Anton Mattsson,Juha Kekäläinen,Jussi Paananen:
  Varanto: variant enrichment analysis and annotation.3154-3156

Sequence Analysis

• 
  Weitai Huang,Yu Amanda Guo,Karthik Muthukumar,Probhonjon Baruah,Mei Mei Chang,Anders Jacobsen Skanderup:
  SMuRF: portable and accurate ensemble prediction of somatic mutations.3157-3159
• 
  Davoud Torkamaneh,Jérôme Laroche,Istvan Rajcan,François Belzile:
  SRG extractor: a skinny reference genome approach for reduced-representation sequencing.3160-3162

Phylogenetics

• 
  Bastien Cazaux,Guillaume Castel,Eric Rivals:
  AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees.3163-3165

Structural Bioinformatics

• 
  Aleksandra Maria Gierut,Pawel Dabrowski-Tumanski,Wanda Niemyska,Kenneth C. Millett,Joanna I. Sulkowska:
  PyLink: a PyMOL plugin to identify links.3166-3168
• 
  Allan J. R. Ferrari,Milan A. Clasen,Louise U. Kurt,Paulo C. Carvalho,Fábio C. Gozzo,Leandro Martínez:
  TopoLink: evaluation of structural models using chemical crosslinking distance constraints.3169-3170
• 
  Andy M. C. Lau,Zainab Ahdash,Chloe Martens,Argyris Politis:
  Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry.3171-3173
• 
  Lars Olsen,Marco Montefiori,Khanhvi Phuc Tran,Flemming Steen Jørgensen:
  SMARTCyp 3.0: enhanced cytochrome P450 site-of-metabolism prediction server.3174-3175

Gene expression

• 
  Eric J. Kort,Stefan Jovinge:
  Streamlined analysis of LINCS L1000 data with the slinky package for R.3176-3177
• 
  Michael Banf,Kangmei Zhao,Seung Y. Rhee:
  METACLUSTER - an R package for context-specific expression analysis of metabolic gene clusters.3178-3180
• 
  Patryk Orzechowski,Jason H. Moore:
  EBIC: an open source software for high-dimensional and big data analyses.3181-3183
• 
  Xiao-Fei Zhang,Le Ou-Yang,Shuo Yang,Xiaohua Hu,Hong Yan:
  DiffNetFDR: differential network analysis with false discovery rate control.3184-3186

Genetics and Population Analysis

• 
  Alsamman M. Alsamman,Shafik D. Ibrahim,Aladdin Hamwieh:
  KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping.3187-3190
• 
  Yingzhou Wu,Jochen Weile,Atina G. Coté,Song Sun,Jennifer J. Knapp,Marta Verby,Frederick P. Roth:
  A web application and service for imputing and visualizing missense variant effect maps.3191-3193
• 
  Martin Petr,Benjamin Vernot,Janet Kelso:
  admixr - R package for reproducible analyses using ADMIXTOOLS.3194-3195

Systems Biology

• 
  Tobias Depke,Raimo Franke,Mark Brönstrup:
  CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics.3196-3198

Data and Text Mining

• 
  Yang Zhang,Tianyuan Liu,Liqun Chen,Jinxurong Yang,Jiayi Yin,Yuncong Zhang,Zhixi Yun,Hao Xu,Lin Ning,Feng-Biao Guo,Yongshuai Jiang,Hao Lin,Dong Wang,Yan Huang,Jian Huang:
  RIscoper: a tool for RNA-RNA interaction extraction from the literature.3199-3202

Databases and Ontologies

• 
  Yann Rivault,Olivier Dameron,Nolwenn Le Meur:
  queryMed: Semantic Web functions for linking pharmacological and medical knowledge to data.3203-3205
• 
  Konstantinos A Kyritsis,Bing Wang,Julie M. Sullivan,Rachel Lyne,Gos Micklem:
  InterMineR: an R package for InterMine databases.3206-3207

Bioimage Informatics

• 
  Yangzhen Wang,Feng Su,Shanshan Wang,Chaojuan Yang,Yonglu Tian,Peijiang Yuan,Xiaorong Liu,Wei Xiong,Chen Zhang:
  Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging.3208-3210

Letter to the Editor
Genome Analysis

• 
  Marzia A. Cremona,Hongyan Xu,Kateryna D. Makova,Matthew Reimherr,Francesca Chiaromonte,Pedro Madrigal:
  Functional data analysis for computational biology.3211-3213

Corrigenda
Genome Analysis

• 
  Ian Walsh,Terry Nguyen-Khuong,Katherine Wongtrakul-Kish,Shi Jie Tay,Daniel Chew,Tasha José,Christopher H. Taron,Pauline M. Rudd:
  GlycanAnalyzer: software for automated interpretation of N-glycan profiles after exoglycosidase digestions.3214
• 
  Arthur T. O. Melo,Iago Hale:
  Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP.3215
• 
  Mark R. Zucker,Lynne V. Abruzzo,Carmen D. Herling,Lynn L. Barron,Michael J. Keating,Zachary B. Abrams,Nyla A. Heerema,Kevin R. Coombes:
  Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.3216

Volume 35, Number 18, September 2019

Editorial
Data and Text Mining

• 
  Jonathan D. Wren,Alfonso Valencia,Janet Kelso:
  Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention.3217-3218

Discovery note
Sequence Analysis

• 
  Veronna Marie,Michelle Gordon:
  Gag-protease coevolution shapes the outcome of lopinavir-inclusive treatment regimens in chronically infected HIV-1 subtype C patients.3219-3223

Original Papers
Genome Analysis

• 
  David B. Sauer,Da-Neng Wang:
  Predicting the optimal growth temperatures of prokaryotes using only genome derived features.3224-3231
• 
  Tahmid F. Mehdi,Gurdeep Singh,Jennifer A Mitchell,Alan M. Moses:
  Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers.3232-3239
• 
  Yang Yang,Timothy M. Walker,A. Sarah Walker,Daniel J. Wilson,Timothy E. A Peto,Derrick W. Crook,Farah Shamout,CRyPTIC Consortium,Tingting Zhu,David A. Clifton:
  DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis.3240-3249
• 
  Kingshuk Mukherjee,Bahar Alipanahi,Tamer Kahveci,Leena Salmela,Christina Boucher:
  Aligning optical maps to de Bruijn graphs.3250-3256
• 
  Jordi Martorell-Marugan,Víctor González-Rumayor,Pedro Carmona-Saez:
  mCSEA: detecting subtle differentially methylated regions.3257-3262
• 
  Sahand Khakabimamaghani,Yogeshwar D. Kelkar,Bruno M. Grande,Ryan D. Morin,Martin Ester,Daniel Ziemek:
  SUBSTRA: Supervised Bayesian Patient Stratification.3263-3272
• 
  Peng Wu,Yan Gao,Weilong Guo,Ping Zhu:
  Using local alignment to enhance single-cell bisulfite sequencing data efficiency.3273-3278

Sequence Analysis

• 
  Enrico Siragusa,Niina Haiminen,Richard Finkers,Richard G. F. Visser,Laxmi Parida:
  Haplotype assembly of autotetraploid potato using integer linear programing.3279-3286
• 
  Vu Ngo,Mengchi Wang,Wei Wang:
  Finding de novo methylated DNA motifs.3287-3293
• 
  Dexiong Chen,Laurent Jacob,Julien Mairal:
  Biological sequence modeling with convolutional kernel networks.3294-3302

Phylogenetics

• 
  Benjamin Linard,Krister M. Swenson,Fabio Pardi:
  Rapid alignment-free phylogenetic identification of metagenomic sequences.3303-3312

Structural Bioinformatics

• 
  Guillaume Pagès,Benoit Charmettant,Sergei Grudinin:
  Protein model quality assessment using 3D oriented convolutional neural networks.3313-3319
• 
  Debswapna Bhattacharya:
  refineD: improved protein structure refinement using machine learning based restrained relaxation.3320-3328
• 
  Mostafa Karimi,Di Wu,Zhangyang Wang,Yang Shen:
  DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks.3329-3338

Gene expression

• 
  Rachel Jeitziner,Mathieu Carrière,Jacques Rougemont,Steve Oudot,Kathryn Hess,Cathrin Brisken:
  Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis.3339-3347
• 
  Nimrod Rappoport,Ron Shamir:
  NEMO: cancer subtyping by integration of partial multi-omic data.3348-3356
• 
  Holger Weishaupt,Patrik Johansson,Anders Sundström,Zelmina Lubovac-Pilav,Björn Olsson,Sven Nelander,Fredrik J. Swartling:
  Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes.3357-3364
• 
  Alon Diament,Iddo Weiner,Noam Shahar,Shira Landman,Yael Feldman,Shimshi Atar,Meital Avitan,Shira Schweitzer,Iftach Yacoby,Tamir Tuller:
  ChimeraUGEM: unsupervised gene expression modeling in any given organism.3365-3371
• 
  Kimon Froussios,Nick J. Schurch,Katarzyna Mackinnon,Marek Gierlinski,Céline Duc,Gordon G. Simpson,Geoffrey J. Barton:
  How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana.3372-3377

Systems Biology

• 
  Marco S. Nobile,Thalia Vlachou,Simone Spolaor,Daniela Bossi,Paolo Cazzaniga,Luisa Lanfrancone,Giancarlo Mauri,Pier Giuseppe Pelicci,Daniela Besozzi:
  Modeling cell proliferation in human acute myeloid leukemia xenografts.3378-3386
• 
  Yannis Pantazis,Ioannis Tsamardinos:
  A unified approach for sparse dynamical system inference from temporal measurements.3387-3396
• 
  James P. Gilbert,Nicole Pearcy,Rupert Norman,Thomas Millat,Klaus Winzer,John R. King,Charlie Hodgman,Nigel P. Minton,Jamie Twycross:
  Gsmodutils: a python based framework for test-driven genome scale metabolic model development.3397-3403
• 
  Huili Yuan,Shun He,Minghua Deng:
  Compositional data network analysis via lasso penalized D-trace loss.3404-3411
• 
  Evi Berchtold,Martina Vetter,Melanie Gündert,Gergely Csaba,Christine Fathke,Susanne E. Ulbrich,Christoph Thomssen,Ralf Zimmer,Eva J. Kantelhardt:
  Comparison of six breast cancer classifiers using qPCR.3412-3420
• 
  Joseph J. Muldoon,Jessica S. Yu,Mohammad-Kasim Fassia,Neda Bagheri:
  Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants.3421-3432
• 
  Utku Norman,A. Ercüment Çiçek:
  ST-Steiner: a spatio-temporal gene discovery algorithm.3433-3440
• 
  Jing Ma,Alla Karnovsky,Farsad Afshinnia,Janis E. Wigginton,Daniel J. Rader,Loki Natarajan,Kumar Sharma,Anna C. Porter,Mahboob Rahman,Jiang He,Lee Hamm,Tariq Shafi,Debbie S. Gipson,Crystal Gadegbeku,Harold Feldman,George Michailidis:
  Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease.3441-3452

Data and Text Mining

• 
  Anastasia Tyryshkina,Nate Coraor,Anton Nekrutenko:
  Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage.3453-3460

Bioimage Informatics

• 
  Mohamed Amgad,Habiba Elfandy,Hagar Hussein,Lamees A. Atteya,Mai A. T. Elsebaie,Lamia S. Abo Elnasr,Rokia Adel Sakr,Hazem S. E. Salem,Ahmed F. Ismail,Anas M. Saad,Joumana Ahmed,Maha A. T. Elsebaie,Mustafijur Rahman,Inas A. Ruhban,Nada M. Elgazar,Yahya Alagha,Mohamed H. Osman,Ahmed M. Alhusseiny,Mariam M. Khalaf,Abo-Alela F. Younes,Ali Abdulkarim,Duaa M. Younes,Ahmed M. Gadallah,Ahmad M. Elkashash,Salma Y. Fala,Basma M. Zaki,Jonathan D. Beezley,Deepak Roy Chittajallu,David Manthey,David A. Gutman,Lee A. D. Cooper:
  Structured crowdsourcing enables convolutional segmentation of histology images.3461-3467
• 
  Ismail M. Khater,Fanrui Meng,Ivan Robert Nabi,Ghassan Hamarneh:
  Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data.3468-3475

Applications Notes
Genome Analysis

• 
  Alla Mikheenko,Mikhail Kolmogorov:
  Assembly Graph Browser: interactive visualization of assembly graphs.3476-3478
• 
  Akihiro Kuno,Seiya Mizuno,Satoru Takahashi:
  KOnezumi: a web application for automating gene disruption strategies to generate knockout mice.3479-3481
• 
  Javier López-Ibáñez,Laura T. Martín,Monica Chagoyen,Florencio Pazos:
  Bacterial Feature Finder (BaFF) - a system for extracting features overrepresented in sets of prokaryotic organisms.3482-3483
• 
  Tao Jiang,Bo Liu,Junyi Li,Yadong Wang:
  rMETL: sensitive mobile element insertion detection with long read realignment.3484-3486
• 
  Frédéric Lopez,Guillaume Charbonnier,Yasmina Kermezli,Mohamed Belhocine,Quentin Ferré,N. Zweig,Mourad Aribi,Aitor González,Salvatore Spicuglia,Denis Puthier:
  Explore, edit and leverage genomic annotations using Python GTF toolkit.3487-3488

Sequence Analysis

• 
  Diogo B. Lima,André Ramos Fernandes Da Silva,Mathieu Dupré,Marlon D. M. Santos,Milan A. Clasen,Louise U. Kurt,Priscila F. Aquino,Valmir C. Barbosa,Paulo C. Carvalho,Julia Chamot-Rooke:
  Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra.3489-3490
• 
  Braslav Rabar,Maja Zagorscak,Strahil Ristov,Martin Rosenzweig,Pavle Goldstein:
  IGLOSS: iterative gapless local similarity search.3491-3492
• 
  Václav Brázda,Jan Kolomazník,Jirí Lýsek,Martin Bartas,Miroslav Fojta,Jirí Stastný,Jean-Louis Mergny:
  G4Hunter web application: a web server for G-quadruplex prediction.3493-3495

Phylogenetics

• 
  Soumya Kundu,Mukul S. Bansal:
  SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.3496-3498

Structural Bioinformatics

• 
  Judemir Ribeiro,Carlos Ríos-Vera,Francisco Melo,Andreas Schüller:
  Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions.3499-3501
• 
  Nagarajan Raju,Ian Setliff,Ivelin S. Georgiev:
  NFPws: a web server for delineating broadly neutralizing antibody specificities from serum HIV-1 neutralization data.3502-3504
• 
  Laura Orellana,Johan Gustavsson,Cathrine Bergh,Ozge Yoluk,Erik Lindahl:
  eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces.3505-3507
• 
  Tharindu Senapathi,Simon Bray,Christopher B. Barnett,Björn A. Grüning,Kevin J. Naidoo:
  Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE).3508-3509
• 
  Abhik Mukhopadhyay,Neera Borkakoti,Lukás Pravda,Jonathan D. Tyzack,Janet M. Thornton,Sameer Velankar:
  Finding enzyme cofactors in Protein Data Bank.3510-3511
• 
  Joan Segura,Rubén Sánchez García,Carlos Oscar Sánchez Sorzano,José María Carazo:
  3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations.3512-3513

Gene expression

• 
  Danyue Dong,Yuan Tian,Shijie C. Zheng,Andrew E. Teschendorff:
  ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies.3514-3516
• 
  Nikolaos Papadopoulos,R. Gonzalo Parra,Johannes Söding:
  PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.3517-3519

Genetics and Population Analysis

• 
  Martin Maiers,Michael Halagan,Loren Gragert,Pradeep Bashyal,Jason Brelsford,Joel Schneider,Polina Lutsker,Yoram Louzoun:
  GRIMM: GRaph IMputation and matching for HLA genotypes.3520-3523

Systems Biology

• 
  Yonghui Dong,Liron Feldberg,Asaph Aharoni:
  Miso: an R package for multiple isotope labeling assisted metabolomics data analysis.3524-3526
• 
  David Oliveira Aparício,Pedro Ribeiro,Tijana Milenkovic,Fernando Silva:
  Temporal network alignment via GoT-WAVE.3527-3529

Data and Text Mining

• 
  Francesco Ronzano,Alba Gutiérrez-Sacristán,Laura I. Furlong:
  Comorbidity4j: a tool for interactive analysis of disease comorbidities over large patient datasets.3530-3532
• 
  Donald C. Comeau,Chih-Hsuan Wei,Rezarta Islamaj Dogan,Zhiyong Lu:
  PMC text mining subset in BioC: about three million full-text articles and growing.3533-3535
• 
  Akul Y. Mehta,Richard D. Cummings:
  GLAD: GLycan Array Dashboard, a visual analytics tool for glycan microarrays.3536-3537
• 
  Mehdi Ali,Charles Tapley Hoyt,Daniel Domingo-Fernández,Jens Lehmann,Hajira Jabeen:
  BioKEEN: a library for learning and evaluating biological knowledge graph embeddings.3538-3540

Databases and Ontologies

• 
  Sumit Mukherjee,Sukhen Das Mandal,Nikita Gupta,Matan Drory Retwitzer,Danny Barash,Supratim Sengupta:
  RiboD: a comprehensive database for prokaryotic riboswitches.3541-3543

Bioimage Informatics

• 
  Douglas H. Roossien,Benjamin V. Sadis,Yan Yan,John M. Webb,Lia Y. Min,Aslan S. Dizaji,Luke J. Bogart,Cristina Mazuski,Robert S. Huth,Johanna S. Stecher,Sriakhila Akula,Fred Y. Shen,Ye Li,Tingxin Xiao,Madeleine Vandenbrink,Jeff W. Lichtman,Takao K. Hensch,Erik D. Herzog,Dawen Cai:
  Multispectral tracing in densely labeled mouse brain with nTracer.3544-3546

Volume 35, Number 19, October 2019

Review
Genome Analysis

• 
  Gregory Kucherov:
  Evolution of biosequence search algorithms: a brief survey.3547-3552

Discovery note
Structural Bioinformatics

• 
  Henry J. Martell,Stuart G. Masterson,Jake E. McGreig,Martin Michaelis,Mark N. Wass:
  Is the Bombali virus pathogenic in humans?3553-3558

Original Papers
Genome Analysis

• 
  Zixiu Li,Feng Zhang,Yukai Wang,Yue Qiu,Yang Wu,Yulan Lu,Lin Yang,William J. Qu,Huijun Wang,Wenhao Zhou,Weidong Tian:
  PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease.3559-3566
• 
  Anna M. Plantinga,Jun Chen,Robert R. Jenq,Michael C. Wu:
  pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis.3567-3575
• 
  Chong Wu,Wei Pan:
  Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes.3576-3583

Sequence Analysis

• 
  Sherif Farag,Rachel M. Bleich,Elizabeth A. Shank,Olexandr Isayev,Albert A Bowers,Alexander Tropsha:
  Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides.3584-3591
• 
  Justin G. Chitpin,Aseel Awdeh,Theodore J. Perkins:
  RECAP reveals the true statistical significance of ChIP-seq peak calls.3592-3598
• 
  Mikko Rautiainen,Veli Mäkinen,Tobias Marschall:
  Bit-parallel sequence-to-graph alignment.3599-3607

Phylogenetics

• 
  Ashley A Superson,Doug Phelan,Allyson Dekovich,Fabia U. Battistuzzi:
  Choice of species affects phylogenetic stability of deep nodes: an empirical example in Terrabacteria.3608-3616
• 
  Zebulun Arendsee,Jing Li,Urminder Singh,Arun S. Seetharam,Karin S. Dorman,Eve Syrkin Wurtele:
  phylostratr: a framework for phylostratigraphy.3617-3627

Gene expression

• 
  Soufiane Ajana,Niyazi Acar,Lionel Bretillon,Boris P. Hejblum,Hélène Jacqmin-Gadda,Cécile Delcourt:
  Benefits of dimension reduction in penalized regression methods for high-dimensional grouped data: a case study in low sample size.3628-3634
• 
  Yue Wang,Jennifer M. Franks,Michael L. Whitfield,Chao Cheng:
  BioMethyl: an R package for biological interpretation of DNA methylation data.3635-3641
• 
  Ruiqing Zheng,Min Li,Zhenlan Liang,Fang-Xiang Wu,Yi Pan,Jianxin Wang:
  SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation.3642-3650
• 
  Francisco J. Campos-Laborie,Alberto Risueño,M. Ortiz-Estévez,B. Rosón-Burgo,Conrad Droste,Celia Fontanillo,Remco Loos,Jose Manuel Sánchez-Santos,Matthew W. B. Trotter,Javier De Las Rivas:
  DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling.3651-3662
• 
  Stephan Seifert,Sven Gundlach,Silke Szymczak:
  Surrogate minimal depth as an importance measure for variables in random forests.3663-3671
• 
  Nafiseh Saberian,Azam Peyvandi-Pour,Michele Donato,Sahar Ansari,Sorin Draghici:
  A new computational drug repurposing method using established disease-drug pair knowledge.3672-3678

Genetics and Population Analysis

• 
  Aritra Bose,Vassilis Kalantzis,Eugenia-Maria Kontopoulou,Mai Elkady,Peristera Paschou,Petros Drineas:
  TeraPCA: a fast and scalable software package to study genetic variation in tera-scale genotypes.3679-3683
• 
  Jarno Vanhatalo,Zitong Li,Mikko J. Sillanpää:
  A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data.3684-3692
• 
  Xingjie Shi,Yuling Jiao,Yi Yang,Ching-Yu Cheng,Can Yang,Xinyi Lin,Jin Liu:
  VIMCO: variational inference for multiple correlated outcomes in genome-wide association studies.3693-3700
• 
  Gulnara R. Svishcheva,Nadezhda M. Belonogova,Irina V. Zorkoltseva,Anatoly V. Kirichenko,Tatiana I. Axenovich:
  Gene-based association tests using GWAS summary statistics.3701-3708

Systems Biology

• 
  Lei Huang,David Brunell,Clifford Stephan,James J. Mancuso,Xiaohui Yu,Bin He,Timothy C. Thompson,Ralph Zinner,Jeri Kim,Peter Davies,Stephen T. C. Wong:
  Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction.3709-3717
• 
  Peifeng Ruan,Ya Wang,Ronglai Shen,Shuang Wang:
  Using association signal annotations to boost similarity network fusion.3718-3726
• 
  Noël Malod-Dognin,Natasa Przulj:
  Functional geometry of protein interactomes.3727-3734
• 
  Ping Luo,Yuanyuan Li,Li-Ping Tian,Fang-Xiang Wu:
  Enhancing the prediction of disease-gene associations with multimodal deep learning.3735-3742
• 
  Ladislav Rampásek,Daniel Hidru,Petr Smirnov,Benjamin Haibe-Kains,Anna Goldenberg:
  Dr.VAE: improving drug response prediction via modeling of drug perturbation effects.3743-3751
• 
  Payam Emami Khoonsari,Pablo A. Moreno,Sven Bergmann,Joachim Burman,Marco Capuccini,Matteo Carone,Marta Cascante,Pedro de Atauri,Carles Foguet,Alejandra N. González-Beltrán,Thomas Hankemeier,Kenneth Haug,Sijin He,Stephanie Herman,David Johnson,Namrata Kale,Anders Larsson,Steffen Neumann,Kristian Peters,Luca Pireddu,Philippe Rocca-Serra,Pierrick Roger,Rico Rueedi,Christoph Ruttkies,Noureddin Sadawi,Reza M. Salek,Susanna-Assunta Sansone,Daniel Schober,Vitaly A. Selivanov,Etienne A. Thévenot,Michael van Vliet,Gianluigi Zanetti,Christoph Steinbeck,Kim Kultima,Ola Spjuth:
  Interoperable and scalable data analysis with microservices: applications in metabolomics.3752-3760

Data and Text Mining

• 
  Di Du,Chia-Hua Chang,Yumeng Wang,Pan Tong,Wai Kin Chan,Yulun Chiu,Bo Peng,Lin Tan,John N. Weinstein,Philip L. Lorenzi:
  Response envelope analysis for quantitative evaluation of drug combinations.3761-3770
• 
  Zhaowen Liu,Edmund T. Rolls,Zhi Liu,Kai Zhang,Ming Yang,Jingnan Du,Weikang Gong,Wei Cheng,Fei Dai,He Wang,Kâmil Ugurbil,Jie Zhang,Jianfeng Feng:
  Brain annotation toolbox: exploring the functional and genetic associations of neuroimaging results.3771-3778
• 
  Livia Perfetto,Marcio Luis Acencio,Glyn Bradley,Gianni Cesareni,Noemi del-Toro,Dávid Fazekas,Henning Hermjakob,Tamás Korcsmáros,Martin Kuiper,Astrid Lægreid,Prisca Lo Surdo,Ruth C. Lovering,Sandra E. Orchard,Pablo Porras,Paul D. Thomas,Vasundra Touré,John Zobolas,Luana Licata:
  CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.3779-3785
• 
  Pietro Di Lena,Claudia Sala,Andrea Prodi,Christine Nardini:
  Missing value estimation methods for DNA methylation data.3786-3793
• 
  Guangxu Xun,Kishlay Jha,Ye Yuan,Yaqing Wang,Aidong Zhang:
  MeSHProbeNet: a self-attentive probe net for MeSH indexing.3794-3802
• 
  Oksana E. Glushchenko,Nikita A. Prianichnikov,Evgenii I Olekhnovich,Alexander I Manolov,Alexander V. Tyakht,Elizaveta V. Starikova,Vera Odintsova,Elena S. Kostryukova,Elena Ilina:
  VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota.3803-3811

Applications Notes
Genome Analysis

• 
  Mohamad Koohi-Moghadam,Mitesh J. Borad,Nhan L. Tran,Kristin R. Swanson,Lisa Boardman,Hong-Zhe Su,Junwen Wang:
  MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers.3812-3814
• 
  Alejandra Cervera,Ville Rantanen,Kristian Ovaska,Marko Laakso,Javier Nuñez-Fontarnau,Amjad Alkodsi,Julia Casado,Chiara Facciotto,Antti Häkkinen,Riku Louhimo,Sirkku Karinen,Kaiyang Zhang,Kari Lavikka,Lauri Lyly,Maninder Pal Singh,Sampsa Hautaniemi:
  Anduril 2: upgraded large-scale data integration framework.3815-3817
• 
  Eugene Urrutia,Li Chen,Haibo Zhou,Yuchao Jiang:
  Destin: toolkit for single-cell analysis of chromatin accessibility.3818-3820
• 
  Saori Sakaue,Yukinori Okada:
  GREP: genome for REPositioning drugs.3821-3823
• 
  He Zhang,Xiaowei Zhan,James Brugarolas,Yang Xie:
  DEFOR: depth- and frequency-based somatic copy number alteration detector.3824-3825

Sequence Analysis

• 
  Kirill Kryukov,Mahoko Ueda Takahashi,So Nakagawa,Tadashi Imanishi:
  Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences.3826-3828
• 
  Shaun P. Wilkinson:
  aphid: an R package for analysis with profile hidden Markov models.3829-3830
• 
  Rafsanjani Muhammod,Sajid Ahmed,Dewan Md. Farid,Swakkhar Shatabda,Alok Sharma,Abdollah Dehzangi:
  PyFeat: a Python-based effective feature generation tool for DNA, RNA and protein sequences.3831-3833

Structural Bioinformatics

• 
  Aleksander Kuriata,Valentin Iglesias,Mateusz Kurcinski,Salvador Ventura,Sebastian Kmiecik:
  Aggrescan3D standalone package for structure-based prediction of protein aggregation properties.3834-3835
• 
  Juan Pablo Arcon,Carlos P. Modenutti,Demian Avendaño,Elias D. López,Lucas A. Defelipe,Francesca Alessandra Ambrosio,Adrian Gustavo Turjanski,Stefano Forli,Marcelo A. Marti:
  AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.3836-3838

Gene expression

• 
  Artem Babaian,I. Richard Thompson,Jake Lever,Liane Gagnier,Mohammad M. Karimi,Dixie L. Mager:
  LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq.3839-3841
• 
  Guangsheng Pei,Yulin Dai,Zhongming Zhao,Peilin Jia:
  deTS: tissue-specific enrichment analysis to decode tissue specificity.3842-3845
• 
  Lisa-Katrin Turnhoff,Ali Hadizadeh Esfahani,Maryam Montazeri,Nina Kusch,Andreas Schuppert:
  FORESEE: a tool for the systematic comparison of translational drug response modeling pipelines.3846-3848

Genetics and Population Analysis

• 
  Jeremy Ferlic,Jiantao Shi,Thomas O. McDonald,Franziska Michor:
  DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding.3849-3851
• 
  You Tang,Xiaolei Liu:
  G2P: a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation.3852-3854
• 
  Emma A. Fox,Alison E. Wright,Matteo Fumagalli,Filipe G. Vieira:
  ngsLD: evaluating linkage disequilibrium using genotype likelihoods.3855-3856

Systems Biology

• 
  Timo Lubitz,Wolfram Liebermeister:
  Parameter balancing: consistent parameter sets for kinetic metabolic models.3857-3858
• 
  Jonathan Naylor,Harold Fellermann,Natalio Krasnogor:
  Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations.3859-3860
• 
  Chuang Li,Kenli Li,Tao Chen,Yunping Zhu,Qiang He:
  SW-Tandem: a highly efficient tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight.3861-3863
• 
  Bernhard Mlecnik,Jérôme Galon,Gabriela Bindea:
  Automated exploration of gene ontology term and pathway networks with ClueGO-REST.3864-3866

Data and Text Mining

• 
  Ezra Kitson,Curtis A Suttle:
  VHost-Classifier: virus-host classification using natural language processing.3867-3869

Databases and Ontologies

• 
  Nathan D. Olson,Nidhi Shah,Jayaram Kancherla,Justin Wagner,Joseph N. Paulson,Héctor Corrada Bravo:
  metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data.3870-3872
• 
  Bruno Henrique Ribeiro Da Fonseca,Douglas Silva Domingues,Alexandre Rossi Paschoal:
  mirtronDB: a mirtron knowledge base.3873-3874

Bioimage Informatics

• 
  Jan Kozuszník,Petr Bainar,Jana Klímová,Michal Krumnikl,Pavel Moravec,Václav Svaton,Pavel Tomancák:
  SPIM workflow manager for HPC.3875-3876

Volume 35, Number 20, October 2019

Review
Sequence Analysis

• 
  Amlan Talukder,Samaneh Saadat,Xiaoman Li,Haiyan Hu:
  EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction.3877-3883

Discovery note
Sequence Analysis

• 
  Syed Faraz Ahmed,Ahmed A. Quadeer,David Morales-Jiménez,Matthew R. McKay:
  Sub-dominant principal components inform new vaccine targets for HIV Gag.3884-3889

Original Papers
Genome Analysis

• 
  Ho Jang,Hyunju Lee:
  Multiresolution correction of GC bias and application to identification of copy number alterations.3890-3897
• 
  Ziyi Li,Zhijin Wu,Peng Jin,Hao Wu:
  Dissecting differential signals in high-throughput data from complex tissues.3898-3905
• 
  Felix Richter,Gabriel E. Hoffman,K. B. Manheimer,Nihir Patel,A J. Sharp,D. McKean,Sarah U. Morton,S. DePalma,J. Gorham,A Kitaygorodksy,George A. Porter,A Giardini,Y. Shen,Wendy K. Chung,J. G. Seidman,Christine E. Seidman,Eric E. Schadt,Bruce D. Gelb:
  ORE identifies extreme expression effects enriched for rare variants.3906-3912
• 
  Xun Chen,Dawei Li:
  ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data.3913-3922
• 
  Arda Soylev,Thong Minh Le,Hajar Amini,Can Alkan,Fereydoun Hormozdiari:
  Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.3923-3930
• 
  Xin Huang,Xudong Gao,Wanying Li,Shuai Jiang,Ruijiang Li,Hao Hong,Chenghui Zhao,Pingkun Zhou,Hebing Chen,Xiaochen Bo,Hao Li:
  Stable H3K4me3 is associated with transcription initiation during early embryo development.3931-3936

Sequence Analysis

• 
  Christopher Blum,Markus Kollmann:
  Neural networks with circular filters enable data efficient inference of sequence motifs.3937-3943
• 
  Dennis C. Wylie,Hans A. Hofmann,Boris V. Zemelman:
  SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.3944-3952
• 
  Ergude Bao,Fei Xie,Chang-Jin Song,Dandan Song:
  FLAS: fast and high-throughput algorithm for PacBio long-read self-correction.3953-3960

Phylogenetics

• 
  John Yin,Chao Zhang,Siavash Mirarab:
  ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization.3961-3969

Structural Bioinformatics

• 
  Mathilde Carpentier,Jacques Chomilier:
  Protein multiple alignments: sequence-based versus structure-based programs.3970-3980
• 
  Hao Zhu,Zheng Wang:
  SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data.3981-3988
• 
  Hongjian Li,Jiangjun Peng,Pavel Sidorov,Yee Leung,Kwong-Sak Leung,Man Hon Wong,Gang Lu,Pedro J. Ballester:
  Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data.3989-3995
• 
  Insha Ullah,Sudhir Paul,Zhenjie Hong,You-Gan Wang:
  Significance tests for analyzing gene expression data with small sample sizes.3996-4003
• 
  Zafer Aydin,Nuh Azginoglu,Halil Ibrahim Bilgin,Mete Celik:
  Developing structural profile matrices for protein secondary structure and solvent accessibility prediction.4004-4010

Gene expression

• 
  Ghislain Durif,Laurent Modolo,Jeff E. Mold,Sophie Lambert-Lacroix,Franck Picard:
  Probabilistic count matrix factorization for single cell expression data analysis.4011-4019
• 
  Malik Yousef,Loai AbdAllah,Jens Allmer:
  maTE: discovering expressed interactions between microRNAs and their targets.4020-4028
• 
  Yun Yu,Lei-Hong Zhang,Shuqin Zhang:
  Simultaneous clustering of multiview biomedical data using manifold optimization.4029-4037

Genetics and Population Analysis

• 
  Lei Song,Aiyi Liu,Jianxin Shi,Molecular Genetics of Schizophrenia Consortium:
  SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics.4038-4044
• 
  Jussi Gillberg,Pekka Marttinen,Hiroshi Mamitsuka,Samuel Kaski:
  Modelling G×E with historical weather information improves genomic prediction in new environments.4045-4052

Systems Biology

• 
  Louis Gauthier,Rémicia Di Franco,Adrian W. R. Serohijos:
  SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes.4053-4062
• 
  Tamim Abdelaal,Thomas Höllt,Vincent van Unen,Boudewijn P. F. Lelieveldt,Frits Koning,Marcel J. T. Reinders,Ahmed Mahfouz:
  CyTOFmerge: integrating mass cytometry data across multiple panels.4063-4071
• 
  Timo Deist,Andrew Patti,Zhaoqi Wang,David Krane,Taylor Sorenson,David Craft:
  Simulation-assisted machine learning.4072-4080
• 
  Hosein Fooladi,Parsa Moradi,Ali Sharifi-Zarchi,Babak Hossein Khalaj:
  Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization.4081-4088
• 
  Oriol Senan,Antoni Aguilar-Mogas,Miriam Navarro,Jordi Capellades,Luke Noon,Deborah Burks,Oscar Yanes,Roger Guimerà,Marta Sales-Pardo:
  CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.4089-4097
• 
  Reshmi Ramakrishnan,Bert Houben,Frederic Rousseau,Joost Schymkowitz:
  Differential proteostatic regulation of insoluble and abundant proteins.4098-4107

Data and Text Mining

• 
  Ping Xuan,Yangkun Cao,Tiangang Zhang,Xiao Wang,Shuxiang Pan,Tonghui Shen:
  Drug repositioning through integration of prior knowledge and projections of drugs and diseases.4108-4119
• 
  Gonzalo Navarro,Victor Sepulveda,Mauricio Marín,Senén González:
  Compressed filesystem for managing large genome collections.4120-4128
• 
  Zan-Xia Jin,Bo-Wen Zhang,Fan Fang,Le-Le Zhang,Xu-Cheng Yin:
  Health assistant: answering your questions anytime from biomedical literature.4129-4139
• 
  Ghazaleh Taherzadeh,Abdollah Dehzangi,Maryam Golchin,Yaoqi Zhou,Matthew P. Campbell:
  SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties.4140-4146

Databases and Ontologies

• 
  Peter Selby,Rafael Abbeloos,Jan Erik Backlund,Martin Basterrechea Salido,Guillaume Bauchet,Omar E. Benites-Alfaro,Clayton L. Birkett,Viana C. Calaminos,Pierre Carceller,Guillaume Cornut,Bruno Vasques Costa,Jeremy D. Edwards,Richard Finkers,Star Yanxin Gao,Mehmood Ghaffar,Philip Glaser,Valentin Guignon,Puthick Hok,Andrzej Kilian,Patrick König,Jack Elendil B. Lagare,Matthias Lange,Marie-Angélique Laporte,Pierre Larmande,David S. LeBauer,David A Lyon,David F. Marshall,Dave Matthews,Iain Milne,Naymesh Mistry,Nicolas Morales,Lukas A. Mueller,Pascal Neveu,Evangelia Papoutsoglou,Brian Pearce,Ivan Perez-Masias,Cyril Pommier,Ricardo H. Ramirez-Gonzalez,Abhishek Rathore,Angel Manica Raquel,Sebastian Raubach,Trevor Rife,Kelly Robbins,Mathieu Rouard,Chaitanya Sarma,Uwe Scholz,Guilhem Sempéré,Paul D. Shaw,Reinhard Simon,Nahuel Soldevilla,Gordon Stephen,Qi Sun,Clarysabel Tovar,Grzegorz Uszynski,Maikel Verouden,BrAPI Consortium:
  BrAPI - an application programming interface for plant breeding applications.4147-4155

Applications Notes
Genome Analysis

• 
  Muhammad Tahir Ul Qamar,Xitong Zhu,Feng Xing,Ling-Ling Chen:
  ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline.4156-4158
• 
  Ting-You Wang,Li Wang,Sk Kayum Alam,Luke H. Hoeppner,Rendong Yang:
  ScanNeo: identifying indel-derived neoantigens using RNA-Seq data.4159-4161

Phylogenetics

• 
  Michael D. Lee:
  GToTree: a user-friendly workflow for phylogenomics.4162-4164

Structural Bioinformatics

• 
  Jonathan Fine,Gaurav Chopra:
  Lemon: a framework for rapidly mining structural information from the Protein Data Bank.4165-4167
• 
  Javier Delgado,Leandro G. Radusky,Damiano Cianferoni,Luis Serrano:
  FoldX 5.0: working with RNA, small molecules and a new graphical interface.4168-4169
• 
  Mateusz Kurcinski,Maciej Pawel Ciemny,Tymoteusz Oleniecki,Aleksander Kuriata,Aleksandra E. Badaczewska-Dawid,Andrzej Kolinski,Sebastian Kmiecik:
  CABS-dock standalone: a toolbox for flexible protein-peptide docking.4170-4172

Gene expression

• 
  Ling-Hong Hung,Wes Lloyd,Radhika Agumbe Sridhar,Saranya Devi Athmalingam Ravishankar,Yuguang Xiong,Eric Sobie,Ka Yee Yeung:
  Holistic optimization of an RNA-seq workflow for multi-threaded environments.4173-4175
• 
  Benjamin R. Jack,Claus O. Wilke:
  Pinetree: a step-wise gene expression simulator with codon-specific translation rates.4176-4178

Genetics and Population Analysis

• 
  Xiaoyi Raymond Gao,Hua Huang:
  PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits.4179-4180
• 
  Wen Yao,Fangfang Huang,Xuehai Zhang,Jihua Tang:
  ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices.4181-4183
• 
  Bremen L. Braun,David A. Schott,John L. Portwood II,Carson M. Andorf,Taner Z. Sen:
  PedigreeNet: a web-based pedigree viewer for biological databases.4184-4186

Systems Biology

• 
  Adrien Leite Pereira,Olivier Lambotte,Roger Le Grand,Antonio Cosma,Nicolas Tchitchek:
  CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles.4187-4189

Data and Text Mining

• 
  Vincenzo Belcastro,Stephane Cano,Diego Marescotti,Stefano Acali,Carine Poussin,Ignacio Gonzalez-Suarez,Florian Martin,Filipe Bonjour,Nikolai V. Ivanov,Manuel C. Peitsch,Julia Hoeng:
  GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology.4190-4192
• 
  Pei-Hua Wang,Yi-shu Tu,Yufeng J. Tseng:
  PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors.4193-4195

Databases and Ontologies

• 
  David S. Robertson,Jan Wildenhain,Adel Javanmard,Natasha A. Karp:
  onlineFDR: an R package to control the false discovery rate for growing data repositories.4196-4199
• 
  Beibei Ru,Ching Ngar Wong,Yin Tong,Jia Yi Zhong,Sophia Shek Wa Zhong,Wai Chung Wu,Ka Chi Chu,Choi Yiu Wong,Chit Ying Lau,Ian Chen,Nam Wai Chan,Jiangwen Zhang:
  TISIDB: an integrated repository portal for tumor-immune system interactions.4200-4202

Structural genomics

• 
  Julia Varga,Gábor E. Tusnády:
  The TMCrys server for supporting crystallization of transmembrane proteins.4203-4204

Corrigenda
Structural genomics

• 
  Sébastien Morin,Troels E. Linnet,Mathilde Lescanne,Paul Schanda,Gary S. Thompson,Martin Tollinger,Kaare Teilum,Stéphane Gagné,Dominique Marion,Christian Griesinger,Martin Blackledge,Edward J. d'Auvergne:
  relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data.4205
• 
  Shahar Alon,Eli Eisenberg,Jasmine Jacob-Hirsch,Gideon Rechavi,Gad Vatine,Reiko Toyama,Steven L. Coon,David C. Klein,Yoav Gothilf:
  Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland.4206

Volume 35, Number 21, November 2019

Original Papers
Genome Analysis

• 
  Narciso M. Quijada,David Rodríguez-Lázaro,Jose María Eiros,Marta Hernández:
  TORMES: an automated pipeline for whole bacterial genome analysis.4207-4212
• 
  Alberto Magi,Davide Bolognini,Niccoló Bartalucci,Alessandra Mingrino,Roberto Semeraro,Luna Giovannini,Stefania Bonifacio,Daniela Parrini,Elisabetta Pelo,Francesco Mannelli,Paola Guglielmelli,Alessandro Maria Vannucchi:
  Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data.4213-4221
• 
  Tong Liu,Zheng Wang:
  HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data.4222-4228
• 
  Ziye Wang,Zhengyang Wang,Yang Young Lu,Fengzhu Sun,Shanfeng Zhu:
  SolidBin: improving metagenome binning with semi-supervised normalized cut.4229-4238

Sequence Analysis

• 
  Pierre Marijon,Rayan Chikhi,Jean-Stéphane Varré:
  Graph analysis of fragmented long-read bacterial genome assemblies.4239-4246
• 
  Takuya Moriyama,Seiya Imoto,Shuto Hayashi,Yuichi Shiraishi,Satoru Miyano,Rui Yamaguchi:
  A Bayesian model integration for mutation calling through data partitioning.4247-4254
• 
  Mohammed Alser,Hasan Hassan,Akash Kumar,Onur Mutlu,Can Alkan:
  Shouji: a fast and efficient pre-alignment filter for sequence alignment.4255-4263
• 
  Juntao Liu,Xiangyu Liu,Xianwen Ren,Guojun Li:
  scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions.4264-4271
• 
  Leyi Wei,Chen Zhou,Ran Su,Quan Zou:
  PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning.4272-4280
• 
  Jasmijn A. Baaijens,Alexander Schönhuth:
  Overlap graph-based generation of haplotigs for diploids and polyploids.4281-4289

Phylogenetics

• 
  Adrien Oliva,Sylvain Pulicani,Vincent Lefort,Laurent Bréhélin,Olivier Gascuel,Stéphane Guindon:
  Accounting for ambiguity in ancestral sequence reconstruction.4290-4297

Structural Bioinformatics

• 
  Max Ward,Hongying Sun,Amitava Datta,Michael J. Wise,David H. Mathews:
  Determining parameters for non-linear models of multi-loop free energy change.4298-4306

Gene expression

• 
  Laura Cantini,Ulykbek Kairov,Aurélien de Reyniès,Emmanuel Barillot,François Radvanyi,Andrei Yu. Zinovyev:
  Assessing reproducibility of matrix factorization methods in independent transcriptomes.4307-4313
• 
  Ling-Yun Chen,Diego F. Morales-Briones,Courtney N. Passow,Ya Yang:
  Performance of gene expression analyses using de novo assembled transcripts in polyploid species.4314-4320

Genetics and Population Analysis

• 
  Mark Abney,Aisha ElSherbiny:
  Kinpute: using identity by descent to improve genotype imputation.4321-4326
• 
  Meiyue Wang,Shizhong Xu:
  A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies.4327-4335

Systems Biology

• 
  W. Jenny Shi,Yonghua Zhuang,Pamela H. Russell,Brian D. Hobbs,Margaret M. Parker,Peter J. Castaldi,Pratyaydipta Rudra,Brian Vestal,Craig P. Hersh,Laura M. Saba,Katerina J. Kechris:
  Unsupervised discovery of phenotype-specific multi-omics networks.4336-4343
• 
  Yuwei Zhang,Yang Tao,Huihui Ji,Wei Li,Xingli Guo,Derry Minyao Ng,Maria Haleem,Yang Xi,Changzheng Dong,Jinshun Zhao,Lina Zhang,Xiaohong Zhang,Yangyang Xie,Xiaoyu Dai,Qi Liao:
  Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer.4344-4349
• 
  Luis Vitores Valcarcel,Verónica Torrano,Luis Tobalina,Arkaitz Carracedo,Francisco J. Planes:
  rMTA: robust metabolic transformation analysis.4350-4355
• 
  Gaëlle Lefort,Laurence Liaubet,Cécile Canlet,Patrick Tardivel,Marie-Christine Père,Hélène Quesnel,Alain Paris,Nathalie Iannuccelli,Nathalie Vialaneix,Rémi Servien:
  ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra.4356-4363
• 
  Jiajie Peng,Weiwei Hui,Qianqian Li,Bolin Chen,Jianye Hao,Qinghua Jiang,Xuequn Shang,Zhongyu Wei:
  A learning-based framework for miRNA-disease association identification using neural networks.4364-4371

Data and Text Mining

• 
  Jin-Dong Kim,Yue Wang,Toyofumi Fujiwara,Shujiro Okuda,Tiffany J. Callahan,K. Bretonnel Cohen:
  Open Agile text mining for bioinformatics: the PubAnnotation ecosystem.4372-4380
• 
  Pengyuan Li,Xiangying Jiang,Hagit Shatkay:
  Figure and caption extraction from biomedical documents.4381-4388

Applications Notes
Genome Analysis

• 
  Cory Y. McLean,Yeongwoo Hwang,Ryan Poplin,Mark A. DePristo:
  GenomeWarp: an alignment-based variant coordinate transformation.4389-4391
• 
  Endre Bakken Stovner,Pål Sætrom:
  epic2 efficiently finds diffuse domains in ChIP-seq data.4392-4393
• 
  Alexander T. Dilthey,Alexander J. Mentzer,Raphael Carapito,Clare Cutland,Nezih Cereb,Shabir A Madhi,Arang Rhie,Sergey Koren,Seiamak Bahram,Gil McVean,Adam M. Phillippy:
  HLA*LA - HLA typing from linearly projected graph alignments.4394-4396
• 
  Stephanie U. Greer,Hanlee P. Ji:
  Structural variant analysis for linked-read sequencing data with gemtools.4397-4399
• 
  Dapeng Wang:
  IntronDB: a database for eukaryotic intron features.4400-4401
• 
  Carol L. Ecale Zhou,Stephanie Malfatti,Jeffrey A. Kimbrel,Casandra Philipson,Katelyn McNair,Theron Hamilton,Robert A. Edwards,Brian Souza:
  multiPhATE: bioinformatics pipeline for functional annotation of phage isolates.4402-4404
• 
  Steven Monger,Michael Troup,Eddie Ip,Sally L. Dunwoodie,Eleni Giannoulatou:
  Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants.4405-4407
• 
  Heng Li:
  Identifying centromeric satellites with dna-brnn.4408-4410
• 
  Vinhthuy Phan,Diem-Trang Pham,Caroline Melton,Adam J. Ramsey,Bernie J. Daigle Jr.,Jennifer R. Mandel:
  icHET: interactive visualization of cytoplasmic heteroplasmy.4411-4412
• 
  Mustafa Solmaz,Adam Lane,Bilal Gonen,Ogulsheker Akmamedova,Mehmet Hadi Gunes,Kakajan Komurov:
  Graphical data mining of cancer mechanisms with SEMA.4413-4418
• 
  Sun-Ah Kim,Myriam Brossard,Delnaz Roshandel,Andrew D. Paterson,Shelley B. Bull,Yun Joo Yoo:
  gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.4419-4421
• 
  Yating Liu,Luke Sargent,Wilson Leung,Sarah C. R. Elgin,Jeremy Goecks:
  G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes.4422-4423
• 
  Soohyun Lee,Jeremy Johnson,Carl Vitzthum,Koray Kirli,Burak Han Alver,Peter J. Park:
  Tibanna: software for scalable execution of portable pipelines on the cloud.4424-4426
• 
  (Withdrawn)Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants.4427-4429
• 
  René L. Warren,Lauren Coombe,Hamid Mohamadi,Jessica Zhang,Barry Jaquish,Nathalie Isabel,Steven J. M. Jones,Jean Bousquet,Jörg Bohlmann,Inanç Birol:
  ntEdit: scalable genome sequence polishing.4430-4432
• 
  Alessio Locallo,Davide Prandi,Tarcisio Fedrizzi,Francesca Demichelis:
  TPES: tumor purity estimation from SNVs.4433-4435
• 
  Robert Müller,Cédric Chauve:
  HyAsP, a greedy tool for plasmids identification.4436-4439
• 
  Romain Groux,Philipp Bucher:
  SPar-K: a method to partition NGS signal data.4440-4441
• 
  Jia-Xing Yue,Gianni Liti:
  simuG: a general-purpose genome simulator.4442-4444

Sequence Analysis

• 
  Roberto Semeraro,Alberto Magi:
  PyPore: a python toolbox for nanopore sequencing data handling.4445-4447
• 
  Shaun D. Jackman,Tatyana Mozgacheva,Susie Chen,Brendan O'Huiginn,Lance Bailey,Inanç Birol,Steven J. M. Jones:
  ORCA: a comprehensive bioinformatics container environment for education and research.4448-4450
• 
  Robert M. Buels,Shihab Dider,Colin M. Diesh,James Robinson,Ian H. Holmes:
  Cram-JS: reference-based decompression in node and the browser.4451-4452

Phylogenetics

• 
  Alexey M. Kozlov,Diego Darriba,Tomás Flouri,Benoit Morel,Alexandros Stamatakis:
  RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.4453-4455

Structural Bioinformatics

• 
  Maksim V. Shegay,Dmitry A. Suplatov,Nina N. Popova,Vytas K. Svedas,Vladimir V. Voevodin:
  parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems.4456-4458
• 
  Sha Gong,Chengxin Zhang,Yang Zhang:
  RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.4459-4461
• 
  Jordan H. Creed,Garrick Aden-Buie,Alvaro N. A. Monteiro,Travis A. Gerke:
  epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology.4462-4464

Gene expression

• 
  Xin Gao,Yuan Zhong:
  FusionLearn: a biomarker selection algorithm on cross-platform data.4465-4468
• 
  Kristoffer Vitting-Seerup,Albin Sandelin:
  IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences.4469-4471
• 
  Páll Melsted,Vasilis Ntranos,Lior Pachter:
  The barcode, UMI, set format and BUStools.4472-4473
• 
  Anjun Ma,Minxuan Sun,Adam McDermaid,Bingqiang Liu,Qin Ma:
  MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.4474-4477

Genetics and Population Analysis

• 
  Juanjiangmeng Du,Monica Sudarsanam,Eduardo Pérez-Palma,Andrea Ganna,Laurent C. Francioli,Sumaiya Iqbal,Lisa-Marie Niestroj,Costin Leu,Ben Weisburd,Timothy Poterba,Peter Nürnberg,Mark J. Daly,Aarno Palotie,Patrick May,Dennis Lal:
  Variant Score Ranker - a web application for intuitive missense variant prioritization.4478-4479
• 
  Mathias Currat,Miguel Arenas,Claudio S. Quilodràn,Laurent Excoffier,Nicolas Ray:
  SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.4480-4483

Systems Biology

• 
  Pierre Millard,Baudoin Delépine,Matthieu Guionnet,Maud Heuillet,Floriant Bellvert,Fabien Létisse:
  IsoCor: isotope correction for high-resolution MS labeling experiments.4484-4487
• 
  Clarice S. Groeneveld,Vinicius S. Chagas,Steven J. M. Jones,A. Gordon Robertson,Bruce A. J. Ponder,Kerstin B. Meyer,Mauro A. A. Castro:
  RTNsurvival: an R/Bioconductor package for regulatory network survival analysis.4488-4489
• 
  Bence Ágg,Andrea Császár,Máté Szalay-Beko,Dániel V. Veres,Réka Mizsei,Péter Ferdinandy,Péter Csermely,István A. Kovács:
  The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks.4490-4492
• 
  Michael Schubert:
  clustermq enables efficient parallelization of genomic analyses.4493-4495
• 
  David Hoksza,Piotr Gawron,Marek Ostaszewski,Ewa Smula,Reinhard Schneider:
  MINERVA API and plugins: opening molecular network analysis and visualization to the community.4496-4498
• 
  Adrien Rougny:
  sbgntikz - a TikZ library to draw SBGN maps.4499-4500
• 
  Petar V. Todorov,Benjamin M. Gyori,John A. Bachman,Peter K. Sorger:
  INDRA-IPM: interactive pathway modeling using natural language with automated assembly.4501-4503
• 
  Jennifer L. Wilson,Mike Wong,Ajinkya Chalke,Nicholas Stepanov,Dragutin Petkovic,Russ B. Altman:
  PathFXweb: a web application for identifying drug safety and efficacy phenotypes.4504-4506

Data and Text Mining

• 
  Geremy Clair,Sarah Reehl,Kelly G. Stratton,Matthew E. Monroe,Malak M. Tfaily,Charles Ansong,Jennifer E. Kyle:
  Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data.4507-4508
• 
  Neil Pearson,Karim Malki,David Evans,Lewis Vidler,Cara Ruble,James Scherschel,Brian Eastwood,David A. Collier:
  TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability.4509-4510
• 
  Jan P. Buchmann,Edward C. Holmes:
  Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases.4511-4514
• 
  Benjamin S. Glicksberg,Boris Oskotsky,Phyllis M. Thangaraj,Nicholas Giangreco,Marcus A. Badgeley,Kipp W. Johnson,Debajyoti Datta,Vivek A. Rudrapatna,Nadav Rappoport,Mark M. Shervey,Riccardo Miotto,Theodore C. Goldstein,Eugenia Rutenberg,Remi Frazier,Nelson Lee,Sharat Israni,Rick Larsen,Bethany Percha,Li Li,Joel T. Dudley,Nicholas P. Tatonetti,Atul J. Butte:
  PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.4515-4518

Databases and Ontologies

• 
  Youssef Darzi,Yuta Yamate,Takuji Yamada:
  FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization.4519-4521

Bioimage Informatics

• 
  Marcus D. Bloice,Peter M. Roth,Andreas Holzinger:
  Biomedical image augmentation using Augmentor.4522-4524
• 
  Alex X. Lu,Taraneh Zarin,Ian Shenyen Hsu,Alan M. Moses:
  YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.4525-4527
• 
  Michael J. Whitehead,George A. McCanney,Hugh J. Willison,Susan C. Barnett:
  MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures.4528-4530
• 
  David Wiesner,David Svoboda,Martin Maska,Michal Kozubek:
  CytoPacq: a web-interface for simulating multi-dimensional cell imaging.4531-4533

Corrigenda
Bioimage Informatics

• 
  Enrico Siragusa,Niina Haiminen,Richard Finkers,Richard G. F. Visser,Laxmi Parida:
  Haplotype assembly of autotetraploid potato using integer linear programing.4534
• 
  Pei-Hua Wang,Yi-shu Tu,Yufeng J. Tseng:
  PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors.4535
• 
  Pay Giesselmann,Sara Hetzel,Franz-Josef Müller,Alexander Meissner,Helene Kretzmer:
  Nanopype: a modular and scalable nanopore data processing pipeline.4536

Volume 35, Number 22, November 2019

Original Papers
Genome Analysis

• 
  Katelyn McNair,Carol Zhou,Elizabeth A. Dinsdale,Brian Souza,Robert A. Edwards:
  PHANOTATE: a novel approach to gene identification in phage genomes.4537-4542
• 
  Taro Matsutani,Yuki Ueno,Tsukasa Fukunaga,Michiaki Hamada:
  Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference.4543-4552
• 
  Ali M. Yazbeck,Peter F. Stadler,Kifah Tout,Jörg Fallmann:
  Automatic curation of large comparative animal MicroRNA datasets.4553-4559
• 
  Yuansheng Liu,Leo Yu Zhang,Jinyan Li:
  Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers.4560-4567
• 
  Sheila M. Gaynor,Ryan Sun,Xihong Lin,John Quackenbush:
  Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic.4568-4576
• 
  Ashraful Arefeen,Xinshu Xiao,Tao Jiang:
  DeepPASTA: deep neural network based polyadenylation site analysis.4577-4585
• 
  Peng Ni,Neng Huang,Zhi Zhang,De-Peng Wang,Fan Liang,Yu Miao,Chuan-Le Xiao,Feng Luo,Jianxin Wang:
  DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning.4586-4595

Sequence Analysis

• 
  Sijie Chen,Yixin Chen,Fengzhu Sun,Michael S. Waterman,Xuegong Zhang:
  A new statistic for efficient detection of repetitive sequences.4596-4606
• 
  Fabio Cunial,Jarno Alanko,Djamal Belazzougui:
  A framework for space-efficient variable-order Markov models.4607-4616
• 
  Gabriele Orlando,Daniele Raimondi,Francesco Tabaro,Francesco Codicè,Yves Moreau,Wim F. Vranken:
  Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates.4617-4623
• 
  Xin Li,Samaneh Saadat,Haiyan Hu,Xiaoman Li:
  BHap: a novel approach for bacterial haplotype reconstruction.4624-4631
• 
  Yang Li,Pengyu Ni,Shaoqiang Zhang,Guojun Li,Zhengchang Su:
  ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.4632-4639
• 
  Xi Han,Xiaonan Wang,Kang Zhou:
  Develop machine learning-based regression predictive models for engineering protein solubility.4640-4646

Structural Bioinformatics

• 
  Yang Li,Jun Hu,Chengxin Zhang,Dong-Jun Yu,Yang Zhang:
  ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.4647-4655
• 
  Oliver P. Watson,Isidro Cortes-Ciriano,Aimee R. Taylor,James A. Watson:
  A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery.4656-4663
• 
  Quan Li,Ray Luo,Hai-Feng Chen:
  Dynamical important residue network (DIRN): network inference via conformational change.4664-4670

Gene expression

• 
  Justin D. Finkle,Neda Bagheri:
  Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights.4671-4678
• 
  Trung-Nghia Vu,Ha-Nam Nguyen,Stefano Calza,Krishna R. Kalari,Liewei Wang,Yudi Pawitan:
  Cell-level somatic mutation detection from single-cell RNA sequencing.4679-4687
• 
  Rui Hou,Elena Denisenko,Alistair R. R. Forrest:
  scMatch: a single-cell gene expression profile annotation tool using reference datasets.4688-4695
• 
  Travis S. Johnson,Tongxin Wang,Zhi Huang,Christina Y. Yu,Yi Wu,Yatong Han,Yan Zhang,Kun Huang,Jie Zhang:
  LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection.4696-4706
• 
  Chieh Lin,Ziv Bar-Joseph:
  Continuous-state HMMs for modeling time-series single-cell RNA-Seq data.4707-4715

Genetics and Population Analysis

• 
  Daniel Tello,Juanita Gil,Cristian D. Loaiza,John J. Riascos,Nicolás Cardozo,Jorge Duitama:
  NGSEP3: accurate variant calling across species and sequencing protocols.4716-4723

Systems Biology

• 
  Wujuan Zhong,Cassandra N. Spracklen,Karen L. Mohlke,Xiaojing Zheng,Jason Fine,Yun Li:
  Multi-SNP mediation intersection-union test.4724-4729
• 
  Yan Zhao,Xing Chen,Jun Yin:
  Adaptive boosting-based computational model for predicting potential miRNA-disease associations.4730-4738

Data and Text Mining

• 
  Longendri Aguilera-Mendoza,Yovani Marrero-Ponce,Jesus A. Beltran,Roberto Tellez-Ibarra,Hugo A. Guillen-Ramirez,Carlos A. Brizuela:
  Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis.4739-4747
• 
  Ahmad Borzou,Razie Yousefi,Rovshan G. Sadygov:
  Another look at matrix correlations.4748-4753

Applications Notes
Genome Analysis

• 
  Egor Dolzhenko,Viraj Deshpande,Felix Schlesinger,Peter Krusche,Roman Petrovski,Sai Chen,Dorothea Emig-Agius,Andrew Gross,Giuseppe Narzisi,Brett Bowman,Konrad Scheffler,Joke J. F. A van Vugt,Courtney E. French,Alba Sanchis-Juan,Kristina Ibáñez,Arianna Tucci,Bryan R. Lajoie,Jan H. Veldink,F. Lucy Raymond,Ryan J. Taft,David R. Bentley,Michael A. Eberle:
  ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.4754-4756
• 
  Vivek Bhardwaj,Steffen Heyne,Katarzyna Sikora,Leily Rabbani,Michael Rauer,Fabian Kilpert,Andreas S. Richter,Devon Patrick Ryan,Thomas Manke:
  snakePipes: facilitating flexible, scalable and integrative epigenomic analysis.4757-4759
• 
  Saber HafezQorani,Aissa Houdjedj,Mehmet Arici,Abdesselam Said,Hilal Kazan:
  RBPSponge: genome-wide identification of lncRNAs that sponge RBPs.4760-4763
• 
  Jonathan M. Cairns,William R. Orchard,Valeriya Malysheva,Mikhail Spivakov:
  Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.4764-4766
• 
  Charles E. Breeze,Alex P. Reynolds,Jenny van Dongen,Ian Dunham,John Lazar,Shane J. Neph,Jeff Vierstra,Guillaume Bourque,Andrew E. Teschendorff,John A. Stamatoyannopoulos,Stephan Beck:
  eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.4767-4769
• 
  Pay Giesselmann,Sara Hetzel,Franz-Josef Müller,Alexander Meissner,Helene Kretzmer:
  Nanopype: a modular and scalable nanopore data processing pipeline.4770-4772
• 
  Adam Buckle,Nick Gilbert,Davide Marenduzzo,Chris A. Brackley:
  capC-MAP: software for analysis of Capture-C data.4773-4775
• 
  Audrey Mauguen,Venkatraman E. Seshan,Colin B. Begg,Irina Ostrovnaya:
  Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package.4776-4778
• 
  Rens Holmer,Robin van Velzen,René Geurts,Ton Bisseling,Dick de Ridder,Sandra Smit:
  GeneNoteBook, a collaborative notebook for comparative genomics.4779-4781
• 
  David E. Larson,Haley J. Abel,Colby Chiang,Abhijit Badve,Indraniel Das,James M. Eldred,Ryan M. Layer,Ira M. Hall:
  svtools: population-scale analysis of structural variation.4782-4787
• 
  Claudia Arnedo-Pac,Loris Mularoni,Ferran Muiños,Abel Gonzalez-Perez,Núria López-Bigas:
  OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers.4788-4790
• 
  Sebastian Deorowicz,Agnieszka Danek:
  GTShark: genotype compression in large projects.4791-4793

Sequence Analysis

• 
  Qingzhen Hou,Paul F. G. De Geest,Christian J. Griffioen,Sanne Abeln,Jaap Heringa,K. Anton Feenstra:
  SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions.4794-4796
• 
  Rahul Nikam,M. Michael Gromiha:
  Seq2Feature: a comprehensive web-based feature extraction tool.4797-4799
• 
  Antonio Solano-Román,Carlos Cruz-Castillo,Dietmar Offenhuber,Andrés Colubri:
  NX4: a web-based visualization of large multiple sequence alignments.4800-4802
• 
  Raul Ossio,O. Isaac Garcia-Salinas,Diego Said Anaya-Mancilla,Jair S. García-Sotelo,Luis A. Aguilar,David J. Adams,Carla Daniela Robles-Espinoza:
  VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects.4803-4805
• 
  Hein Chun,Sangwoo Kim:
  BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort.4806-4808
• 
  Robert S. Harris,Monika Cechova,Kateryna D. Makova:
  Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data.4809-4811
• 
  Jan Grau,Martin Nettling,Jens Keilwagen:
  DepLogo: visualizing sequence dependencies in R.4812-4814

Phylogenetics

• 
  Amanda Kowalczyk,Wynn K. Meyer,Raghavendran Partha,Weiguang Mao,Nathan L. Clark,Maria Chikina:
  RERconverge: an R package for associating evolutionary rates with convergent traits.4815-4817
• 
  Muhsen Hammoud,Charles Morphy D. Santos,João Paulo Gois:
  iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis.4818-4820

Structural Bioinformatics

• 
  Brian Jiménez-García,Katarina Elez,Panagiotis I. Koukos,Alexandre M. J. J. Bonvin,Anna Vangone:
  PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes.4821-4823
• 
  Jing Ma,Ke An,Jing-Bo Zhou,Nuo-Si Wu,Yang Wang,Zhi-Qiang Ye,Yun-Dong Wu:
  WDSPdb: an updated resource for WD40 proteins.4824-4826

Gene expression

• 
  Xiao-Fei Zhang,Le Ou-Yang,Shuo Yang,Xing-Ming Zhao,Xiaohua Hu,Hong Yan:
  EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning.4827-4829
• 
  Seyed Ali Madani Tonekaboni,Venkata Satya Kumar Manem,Nehme El-Hachem,Benjamin Haibe-Kains:
  SIGN: similarity identification in gene expression.4830-4833
• 
  Tim Jeske,Peter Huypens,Laura Stirm,Selina Höckele,Christine M. Wurmser,Anja Böhm,Cora Weigert,Harald Staiger,Christoph Klein,Johannes Beckers,Maximilian Hastreiter:
  DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences.4834-4836

Genetics and Population Analysis

• 
  Hanna Julienne,Huwenbo Shi,Bogdan Pasaniuc,Hugues Aschard:
  RAISS: robust and accurate imputation from summary statistics.4837-4839
• 
  Ayelet Peres,Moriah Gidoni,Pazit Polak,Gur Yaari:
  RAbHIT: R Antibody Haplotype Inference Tool.4840-4842

Systems Biology

• 
  Phaedra Agius,Heather Geiger,Nicolas Robine:
  SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions.4843-4845
• 
  Javier Perales-Patón,Tomás Di Domenico,Coral Fustero Torre,Elena Piñeiro-Yáñez,Carlos Carretero-Puche,Héctor Tejero,Alfonso Valencia,Gonzalo Gómez-López,Fátima Al-Shahrour:
  vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer.4846-4848

Databases and Ontologies

• 
  Héctor Valverde,Francisco R. Cantón,Juan Carlos Aledo:
  MetOSite: an integrated resource for the study of methionine residues sulfoxidation.4849-4850
• 
  Mihir A. Kamat,James A. Blackshaw,Robin Young,Praveen Surendran,Stephen Burgess,John Danesh,Adam S. Butterworth,James R. Staley:
  PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.4851-4853
• 
  James D. Stephenson,Roman A. Laskowski,Andrew Nightingale,Matthew E. Hurles,Janet M. Thornton:
  VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.4854-4856
• 
  Adrienne Hoarfrost,Nick Brown,C. Titus Brown,Carol Arnosti:
  Sequencing data discovery with MetaSeek.4857-4859

Bioimage Informatics

• 
  Mina Khoshdeli,Garrett Winkelmaier,Bahram Parvin:
  Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes.4860-4861

Letter to the Editor
Structural Bioinformatics

• 
  Mohammed AlQuraishi:
  AlphaFold at CASP13.4862-4865

Volume 35, Number 23, December 2019

Discovery note
Sequence analysis

• 
  Chengyu Liu,Yu-Chen Liu,Hsien-Da Huang,Wei Wang:
  Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.4867-4870

Original Papers
Genome analysis

• 
  Peng Jiang,Jie Luo,Yiqi Wang,Pingji Deng,Bertil Schmidt,Xiangjun Tang,Ningjiang Chen,Limsoon Wong,Liang Zhao:
  kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.4871-4878
• 
  Chao Ning,Dan Wang,Lei Zhou,Julong Wei,Yuanxin Liu,Huimin Kang,Shengli Zhang,Xiang Zhou,Shizhong Xu,Jianfeng Liu:
  Efficient multivariate analysis algorithms for longitudinal genome-wide association studies.4879-4885
• 
  David M. Swanson,Tonje Lien,Helga Bergholtz,Therese Sørlie,Arnoldo Frigessi:
  A Bayesian two-way latent structure model for genomic data integration reveals few pan-genomic cluster subtypes in a breast cancer cohort.4886-4897
• 
  Minhyeok Lee,Sung Won Han,Junhee Seok:
  Prediction of survival risks with adjusted gene expression through risk-gene networks.4898-4906
• 
  Jianglin Feng,Aakrosh Ratan,Nathan C. Sheffield:
  Augmented Interval List: a novel data structure for efficient genomic interval search.4907-4911
• 
  Miroslav Nuriddinov,Veniamin Fishman:
  C-InterSecture - a computational tool for interspecies comparison of genome architecture.4912-4921

Sequence analysis

• 
  Zhao-Chun Xu,Peng-Mian Feng,Hui Yang,Wangren Qiu,Wei Chen,Hao Lin:
  iRNAD: a computational tool for identifying D modification sites in RNA sequence.4922-4929
• 
  Leyi Wei,Ran Su,Shasha Luan,Zhijun Liao,Balachandran Manavalan,Quan Zou,Xiaolong Shi:
  Iterative feature representations improve N4-methylcytosine site prediction.4930-4937
• 
  Carolin Walter,Daniel Schuetzmann,Frank Rosenbauer,Martin Dugas:
  Benchmarking of 4C-seq pipelines based on real and simulated data.4938-4945
• 
  Yan Hu,Ziqiang Wang,Hailin Hu,Fangping Wan,Lin Chen,Yuanpeng Xiong,Xiaoxia Wang,Dan Zhao,Weiren Huang,Jianyang Zeng:
  ACME: pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks.4946-4954
• 
  Yongzhuang Liu,Jian Liu,Yadong Wang:
  Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs.4955-4961

Phylogenetics

• 
  Xiangqi Bai,Liang Ma,Lin Wan:
  Statistical test of structured continuous trees based on discordance matrix.4962-4970

Structural bioinformatics

• 
  Alvaro Alfayate,Carlos Rodriguez Caceres,Helena G. Dos Santos,Ugo Bastolla:
  Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery.4971-4978
• 
  Woosung Jeon,Dongsup Kim:
  FP2VEC: a new molecular featurizer for learning molecular properties.4979-4985
• 
  Ondrej Vavra,Jiri Filipovic,Jan Plhak,David Bednar,Sérgio M. Marques,Jan Brezovsky,Jan Stourac,Ludek Matyska,Jirí Damborský:
  CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.4986-4993
• 
  Jiahua He,Huanyu Tao,Sheng-You Huang:
  Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models.4994-5002
• 
  Maria Elisa Ruiz Echartea,Isaure Chauvot de Beauchêne,David W. Ritchie:
  EROS-DOCK: protein-protein docking using exhaustive branch-and-bound rotational search.5003-5010

Gene expression

• 
  Victor Bernal,Rainer Bischoff,Victor Guryev,Marco Grzegorczyk,Peter Horvatovich:
  Exact hypothesis testing for shrinkage-based Gaussian graphical models.5011-5017
• 
  Viren Amin,Didem Agaç,Spencer D. Barnes,Murat Can Cobanoglu:
  Accurate differential analysis of transcription factor activity from gene expression.5018-5029
• 
  Xun Gu,Hang Ruan,Jingwen Yang:
  Estimating the strength of expression conservation from high throughput RNA-seq data.5030-5038
• 
  Gabrielle Deschamps-Francoeur,Vincent Boivin,Sherif Abou Elela,Michelle S. Scott:
  CoCo: RNA-seq read assignment correction for nested genes and multimapped reads.5039-5047
• 
  Kuan-Ting Lin,Adrian R. Krainer:
  PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.5048-5054

Genetics and population analysis

• 
  Ivan Vogel,Robert C. Blanshard,Eva R. Hoffmann:
  SureTypeSC - a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data.5055-5062

Applications note
Genome analysis

• 
  Lee H. Bergstrand,Josh D. Neufeld,Andrew C. Doxey:
  Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties.5063-5065

Volume 35, Number 24, December 2019

Original Papers
Genome analysis

• 
  Jiyun Zhou,Qin Lu,Lin Gui,Ruifeng Xu,Yunfei Long,Hongpeng Wang:
  MTTFsite: cross-cell type TF binding site prediction by using multi-task learning.5067-5077
• 
  Javad Ansarifar,Lizhi Wang:
  New algorithms for detecting multi-effect and multi-way epistatic interactions.5078-5085

Sequence analysis

• 
  Jasmijn A. Baaijens,Bastiaan Van der Roest,Johannes Köster,Leen Stougie,Alexander Schönhuth:
  Full-length de novo viral quasispecies assembly through variation graph construction.5086-5094
• 
  Rose Du,Vincent J. Carey,Scott T. Weiss:
  deconvSeq: deconvolution of cell mixture distribution in sequencing data.5095-5102

Structural bioinformatics

• 
  Albert Y. Xue,Angela M. Yu,Julius B. Lucks,Neda Bagheri:
  DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.5103-5112
• 
  Guillaume Pagès,Sergei Grudinin:
  DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures.5113-5120
• 
  Yuqi Zhang,Michel F. Sanner:
  AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes.5121-5127
• 
  Qiang Shi,Weiya Chen,Siqi Huang,Fanglin Jin,Yinghao Dong,Yan Wang,Zhidong Xue:
  DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network.5128-5136

Gene expression

• 
  Onur Dereli,Ceyda Oguz,Mehmet Gönen:
  Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning.5137-5145
• 
  Joanna Zyla,Michal Marczyk,Teresa Domaszewska,Stefan H. E. Kaufmann,Joanna Polanska,January 3rd Weiner:
  Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms.5146-5154
• 
  Chengzhong Ye,Terence P. Speed,Agus Salim:
  DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data.5155-5162

Genetics and population analysis

• 
  Jiaqi Luo,Tianliangwen Zhou,Xiaobin You,Yi Zi,Xiaoting Li,Yangming Wu,Zhaoji Lan,Qihuan Zhi,Dandan Yi,Lei Xu,Ang Li,Zaixuan Zhong,Mei Zhu,Gang Sun,Tao Zhu,Jianmei Rao,Luhua Lin,Jianfeng Sang,Yujian Shi:
  Assessing concordance among human, in silico predictions and functional assays on genetic variant classification.5163-5170

Systems biology

• 
  Lara Schneider,Tim Kehl,Kristina Thedinga,Nadja Liddy Grammes,Christina Backes,Christopher Mohr,Benjamin Schubert,Kerstin Lenhof,Nico Gerstner,Andreas Daniel Hartkopf,Markus Wallwiener,Oliver Kohlbacher,Andreas Keller,Eckart Meese,Norbert M. Graf,Hans-Peter Lenhof:
  ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification.5171-5181
• 
  Luis G. Leal,Alessia David,Marjo-Riitta Järvelin,Sylvain Sebert,Minna Männikkö,Ville Karhunen,Eleanor Seaby,Clive J. Hoggart,Michael J. E. Sternberg:
  Identification of disease-associated loci using machine learning for genotype and network data integration.5182-5190
• 
  Xiangxiang Zeng,Siyi Zhu,Xiangrong Liu,Yadi Zhou,Ruth Nussinov,Feixiong Cheng:
  deepDR: a network-based deep learning approach to in silico drug repositioning.5191-5198
• 
  Fredrik Wrede,Andreas Hellander:
  Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning.5199-5206
• 
  Peilin Jia,Guangsheng Pei,Zhongming Zhao:
  CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures.5207-5215
• 
  Shyam Srinivasan,William R. Cluett,Radhakrishnan Mahadevan:
  A scalable method for parameter identification in kinetic models of metabolism using steady-state data.5216-5225
• 
  Sam F. L. Windels,Noël Malod-Dognin,Natasa Przulj:
  Graphlet Laplacians for topology-function and topology-disease relationships.5226-5234

Data and text mining

• 
  Jun Wang,Liangjiang Wang:
  Deep learning of the back-splicing code for circular RNA formation.5235-5242
• 
  Ana S. C. Silva,Robbin Bouwmeester,Lennart Martens,Sven Degroeve:
  Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions.5243-5248
• 
  Minji Jeon,Donghyeon Park,Jinhyuk Lee,Hwisang Jeon,Miyoung Ko,Sunkyu Kim,Yonghwa Choi,Aik Choon Tan,Jaewoo Kang:
  ReSimNet: drug response similarity prediction using Siamese neural networks.5249-5256
• 
  Camilo L. M. Morais,Marfran C. D. Santos,Kássio M. G. Lima,Francis L. Martin:
  Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach.5257-5263

Databases and ontologies

• 
  Jennifer D. Warrender,Anthony V. Moorman,Phillip Lord:
  A fully computational and reasonable representation for karyotypes.5264-5270

Bioimage informatics

• 
  Meiyan Huang,Yuwei Yu,Wei Yang,Qianjin Feng,Alzheimer's Disease Neuroimaging Initiative:
  Incorporating spatial-anatomical similarity into the VGWAS framework for AD biomarker detection.5271-5280
• 
  Qi Shen,Goayu Xiao,Yingwei Zheng,Jie Wang,Yue Liu,Xutao Zhu,Fan Jia,Peng Su,Binbin Nie,Fuqiang Xu,Bin Zhang:
  ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques.5281-5289
• 
  Arttu Miettinen,Ioannis Vogiatzis Oikonomidis,Anne Bonnin,Marco Stampanoni:
  NRStitcher: non-rigid stitching of terapixel-scale volumetric images.5290-5297

Applications Notes
Genome analysis

• 
  Bowen Liu,Xiaofei Yang,Tingjie Wang,Jiadong Lin,Yongyong Kang,Peng Jia,Kai Ye:
  MEpurity: estimating tumor purity using DNA methylation data.5298-5300
• 
  Marta Sampaio,Miguel Rocha,Hugo Oliveira,Oscar Dias:
  Predicting promoters in phage genomes using PhagePromoter.5301-5302
• 
  Jaehee Jung,Jong Im Kim,Gangman Yi:
  geneCo: a visualized comparative genomic method to analyze multiple genome structures.5303-5305
• 
  Qi Liu,Quanhu Sheng,Jie Ping,Marisol Adelina Ramirez,Ken S. Lau,Robert J. Coffey,Yu Shyr:
  scRNABatchQC: multi-samples quality control for single cell RNA-seq data.5306-5308

Sequence analysis

• 
  Ioannis A. Tamposis,Konstantinos D. Tsirigos,Margarita C. Theodoropoulou,Panagiota I. Kontou,Georgios N. Tsaousis,Dimitra Sarantopoulou,Zoi I. Litou,Pantelis G. Bagos:
  JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis.5309-5312
• 
  Thammakorn Saethang,Kenneth Hodge,Chin-Rang Yang,Yue Zhao,Ingorn Kimkong,Mark A. Knepper,Trairak Pisitkun:
  PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities.5313-5314
• 
  Maurits J. J. Dijkstra,Atze van der Ploeg,K. Anton Feenstra,Wan J. Fokkink,Sanne Abeln,Jaap Heringa:
  Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.5315-5317
• 
  Wolfgang Beyer,Adam M. Novak,Glenn Hickey,Jeffrey Chan,Vanessa Tan,Benedict Paten,Daniel R. Zerbino:
  Sequence tube maps: making graph genomes intuitive to commuters.5318-5320

Phylogenetics

• 
  Mark N. Puttick:
  MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees.5321-5322

Structural bioinformatics

• 
  Ragul Gowthaman,Brian G. Pierce:
  TCR3d: The T cell receptor structural repertoire database.5323-5325
• 
  Liisa Holm:
  Benchmarking fold detection by DaliLite v.5.5326-5327
• 
  Simone Aureli,Daniele Di Marino,Stefano Raniolo,Vittorio Limongelli:
  DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis.5328-5330
• 
  David Bouyssié,Jean Lesne,Marie Locard-Paulet,Renaud Albigot,Odile Burlet-Schiltz,Julien Marcoux:
  HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data.5331-5333
• 
  Diego Gallego,Leonardo Darré,Pablo D. Dans,Modesto Orozco:
  VeriNA3d: an R package for nucleic acids data mining.5334-5336
• 
  Oskar Taubert,Ines Reinartz,Henning Meyerhenke,Alexander Schug:
  diSTruct v1.0: generating biomolecular structures from distance constraints.5337-5338

Gene expression

• 
  Laura Puente-Santamaria,Wyeth W. Wasserman,Luis del Peso:
  TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.5339-5340

Genetics and population analysis

• 
  Yeongjun Jang,Jihae Seo,Insu Jang,Byungwook Lee,Sun Kim,Sanghyuk Lee:
  CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data.5341-5343
• 
  Carles Hernandez-Ferrer,Gregory A. Wellenius,Ibon Tamayo,Xavier Basagaña,Jordi Sunyer,Martine Vrijheid,Juan R. González:
  Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages.5344-5345
• 
  Stephanie M. Gogarten,Tamar Sofer,Han Chen,Chaoyu Yu,Jennifer A. Brody,Timothy A. Thornton,Kenneth M. Rice,Matthew P. Conomos:
  Genetic association testing using the GENESIS R/Bioconductor package.5346-5348
• 
  Nils Koelling,Marie Bernkopf,Eduardo Calpena,Geoffrey J. Maher,Kerry A. Miller,Hannah K. Ralph,Anne Goriely,Andrew O. M. Wilkie:
  amplimap: a versatile tool to process and analyze targeted NGS data.5349-5350
• 
  Abhishek Niroula,Ram Ajore,Björn Nilsson:
  MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.5351-5353

Systems biology

• 
  Zhaojun Li,Xutong Li,Xiaohong Liu,Zunyun Fu,Zhaoping Xiong,Xiaolong Wu,Xiaoqin Tan,Jihui Zhao,Feisheng Zhong,Xiaozhe Wan,Xiaomin Luo,Kaixian Chen,Hualiang Jiang,Mingyue Zheng:
  KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules.5354-5356
• 
  Vinicius S. Chagas,Clarice S. Groeneveld,Kelin G. Oliveira,Sheyla Trefflich,Rodrigo C. de Almeida,Bruce A. J. Ponder,Kerstin B. Meyer,Steven J. M. Jones,A. Gordon Robertson,Mauro A. A. Castro:
  RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons.5357-5358
• 
  Caroline J. Sands,Arnaud M. Wolfer,Gonçalo D. S. Correia,Noureddin Sadawi,Arfan Ahmed,Beatriz Jiménez,Matthew R. Lewis,Robert C. Glen,Jeremy K. Nicholson,Jake T. M. Pearce:
  The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets.5359-5360
• 
  Vítor Vieira,Miguel Rocha:
  CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.5361-5362
• 
  Sridevi Maharaj,Brennan Tracy,Wayne B. Hayes:
  BLANT - fast graphlet sampling tool.5363-5364

Data and text mining

• 
  Zachary B. Abrams,Lin Zhang,Lynne V. Abruzzo,Nyla A. Heerema,Suli Li,Tom Dillon,Ricky Rodriguez,Kevin R. Coombes,Philip R. O. Payne:
  CytoGPS: a web-enabled karyotype analysis tool for cytogenetics.5365-5366
• 
  Raphael Scheible,Stephan Rusch,David Guzman,Nizar Mahlaoui,Stephan Ehl,Gerhard Kindle:
  The NEW ESID online database network.5367-5369
• 
  Melissa Y. Yan,Betsy Ferguson,Benjamin N. Bimber:
  VariantQC: a visual quality control report for variant evaluation.5370-5371
• 
  James M. Ferguson,Martin A. Smith:
  SquiggleKit: a toolkit for manipulating nanopore signal data.5372-5373
• 
  Oleksandr Narykov,Dmytro Bogatov,Dmitry Korkin:
  DISPOT: a simple knowledge-based protein domain interaction statistical potential.5374-5378
• 
  Joshua J. Levy,Alexander J. Titus,Lucas A. Salas,Brock C. Christensen:
  PyMethylProcess - convenient high-throughput preprocessing workflow for DNA methylation data.5379-5381
• 
  Kenneth Morton,Patrick Wang,Chris Bizon,Steven Cox,James P. Balhoff,Yaphet Kebede,Karamarie Fecho,Alexander Tropsha:
  ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.5382-5384

Databases and ontologies

• 
  Vid Podpecan,Ziva Ramsak,Kristina Gruden,Hannu Toivonen,Nada Lavrac:
  Interactive exploration of heterogeneous biological networks with Biomine Explorer.5385-5388
• 
  Vladimír Horský,Veronika Bendová,Dominik Tousek,Jaroslav Koca,Radka Svobodová Vareková:
  ValTrendsDB: bringing Protein Data Bank validation information closer to the user.5389-5390
• 
  Alejandro Aguayo-Orozco,Karine Audouze,Troels Siggaard,Robert Barouki,Søren Brunak,Olivier Taboureau:
  sAOP: linking chemical stressors to adverse outcomes pathway networks.5391-5392

Bioimage informatics

• 
  Eric Wait,Mark R. Winter,Andrew R. Cohen:
  Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers.5393-5395

Corrigenda
Bioimage informatics

• 
  Claudia Arnedo-Pac,Loris Mularoni,Ferran Muiños,Abel Gonzalez-Perez,Núria López-Bigas:
  OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers.5396
• 
  Anjun Ma,Minxuan Sun,Adam McDermaid,Bingqiang Liu,Qin Ma:
  MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.5397