Bioinformatics, Volume 34

Volume 34, Number 1, January 2018

Original Papers
Genome Analysis

• 
  Karolina Elzbieta Kaczor-Urbanowicz,Yong Kim,Feng Li,Timur Galeev,Robert R. Kitchen,Mark Gerstein,Kikuye Koyano,Sung-Hee Jeong,Xiaoyan Wang,David Elashoff,So Young Kang,Su Mi Kim,Kyoung Kim,Sung Kim,David Chia,Xinshu Xiao,Joel S. Rozowsky,David T. W. Wong:
  Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.1-8
• 
  Sha Joe Zhu,Jacob Almagro-Garcia,Gil McVean:
  Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data.9-15
• 
  Brian J. Mendoza,Cong T. Trinh:
  Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms.16-23

Sequence Analysis

• 
  Ergude Bao,Chang-Jin Song,Lingxiao Lan:
  ReMILO: reference assisted misassembly detection algorithm using short and long reads.24-32
• 
  Bin Liu,Fan Yang,De-Shuang Huang,Kuo-Chen Chou:
  iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.33-40

Structural Bioinformatics

• 
  Konrad Krawczyk,Samuel Demharter,Bernhard Knapp,Charlotte M. Deane,Peter Minary:
  In silico structural modeling of multiple epigenetic marks on DNA.41-48
• 
  Brian Jiménez-García,Jorge Roel-Touris,Miguel Romero-Durana,Miquel Vidal,Daniel Jiménez-González,Juan Fernández-Recio:
  LightDock: a new multi-scale approach to protein-protein docking.49-55

Gene expression

• 
  Xu Shi,Xiao Wang,Tian-Li Wang,Leena Hilakivi-Clarke,Robert Clarke,Jianhua Xuan:
  SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data.56-63

Systems Biology

• 
  Andrew Elliott,Elizabeth Leicht,Alan Whitmore,Gesine Reinert,Felix Reed-Tsochas:
  A nonparametric significance test for sampled networks.64-71

Data and Text Mining

• 
  Lewis H. Mervin,Krishna C. Bulusu,Leen Kalash,Avid M. Afzal,Fredrik Svensson,Mike A. Firth,Ian P. Barrett,Ola Engkvist,Andreas Bender:
  Orthologue chemical space and its influence on target prediction.72-79
• 
  Chih-Hsuan Wei,Lon Phan,Juliana Feltz,Rama Maiti,Tim Hefferon,Zhiyong Lu:
  tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine.80-87

Bioimage Informatics

• 
  Elco Bakker,Peter S. Swain,Matthew M. Crane:
  Morphologically constrained and data informed cell segmentation of budding yeast.88-96
• 
  Carlo Biffi,Antonio de Marvao,Mark I Attard,Timothy J. W. Dawes,Nicola Whiffin,Wenjia Bai,Wenzhe Shi,Catherine Francis,Hannah Meyer,Rachel J. Buchan,Stuart A. Cook,Daniel Rueckert,Declan P. O'Regan:
  Three-dimensional cardiovascular imaging-genetics: a mass univariate framework.97-103

Applications Notes
Genome Analysis

• 
  Laura Seaman,Indika Rajapakse:
  4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities.104-106
• 
  Jochen Singer,Hans-Joachim Ruscheweyh,Ariane L. Hofmann,Thomas Thurnherr,Franziska Singer,Nora C. Toussaint,Charlotte K. Y. Ng,Salvatore Piscuoglio,Christian Beisel,Gerhard Christofori,Reinhard Dummer,Michael N. Hall,Wilhelm Krek,Mitchell P. Levesque,Markus G. Manz,Holger Moch,Andreas Papassotiropoulos,Daniel J. Stekhoven,Peter Wild,Thomas Wüst,Bernd Rinn,Niko Beerenwinkel:
  NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.107-108
• 
  Kun-Tze Chen,Chia-Liang Liu,Shang-Hao Huang,Hsin-Ting Shen,Yi-Kung Shieh,Hsien-Tai Chiu,Chin Lung Lu:
  CSAR: a contig scaffolding tool using algebraic rearrangements.109-111
• 
  Nils Ternès,Federico Rotolo,Stefan Michiels:
  biospear: an R package for biomarker selection in penalized Cox regression.112-113

Sequence Analysis

• 
  Christopher Wilks,Phani Gaddipati,Abhinav Nellore,Ben Langmead:
  Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.114-116
• 
  Houxiang Zhu,Emily Richmond,Chun Liang:
  CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity.117-119

Structural Bioinformatics

• 
  Yuri Binev,Daniela Peixoto,Florbela Pereira,Ian Rodrigues,Sofia Cavaco,Ana M. Lobo,João Aires-de-Sousa:
  NavMol 3.0: enabling the representation of metabolic reactions by blind users.120-121
• 
  Damiano Piovesan,Silvio C. E. Tosatto:
  Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures.122-123

Systems Biology

• 
  Carl D. Christensen,Jan-Hendrik S. Hofmeyr,Johann M. Rohwer:
  PySCeSToolbox: a collection of metabolic pathway analysis tools.124-125
• 
  Sara Brin Rosenthal,Julia Len,Mikayla Webster,Aaron Gary,Amanda Birmingham,Kathleen M. Fisch:
  Interactive network visualization in Jupyter notebooks: visJS2jupyter.126-128

Data and Text Mining

• 
  Oded Rimon,Dana Reichmann:
  Kfits: a software framework for fitting and cleaning outliers in kinetic measurements.129-130

Databases and Ontologies

• 
  Oriol López-Massaguer,Ferran Sanz,Manuel Pastor:
  An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies.131-133

Bioimage Informatics

• 
  Rani Arielly,Yuval Ebenstein:
  Irys Extract.134-136
• 
  Kristoffer Bernhem,Hjalmar Brismar:
  SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy.137-138

Special Issue:RECOMB-Seq/RECOMB-CCB/RECOMB-CG
Gene expression

• 
  Zhe Sun,Ting Wang,Ke Deng,Xiao-Feng Wang,Robert Lafyatis,Ying Ding,Ming Hu,Wei Chen:
  DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data.139-146

Genome Analysis

• 
  Roye Rozov,Gil Goldshlager,Eran Halperin,Ron Shamir:
  Faucet: streaming de novo assembly graph construction.147-154

Sequence Analysis

• 
  Vikas Bansal:
  An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.155-162
• 
  Pavel Skums,Alex Zelikovsky,Rahul Singh,Walker Gussler,Zoya Dimitrova,Sergey Knyazev,Igor Mandric,Sumathi Ramachandran,David S. Campo,Deeptanshu Jha,Leonid Bunimovich,Elizabeth Costenbader,Connie Sexton,Siobhán O'Connor,Guo-liang Xia,Yury Khudyakov:
  QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.163-170
• 
  Xinan Liu,Ye Yu,Jinpeng Liu,Corrine F. Elliott,Chen Qian,Jinze Liu:
  A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.171-178

Corrigendum
Sequence Analysis

• 
  Greg Malysa,Mikel Hernaez,Idoia Ochoa,Milind Rao,Karthik Ganesan,Tsachy Weissman:
  QVZ: lossy compression of quality values.179

Erratum
Sequence Analysis

• 
  Zhi-Kai Yang,Feng Gao:
  The systematic analysis of ultraconserved genomic regions in the budding yeast.180

Volume 34, Number 2, January 2018

Original Papers
Genome Analysis

• 
  Gulce Kale,Erman Ayday,Öznur Tastan:
  A utility maximizing and privacy preserving approach for protecting kinship in genomic databases.181-189

Sequence Analysis

• 
  Hsin-Nan Lin,Wen-Lian Hsu:
  DART: a fast and accurate RNA-seq mapper with a partitioning strategy.190-197
• 
  Jun Ding,Xiaoman Li,Haiyan Hu:
  CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.198-206

Structural Bioinformatics

• 
  Matteo Tiberti,Alessandro Pandini,Franca Fraternali,Arianna Fornili:
  In silico identification of rescue sites by double force scanning.207-214
• 
  Dmytro Guzenko,Sergei V. Strelkov:
  CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments.215-222
• 
  Thomas C. Northey,Anja Baresic,Andrew C. R. Martin:
  IntPred: a structure-based predictor of protein-protein interaction sites.223-229
• 
  Jing Yang,Hong-Bin Shen:
  MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain.230-238

Systems Biology

• 
  Qiu Xiao,Jiawei Luo,Cheng Liang,Jie Cai,Pingjian Ding:
  A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations.239-248
• 
  Yiming Kang,Hien-Haw Liow,Ezekiel J. Maier,Michael R. Brent:
  NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources.249-257
• 
  Nan Papili Gao,S. M. Minhaz Ud-Dean,Olivier Gandrillon,Rudiyanto Gunawan:
  SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.258-266

Data and Text Mining

• 
  Yingli Zhong,Ping Xuan,Xiao Wang,Tiangang Zhang,Jianzhong Li,Yong Liu,Weixiong Zhang:
  A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network.267-277

Bioimage Informatics

• 
  Lei Du,Kefei Liu,Tuo Zhang,Xiaohui Yao,Jingwen Yan,Shannon L. Risacher,Junwei Han,Lei Guo,Andrew J. Saykin,Li Shen:
  A novel SCCA approach via truncated ℓ1-norm and truncated group lasso for brain imaging genetics.278-285

Applications Notes
Genome Analysis

• 
  Chris Chatzinakos,Donghyung Lee,Bradley Todd Webb,Vladimir I. Vladimirov,Kenneth S. Kendler,Silviu-Alin Bacanu:
  JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.286-288
• 
  Roberto Vera Alvarez,Shan Li,David Landsman,Ivan Ovcharenko:
  SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome.289-291

Phylogenetics

• 
  James Hadfield,Nicholas J. Croucher,Richard J. Goater,Khalil AbuDahab,David M. Aanensen,Simon R. Harris:
  Phandango: an interactive viewer for bacterial population genomics.292-293

Structural Bioinformatics

• 
  Guillaume Brysbaert,Kevin Lorgouilloux,Wim F. Vranken,Marc F. Lensink:
  RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction.294-296
• 
  Anastasia A. Anashkina,Yuri Kravatsky,Eugene N. Kuznetsov,Alexander A. Makarov,Alexei A. Adzhubei:
  Meta-server for automatic analysis, scoring and ranking of docking models.297-299

Gene expression

• 
  Christopher J. Green,Matthew R. Gazzara,Yoseph Barash:
  MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data.300-302

Genetics and Population Analysis

• 
  Daniel Boloc,Natalia Rodríguez,Patricia Gassó,Josep F. Abril,Miquel Bernardo,Amalia Lafuente,Sergi Mas:
  SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling.303-305
• 
  Lisa A. Ouellette,Robert W. Reid,Steven G. Blanchard,Cory R. Brouwer:
  LinkageMapView - rendering high-resolution linkage and QTL maps.306-307

Systems Biology

• 
  Michael Seifert,Andreas Beyer:
  regNet: an R package for network-based propagation of gene expression alterations.308-311
• 
  Maxime Chazalviel,Clément Frainay,Nathalie Poupin,Florence Vinson,Benjamin Merlet,Yoann Gloaguen,Ludovic Cottret,Fabien Jourdan:
  MetExploreViz: web component for interactive metabolic network visualization.312-313
• 
  Huey-Eng Chua,Sourav S. Bhowmick,Jie Zheng:
  TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks.314-316

Data and Text Mining

• 
  Joe Wandy,Yunfeng Zhu,Justin J. J. van der Hooft,Rónán Daly,Michael P. Barrett,Simon Rogers:
  Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.317-318

Databases and Ontologies

• 
  Kun-Hsing Yu,Michael R. Fitzpatrick,Luke Pappas,Warren Chan,Jessica Kung,Michael Snyder:
  Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction.319-320
• 
  Jonathan Lo,Deric Zhang,Emily Speranza,Jose A. Negron,John H. Connor:
  HoTResDB: host transcriptional response database for viral hemorrhagic fevers.321-322

Letter to the Editor
Genome Analysis

• 
  Kristoffer Forslund,Cécile Pereira,Salvador Capella-Gutiérrez,Alan W. Sousa da Silva,Adrian M. Altenhoff,Jaime Huerta-Cepas,Matthieu Muffato,Mateus Patricio,Klaas Vandepoele,Ingo Ebersberger,Judith A. Blake,Jesualdo Tomás Fernández-Breis,Quest for Orthologs Consortium,Brigitte Boeckmann,Toni Gabaldón,Erik L. L. Sonnhammer,Christophe Dessimoz,Suzanna Lewis:
  Gearing up to handle the mosaic nature of life in the quest for orthologs.323-329

SPECIAL ISSUE:RECOMB-CCB2017
Genome Analysis

• 
  Xiaoqing Huang,Damian Wójtowicz,Teresa M. Przytycka:
  Detecting presence of mutational signatures in cancer with confidence.330-337
• 
  Abhijit Chakraborty,Ferhat Ay:
  Identification of copy number variations and translocations in cancer cells from Hi-C data.338-345

Sequence Analysis

• 
  Layla Oesper,Simone Dantas,Benjamin J. Raphael:
  Identifying simultaneous rearrangements in cancer genomes.346-352
• 
  Rebecca Elyanow,Hsin-Ta Wu,Benjamin J. Raphael:
  Identifying structural variants using linked-read sequencing data.353-360

Volume 34, Number 3, February 2018

Discovery Notes
Genome Analysis

• 
  Zhi-Kai Yang,Feng Gao:
  The systematic analysis of ultraconserved genomic regions in the budding yeast.361-366

Gene expression

• 
  Zeljko Tomljanovic,Mitesh Patel,William Shin,Andrea Califano,Andrew F. Teich:
  ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.367-371

Original Papers
Genome Analysis

• 
  Tarmo Äijö,Christian L. Müller,Richard Bonneau:
  Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.372-380
• 
  Weilong Guo,Ping Zhu,Matteo Pellegrini,Michael Q. Zhang,Xiangfeng Wang,Zhongfu Ni:
  CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.381-387
• 
  Sun-Ah Kim,Chang-Sung Cho,Suh-Ryung Kim,Shelley B. Bull,Yun Joo Yoo:
  A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs.388-397
• 
  Wei Tang,Shixiang Wan,Zhen Yang,Andrew E. Teschendorff,Quan Zou:
  Tumor origin detection with tissue-specific miRNA and DNA methylation markers.398-406

Sequence Analysis

• 
  Paul D. Blischak,Laura Salter Kubatko,Andrea D. Wolfe:
  SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data.407-415
• 
  Haoyu Cheng,Ming Wu,Yun Xu:
  FMtree: a fast locating algorithm of FM-indexes for genomic data.416-424
• 
  Tom Paridaens,Glenn Van Wallendael,Wesley De Neve,Peter Lambert:
  AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality.425-433
• 
  Evgenii I Olekhnovich,Artem T. Vasilyev,Vladimir Ulyantsev,Elena S. Kostryukova,Alexander V. Tyakht:
  MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.434-444

Structural Bioinformatics

• 
  Marco Necci,Damiano Piovesan,Zsuzsanna Dosztányi,Peter Tompa,Silvio C. E. Tosatto:
  A comprehensive assessment of long intrinsic protein disorder from the DisProt database.445-452
• 
  Yumeng Yan,Sheng-You Huang:
  RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring.453-458
• 
  Francesca Nadalin,Alessandra Carbone:
  Protein-protein interaction specificity is captured by contact preferences and interface composition.459-468
• 
  Hyun-Ho Kyeong,Yoonjoo Choi,Hak-Sung Kim:
  GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking.469-476
• 
  Ghazaleh Taherzadeh,Yaoqi Zhou,Alan Wee-Chung Liew,Yuedong Yang:
  Structure-based prediction of protein- peptide binding regions using Random Forest.477-484

Gene expression

• 
  Ghislain Durif,Laurent Modolo,Jakob Michaelsson,Jeff E. Mold,Sophie Lambert-Lacroix,Franck Picard:
  High dimensional classification with combined adaptive sparse PLS and logistic regression.485-493

Systems Biology

• 
  Claudio Angione:
  Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism.494-501
• 
  Zhengwei Xie,Tianyu Zhang,Qi Ouyang:
  Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm.502-510

Applications Notes
Genome Analysis

• 
  Mark F. Rogers,Hashem A. Shihab,Matthew E. Mort,David N. Cooper,Tom R. Gaunt,Colin Campbell:
  FATHMM-XF: accurate prediction of pathogenic point mutations via extended features.511-513
• 
  Fabiano B. Menegidio,Daniela L. Jabes,Regina Costa de Oliveira,Luiz R. Nunes:
  Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.514-515
• 
  Sergii Ivakhno,Eric Roller,Camilla Colombo,Philip Tedder,Anthony J. Cox:
  Canvas SPW: calling de novo copy number variants in pedigrees.516-518
• 
  Ho Jang,Hyunju Lee:
  Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data.519-521
• 
  Javier Palarea-Albaladejo,Kevin McLean,Frank Wright,David G. E. Smith:
  MALDIrppa: quality control and robust analysis for mass spectrometry data.522-523

Gene expression

• 
  María José Nueda,Jordi Martorell-Marugan,Cristina Martí,Sonia Tarazona,Ana Conesa:
  Identification and visualization of differential isoform expression in RNA-seq time series.524-526

Genetics and Population Analysis

• 
  Anna Okula Basile,Marta Byrska-Bishop,John R. Wallace,Alex Thomas Frase,Marylyn D. Ritchie:
  Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants.527-529

Systems Biology

• 
  Mahito Sugiyama,M. Elisabetta Ghisu,Felipe Llinares-López,Karsten M. Borgwardt:
  graphkernels: R and Python packages for graph comparison.530-532

Data and Text Mining

• 
  Sergio Picart-Armada,Wesley K. Thompson,Alfonso Buil,Alexandre Perera-Lluna:
  diffuStats: an R package to compute diffusion-based scores on biological networks.533-534

Databases and Ontologies

• 
  Éva Schád,Erzsébet Fichó,Rita Pancsa,István Simon,Zsuzsanna Dosztányi,Bálint Mészáros:
  DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.535-537

Bioimage Informatics

• 
  Virginie Uhlmann,Carsten Haubold,Fred A. Hamprecht,Michael Unser:
  DiversePathsJ: diverse shortest paths for bioimage analysis.538-540

Volume 34, Number 4, February 2018

Original Papers
Genome Analysis

• 
  Cristian A. Yones,Georgina Stegmayer,Diego H. Milone:
  Genome-wide pre-miRNA discovery from few labeled examples.541-549
• 
  Hequan Sun,Jia Ding,Mathieu Piednoël,Korbinian Schneeberger:
  findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies.550-557
• 
  Shubham Chandak,Kedar Tatwawadi,Tsachy Weissman:
  Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis.558-567

Sequence Analysis

• 
  Prashant Pandey,Michael A. Bender,Rob Johnson,Rob Patro:
  Squeakr: an exact and approximate k-mer counting system.568-575
• 
  Taikai Takeda,Michiaki Hamada:
  Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm.576-584
• 
  Pierre Pericard,Yoann Dufresne,Loïc Couderc,Samuel Blanquart,Hélène Touzet:
  MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.585-591

Structural Bioinformatics

• 
  Manuel Alejandro Marín-López,Joan Planas-Iglesias,Joaquim Aguirre-Plans,Jaume Bonet,Javier García-García,Narcis Fernandez-Fuentes,Baldo Oliva:
  On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.592-598
• 
  Stanislav A. Bondarev,Olga V. Bondareva,Galina A. Zhouravleva,Andrey V. Kajava:
  BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures.599-608
• 
  Jasmin Cevost,Cédric Vaillant,Sam Meyer:
  ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes.609-616

Gene expression

• 
  Y. X. Rachel Wang,Ke Liu,Elizabeth Theusch,Jerome I. Rotter,Marisa W. Medina,Michael S. Waterman,Haiyan Huang:
  Generalized correlation measure using count statistics for gene expression data with ordered samples.617-624
• 
  Angela Serra,Pietro Coretto,Michele Fratello,Roberto Tagliaferri:
  Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data.625-634

Genetics and Population Analysis

• 
  Xiayuan Huang,Robert C. Elston,Guilherme J. M. Rosa,John Mayer,Zhan Ye,Terrie E. Kitchner,Murray H. Brilliant,David Page,Scott J. Hebbring:
  Applying family analyses to electronic health records to facilitate genetic research.635-642
• 
  Jun Chen,Emily King,Rebecca Deek,Zhi Wei,Yue Yu,Diane E. Grill,Karla V. Ballman:
  An omnibus test for differential distribution analysis of microbiome sequencing data.643-651

Data and Text Mining

• 
  Jake Lever,Sitanshu Gakkhar,Michael Gottlieb,Tahereh Rashnavadi,Santina Lin,Celia Siu,Maia Smith,Martin R. Jones,Martin Krzywinski,Steven J. M. Jones:
  A collaborative filtering-based approach to biomedical knowledge discovery.652-659

Databases and Ontologies

• 
  Maxat Kulmanov,Mohammad Asif Khan,Robert Hoehndorf:
  DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.660-668

Applications Notes
Genome Analysis

• 
  Rachel C. W. Chan,Maxwell W. Libbrecht,Eric G. Roberts,Jeffrey A. Bilmes,William Stafford Noble,Michael M. Hoffman:
  Segway 2.0: Gaussian mixture models and minibatch training.669-671
• 
  Caleb A. Lareau,Martin J. Aryee:
  diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.672-674
• 
  Anandashankar Anil,Rapolas Spalinskas,Örjan Åkerborg,Pelin Sahlén:
  HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.675-677
• 
  Michael Molnar,Ehsan Haghshenas,Lucian Ilie:
  SAGE2: parallel human genome assembly.678-680
• 
  Lianming Du,Chi Zhang,Qin Liu,Xiuyue Zhang,Bisong Yue:
  Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design.681-683

Sequence Analysis

• 
  Jiangning Song,Fuyi Li,André Leier,Tatiana T. Marquez-Lago,Tatsuya Akutsu,Gholamreza Haffari,Kuo-Chen Chou,Geoffrey I. Webb,Robert N. Pike:
  PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.684-687
• 
  Marie-Elisa Pinson,Romain Pogorelcnik,Franck Court,Philippe Arnaud,Catherine Vaurs-Barrière:
  CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data.688-690

Gene expression

• 
  Charlotte Soneson,Mark D. Robinson:
  Towards unified quality verification of synthetic count data with countsimQC.691-692

Proteomics

• 
  Sohrab Saraei,Tomi Suomi,Otto Kauko,Laura L. Elo:
  Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics.693-694

Systems Biology

• 
  Erin M. Shockley,Jasper A. Vrugt,Carlos F. Lopez:
  PyDREAM: high-dimensional parameter inference for biological models in python.695-697
• 
  Nozomu Sakurai,Takafumi Narise,Joon-Soo Sim,Chang-Muk Lee,Chiaki Ikeda,Nayumi Akimoto,Shigehiko Kanaya:
  UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics.698-700
• 
  Karan Uppal,Chunyu Ma,Young-Mi Go,Dean P. Jones:
  xMWAS: a data-driven integration and differential network analysis tool.701-702
• 
  Charles Tapley Hoyt,Andrej Konotopez,Christian Ebeling:
  PyBEL: a computational framework for Biological Expression Language.703-704
• 
  Paul Stapor,Daniel Weindl,Benjamin Ballnus,Sabine Hug,Carolin Loos,Anna Fiedler,Sabrina Krause,Sabrina Hross,Fabian Fröhlich,Jan Hasenauer:
  PESTO: Parameter EStimation TOolbox.705-707

Data and Text Mining

• 
  Xiaosan Huang,Shaoling Zhang,Kongqing Li,Jyothi Thimmapuram,Shaojun Xie:
  ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data.708-709
• 
  Alexey Lagunin,Anastasia V. Rudik,Dmitry S. Druzhilovskiy,Dmitry Filimonov,Vladimir Poroikov:
  ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction.710-712

Databases and Ontologies

• 
  Nathan W. Wong,Yuhao Chen,Shuai Chen,Xiaowei Wang:
  OncomiR: an online resource for exploring pan-cancer microRNA dysregulation.713-715
• 
  Florian Auer,Zaynab Hammoud,Alexandr Ishkin,Dexter Pratt,Trey Ideker,Frank Kramer:
  ndexr - an R package to interface with the network data exchange.716-717

Bioimage Informatics

• 
  Michaël Barbier,Astrid Bottelbergs,Rony Nuydens,Andreas Ebneth,Winnok De Vos:
  SliceMap: an algorithm for automated brain region annotation.718-720

Volume 34, Number 5, March 2018

Discovery note
Sequence Analysis

• 
  Luis Sánchez-Pulido,Chris P. Ponting:
  TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules.721-724

Original Papers
Genome Analysis

• 
  Sarah Yeo,Lauren Coombe,René L. Warren,Justin Chu,Inanç Birol:
  ARCS: scaffolding genome drafts with linked reads.725-731
• 
  Qiao Liu,Fei Xia,Qijin Yin,Rui Jiang:
  Chromatin accessibility prediction via a hybrid deep convolutional neural network.732-738

Sequence Analysis

• 
  Lu Zhao,Zhimin Liu,Sasha F. Levy,Song Wu:
  Bartender: a fast and accurate clustering algorithm to count barcode reads.739-747
• 
  Kresimir Krizanovic,Amina Echchiki,Julien Roux,Mile Sikic:
  Evaluation of tools for long read RNA-seq splice-aware alignment.748-754
• 
  Alejandro A. Schäffer,Eric P. Nawrocki,Yoon Choi,Paul A. Kitts,Ilene Karsch-Mizrachi,Richard McVeigh:
  VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening.755-759
• 
  Yu Li,Sheng Wang,Ramzan Umarov,Bingqing Xie,Ming Fan,Lihua Li,Xin Gao:
  DEEPre: sequence-based enzyme EC number prediction by deep learning.760-769

Structural Bioinformatics

• 
  Kei Terayama,Hiroaki Iwata,Mitsugu Araki,Yasushi Okuno,Koji Tsuda:
  Machine learning accelerates MD-based binding pose prediction between ligands and proteins.770-778
• 
  Yunhui Peng,Lexuan Sun,Zhe Jia,Lin Li,Emil Alexov:
  Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.779-786

Genetics and Population Analysis

• 
  Cynthia A. Kalita,Gregory A. Moyerbrailean,Christopher Brown,Xiaoquan Wen,Francesca Luca,Roger Pique-Regi:
  QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.787-794

Systems Biology

• 
  Xuan Guo,Zhou Li,Qiuming Yao,Ryan S. Mueller,Jimmy K. Eng,David L. Tabb,IV William Judson Hervey,Chongle Pan:
  Sipros Ensemble improves database searching and filtering for complex metaproteomics.795-802
• 
  Bram Thijssen,Tjeerd Dijkstra,Tom Heskes,Lodewyk F. A. Wessels:
  Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates.803-811
• 
  Yu-An Huang,Keith C. C. Chan,Zhu-Hong You:
  Constructing prediction models from expression profiles for large scale lncRNA-miRNA interaction profiling.812-819

Data and Text Mining

• 
  Jinglong Niu,Yan Shi,Maolin Cai,Zhixin Cao,Dandan Wang,Zhaozhi Zhang,Xiaohua Douglas Zhang:
  Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques.820-827
• 
  Yijia Zhang,Wei Zheng,Hongfei Lin,Jian Wang,Zhihao Yang,Michel Dumontier:
  Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths.828-835
• 
  Ramón Díaz-Uriarte:
  Cancer progression models and fitness landscapes: a many-to-many relationship.836-844

Bioimage Informatics

• 
  Blazej Ruszczycki,Tytus Bernas:
  Quality of biological images, reconstructed using localization microscopy data.845-852
• 
  Renmin Han,Fa Zhang,Xin Gao:
  A fast fiducial marker tracking model for fully automatic alignment in electron tomography.853-863

Applications Notes
Genome Analysis

• 
  Markus Hollander,Mohamed Hamed,Volkhard Helms,Kerstin Neininger:
  MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks.864-866
• 
  Brent S. Pedersen,Aaron R. Quinlan:
  Mosdepth: quick coverage calculation for genomes and exomes.867-868

Sequence Analysis

• 
  Sergio Díaz Del Pino,Juan Falgueras Cano,Esteban Pérez-Wohlfeil,Oswaldo Trelles:
  mORCA: sailing bioinformatics world with mobile devices.869-870
• 
  Marco Beccuti,Francesca Cordero,Maddalena Arigoni,Riccardo Panero,Elvio Gilberto Amparore,Susanna Donatelli,Raffaele A. Calogero:
  SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.871-872
• 
  Minh Duc Cao,Devika Ganesamoorthy,Chenxi Zhou,Lachlan J. M. Coin:
  Simulating the dynamics of targeted capture sequencing with CapSim.873-874

Structural Bioinformatics

• 
  Soundhararajan Gopi,Devanshu Devanshu,Praveen Krishna,Athi N. Naganathan:
  pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration.875-877
• 
  Daniele Toti,Le Viet Hung,Valentina Tortosa,Valentina Brandi,Fabio Polticelli:
  LIBRA-WA: a web application for ligand binding site detection and protein function recognition.878-880

Gene expression

• 
  Jinting Guan,Moliang Chen,Congting Ye,James J. Cai,Guoli Ji:
  AEGS: identifying aberrantly expressed gene sets for differential variability analysis.881-883
• 
  Krzysztof Polanski,Bo Gao,Sam A. Mason,Paul Brown,Sascha Ott,Katherine J. Denby,David L. Wild:
  Bringing numerous methods for expression and promoter analysis to a public cloud computing service.884-886

Genetics and Population Analysis

• 
  Mitchell J. Machiela,Stephen J. Chanock:
  LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation.887-889

Systems Biology

• 
  Andrea Rodriguez-Martinez,Joram M. Posma,Rafael Ayala,Ana Luísa Neves,Maryam Anwar,Enrico Petretto,Costanza Emanueli,Dominique Gauguier,Jeremy K. Nicholson,Marc-Emmanuel Dumas:
  MWASTools: an R/bioconductor package for metabolome-wide association studies.890-892
• 
  Manuel Pájaro,Irene Otero-Muras,Carlos Vázquez,Antonio A. Alonso:
  SELANSI: a toolbox for simulation of stochastic gene regulatory networks.893-895

Data and Text Mining

• 
  Simon Dirmeier,Christiane Fuchs,Nikola S. Müller,Fabian J. Theis:
  netReg: network-regularized linear models for biological association studies.896-898

Bioimage Informatics

• 
  Kyle I. S. Harrington,Curtis T. Rueden,Kevin W. Eliceiri:
  FunImageJ: a Lisp framework for scientific image processing.899-900

Volume 34, Number 6, March 2018

Original Papers
Genome Analysis

• 
  Zaixiang Tang,Yueping Shen,Yan Li,Xinyan Zhang,Jia Wen,Chen'ao Qian,Wenzhuo Zhuang,Xinghua Shi,Nengjun Yi:
  Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information.901-910
• 
  Vida Ravanmehr,Minji Kim,Zhiying Wang,Olgica Milenkovic:
  ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.911-919
• 
  Bethany Signal,Brian S. Gloss,Marcel E. Dinger,Tim R. Mercer:
  Machine learning annotation of human branchpoints.920-927
• 
  Altti Ilari Maarala,Zurab Bzhalava,Joakim Dillner,Keijo Heljanko,Davit Bzhalava:
  ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.928-935
• 
  Clinton L. Cario,John S. Witte:
  Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations.936-942

Sequence Analysis

• 
  Akshay Kumar Avvaru,Divya Tej Sowpati,Rakesh Kumar Mishra:
  PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences.943-948

Structural Bioinformatics

• 
  Claire Marks,Jiye Shi,Charlotte M. Deane:
  Predicting loop conformational ensembles.949-956
• 
  Roman R. Kapaev,Philip V. Toukach:
  GRASS: semi-automated NMR-based structure elucidation of saccharides.957-963

Gene expression

• 
  Manuel Sanchez-Castillo,David Blanco,Isabel M. Tienda-Luna,Maria Carmen Carrion Perez,Yufei Huang:
  A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data.964-970
• 
  Matthew M. Parks:
  An exact test for comparing a fixed quantitative property between gene sets.971-977

Genetics and Population Analysis

• 
  Weiqi Tang,Likun Huang,Suhong Bu,Xuzhang Zhang,Weiren Wu:
  Estimation of QTL heritability based on pooled sequencing data.978-984

Systems Biology

• 
  Lichy Han,Mateusz Maciejewski,Christoph Brockel,William Gordon,Scott B. Snapper,Joshua R. Korzenik,Lovisa Afzelius,Russ B. Altman:
  A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease.985-993
• 
  Malte Lücken,M. J. T. Page,A. J. Crosby,S. Mason,Gesine Reinert,Charlotte M. Deane:
  CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.994-1000

Data and Text Mining

• 
  Somrudee Deepaisarn,Paul D. Tar,Neil A. Thacker,A. Seepujak,A. W. McMahon:
  Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra.1001-1008
• 
  Jérôme Mariette,Nathalie Villa-Vialaneix:
  Unsupervised multiple kernel learning for heterogeneous data integration.1009-1015

Databases and Ontologies

• 
  Sergio Castillo-Lara,Josep F. Abril:
  PlanNET: homology-based predicted interactome for multiple planarian transcriptomes.1016-1023

Bioimage Informatics

• 
  Jun Cheng,Xiaokui Mo,Xusheng Wang,Anil Parwani,Qianjin Feng,Kun Huang:
  Identification of topological features in renal tumor microenvironment associated with patient survival.1024-1030

Applications Notes
Genome Analysis

• 
  Lucas Lochovsky,Jing Zhang,Mark Gerstein:
  MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.1031-1033
• 
  Dorota H. Sendorek,Emilie Lalonde,Cindy Q. Yao,Veronica Y. Sabelnykova,Robert G. Bristow,Paul C. Boutros:
  NanoStringNormCNV: pre-processing of NanoString CNV data.1034-1036
• 
  Yasuhiro Tanizawa,Takatomo Fujisawa,Yasukazu Nakamura:
  DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.1037-1039
• 
  Lauro Ângelo Gonçalves de Moraes,Érica Barbosa Felestrino,Renata de Almeida Barbosa Assis,Diogo Matos,Joubert de Castro Lima,Leandro de Araújo Lima,Nalvo F. de Almeida Jr.,João Carlos Setubal,Camila Carrião Machado Garcia,Leandro Márcio Moreira:
  TabPath: interactive tables for metabolic pathway analysis.1040-1042
• 
  Antonio Carvajal-Rodríguez:
  Myriads: P-value-based multiple testing correction.1043-1045
• 
  Tong Liu,Zheng Wang:
  scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data.1046-1047

Sequence Analysis

• 
  Antonio Solano-Román,Verónica Alfaro-Arias,Carlos Cruz-Castillo,Allan Orozco-Solano:
  Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.1048-1049

Phylogenetics

• 
  Brian D. Piccolo,Umesh D. Wankhade,Sree V. Chintapalli,Sudeepa Bhattacharyya,Luo Chunqiao,Kartik Shankar:
  Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.1050-1052
• 
  Stilianos Louca,Michael Doebeli:
  Efficient comparative phylogenetics on large trees.1053-1055
• 
  Sarah Bastkowski,Daniel Mapleson,Andreas Spillner,Taoyang Wu,Monika Balvociute,Vincent Moulton:
  SPECTRE: a suite of phylogenetic tools for reticulate evolution.1056-1057

Structural Bioinformatics

• 
  Marco Pietrosanto,Marta Adinolfi,Riccardo Casula,Gabriele Ausiello,Fabrizio Ferrè,Manuela Helmer-Citterich:
  BEAM web server: a tool for structural RNA motif discovery.1058-1060
• 
  Andrei L. Lomize,Jacob M. Hage,Irina D. Pogozheva:
  Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers.1061-1062
• 
  Lim Heo,Michael Feig:
  PREFMD: a web server for protein structure refinement via molecular dynamics simulations.1063-1065

Gene expression

• 
  Gero Doose,Stephan H. Bernhart,Rabea Wagener,Steve Hoffmann:
  DIEGO: detection of differential alternative splicing using Aitchison's geometry.1066-1068

Genetics and Population Analysis

• 
  Tim Carver,Alex P. Cunningham,Chantal Babb de Villiers,Andrew Lee,Simon Hartley,Marc Tischkowitz,Fiona M. Walter,Douglas F. Easton,Antonis C. Antoniou:
  pedigreejs: a web-based graphical pedigree editor.1069-1071
• 
  Richard H. Adams,Drew R. Schield,Daren C. Card,Andrew Corbin,Todd A. Castoe:
  ThetaMater: Bayesian estimation of population size parameter θ from genomic data.1072-1073

Databases and Ontologies

• 
  Sandy S. Pineda,Pierre-Alain Chaumeil,Anne Kunert,Quentin Kaas,Mike W. C. Thang,Lien Le,Michael Nuhn,Volker Herzig,Natalie J. Saez,Ben Cristofori-Armstrong,Raveendra Anangi,Sebastian Senff,Dominique Gorse,Glenn F. King:
  ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.1074-1076
• 
  Jeongbin Park,Sangsu Bae:
  Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1.1077-1079

Volume 34, Number 7, April 2018

Discovery note
Genome Analysis

• 
  Jana Cechová,Jirí Lýsek,Martin Bartas,Václav Brázda:
  Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.1081-1085

Original Papers
Genome Analysis

• 
  Minjeong Kim,Jai-Hoon Kim,Kangseok Kim,Sunshin Kim:
  Cost-effective and accurate method of measuring fetal fraction using SNP imputation.1086-1091

Sequence Analysis

• 
  Reda Rawi,Raghvendra Mall,Khalid Kunji,Chen-Hsiang Shen,Peter D. Kwong,Gwo-Yu Chuang:
  PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine.1092-1098
• 
  Rui Guo,Yan-Ran Li,Shan He,Le Ou-Yang,Yiwen Sun,Zexuan Zhu:
  RepLong: de novo repeat identification using long read sequencing data.1099-1107
• 
  Kuan-Chieh Tseng,Yi-Fan Chiang-Hsieh,Hsuan Pai,Chi-Nga Chow,Shu-Chuan Lee,Han-Qin Zheng,Po-Li Kuo,Guan-Zhen Li,Yu-Cheng Hung,Na-Sheng Lin,Wen-Chi Chang:
  microRPM: a microRNA prediction model based only on plant small RNA sequencing data.1108-1115
• 
  Anne Hoffmann,Jörg Fallmann,Elisa Vilardo,Mario Mörl,Peter F. Stadler,Fabian Amman:
  Accurate mapping of tRNA reads.1116-1124
• 
  Samarth Rangavittal,Robert S. Harris,Monika Cechova,Marta Tomaszkiewicz,Rayan Chikhi,Kateryna D. Makova,Paul Medvedev:
  RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.1125-1131

Structural Bioinformatics

• 
  Saulo Henrique Pires de Oliveira,Eleanor C. Law,Jiye Shi,Charlotte M. Deane:
  Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.1132-1140

Gene expression

• 
  Haidong Yi,Ayush T. Raman,Han Zhang,Genevera I. Allen,Zhandong Liu:
  Detecting hidden batch factors through data-adaptive adjustment for biological effects.1141-1147
• 
  Phan Nguyen,Rosemary Braun:
  Semi-supervised network inference using simulated gene expression dynamics.1148-1156

Genetics and Population Analysis

• 
  Peizhou Liao,Glen A. Satten,Yi-Juan Hu:
  Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing.1157-1163

Systems Biology

• 
  Rawan S. Olayan,Haitham Ashoor,Vladimir B. Bajic:
  DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches.1164-1173
• 
  Carlos Ramírez,Luis Mendoza:
  Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network.1174-1182
• 
  Andrei A. Ivanov,Brian Revennaugh,Lauren Rusnak,Valentina Gonzalez-Pecchi,Xiulei Mo,Margaret A. Johns,Yuhong Du,Lee A. D. Cooper,Carlos Sanchez Moreno,Fadlo R. Khuri,Haian Fu:
  The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery.1183-1191

Data and Text Mining

• 
  Pengyuan Li,Xiangying Jiang,Chandra Kambhamettu,Hagit Shatkay:
  Compound image segmentation of published biomedical figures.1192-1199

Databases and Ontologies

• 
  Fritz Lekschas,Nils Gehlenborg:
  SATORI: a system for ontology-guided visual exploration of biomedical data repositories.1200-1207
• 
  Antonio Fabregat,Konstantinos Sidiropoulos,Guilherme Viteri,Pablo Marín-García,Peipei Ping,Lincoln Stein,Peter D'Eustachio,Henning Hermjakob:
  Reactome diagram viewer: data structures and strategies to boost performance.1208-1214

Bioimage Informatics

• 
  Jens Behrmann,Christian Etmann,Tobias Boskamp,Rita Casadonte,Jörg Kriegsmann,Peter Maaß:
  Deep learning for tumor classification in imaging mass spectrometry.1215-1223

Applications Notes
Genome Analysis

• 
  Pierre Lindenbaum,Richard Redon:
  bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.1224-1225
• 
  Thomas Cokelaer,Elisabeth Chen,Francesco Iorio,Michael P. Menden,Howard Lightfoot,Julio Saez-Rodriguez,Mathew Garnett:
  GDSCTools for mining pharmacogenomic interactions in cancer.1226-1228
• 
  Yiming Yu,Yidan Ouyang,Wen Yao:
  shinyCircos: an R/Shiny application for interactive creation of Circos plot.1229-1231

Sequence Analysis

• 
  Sunguk Shin,Hanna Lee,Hyeonju Son,Soonmyung Paik,Sangwoo Kim:
  AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing.1232-1234
• 
  Lauren J. McIver,Galeb Abu-Ali,Eric A. Franzosa,Randall Schwager,Xochitl C. Morgan,Levi Waldron,Nicola Segata,Curtis Huttenhower:
  bioBakery: a meta'omic analysis environment.1235-1237

Structural Bioinformatics

• 
  Yangyu Huang,Haotian Li,Yi Xiao:
  3dRPC: a web server for 3D RNA-protein structure prediction.1238-1240
• 
  Hai Nguyen,David A. Case,Alexander S. Rose:
  NGLview-interactive molecular graphics for Jupyter notebooks.1241-1242

Gene expression

• 
  Caleb A. Class,Min Jin Ha,Veerabhadran Baladandayuthapani,Kim-Anh Do:
  iDINGO - integrative differential network analysis in genomics with Shiny application.1243-1245
• 
  Caleb Weinreb,Samuel L. Wolock,Allon M. Klein:
  SPRING: a kinetic interface for visualizing high dimensional single-cell expression data.1246-1248

Systems Biology

• 
  Leander Dony,Jonas Mackerodt,Scott Ward,Sarah Filippi,Michael P. H. Stumpf,Juliane Liepe:
  PEITH(Θ): perfecting experiments with information theory in Python with GPU support.1249-1250

Databases and Ontologies

• 
  Justin Nelson,Scott W. Simpkins,Hamid Safizadeh,Sheena C. Li,Jeff S. Piotrowski,Hiroyuki Hirano,Yoko Yashiroda,Hiroyuki Osada,Minoru Yoshida,Charles Boone,Chad L. Myers:
  MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action.1251-1252

Review
Systems Biology

• 
  Mariano Rubiolo,Diego H. Milone,Georgina Stegmayer:
  Extreme learning machines for reverse engineering of gene regulatory networks from expression time series.1253-1260

Volume 34, Number 8, April 2018

Original Papers
Sequence Analysis

• 
  Ziga Avsec,Mohammadamin Barekatain,Jun Cheng,Julien Gagneur:
  Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.1261-1269
• 
  Brittney N. Keel,Bo Deng,Etsuko N. Moriyama:
  MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks.1270-1277
• 
  Nelson Gil,András Fiser:
  Identifying functionally informative evolutionary sequence profiles.1278-1286
• 
  Frédéric Escudié,Lucas Auer,Maria Bernard,Mahendra Mariadassou,Laurent Cauquil,Katia Vidal,Sarah Maman,Guillermina Hernandez-Raquet,Sylvie Combes,Géraldine Pascal:
  FROGS: Find, Rapidly, OTUs with Galaxy Solution.1287-1294

Structural Bioinformatics

• 
  Jie Hou,Badri Adhikari,Jianlin Cheng:
  DeepSF: deep convolutional neural network for mapping protein sequences to folds.1295-1303
• 
  Maciej Antczak,Mariusz Popenda,Tomasz Zok,Michal Zurkowski,Ryszard W. Adamiak,Marta Szachniuk:
  New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.1304-1312

Gene expression

• 
  Zong Miao,Marcus Alvarez,Päivi Pajukanta,Arthur Ko:
  ASElux: an ultra-fast and accurate allelic reads counter.1313-1320
• 
  Sunghwan Kim,Dongwan D. Kang,Zhiguang Huo,Yongseok Park,George C. Tseng:
  Meta-analytic principal component analysis in integrative omics application.1321-1328
• 
  Yan Zhou,Xiang Wan,Baoxue Zhang,Tiejun Tong:
  Classifying next-generation sequencing data using a zero-inflated Poisson model.1329-1335
• 
  Joshua Mayer,Raziur Rahman,Souparno Ghosh,Ranadip Pal:
  Sequential feature selection and inference using multi-variate random forests.1336-1344

Systems Biology

• 
  Wayne B. Hayes,Nil Mamano:
  SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments.1345-1352
• 
  Mehreen Ali,Suleiman A. Khan,Krister Wennerberg,Tero Aittokallio:
  Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach.1353-1362
• 
  Shyam Srinivasan,William R. Cluett,Radhakrishnan Mahadevan:
  Model-based design of bistable cell factories for metabolic engineering.1363-1371

Data and Text Mining

• 
  Ine Melckenbeeck,Pieter Audenaert,Didier Colle,Mario Pickavet:
  Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations.1372-1380
• 
  Ling Luo,Zhihao Yang,Pei Yang,Yin Zhang,Lei Wang,Hongfei Lin,Jian Wang:
  An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition.1381-1388
• 
  Axel J. Soto,Chrysoula Zerva,Riza Batista-Navarro,Sophia Ananiadou:
  LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models.1389-1397

Applications Notes
Genome Analysis

• 
  Gabriel Renaud:
  glactools: a command-line toolset for the management of genotype likelihoods and allele counts.1398-1400
• 
  Jasper J. Koehorst,Jesse C. J. van Dam,Edoardo Saccenti,Vítor A. P. Martins dos Santos,María Suárez-Diez,Peter J. Schaap:
  SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.1401-1403
• 
  Askarbek N. Orakov,Nazgul Sakenova,Anatoly A. Sorokin,Igor Goryanin:
  ASAR: visual analysis of metagenomes in R.1404-1405
• 
  Katherine J. Harrison,Valérie de Crécy-Lagard,Rémi Zallot:
  Gene Graphics: a genomic neighborhood data visualization web application.1406-1408
• 
  Bixia Tang,Feifei Li,Jing Li,Wenming Zhao,Zhihua Zhang:
  Delta: a new web-based 3D genome visualization and analysis platform.1409-1410

Sequence Analysis

• 
  Nick Weber,David Liou,Jennifer Dommer,Philip MacMenamin,Mariam Quiñones,Ian Misner,Andrew J. Oler,Joe Wan,Lewis Kim,Meghan Coakley McCarthy,Samuel Ezeji,Karlynn Noble,Darrell E. Hurt:
  Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.1411-1413
• 
  Osvaldo Graña,Hugo López-Fernández,Florentino Fdez-Riverola,David G. Pisano,Daniel Glez-Peña:
  Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.1414-1415

Gene expression

• 
  Mattia Chiesa,Gualtiero I. Colombo,Luca Piacentini:
  DaMiRseq - an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification.1416-1418

Genetics and Population Analysis

• 
  Robert Kofler:
  SimulaTE: simulating complex landscapes of transposable elements of populations.1419-1420

Systems Biology

• 
  Thomas S. Ligon,Fabian Fröhlich,Oana Chis,Julio R. Banga,Eva Balsa-Canto,Jan Hasenauer:
  GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.1421-1423
• 
  Tom Warnke,Tobias Helms,Adelinde M. Uhrmacher:
  Reproducible and flexible simulation experiments with ML-Rules and SESSL.1424-1427
• 
  Lin Wu,Min Li,Jianxin Wang,Fang-Xiang Wu:
  CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis.1428-1430

Data and Text Mining

• 
  Alba Gutiérrez-Sacristán,Romain Guedj,Gabor Korodi,Jason Stedman,Laura Inés Furlong,Chirag J. Patel,Isaac S. Kohane,Paul Avillach:
  Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.1431-1432

Databases and Ontologies

• 
  Daniel Probst,Jean-Louis Reymond:
  FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web.1433-1435
• 
  Andrew Palmer,Prasad Phapale,Dominik Fay,Theodore Alexandrov:
  Curatr: a web application for creating, curating and sharing a mass spectral library.1436-1438

Corrigendum
Databases and Ontologies

• 
  Robert Kofler:
  SimulaTE: simulating complex landscapes of transposable elements of populations.1439

Erratum
Databases and Ontologies

• 
  Xing Chen,Yu-An Huang,Zhu-Hong You,Guiying Yan,Xuesong Wang:
  A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases.1440

Volume 34, Number 9, May 2018

Original Papers
Genome Analysis

• 
  Cristina Mitrea,Priyanga Wijesinghe,Gregory Dyson,Adéle Kruger,Douglas M. Ruden,Sorin Draghici,Aliccia Bollig-Fischer:
  Integrating 5hmC and gene expression data to infer regulatory mechanisms.1441-1447

Sequence Analysis

• 
  Xiang Cheng,Xuan Xiao,Kuo-Chen Chou:
  pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information.1448-1456
• 
  Liren Huang,Jan Krüger,Alexander Sczyrba:
  Analyzing large scale genomic data on the cloud with Sparkhit.1457-1465

Structural Bioinformatics

• 
  Badri Adhikari,Jie Hou,Jianlin Cheng:
  DNCON2: improved protein contact prediction using two-level deep convolutional neural networks.1466-1472
• 
  Yuliang Pan,Zixiang Wang,Weihua Zhan,Lei Deng:
  Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.1473-1480
• 
  S. M. Ashiqul Islam,Benjamin J. Heil,Christopher Michel Kearney,Erich J. Baker:
  Protein classification using modified n-grams and skip-grams.1481-1487

Gene expression

• 
  Scott S. Norton,Jorge Vaquero-Garcia,Nicholas F. Lahens,Gregory R. Grant,Yoseph Barash:
  Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.1488-1497
• 
  Francesco Napolitano,Diego Carrella,Barbara Mandriani,Sandra Pisonero-Vaquero,Francesco Sirci,Diego L. Medina,Nicola Brunetti-Pierri,Diego di Bernardo:
  gene2drug: a computational tool for pathway-based rational drug repositioning.1498-1505

Genetics and Population Analysis

• 
  Andriy Derkach,Haoyu Zhang,Nilanjan Chatterjee:
  Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies.1506-1513

Systems Biology

• 
  Mitra Ansariola,Molly Megraw,David Koslicki:
  IndeCut evaluates performance of network motif discovery algorithms.1514-1521
• 
  Massimo Andreatta,Thomas Trolle,Zhen Yan,Jason A. Greenbaum,Bjoern Peters,Morten Nielsen:
  An automated benchmarking platform for MHC class II binding prediction methods.1522-1528

Data and Text Mining

• 
  Guangyuan Fu,Jun Wang,Carlotta Domeniconi,Guoxian Yu:
  Matrix factorization-based data fusion for the prediction of lncRNA-disease associations.1529-1537
• 
  Kristina Preuer,Richard P. I. Lewis,Sepp Hochreiter,Andreas Bender,Krishna C. Bulusu,Günter Klambauer:
  DeepSynergy: predicting anti-cancer drug synergy with Deep Learning.1538-1546
• 
  Qile Zhu,Xiaolin Li,Ana Conesa,Cécile Pereira:
  GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text.1547-1554
• 
  Zhuxuan Jin,Jian Kang,Tianwei Yu:
  Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations.1555-1561

Applications Notes
Genome Analysis

• 
  Alan M. Cleary,Andrew D. Farmer:
  Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny.1562-1564
• 
  Jacob M. Luber,Braden T. Tierney,Evan M. Cofer,Chirag J. Patel,Aleksandar D. Kostic:
  Aether: leveraging linear programming for optimal cloud computing in genomics.1565-1567
• 
  Xiaobin Zheng,Yixian Zheng:
  CscoreTool: fast Hi-C compartment analysis at high resolution.1568-1570
• 
  Xiao-Fei Zhang,Le Ou-Yang,Shuo Yang,Xiaohua Hu,Hong Yan:
  DiffGraph: an R package for identifying gene network rewiring using differential graphical models.1571-1573

Sequence Analysis

• 
  Xuan Ma,Chunyan Liu,Lian-Feng Gu,Beixin Mo,Xiaofeng Cao,Xuemei Chen:
  TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants.1574-1576
• 
  Duong Vu,Sonja Georgievska,Szaniszlo Szoke,Arnold Kuzniar,Vincent Robert:
  fMLC: fast multi-level clustering and visualization of large molecular datasets.1577-1579
• 
  Yubang Gao,Huiyuan Wang,Hangxiao Zhang,Yongsheng Wang,Jinfeng Chen,Lian-Feng Gu:
  PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.1580-1582
• 
  Dmitry A. Suplatov,Kirill E. Kopylov,Nina N. Popova,Vladimir V. Voevodin,Vytas K. Svedas:
  Mustguseal: a server for multiple structure-guided sequence alignment of protein families.1583-1585

Structural Bioinformatics

• 
  Woonghee Lee,John L. Markley:
  PINE-SPARKY.2 for automated NMR-based protein structure research.1586-1588

Gene expression

• 
  Hajk-Georg Drost,Alexander Gabel,Jialin Liu,Marcel Quint,Ivo Grosse:
  myTAI: evolutionary transcriptomics with R.1589-1590

Genetics and Population Analysis

• 
  Khalid Kunji,Ehsan Ullah,Alejandro Q. Nato,Ellen M. Wijsman,Mohamad Saad:
  GIGI-Quick: a fast approach to impute missing genotypes in genome-wide association family data.1591-1593

Systems Biology

• 
  Brendan King,Terry Farrah,Matthew A. Richards,Michael B. Mundy,Evangelos Simeonidis,Nathan D. Price:
  ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions.1594-1596
• 
  Min Li,Jie Yang,Fang-Xiang Wu,Yi Pan,Jianxin Wang:
  DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization.1597-1599

Data and Text Mining

• 
  Tal Galili,Alan O'Callaghan,Jonathan Sidi,Carson Sievert:
  heatmaply: an R package for creating interactive cluster heatmaps for online publishing.1600-1602
• 
  Anbo Zhou,Yeting Zhang,Yazhou Sun,Jinchuan Xing:
  PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool.1603-1605
• 
  Tasnia Tahsin,Davy Weissenbacher,Karen O'Connor,Arjun Magge,Matthew Scotch,Graciela Gonzalez-Hernandez:
  GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.1606-1608
• 
  Xiaohua Douglas Zhang,Zhaozhi Zhang,Dandan Wang:
  CGManalyzer: an R package for analyzing continuous glucose monitoring studies.1609-1611

Databases and Ontologies

• 
  Aziz Khan,Anthony Mathelier:
  JASPAR RESTful API: accessing JASPAR data from any programming language.1612-1614
• 
  Lin Wei,Zhilin Jin,Shengjie Yang,Yanxun Xu,Yitan Zhu,Yuan Ji:
  TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data.1615-1617
• 
  Yuhan Fei,Rui Wang,Haoyuan Li,Shu Liu,Hongsheng Zhang,Ji Huang:
  DPMIND: degradome-based plant miRNA-target interaction and network database.1618-1620

Volume 34, Number 10, May 2018

Original Papers
Genome Analysis

• 
  Tobias Fehlmann,Christina Backes,Julia Alles,Ulrike Fischer,Martin Hart,Fabian Kern,Hilde Langseth,Trine Rounge,Sinan Ugur Umu,Mustafa Kahraman,Thomas Laufer,Jan Haas,Cord Staehler,Nicole Ludwig,Matthias Hübenthal,Benjamin Meder,Andre Franke,Hans-Peter Lenhof,Eckart Meese,Andreas Keller:
  A high-resolution map of the human small non-coding transcriptome.1621-1628
• 
  Athanasios Gaitatzes,Sarah H. Johnson,James B. Smadbeck,George Vasmatzis:
  Genome U-Plot: a whole genome visualization.1629-1634
• 
  Damien Drubay,Daniel Gautheret,Stefan Michiels:
  A benchmark study of scoring methods for non-coding mutations.1635-1641
• 
  Matteo Benelli,Dario Romagnoli,Francesca Demichelis:
  Tumor purity quantification by clonal DNA methylation signatures.1642-1649

Sequence Analysis

• 
  Jan Voges,Jörn Ostermann,Mikel Hernaez:
  CALQ: compression of quality values of aligned sequencing data.1650-1658
• 
  Peter Audano,Shashidhar Ravishankar,Fredrik Vannberg:
  Mapping-free variant calling using haplotype reconstruction from k-mer frequencies.1659-1665
• 
  Yang Yang,Katherine E. Niehaus,Timothy M. Walker,Zamin Iqbal,A. Sarah Walker,Daniel J. Wilson,Tim E. A. Peto,Derrick W. Crook,E. Grace Smith,Tingting Zhu,David A. Clifton:
  Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.1666-1671
• 
  Yen-Yi Lin,Alexander Gawronski,Faraz Hach,Sujun Li,Ibrahim Numanagic,Iman Sarrafi,Swati Mishra,Andrew W. McPherson,Colin C. Collins,Milan Radovich,Haixu Tang,Süleyman Cenk Sahinalp:
  Computational identification of micro-structural variations and their proteogenomic consequences in cancer.1672-1681
• 
  Jie Lin,Donald A. Adjeroh,Bing-Hua Jiang,Yue Jiang:
  K2 and K 2 * : efficient alignment-free sequence similarity measurement based on Kendall statistics.1682-1689
• 
  Castrense Savojardo,Pier Luigi Martelli,Piero Fariselli,Rita Casadio:
  DeepSig: deep learning improves signal peptide detection in proteins.1690-1696
• 
  Hamza Khan,Hamid Mohamadi,Benjamin P. Vandervalk,René L. Warren,Justin Chu,Inanç Birol:
  ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.1697-1704
• 
  Juhua Zhang,Wenbo Peng,Lei Wang:
  LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks.1705-1712
• 
  Brian K. Mannakee,Uthra Balaji,Agnieszka K. Witkiewicz,Ryan N. Gutenkunst,Erik S. Knudsen:
  Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors.1713-1718

Structural Bioinformatics

• 
  Runze Dong,Zhenling Peng,Yang Zhang,Jianyi Yang:
  mTM-align: an algorithm for fast and accurate multiple protein structure alignment.1719-1725

Gene expression

• 
  Alyssa Imbert,Armand Valsesia,Caroline Le Gall,Claudia Armenise,Gregory Lefebvre,Pierre-Antoine Gourraud,Nathalie Viguerie,Nathalie Villa-Vialaneix:
  Multiple hot-deck imputation for network inference from RNA sequencing data.1726-1732
• 
  Xi Chen,Jinghua Gu,Xiao Wang,Jin-Gyoung Jung,Tian-Li Wang,Leena Hilakivi-Clarke,Robert Clarke,Jianhua Xuan:
  CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.1733-1740

Genetics and Population Analysis

• 
  Danny Kit-Sang Yip,Landon L. Chan,Iris K. Pang,Wei Jiang,Nelson L. S. Tang,Weichuan Yu,Kevin Y. Yip:
  A network approach to exploring the functional basis of gene-gene epistatic interactions in disease susceptibility.1741-1749

Systems Biology

• 
  Jingpu Zhang,Zuping Zhang,Zixiang Wang,Yuting Liu,Lei Deng:
  Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification.1750-1757

Data and Text Mining

• 
  Constantin Georgescu,Jonathan D. Wren:
  Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values.1758-1766

Bioimage Informatics

• 
  Ching-Wei Wang,Yu-Ching Lee,Evelyne Calista,Fan Zhou,Hongtu Zhu,Ryohei Suzuki,Daisuke Komura,Shumpei Ishikawa,Shih-Ping Cheng:
  A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays.1767-1773

Applications Notes
Genome Analysis

• 
  Danny Antaki,William M. Brandler,Jonathan Sebat:
  SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes.1774-1777
• 
  Sigve Nakken,Ghislain Fournous,Daniel Vodák,Lars Birger Aasheim,Ola Myklebost,Eivind Hovig:
  Personal Cancer Genome Reporter: variant interpretation report for precision oncology.1778-1780
• 
  Yoann Pageaud,Christoph Plass,Yassen Assenov:
  Enrichment analysis with EpiAnnotator.1781-1783

Structural Bioinformatics

• 
  Jaime Rodríguez-Guerra Pedregal,Jean-Didier Maréchal:
  PyChimera: use UCSF Chimera modules in any Python 2.7 project.1784-1785

Genetics and Population Analysis

• 
  Jhih-rong Lin,Daniel Jaroslawicz,Ying Cai,Quanwei Zhang,Zhen Wang,Zhengdong D. Zhang:
  PGA: post-GWAS analysis for disease gene identification.1786-1788

Systems Biology

• 
  Ryne C. Ramaker,Emily R. Gordon,Sara J. Cooper:
  R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R.1789-1791
• 
  Mengci Li,Shouli Wang,Guoxiang Xie,Xiaohui Ma,Tianlu Chen,Wei Jia:
  polyPK: an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach.1792-1794
• 
  Vipin Vijayan,Tijana Milenkovic:
  Aligning dynamic networks with DynaWAVE.1795-1798

Data and Text Mining

• 
  Nilesh R. Tawari,Justine Jia Wen Seow,Dharuman Perumal,Jack L. Ow,Shimin Ang,Arun George Devasia,Pauline C. Ng:
  ChronQC: a quality control monitoring system for clinical next generation sequencing.1799-1800

Volume 34, Number 11, June 2018

Original Papers
Genome Analysis

• 
  Joong Chae Na,Jongchan Lee,Je-Keun Rhee,Soo-Yong Shin:
  PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling.1801-1807
• 
  Paul Deveau,Leo Colmet Daage,Derek Oldridge,Virginie Bernard,Angela Bellini,Mathieu Chicard,Nathalie Clement,Eve Lapouble,Valerie Combaret,Anne Boland,Vincent Meyer,Jean-Francois Deleuze,Isabelle Janoueix-Lerosey,Emmanuel Barillot,Olivier Delattre,John M. Maris,Gudrun Schleiermacher,Valentina Boeva:
  QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.1808-1816
• 
  Chao Ning,Dan Wang,Huimin Kang,Raphael Mrode,Lei Zhou,Shizhong Xu,Jianfeng Liu:
  A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values.1817-1825
• 
  Umberto Ferraro Petrillo,Gianluca Roscigno,Giuseppe Cattaneo,Raffaele Giancarlo:
  Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms.1826-1833
• 
  Agnieszka Danek,Sebastian Deorowicz:
  GTC: how to maintain huge genotype collections in a compressed form.1834-1840
• 
  Congting Ye,Yuqi Long,Guoli Ji,Qingshun Quinn Li,Xiaohui Wu:
  APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data.1841-1849

Sequence Analysis

• 
  Ronesh Sharma,Gaurav Raicar,Tatsuhiko Tsunoda,Ashwini Patil,Alok Sharma:
  OPAL: prediction of MoRF regions in intrinsically disordered protein sequences.1850-1858

Gene expression

• 
  Bahman Afsari,Theresa Guo,Michael Considine,Liliana Florea,Luciane T. Kagohara,Genevieve L. Stein-O'Brien,Dylan Kelley,Emily Flam,Kristina D. Zambo,Patrick K. Ha,Donald Geman,Michael F. Ochs,Joseph A. Califano,Daria A. Gaykalova,Alexander V. Favorov,Elana J. Fertig:
  Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.1859-1867
• 
  Jennifer M. Franks,Guoshuai Cai,Michael L. Whitfield:
  Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data.1868-1874

Genetics and Population Analysis

• 
  Jie Zhang,Zhi Wei,Jun Chen:
  A distance-based approach for testing the mediation effect of the human microbiome.1875-1883

Systems Biology

• 
  Irina M. Armean,Kathryn S. Lilley,Matthew W. B. Trotter,Nicholas Charles Victor Pilkington,Sean B. Holden:
  Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.1884-1892
• 
  Weifeng Guo,Shao-Wu Zhang,Li-Li Liu,Fei Liu,Qianqian Shi,Lei Zhang,Ying Tang,Tao Zeng,Luonan Chen:
  Discovering personalized driver mutation profiles of single samples in cancer by network control strategy.1893-1903
• 
  Huimin Luo,Min Li,Shaokai Wang,Quan Liu,Yaohang Li,Jianxin Wang:
  Computational drug repositioning using low-rank matrix approximation and randomized algorithms.1904-1912
• 
  Clemens Kreutz:
  An easy and efficient approach for testing identifiability.1913-1921

Applications Notes
Genome Analysis

• 
  Thorhildur Juliusdottir,Karina Banasik,Neil R. Robertson,Richard Mott,Mark I. McCarthy:
  Toppar: an interactive browser for viewing association study results.1922-1924
• 
  Chunpeng James Chen,Zhiwu Zhang:
  iPat: intelligent prediction and association tool for genomic research.1925-1927
• 
  Marius Wöste,Martin Dugas:
  VIPER: a web application for rapid expert review of variant calls.1928-1929
• 
  Luca Pinello,Rick Farouni,Guo-Cheng Yuan:
  Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.1930-1933
• 
  Dimitri Desvillechabrol,Rachel Legendre,Claire Rioualen,Christiane Bouchier,Jacques van Helden,Sean Kennedy,Thomas Cokelaer:
  Sequanix: a dynamic graphical interface for Snakemake workflows.1934-1936

Sequence Analysis

• 
  Triinu Koressaar,Maarja Lepamets,Lauris Kaplinski,Kairi Raime,Reidar Andreson,Maido Remm:
  Primer3_masker: integrating masking of template sequence with primer design software.1937-1938
• 
  Peter V. Troshin,James B. Procter,Alexander Sherstnev,Daniel L. Barton,Fábio Madeira,Geoffrey J. Barton:
  JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure.1939-1940

Structural Bioinformatics

• 
  Bernhard Knapp,Marta Alcalá,Hao Zhang,Clare E. West,P. Anton van der Merwe,Charlotte M. Deane:
  pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.1941-1943
• 
  Alejandro Panjkovich,Dmitri I. Svergun:
  CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data.1944-1946
• 
  Lucia Fusani,Ian D. Wall,David Palmer,Álvaro Cortés Cabrera:
  Optimal water networks in protein cavities with GAsol and 3D-RISM.1947-1948
• 
  Juexin Wang,Robert Sheridan,Selçuk Onur Sümer,Nikolaus Schultz,Dong Xu,Jianjiong Gao:
  G2S: a web-service for annotating genomic variants on 3D protein structures.1949-1950

Genetics and Population Analysis

• 
  Corinne E. Sexton,Hayden Z. Smith,Peter D. Newell,Angela E. Douglas,John M. Chaston:
  MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.1951-1952

Systems Biology

• 
  Liang Cheng,Yang Hu,Jie Sun,Meng Zhou,Qinghua Jiang:
  DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function.1953-1956
• 
  Michael J. Dagley,Malcolm J. McConville:
  DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS.1957-1958
• 
  David Amar,Amir Vizel,Carmit Levy,Ron Shamir:
  ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases.1959-1961

Data and Text Mining

• 
  Andon Tchechmedjiev,Amine Abdaoui,Vincent Emonet,Soumia Melzi,Jitendra Jonnagaddala,Clément Jonquet:
  Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+.1962-1965

Bioimage Informatics

• 
  Kim Wong,José Fernández Navarro,Ludvig Bergenstråhle,Patrik L. Ståhl,Joakim Lundeberg:
  ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets.1966-1968

Review
Gene expression

• 
  Francisco Avila Cobos,Jo Vandesompele,Pieter Mestdagh,Katleen De Preter:
  Computational deconvolution of transcriptomics data from mixed cell populations.1969-1979

Corrigendum
Gene expression

• 
  Vipin Vijayan,Tijana Milenkovic:
  Aligning dynamic networks with DynaWAVE.1980

Volume 34, Number 12, June 2018

Discovery note
Structural Bioinformatics

• 
  Gurmeet Kaur,Srikrishna Subramanian:
  Evolutionary relationship between the cysteine and histidine rich domains (CHORDs) and Btk-type zinc fingers.1981-1985

Original Papers
Genome Analysis

• 
  Yuhan Hao,Liying Yang,Antonio Galvao Neto,Milan R. Amin,Dervla Kelly,Stuart M. Brown,Ryan C. Branski,Zhiheng Pei:
  HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA.1986-1995
• 
  Chao Xu,Jian Fang,Hui Shen,Yu-Ping Wang,Hong-Wen Deng:
  EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits.1996-2003
• 
  Zhihui Luo,Xinping Fan,Yao Su,Yu S. Huang:
  Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.2004-2011
• 
  Fei Guo,Dan Wang,Lusheng Wang:
  Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data.2012-2018

Sequence Analysis

• 
  Anqi Wang,Zhanyu Wang,Zheng Li,Lei M. Li:
  BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach.2019-2028
• 
  Cangzhi Jia,Yun Zuo,Quan Zou:
  O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique.2029-2036
• 
  Mindaugas Margelevicius:
  A low-complexity add-on score for protein remote homology search with COMER.2037-2045
• 
  Sung Yong Park,Tanzy M. T. Love,Shivankur Kapoor,Ha Youn Lee:
  HIITE: HIV-1 incidence and infection time estimator.2046-2052

Structural Bioinformatics

• 
  Kamil Tamiola,Ruud M. Scheek,Pieter S. van der Meulen,Frans A. A. Mulder:
  pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides.2053-2060
• 
  Liang Zhao,Shaogui Wu,Jiawen Jiang,Wencui Li,Jie Luo,Jinyan Li:
  Novel overlapping subgraph clustering for the detection of antigen epitopes.2061-2068

Gene expression

• 
  Seyoung Park,Hongyu Zhao:
  Spectral clustering based on learning similarity matrix.2069-2076
• 
  Suoqin Jin,Adam L. Maclean,Tao Peng,Qing Nie:
  scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data.2077-2086

Systems Biology

• 
  Alex J. Cornish,Alessia David,Michael J. E. Sternberg:
  PhenoRank: reducing study bias in gene prioritization through simulation.2087-2095
• 
  Ivan Laponogov,Noureddin Sadawi,Dieter Galea,Reza Mirnezami,Kirill A. Veselkov:
  ChemDistiller: an engine for metabolite annotation in mass spectrometry.2096-2102

Data and Text Mining

• 
  Vishrawas Gopalakrishnan,Kishlay Jha,Guangxu Xun,Hung Q. Ngo,Aidong Zhang:
  Towards self-learning based hypotheses generation in biomedical text domain.2103-2115

Databases and Ontologies

• 
  Thomas A. Darde,Pierre Gaudriault,Rémi Beranger,Clément Lancien,Annaëlle Caillarec-Joly,Olivier Sallou,Nathalie Bonvallot,Cécile Chevrier,Séverine Mazaud-Guittot,Bernard Jégou,Olivier Collin,Emmanuelle Becker,Antoine D. Rolland,Frédéric Chalmel:
  TOXsIgN: a cross-species repository for toxicogenomic signatures.2116-2122

Applications Notes
Genome Analysis

• 
  Guoli Ji,Moliang Chen,Wenbin Ye,Sheng Zhu,Congting Ye,Yaru Su,Haonan Peng,Xiaohui Wu:
  TSAPA: identification of tissue-specific alternative polyadenylation sites in plants.2123-2125
• 
  Eugene Urrutia,Hao Chen,Zilu Zhou,Nancy Ruonan Zhang,Yuchao Jiang:
  Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.2126-2128
• 
  Dapeng Wang:
  GCevobase: an evolution-based database for GC content in eukaryotic genomes.2129-2131

Sequence Analysis

• 
  Alberto Pessia,Jukka Corander:
  Kpax3: Bayesian bi-clustering of large sequence datasets.2132-2133
• 
  Clerk Nuo Xu,Dongfang Fu,Shiang Li,Yuxuan Wang,Aloysius Wong:
  GCPred: a web tool for guanylyl cyclase functional centre prediction from amino acid sequence.2134-2135

Gene expression

• 
  Veer Singh Marwah,Pia Anneli Sofia Kinaret,Angela Serra,Giovanni Scala,Antti Lauerma,Vittorio Fortino,Dario Greco:
  INfORM: Inference of NetwOrk Response Modules.2136-2138

Genetics and Population Analysis

• 
  Hang J. Kim,Zhenning Yu,Andrew Lawson,Hongyu Zhao,Dongjun Chung:
  Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA.2139-2141
• 
  Maarten van Iterson,Davy Cats,Paul Hop,BIOS Consortium,Bastiaan T. Heijmans:
  omicsPrint: detection of data linkage errors in multiple omics studies.2142-2143
• 
  Qi Yan,Zhou Fang,Wei Chen:
  KMgene: a unified R package for gene-based association analysis for complex traits.2144-2146

Systems Biology

• 
  Thierry D. G. A. Mondeel,Frédéric Crémazy,Matteo Barberis:
  GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae.2147-2149
• 
  Zichen Wang,Alexander Lachmann,Alexandra B. Keenan,Avi Ma'ayan:
  L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.2150-2152
• 
  Pablo Carbonell,Jerry Wong,Neil Swainston,Eriko Takano,Nicholas J. Turner,Nigel S. Scrutton,Douglas B. Kell,Rainer Breitling,Jean-Loup Faulon:
  Selenzyme: enzyme selection tool for pathway design.2153-2154
• 
  Nathan Mih,Elizabeth Brunk,Ke Chen,Edward Catoiu,Anand Sastry,Erol S. Kavvas,Jonathan M. Monk,Zhen Zhang,Bernhard O. Palsson:
  ssbio: a Python framework for structural systems biology.2155-2157

Databases and Ontologies

• 
  Thammakorn Saethang,Kenneth Hodge,Ingorn Kimkong,D. Michael Payne,Mark A. Knepper,Trairak Pisitkun:
  AbDesigner3D: a structure-guided tool for peptide-based antibody production.2158-2160

Volume 34, Number 13, July 2018

ISMB 2018 Proceedings July 6 to July 10, 2018, Chicago, IL, United States
Ismb 2018 - Intelligent Systems for molecular Biology Proceedings
Ismb 2018 Proceedings Papers Committee

• 
  ISMB 2018 PROCEEDINGS PAPERS COMMITTEE.i1

ISMB 2018 PROCEEDINGS

• 
  Yana Bromberg,Predrag Radivojac:
  ISMB 2018 proceedings.i2-i3

Bioinformatics Education

• 
  K. Anton Feenstra,Sanne Abeln,Johan A. Westerhuis,Filipe Brancos dos Santos,Douwe Molenaar,Bas Teusink,Huub C. J. Hoefsloot,Jaap Heringa:
  Training for translation between disciplines: a philosophy for life and data sciences curricula.i4-i12

Bioinformatics of Microbes and Microbiomes

• 
  Guillaume Marçais,Dan F. DeBlasio,Carl Kingsford:
  Asymptotically optimal minimizers schemes.i13-i22
• 
  Soyeon Ahn,Ziqi Ke,Haris Vikalo:
  Viral quasispecies reconstruction via tensor factorization with successive read removal.i23-i31
• 
  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.i32-i42

Comparative and Functional genomics

• 
  Weihua Pan,Steve Wanamaker,Audrey M. V. Ah-Fong,Howard S. Judelson,Stefano Lonardi:
  Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.i43-i51
• 
  Fatima Zohra Smaili,Xin Gao,Robert Hoehndorf:
  Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.i52-i60
• 
  Siamak Zamani Dadaneh,Mingyuan Zhou,Xiaoning Qian:
  Covariate-dependent negative binomial factor analysis of RNA sequencing data.i61-i69
• 
  Jean-Pierre Séhi Glouzon,Aïda Ouangraoua:
  aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.i70-i78
• 
  Maziyar Baran Pouyan,Dennis Kostka:
  Random forest based similarity learning for single cell RNA sequencing data.i79-i88
• 
  Hsuan-Lin Her,Yu-Wei Wu:
  A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains.i89-i95
• 
  Jie Liu,Dejun Lin,Galip Gürkan Yardimci,William Stafford Noble:
  Unsupervised embedding of single-cell Hi-C data.i96-i104
• 
  Shilpa Garg,Mikko Rautiainen,Adam M. Novak,Erik Garrison,Richard Durbin,Tobias Marschall:
  A graph-based approach to diploid genome assembly.i105-i114
• 
  Maryam Ghareghani,David Porubsky,Ashley D. Sanders,Sascha Meiers,Evan E. Eichler,Jan O. Korbel,Tobias Marschall:
  Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.i115-i123
• 
  Sumit Mukherjee,Yue Zhang,Joshua Fan,Georg Seelig,Sreeram Kannan:
  Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge.i124-i132
• 
  Ruochi Zhang,Yuchuan Wang,Yang Yang,Yang Zhang,Jian Ma:
  Predicting CTCF-mediated chromatin loops using CTCF-MP.i133-i141
• 
  Alla Mikheenko,Andrey D. Prjibelski,Vladislav Saveliev,Dmitry Antipov,Alexey A. Gurevich:
  Versatile genome assembly evaluation with QUAST-LG.i142-i150

General Computational Biology

• 
  Paul Stapor,Fabian Fröhlich,Jan Hasenauer:
  Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.i151-i159

Genome Privacy and Security

• 
  Bristena Oprisanu,Emiliano De Cristofaro:
  AnoniMME: bringing anonymity to the Matchmaker Exchange platform for rare disease gene discovery.i160-i168
• 
  Fatemeh Almodaresi,Hirak Sarkar,Avi Srivastava,Rob Patro:
  A space and time-efficient index for the compacted colored de Bruijn graph.i169-i177
• 
  Benjamin J. Lengerich,Bryon Aragam,Eric P. Xing:
  Personalized regression enables sample-specific pan-cancer analysis.i178-i186

Genomic variation Analysis

• 
  Yue Wu,Sriram Sankararaman:
  A scalable estimator of SNP heritability for biobank-scale data.i187-i194
• 
  Ruth Johnson,Huwenbo Shi,Bogdan Pasaniuc,Sriram Sankararaman:
  A unifying framework for joint trait analysis under a non-infinitesimal model.i195-i201
• 
  Kendell Clement,Rick Farouni,Daniel E. Bauer,Luca Pinello:
  AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.i202-i210
• 
  Gryte Satas,Benjamin J. Raphael:
  Haplotype phasing in single-cell DNA-sequencing data.i211-i217

Macromolecular sequence, Structure, and function

• 
  Christopher Jürges,Lars Dölken,Florian Erhard:
  Dissecting newly transcribed and old RNA using GRAND-SLAM.i218-i226
• 
  Yixiu Zhao,Xiangrui Zeng,Qiang Guo,Min Xu:
  An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification.i227-i236
• 
  Genta Aoki,Yasubumi Sakakibara:
  Convolutional neural networks for classification of alignments of non-coding RNA sequences.i237-i244
• 
  Yoonjoo Choi,Jacob M. Furlon,Ryan B. Amos,Karl E. Griswold,Chris Bailey-Kellogg:
  DisruPPI: structure-based computational redesign algorithm for protein binding disruption.i245-i253
• 
  Seokjun Seo,Minsik Oh,Youngjune Park,Sun Kim:
  DeepFam: deep learning based alignment-free method for protein family modeling and prediction.i254-i262
• 
  Jianwei Zhu,Sheng Wang,Dongbo Bu,Jinbo Xu:
  Protein threading using residue co-variation and deep learning.i263-i273
• 
  Emmi Jokinen,Markus Heinonen,Harri Lähdesmäki:
  mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion.i274-i283
• 
  Yu Li,Fan Xu,Fa Zhang,Pingyong Xu,Mingshu Zhang,Ming Fan,Lihua Li,Xin Gao,Renmin Han:
  DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy.i284-i294
• 
  Hakime Öztürk,Elif Özkirimli Ölmez,Arzucan Özgür:
  A novel methodology on distributed representations of proteins using their interacting ligands.i295-i303
• 
  Yannick Mahlich,Martin Steinegger,Burkhard Rost,Yana Bromberg:
  HFSP: high speed homology-driven function annotation of proteins.i304-i312
• 
  Yisu Peng,Yuxiang Jiang,Predrag Radivojac:
  Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.i313-i322

Mass spectrometry

• 
  Dai Hai Nguyen,Canh Hao Nguyen,Hiroshi Mamitsuka:
  SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra.i323-i332
• 
  Marcus Ludwig,Kai Dührkop,Sebastian Böcker:
  Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints.i333-i340

Population genomics and molecular Evolution

• 
  Nima Nouri,Steven H. Kleinstein:
  A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.i341-i349
• 
  Edward L. Braun:
  An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins.i350-i356
• 
  Jesse Eaton,Jingyi Wang,Russell Schwartz:
  Deconvolution and phylogeny inference of structural variations in tumor genomic samples.i357-i365
• 
  Manuel Lafond,Mona Meghdari Miardan,David Sankoff:
  Accurate prediction of orthologs in the presence of divergence after duplication.i366-i375
• 
  Jiafan Zhu,Luay Nakhleh:
  Inference of species phylogenies from bi-allelic markers using pseudo-likelihood.i376-i385

Studies of phenotypes and Clinical Applications

• 
  Wenhui Xing,Junsheng Qi,Xiaohui Yuan,Lin Li,Xiaoyu Zhang,Yuhua Fu,Shengwu Xiong,Lun Hu,Jing Peng:
  A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach.i386-i394
• 
  Iiris Sundin,Tomi Peltola,Luana Micallef,Homayun Afrabandpey,Marta Soare,Muntasir Mamun Majumder,Pedram Daee,Chen He,Baris Serim,Aki S. Havulinna,Caroline Heckman,Giulio Jacucci,Pekka Marttinen,Samuel Kaski:
  Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge.i395-i403
• 
  Wensheng Zhang,Erik K. Flemington,Kun Zhang:
  Driver gene mutations based clustering of tumors: methods and applications.i404-i411
• 
  Arezou Rahimi,Mehmet Gönen:
  Discriminating early- and late-stage cancers using multiple kernel learning on gene sets.i412-i421
• 
  Matthew J. McCoy,Alexander J. Paul,Matheus B. Victor,Michelle Richner,Harrison W. Gabel,Haijun Gong,Andrew S. Yoo,Tae-Hyuk Ahn:
  LONGO: an R package for interactive gene length dependent analysis for neuronal identity.i422-i428
• 
  Hannes Bretschneider,Shreshth Gandhi,Amit G. Deshwar,Khalid Zuberi,Brendan J. Frey:
  COSSMO: predicting competitive alternative splice site selection using deep learning.i429-i437
• 
  Christian Bock,Thomas Gumbsch,Michael Moor,Bastian Rieck,Damian Roqueiro,Karsten M. Borgwardt:
  Association mapping in biomedical time series via statistically significant shapelet mining.i438-i446
• 
  Pooya Zakeri,Jaak Simm,Adam Arany,Sarah ElShal,Yves Moreau:
  Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information.i447-i456
• 
  Marinka Zitnik,Monica Agrawal,Jure Leskovec:
  Modeling polypharmacy side effects with graph convolutional networks.i457-i466
• 
  Lisa Gai,Eleazar Eskin:
  Finding associated variants in genome-wide association studies on multiple traits.i467-i474
• 
  Natalie Sauerwald,Carl Kingsford:
  Quantifying the similarity of topological domains across normal and cancer human cell types.i475-i483

Systems Biology and Networks

• 
  Wei Zhang,Jianzhu Ma,Trey Ideker:
  Classifying tumors by supervised network propagation.i484-i493
• 
  Benjamin Ballnus,Steffen Schaper,Fabian J. Theis,Jan Hasenauer:
  Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.i494-i501
• 
  Sushant Patkar,Roded Sharan:
  An optimization framework for network annotation.i502-i508
• 
  Anna Cichonska,Tapio Pahikkala,Sándor Szedmák,Heli Julkunen,Antti Airola,Markus Heinonen,Tero Aittokallio,Juho Rousu:
  Learning with multiple pairwise kernels for drug bioactivity prediction.i509-i518
• 
  Sumana Srivatsa,Jack Kuipers,Fabian Schmich,Simone Eicher,Mario Emmenlauer,Christoph Dehio,Niko Beerenwinkel:
  Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.i519-i527
• 
  Francesca Petralia,Li Wang,Jie Peng,Arthur Yan,Jun Zhu,Pei Wang:
  A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity.i528-i536
• 
  Karel Kalecky,Young-Rae Cho:
  PrimAlign: PageRank-inspired Markovian alignment for large biological networks.i537-i546
• 
  Jinfeng Xiao,Charles Blatti,Saurabh Sinha:
  SigMat: a classification scheme for gene signature matching.i547-i554
• 
  Rani K. Powers,Andrew Goodspeed,Harrison Pielke-Lombardo,Aik Choon Tan,James C. Costello:
  GSEA-InContext: identifying novel and common patterns in expression experiments.i555-i564

Text Mining

• 
  Arjun Magge,Davy Weissenbacher,Abeed Sarker,Matthew Scotch,Graciela Gonzalez-Hernandez:
  Deep neural networks and distant supervision for geographic location mention extraction.i565-i573

Visualisation

• 
  Marwan Abdellah,Juan Hernando,Stefan Eilemann,Samuel Lapere,Nicolas Antille,Henry Markram,Felix Schürmann:
  NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks.i574-i582
• 
  Pierre Boutillier,Mutaamba Maasha,Xing Li,Héctor F. Medina-Abarca,Jean Krivine,Jérôme Feret,Ioana Cristescu,Angus G. Forbes,Walter Fontana:
  The Kappa platform for rule-based modeling.i583-i592

Author Index

• 
  Author Index.i593-i594

Original Papers
Genome Analysis

• 
  Claire Bertelli,Fiona S. L. Brinkman:
  Improved genomic island predictions with IslandPath-DIMOB.2161-2167
• 
  Shuhua Fu,Yingke Ma,Hui Yao,Zhichao Xu,Shilin Chen,Jingyuan Song,Kin Fai Au:
  IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.2168-2176

Sequence Analysis

• 
  Narayanan Raghupathy,Kwangbom Choi,Matthew J. Vincent,Glen L. Beane,Keith S. Sheppard,Steven C. Munger,Ron Korstanje,Fernando Pardo-Manual de Villena,Gary A. Churchill:
  Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression.2177-2184
• 
  Zhen Cao,Xiaoyong Pan,Yang Yang,Yan Huang,Hong-Bin Shen:
  The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier.2185-2194

Phylogenetics

• 
  Sejal Modha,Anil S. Thanki,Susan F. Cotmore,Andrew J. Davison,Joseph Hughes:
  ViCTree: an automated framework for taxonomic classification from protein sequences.2195-2200

Structural Bioinformatics

• 
  Ricardo N. dos Santos,Allan J. R. Ferrari,Hugo C. R. de Jesus,Fábio C. Gozzo,Faruck Morcos,Leandro Martínez:
  Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals.2201-2208
• 
  Jun Hu,Zi Liu,Dong-Jun Yu,Yang Zhang:
  LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.2209-2218
• 
  Saulo Henrique Pires de Oliveira,Charlotte M. Deane:
  Combining co-evolution and secondary structure prediction to improve fragment library generation.2219-2227

Genetics and Population Analysis

• 
  Cheng-Hong Yang,Li-Yeh Chuang,Yu-Da Lin:
  Multiobjective multifactor dimensionality reduction to detect SNP-SNP interactions.2228-2236

Systems Biology

• 
  Aditya Pratapa,Neil Adames,Pavel K. Brazhnik,Nicholas Franzese,John J. Tyson,Jean Peccoud,T. M. Murali:
  CrossPlan: systematic planning of genetic crosses to validate mathematical models.2237-2244
• 
  Markus Lux,Ryan Remy Brinkman,Cédric Chauve,Adam Laing,Anna Lorenc,Lucie Abeler-Dörner,Barbara Hammer:
  flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.2245-2253

Data and Text Mining

• 
  Ajay Anand Kumar,Lut Van Laer,Maaike Alaerts,Amin Ardeshirdavani,Yves Moreau,Kris Laukens,Bart Loeys,Geert Vandeweyer:
  pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion.2254-2262

Databases and Ontologies

• 
  Xiaole Yin,Xiaotao Jiang,Benli Chai,Liguan Li,Ying Yang,James R. Cole,James M. Tiedje,Tong Zhang:
  ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes.2263-2270
• 
  Jiansheng Wu,Qiuming Zhang,Weijian Wu,Tao Pang,Haifeng Hu,Wallace K. B. Chan,Xiaoyan Ke,Yang Zhang:
  WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest.2271-2282

Applications Notes
Genome Analysis

• 
  Andrey A. Shabalin,Mohammad W. Hattab,Shaunna L. Clark,Robin F. Chan,Gaurav Kumar,Karolina A. Åberg,Edwin J. C. G. van den Oord:
  RaMWAS: fast methylome-wide association study pipeline for enrichment platforms.2283-2285
• 
  Selin Jessa,Claudia L. Kleinman:
  chromswitch: a flexible method to detect chromatin state switches.2286-2288
• 
  Marzia A. Cremona,Alessia Pini,Fabio Cumbo,Kateryna D. Makova,Francesca Chiaromonte,Simone Vantini:
  IWTomics: testing high-resolution sequence-based 'Omics' data at multiple locations and scales.2289-2291

Sequence Analysis

• 
  Tomás Vetrovský,Petr Baldrian,Daniel C. Morais:
  SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.2292-2294
• 
  Anna Gogleva,Hajk-Georg Drost,Sebastian Schornack:
  SecretSanta: flexible pipelines for functional secretome prediction.2295-2296

Phylogenetics

• 
  Christopher Monit,Richard A. Goldstein:
  SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny.2297-2299
• 
  David A. Duchêne,Sebastián Duchêne,Simon Y. W. Ho:
  PhyloMAd: efficient assessment of phylogenomic model adequacy.2300-2301

Structural Bioinformatics

• 
  Anssi Nurminen,Vesa P. Hytönen:
  StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data.2302-2304

Gene expression

• 
  Yoojoong Kim,Yeong Seon Kang,Junhee Seok:
  GAIT: Gene expression Analysis for Interval Time.2305-2307

Genetics and Population Analysis

• 
  Aleksi Sipola,Pekka Marttinen,Jukka Corander:
  Bacmeta: simulator for genomic evolution in bacterial metapopulations.2308-2310

Systems Biology

• 
  Nadir Sella,Louis Verny,Guido Uguzzoni,Séverine Affeldt,Hervé Isambert:
  MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data.2311-2313
• 
  Joe Wandy,Mu Niu,Diana Giurghita,Rónán Daly,Simon Rogers,Dirk Husmeier:
  ShinyKGode: an interactive application for ODE parameter inference using gradient matching.2314-2315
• 
  Michaela Gündel,Charles Tapley Hoyt,Martin Hofmann-Apitius:
  BEL2ABM: agent-based simulation of static models in Biological Expression Language.2316-2318
• 
  João G. R. Cardoso,Ahmad A. Zeidan,Kristian Jensen,Nikolaus Sonnenschein,Ana Rute Neves,Markus J. Herrgård:
  MARSI: metabolite analogues for rational strain improvement.2319-2321

Data and Text Mining

• 
  José G. Pérez-Silva,Miguel Araujo-Voces,Víctor Quesada:
  nVenn: generalized, quasi-proportional Venn and Euler diagrams.2322-2324

Databases and Ontologies

• 
  A. Kulandaisamy,S. Binny Priya,R. Sakthivel,Svetlana Tarnovskaya,Ilya Bizin,Peter Hönigschmid,Dmitrij Frishman,M. Michael Gromiha:
  MutHTP: mutations in human transmembrane proteins.2325-2326
• 
  Neil Swainston,Mark Dunstan,Adrian J. Jervis,Christopher J. Robinson,Pablo Carbonell,Alan R. Williams,Jean-Loup Faulon,Nigel S. Scrutton,Douglas B. Kell:
  PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts.2327-2329

Message from the ISCB
Databases and Ontologies

• 
  Christiana N. Fogg,Diane E. Kovats,Ron Shamir:
  2018 ISCB Overton Prize awarded to Cole Trapnell.2330-2331
• 
  Christiana N. Fogg,Diane E. Kovats,Ron Shamir:
  Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award.2332-2333
• 
  Christiana N. Fogg,Diane E. Kovats,Ron Shamir:
  Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman.2334-2335
• 
  Christiana N. Fogg,Diane E. Kovats,Ron Shamir:
  2018 ISCB Innovator Award recognizes M. Madan Babu.2336-2337

Corrigenda
Databases and Ontologies

• 
  Vahid Jalili,Matteo Matteucci,Marco Masseroli,Marco J. Morelli:
  Using combined evidence from replicates to evaluate ChIP-seq peaks.2338
• 
  Anne Hoffmann,Jörg Fallmann,Elisa Vilardo,Mario Mörl,Peter F. Stadler,Fabian Amman:
  Accurate mapping of tRNA reads.2339
• 
  Xiaohua Douglas Zhang,Zhaozhi Zhang,Dandan Wang:
  CGManalyzer: an R package for analyzing continuous glucose monitoring studies.2340

Volume 34, Number 14, July 2018

Original Papers
Genome Analysis

• 
  Shijia Zhu,Gang Fang:
  MatrixEpistasis: ultrafast, exhaustive epistasis scan for quantitative traits with covariate adjustment.2341-2348
• 
  Zilu Zhou,Weixin Wang,Li-San Wang,Nancy Ruonan Zhang:
  Integrative DNA copy number detection and genotyping from sequencing and array-based platforms.2349-2355
• 
  Ryuichiro Nakato,Katsuhiko Shirahige:
  Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile.2356-2363

Sequence Analysis

• 
  Nicholas K. Akers,Eric E. Schadt,Bojan Losic:
  STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts.2364-2370
• 
  Robert C. Edgar:
  Updating the 97% identity threshold for 16S ribosomal RNA OTUs.2371-2375
• 
  Tobias P. Loka,Simon H. Tausch,Piotr Wojtek Dabrowski,Aleksandar Radonic,Andreas Nitsche,Bernhard Y. Renard:
  PriLive: privacy-preserving real-time filtering for next-generation sequencing.2376-2383

Gene expression

• 
  Yu Hu,Jennie Lin,Jian Hu,Gang Hu,Kui Wang,Hanrui Zhang,Muredach P. Reilly,Mingyao Li:
  PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.2384-2391
• 
  Trung-Nghia Vu,Quin F. Wills,Krishna R. Kalari,Nifang Niu,Liewei Wang,Yudi Pawitan,Mattias Rantalainen:
  Isoform-level gene expression patterns in single-cell RNA-sequencing data.2392-2400
• 
  Wanseon Lee,Katharine Plant,Peter Humburg,Julian C. Knight:
  AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes.2401-2408

Systems Biology

• 
  Sahely Bhadra,Peter Blomberg,Sandra Castillo,Juho Rousu:
  Principal metabolic flux mode analysis.2409-2417
• 
  Joshua N. Sampson,Simina M. Boca,Steven C. Moore,Ruth Heller:
  FWER and FDR control when testing multiple mediators.2418-2424
• 
  Xiangxiang Zeng,Li Liu,Linyuan Lü,Quan Zou:
  Prediction of potential disease-associated microRNAs using structural perturbation method.2425-2432
• 
  Nikolaos Tsiantis,Eva Balsa-Canto,Julio R. Banga:
  Optimality and identification of dynamic models in systems biology: an inverse optimal control framework.2433-2440
• 
  Christos Dimitrakopoulos,Sravanth Kumar Hindupur,Luca Häfliger,Jonas Behr,Hesam Montazeri,Michael N. Hall,Niko Beerenwinkel:
  Network-based integration of multi-omics data for prioritizing cancer genes.2441-2448

Data and Text Mining

• 
  Fabio Fabris,Aoife Doherty,Daniel Palmer,João Pedro de Magalhães,Alex Alves Freitas:
  A new approach for interpreting Random Forest models and its application to the biology of ageing.2449-2456
• 
  Willem van den Boom,Callie Mao,Rebecca A. Schroeder,David B. Dunson:
  Extrema-weighted feature extraction for functional data.2457-2464
• 
  Ronghui You,Zihan Zhang,Yi Xiong,Fengzhu Sun,Hiroshi Mamitsuka,Shanfeng Zhu:
  GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank.2465-2473
• 
  Dieter Galea,Ivan Laponogov,Kirill A. Veselkov:
  Exploiting and assessing multi-source data for supervised biomedical named entity recognition.2474-2482

Applications Notes
Genome Analysis

• 
  Giovanna Ambrosini,Romain Groux,Philipp Bucher:
  PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.2483-2484
• 
  Chantriolnt-Andreas Kapourani,Guido Sanguinetti:
  BPRMeth: a flexible Bioconductor package for modelling methylation profiles.2485-2486

Sequence Analysis

• 
  Balázs Szalkai,Vince Grolmusz:
  SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification.2487-2489
• 
  Tsukasa Nakamura,Kazunori D. Yamada,Kentaro Tomii,Kazutaka Katoh:
  Parallelization of MAFFT for large-scale multiple sequence alignments.2490-2492
• 
  Yan-Bo Sun:
  FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data.2493-2495
• 
  Cedric Landerer,Alexander Cope,Russell L. Zaretzki,Michael A. Gilchrist:
  AnaCoDa: analyzing codon data with Bayesian mixture models.2496-2498
• 
  Zhen Chen,Pei Zhao,Fuyi Li,André Leier,Tatiana T. Marquez-Lago,Yanan Wang,Geoffrey I. Webb,Alexander Ian Smith,Roger J. Daly,Kuo-Chen Chou,Jiangning Song:
  iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.2499-2502
• 
  Michele Berselli,Enrico Lavezzo,Stefano Toppo:
  NeSSie: a tool for the identification of approximate DNA sequence symmetries.2503-2505

Phylogenetics

• 
  Merly Escalona,Sara Rocha,David Posada:
  NGSphy: phylogenomic simulation of next-generation sequencing data.2506-2507

Structural Bioinformatics

• 
  Changge Ji,Fredrik Svensson,Azedine Zoufir,Andreas Bender:
  eMolTox: prediction of molecular toxicity with confidence.2508-2509

Gene expression

• 
  Diem-Trang T. Tran,Tian Zhang,Ryan Stutsman,Matthew Might,Umesh R. Desai,Balagurunathan Kuberan:
  anexVis: visual analytics framework for analysis of RNA expression.2510-2512

Data and Text Mining

• 
  M. Kösters,Johannes Leufken,Stefan Schulze,K. Sugimoto,Joshua Klein,R. P. Zahedi,Michael Hippler,S. A Leidel,Christian Fufezan:
  pymzML v2.0: introducing a highly compressed and seekable gzip format.2513-2514
• 
  Ruidong Li,Han Qu,Shibo Wang,Julong Wei,Le Zhang,Renyuan Ma,Jianming Lu,Jianguo Zhu,Wei-De Zhong,Zhenyu Jia:
  GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC.2515-2517

Databases and Ontologies

• 
  R. Shyama Prasad Rao,Ning Zhang,Dong Xu,Ian Max Møller:
  CarbonylDB: a curated data-resource of protein carbonylation sites.2518-2520

Volume 34, Number 15, August 2018

Original Papers
Genome Analysis

• 
  Ashraful Arefeen,Juntao Liu,Xinshu Xiao,Tao Jiang:
  TAPAS: tool for alternative polyadenylation site analysis.2521-2529
• 
  Igor Mandric,Sergey Knyazev,Alex Zelikovsky:
  Repeat-aware evaluation of scaffolding tools.2530-2537
• 
  Claudia Giambartolomei,Jimmy Zhenli Liu,Wen Zhang,Mads Hauberg,Huwenbo Shi,James Boocock,Joe Pickrell,Andrew E. Jaffe,CommonMind Consortium,Bogdan Pasaniuc,Panos Roussos:
  A Bayesian framework for multiple trait colocalization from summary association statistics.2538-2545
• 
  Jiawei Wang,Bingjiao Yang,André Leier,Tatiana T. Marquez-Lago,Morihiro Hayashida,Andrea Rocker,Yanju Zhang,Tatsuya Akutsu,Kuo-Chen Chou,Richard A. Strugnell,Jiangning Song,Trevor Lithgow:
  Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.2546-2555

Sequence Analysis

• 
  Isaac Turner,Kiran V. Garimella,Zamin Iqbal,Gil McVean:
  Integrating long-range connectivity information into de Bruijn graphs.2556-2565
• 
  Matteo Lo Monte,Candida Manelfi,Marica Gemei,Daniela Corda,Andrea Rosario Beccari:
  ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors.2566-2574
• 
  Hannah F. Löchel,Mona Riemenschneider,Dmitrij Frishman,Dominik Heider:
  SCOTCH: subtype A coreceptor tropism classification in HIV-1.2575-2580

Structural Bioinformatics

• 
  Clément Viricel,Simon de Givry,Thomas Schiex,Sophie Barbe:
  Cost function network-based design of protein-protein interactions: predicting changes in binding affinity.2581-2589
• 
  Piotr Klukowski,Michal Augoff,Maciej Zieba,Maciej Drwal,Adam Gonczarek,Michal J. Walczak:
  NMRNet: a deep learning approach to automated peak picking of protein NMR spectra.2590-2597
• 
  Qiaozhen Meng,Zhenling Peng,Jianyi Yang:
  CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction.2598-2604
• 
  Sameer Khurana,Reda Rawi,Khalid Kunji,Gwo-Yu Chuang,Halima Bensmail,Raghvendra Mall:
  DeepSol: a deep learning framework for sequence-based protein solubility prediction.2605-2613

Data and Text Mining

• 
  Bethany Percha,Russ B. Altman:
  A global network of biomedical relationships derived from text.2614-2624
• 
  Paul D. Tar,Neil A. Thacker,M. Babur,Yvonne Watson,Sue Cheung,R. A Little,R. G. Gieling,K. J. Williams,J. P. B. O'Connor:
  A new method for the high-precision assessment of tumor changes in response to treatment.2625-2633
• 
  Teng Fei,Tengjiao Zhang,Weiyang Shi,Tianwei Yu:
  Mitigating the adverse impact of batch effects in sample pattern detection.2634-2641
• 
  Kevin K. Yang,Zachary Wu,Claire N. Bedbrook,Frances H. Arnold:
  Learned protein embeddings for machine learning.2642-2648

Applications Notes
Genome Analysis

• 
  John T. Lawson,Eleni M. Tomazou,Christoph Bock,Nathan C. Sheffield:
  MIRA: an R package for DNA methylation-based inference of regulatory activity.2649-2650
• 
  Andrew D. L. Nelson,Asher Haug-Baltzell,Sean Davey,Brian D. Gregory,Eric Lyons:
  EPIC-CoGe: managing and analyzing genomic data.2651-2653
• 
  Jianhao Peng,Olgica Milenkovic,Idoia Ochoa:
  METHCOMP: a special purpose compression platform for DNA methylation data.2654-2656
• 
  Jing Xu,Linna Zhao,Di Liu,Simeng Hu,Xiuling Song,Jin Li,Hongchao Lv,Lian Duan,Mingming Zhang,Qinghua Jiang,Guiyou Liu,Shuilin Jin,Mingzhi Liao,Meng Zhang,Rennan Feng,Fanwu Kong,Liangde Xu,Yongshuai Jiang:
  EWAS: epigenome-wide association study software 2.0.2657-2658
• 
  David J. Winter,Steven H. Wu,Abigail A. Howell,Ricardo B. R. Azevedo,Rebecca A. Zufall,Reed A. Cartwright:
  accuMUlate: a mutation caller designed for mutation accumulation experiments.2659-2660
• 
  Jaehee Jung,Jong Im Kim,Young-Sik Jeong,Gangman Yi:
  AGORA: organellar genome annotation from the amino acid and nucleotide references.2661-2663

Sequence Analysis

• 
  Zheng Wei,Wei Zhang,Huan Fang,Yanda Li,Xiaowo Wang:
  esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.2664-2665
• 
  Wouter De Coster,Svenn D'Hert,Darrin T. Schultz,Marc Cruts,Christine Van Broeckhoven:
  NanoPack: visualizing and processing long-read sequencing data.2666-2669
• 
  Stephen J. Fletcher,Mikael Bodén,Neena Mitter,Bernard J. Carroll:
  SCRAM: a pipeline for fast index-free small RNA read alignment and visualization.2670-2672
• 
  Richard Wilton,Xin Li,Andrew P. Feinberg,Alexander S. Szalay:
  Arioc: GPU-accelerated alignment of short bisulfite-treated reads.2673-2675

Structural Bioinformatics

• 
  Florian Eggenhofer,Ivo L. Hofacker,Rolf Backofen,Christian Höner zu Siederdissen:
  CMV: visualization for RNA and protein family models and their comparisons.2676-2678
• 
  Ivan Yu Chernyshov,Philip V. Toukach:
  REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates.2679-2681

Gene expression

• 
  Andrew R. Ghazi,Edward S. Chen,David M. Henke,Namrata Madan,Leonard C. Edelstein,Chad A. Shaw:
  Design tools for MPRA experiments.2682-2683

Systems Biology

• 
  Alberto Calderone,Gianni Cesareni:
  SPV: a JavaScript Signaling Pathway Visualizer.2684-2686

Data and Text Mining

• 
  Benedikt G. Brink,Justin Meskas,Ryan Remy Brinkman:
  ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data.2687-2689
• 
  Veronika Suni,Tomi Suomi,Tomoya Tsubosaka,Susumu Y. Imanishi,Laura L. Elo,Garry L. Corthals:
  SimPhospho: a software tool enabling confident phosphosite assignment.2690-2692

Databases and Ontologies

• 
  Anargyros Megalios,Rónán Daly,Karl E. V. Burgess:
  MetaboCraft: building a Minecraft plugin for metabolomics.2693-2694

Bioimage Informatics

• 
  Piotr Baniukiewicz,Sharon Collier,Till Bretschneider:
  QuimP: analyzing transmembrane signalling in highly deformable cells.2695-2697

Letter to the Editor
Data and Text Mining

• 
  Paul Monsarrat,Jean-Noel Vergnes:
  Data mining of effect sizes from PubMed abstracts: a cross-study conceptual replication.2698-2700

Volume 34, Number 16, August 2018

Original Papers
Genome Analysis

• 
  Oana Ursu,Nathan Boley,Maryna Taranova,Y. X. Rachel Wang,Galip Gürkan Yardimci,William Stafford Noble,Anshul Kundaje:
  GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.2701-2707
• 
  Franklin Delehelle,Sylvain Cussat-Blanc,Jean-Marc Alliot,Hervé Luga,Patricia Balaresque:
  ASGART: fast and parallel genome scale segmental duplications mapping.2708-2714
• 
  Xiwei Sun,Yi Han,Liyuan Zhou,Enguo Chen,Bingjian Lu,Yong Liu,Xiaoqing Pan,Allen W. Cowley Jr.,Mingyu Liang,Qingbiao Wu,Yan Lu,Pengyuan Liu:
  A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data.2715-2723
• 
  Mariusz Butkiewicz,Elizabeth E. Blue,Yuk Yee Leung,Xueqiu Jian,Edoardo Marcora,Alan E. Renton,Amanda Kuzma,Li-San Wang,Daniel C. Koboldt,Jonathan L. Haines,William S. Bush:
  Functional annotation of genomic variants in studies of late-onset Alzheimer's disease.2724-2731

Sequence Analysis

• 
  R. W. W. Brouwer,M. C. G. N. van den Hout,C. E. M. Kockx,Erwin Brosens,B. Eussen,A. de Klein,F. Sleutels,Wilfred F. J. van IJcken:
  Nimbus: a design-driven analyses suite for amplicon-based NGS data.2732-2739
• 
  Daniel Veltri,Uday Kamath,Amarda Shehu:
  Deep learning improves antimicrobial peptide recognition.2740-2747
• 
  Lukasz Roguski,Idoia Ochoa,Mikel Hernaez,Sebastian Deorowicz:
  FaStore: a space-saving solution for raw sequencing data.2748-2756

Structural Bioinformatics

• 
  Émilie Neveu,Petr Popov,Alexandre Hoffmann,Angelo Migliosi,Xavier Besseron,Grégoire Danoy,Pascal Bouvry,Sergei Grudinin:
  RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules.2757-2765

Gene expression

• 
  Wanlin Liu,Lai Wei,Jianan Sun,Jinwen Feng,Gaigai Guo,Lizhu Liang,Tianyi Fu,Mingwei Liu,Kai Li,Yin Huang,Weimin Zhu,Bei Zhen,Yi Wang,Chen Ding,Jun Qin:
  A reference peptide database for proteome quantification based on experimental mass spectrum response curves.2766-2772

Genetics and Population Analysis

• 
  Clément Niel,Christine Sinoquet,Christian Dina,Ghislain Rocheleau:
  SMMB: a stochastic Markov blanket framework strategy for epistasis detection in GWAS.2773-2780
• 
  Florian Privé,Hugues Aschard,Andrey Ziyatdinov,Michael G. B. Blum:
  Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr.2781-2787
• 
  Jingsi Ming,Mingwei Dai,Mingxuan Cai,Xiang Wan,Jin Liu,Can Yang:
  LSMM: a statistical approach to integrating functional annotations with genome-wide association studies.2788-2796
• 
  Ping Zeng,Xingjie Hao,Xiang Zhou:
  Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models.2797-2807

Systems Biology

• 
  Xiao He,Lukas Folkman,Karsten M. Borgwardt:
  Kernelized rank learning for personalized drug recommendation.2808-2816
• 
  Azam Peyvandi-Pour,Nafiseh Saberian,Adib Shafi,Michele Donato,Sorin Draghici:
  A novel computational approach for drug repurposing using systems biology.2817-2825
• 
  Gregorio Alanis-Lobato,Pablo Mier,Miguel A. Andrade-Navarro:
  The latent geometry of the human protein interaction network.2826-2834

Data and Text Mining

• 
  Aleksandar Poleksic,Lei Xie:
  Predicting serious rare adverse reactions of novel chemicals.2835-2842

Applications Notes
Genome Analysis

• 
  Amanda Birmingham,Adam M. Mark,Carlo Mazzaferro,Guorong Xu,Kathleen M. Fisch:
  Efficient population-scale variant analysis and prioritization with VAPr.2843-2845
• 
  Simone Rizzetto,David N. P. Koppstein,Jerome Samir,Mandeep Singh,Joanne H. Reed,Curtis H. Cai,Andrew R. Lloyd,Auda A. Eltahla,Christopher C. Goodnow,Fabio Luciani:
  B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle.2846-2847

Phylogenetics

• 
  Ryan A. Leo Elworth,Chabrielle Allen,Travis Benedict,Peter Dulworth,Luay Nakhleh:
  ALPHA: a toolkit for Automated Local PHylogenomic Analyses.2848-2850

Genetics and Population Analysis

• 
  Yeunjoo E. Song,Sungyoung Lee,Kyungtaek Park,Robert C. Elston,Hyeon-Jong Yang,Sungho Won:
  ONETOOL for the analysis of family-based big data.2851-2853
• 
  Ying Zhou,Xiaowen Tian,Brian L. Browning,Sharon R. Browning:
  POPdemog: visualizing population demographic history from simulation scripts.2854-2855

Systems Biology

• 
  Samuel R. Neaves,Sophia Tsoka,Louise A. C. Millard:
  Reactome Pengine: a web-logic API to the Homo sapiens reactome.2856-2858
• 
  Justin K. Huang,Tongqiu Jia,Daniel E. Carlin,Trey Ideker:
  pyNBS: a Python implementation for network-based stratification of tumor mutations.2859-2861
• 
  Andrew Ching-Yuet To,David Ho-Ting Chu,Angela Ruoning Wang,Frances Cheuk-Yau Li,Alan Wai-On Chiu,Daisy Yuwei Gao,Chung Hang Jonathan Choi,Siu-Kai Kong,Ting-Fung Chan,King-Ming Chan,Kevin Y. Yip:
  A comprehensive web tool for toehold switch design.2862-2864

Data and Text Mining

• 
  Hongxu Ding,Wanxin Wang,Andrea Califano:
  iterClust: a statistical framework for iterative clustering analysis.2865-2866
• 
  Zhenjia Wang,Mete Civelek,Clint L. Miller,Nathan C. Sheffield,Michael J. Guertin,Chongzhi Zang:
  BART: a transcription factor prediction tool with query gene sets or epigenomic profiles.2867-2869

Review
Gene expression

• 
  Thomas P. Quinn,Ionas Erb,Mark F. Richardson,Tamsyn M. Crowley:
  Understanding sequencing data as compositions: an outlook and review.2870-2878

Corrigendum
Gene expression

• 
  Xing Tang,Arunima Srivastava,Huayang Liu,Raghu Machiraju,Kun Huang,Gustavo Leone:
  annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.2879

Erratum
Gene expression

• 
  Dennis Pischel,Kai Sundmacher,Robert J. Flassig:
  Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.2880

Volume 34, Number 17, September 2018

ECCB 2018:The 17th European Conference on Computational Biology

• 
  Artemis G. Hatzigeorgiou,Pantelis G. Bagos,Panayiotis V. Benos,Christoforos Nikolaou,Yves Moreau,Ioannis Kavakiotis:
  ECCB 2018: The 17th European Conference on Computational Biology.i595-i598

Genes

• 
  Xiaoqian Wang,Kamran Ghasedi Dizaji,Heng Huang:
  Conditional generative adversarial network for gene expression inference.i603-i611
• 
  Alex Warwick Vesztrocy,Christophe Dessimoz,Henning Redestig:
  Prioritising candidate genes causing QTL using hierarchical orthologous groups.i612-i619
• 
  Ludovic Platon,Farida Zehraoui,Abdelhafid Bendahmane,Fariza Tahi:
  IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection.i620-i628
• 
  Peyton Greenside,Tyler Shimko,Polly Fordyce,Anshul Kundaje:
  Discovering epistatic feature interactions from neural network models of regulatory DNA sequences.i629-i637
• 
  Ilan Ben-Bassat,Benny Chor,Yaron Orenstein:
  A deep neural network approach for learning intrinsic protein-RNA binding preferences.i638-i646
• 
  Simone Tiberi,Mark Walsh,Massimo Cavallaro,Daniel Hebenstreit,Bärbel Finkenstädt:
  Bayesian inference on stochastic gene transcription from flow cytometry data.i647-i655
• 
  Jiecong Lin,Ka-Chun Wong:
  Off-target predictions in CRISPR-Cas9 gene editing using deep learning.i656-i663
• 
  Zhezhen Wang,John M. Cunningham,Xinan Holly Yang:
  CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs.i664-i670

Genome

• 
  Mohammed El-Kebir:
  SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error.i671-i679
• 
  Hongwei Yan,Andreas D. M. Gunawan,Louxin Zhang:
  S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks.i680-i686
• 
  Matteo Togninalli,Damian Roqueiro,COPDGene Investigators,Karsten M. Borgwardt:
  Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts.i687-i696
• 
  Yaxuan Wang,Luay Nakhleh:
  Towards an accurate and efficient heuristic for species/gene tree co-estimation.i697-i705
• 
  Ibrahim Numanagic,Alim S. Gökkaya,Lillian Zhang,Bonnie Berger,Can Alkan,Faraz Hach:
  Fast characterization of segmental duplications in genome assemblies.i706-i714
• 
  Andreas Andrusch,Piotr Wojtek Dabrowski,Jeanette Klenner,Simon H. Tausch,Claudia Kohl,Abdalla Osman,Bernhard Y. Renard,Andreas Nitsche:
  PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples.i715-i721
• 
  Renmin Han,Yu Li,Xin Gao,Sheng Wang:
  An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing.i722-i731
• 
  Alex Salazar,Thomas Abeel:
  Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations.i732-i742
• 
  Lorraine A. K. Ayad,Solon P. Pissis,Dimitris Polychronopoulos:
  CNEFinder: finding conserved non-coding elements in genomes.i743-i747
• 
  Chirag Jain,Sergey Koren,Alexander T. Dilthey,Adam M. Phillippy,Srinivas Aluru:
  A fast adaptive algorithm for computing whole-genome homology maps.i748-i756
• 
  Hui Peng,Yi Zheng,Zhixun Zhao,Tao Liu,Jinyan Li:
  Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions.i757-i765
• 
  Temesgen Hailemariam Dadi,Enrico Siragusa,Vitor Piro,Andreas Andrusch,Enrico Seiler,Bernhard Y. Renard,Knut Reinert:
  DREAM-Yara: an exact read mapper for very large databases with short update time.i766-i772

Proteins

• 
  Yang Liu,Qing Ye,Liwei Wang,Jian Peng:
  Learning structural motif representations for efficient protein structure search.i773-i780
• 
  Nastazia Lesgidou,Elias Eliopoulos,George N. Goulielmos,Metaxia Vlassi:
  Insights on the alteration of functionality of a tyrosine kinase 2 variant: a molecular dynamics study.i781-i786
• 
  Claudio Mirabello,Björn Wallner:
  Topology independent structural matching discovers novel templates for protein interfaces.i787-i794
• 
  E. Sila Ozdemir,Attila Gürsoy,Ozlem Keskin:
  Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces.i795-i801
• 
  Somaye Hashemifar,Behnam Neyshabur,Aly A. Khan,Jinbo Xu:
  Predicting protein-protein interactions through sequence-based deep learning.i802-i810
• 
  Mostafa Karimi,Yang Shen:
  iCFN: an efficient exact algorithm for multistate protein design.i811-i820
• 
  Hakime Öztürk,Arzucan Özgür,Elif Özkirimli Ölmez:
  DeepDTA: deep drug-target binding affinity prediction.i821-i829
• 
  Rundong Zhao,Zixuan Cang,Yiying Tong,Guo-Wei Wei:
  Protein pocket detection via convex hull surface evolution and associated Reeb graph.i830-i837

Data

• 
  Beatriz García Jiménez,Tomás de la Rosa,Mark D. Wilkinson:
  MDPbiome: microbiome engineering through prescriptive perturbations.i838-i847
• 
  Dimitris V. Manatakis,Vineet K. Raghu,Panayiotis V. Benos:
  piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks.i848-i856
• 
  Maxat Kulmanov,Paul N. Schofield,Georgios V. Gkoutos,Robert Hoehndorf:
  Ontology-based validation and identification of regulatory phenotypes.i857-i865
• 
  Xiaoqian Wang,Hong Chen,Jingwen Yan,Kwangsik Nho,Shannon L. Risacher,Andrew J. Saykin,Li Shen,Heng Huang:
  Quantitative trait loci identification for brain endophenotypes via new additive model with random networks.i866-i874
• 
  Eric Bach,Sándor Szedmák,Céline Brouard,Sebastian Böcker,Juho Rousu:
  Liquid-chromatography retention order prediction for metabolite identification.i875-i883
• 
  Shifu Chen,Yanqing Zhou,Yaru Chen,Jia Gu:
  fastp: an ultra-fast all-in-one FASTQ preprocessor.i884-i890
• 
  Arshdeep Sekhon,Ritambhara Singh,Yanjun Qi:
  DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications.i891-i900
• 
  Mona Alshahrani,Robert Hoehndorf:
  Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes.i901-i907
• 
  Florian Schmidt,Markus List,Engin Cukuroglu,Sebastian Köhler,Jonathan Göke,Marcel H. Schulz:
  An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.i908-i916
• 
  Sayaka Miura,Louise A. Huuki,Tiffany Buturla,Tracy Vu,Karen Gomez,Sudhir Kumar:
  Computational enhancement of single-cell sequences for inferring tumor evolution.i917-i926

Systems

• 
  Shohag Barman,Yung-Keun Kwon:
  A Boolean network inference from time-series gene expression data using a genetic algorithm.i927-i933
• 
  Clémence Frioux,Enora Fremy,Camille Trottier,Anne Siegel:
  Scalable and exhaustive screening of metabolic functions carried out by microbial consortia.i934-i943
• 
  Thomas Gaudelet,Noël Malod-Dognin,Natasa Przulj:
  Higher-order molecular organization as a source of biological function.i944-i953
• 
  Beatriz García Jiménez,José Luis García lópez,Juan Nogales:
  FLYCOP: metabolic modeling-based analysis and engineering microbial communities.i954-i963
• 
  Martin Pirkl,Niko Beerenwinkel:
  Single cell network analysis with a mixture of Nested Effects Models.i964-i971
• 
  Matthew A. Reyna,Mark D. M. Leiserson,Benjamin J. Raphael:
  Hierarchical HotNet: identifying hierarchies of altered subnetworks.i972-i980
• 
  Gayathri Sambamoorthy,Karthik Raman:
  Understanding the evolution of functional redundancy in metabolic networks.i981-i987
• 
  Nanne Aben,Johan A. Westerhuis,Yipeng Song,Henk A. L. Kiers,Magali Michaut,Age K. Smilde,Lodewyk F. A. Wessels:
  iTOP: inferring the topology of omics data.i988-i996
• 
  Evert Bosdriesz,Anirudh Prahallad,Bertram Klinger,Anja Sieber,Astrid Bosma,René Bernards,Nils Blüthgen,Lodewyk F. A. Wessels:
  Comparative Network Reconstruction using mixed integer programming.i997-i1004
• 
  Christopher A. Penfold,Anastasiya Sybirna,John E. Reid,Yun Huang,Lorenz Wernisch,Zoubin Ghahramani,Murray Grant,M. Azim Surani:
  Branch-recombinant Gaussian processes for analysis of perturbations in biological time series.i1005-i1013

Original Papers
Genome Analysis

• 
  Trevor Cickovski,Giri Narasimhan:
  Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA).2881-2888
• 
  Michael K. K. Leung,Andrew Delong,Brendan J. Frey:
  Inference of the human polyadenylation code.2889-2898
• 
  Yu Li,Renmin Han,Chongwei Bi,Mo Li,Sheng Wang,Xin Gao:
  DeepSimulator: a deep simulator for Nanopore sequencing.2899-2908
• 
  Emily Goren,Peng Liu,Chao Wang,Chong Wang:
  BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.2909-2917

Sequence Analysis

• 
  Nam S. Vo,Vinhthuy Phan:
  Leveraging known genomic variants to improve detection of variants, especially close-by Indels.2918-2926
• 
  Jiao Chen,Yingchao Zhao,Yanni Sun:
  De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding.2927-2935
• 
  Dongwei Wang,Chunling Xu,Shanwen Ding,Xin Huang,Xi Cheng,Chao Zhang,Chun Chen,Hui Xie:
  Identification and function of FAR protein family genes from a transcriptome analysis of Aphelenchoides besseyi.2936-2943
• 
  Edgar Liberis,Petar Velickovic,Pietro Sormanni,Michele Vendruscolo,Pietro Liò:
  Parapred: antibody paratope prediction using convolutional and recurrent neural networks.2944-2950

Genetics and Population Analysis

• 
  Hannah Verena Meyer,Ewan Birney:
  PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships.2951-2956

Systems Biology

• 
  H. Robert Frost:
  Computation and application of tissue-specific gene set weights.2957-2964
• 
  Veit Schwämmle,Ole Nørregaard Jensen:
  VSClust: feature-based variance-sensitive clustering of omics data.2965-2972

Data and Text Mining

• 
  Anthony Rios,Ramakanth Kavuluru,Zhiyong Lu:
  Generalizing biomedical relation classification with neural adversarial domain adaptation.2973-2981
• 
  Tien-Chueh Kuo,Yufeng Jane Tseng:
  LipidPedia: a comprehensive lipid knowledgebase.2982-2987
• 
  Leena Choi,Robert J. Carroll,Cole Beck,Jonathan D. Mosley,Dan M. Roden,Joshua C. Denny,Sara L. Van Driest:
  Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects.2988-2996

Databases and Ontologies

• 
  Yuxing Liao,R. Dustin Schaeffer,Jimin Pei,Nick V. Grishin:
  A sequence family database built on ECOD structural domains.2997-3003

Bioimage Informatics

• 
  Leonid Andronov,Jonathan Michalon,Khalid Ouararhni,Igor Orlov,Ali Hamiche,Jean-Luc Vonesch,Bruno P. Klaholz:
  3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations.3004-3012
• 
  Kimmo Kartasalo,Leena Latonen,Jorma Vihinen,Tapio Visakorpi,Matti Nykter,Pekka Ruusuvuori:
  Comparative analysis of tissue reconstruction algorithms for 3D histology.3013-3021

Applications Notes
Genome Analysis

• 
  Francesca Giordano,Maximilian R. Stammnitz,Elizabeth P. Murchison,Zemin Ning:
  scanPAV: a pipeline for extracting presence-absence variations in genome pairs.3022-3024
• 
  Ji Zhang,Yanwen Xiong,Lynn Rogers,Glen P. Carter,Nigel French:
  Genome-by-genome approach for fast bacterial genealogical relationship evaluation.3025-3027
• 
  Timothy Dallman,Philip Ashton,Ulf Schafer,Aleksey Jironkin,Anais Painset,Sharif Shaaban,Hassan Hartman,Richard Myers,Anthony Underwood,Claire Jenkins,Kathie Grant:
  SnapperDB: a database solution for routine sequencing analysis of bacterial isolates.3028-3029
• 
  Ali Amiryousefi,Jaakko Hyvönen,Peter Poczai:
  IRscope: an online program to visualize the junction sites of chloroplast genomes.3030-3031
• 
  Thomas H. Clarke,Lauren M. Brinkac,Granger G. Sutton,Derrick E. Fouts:
  GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models.3032-3034

Sequence Analysis

• 
  Stefan Budach,Annalisa Marsico:
  pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks.3035-3037
• 
  Viola Ravasio,Marco Ritelli,Andrea Legati,Edoardo Giacopuzzi:
  GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS.3038-3040

Phylogenetics

• 
  Ngoc-Vinh Tran,Bastian Greshake Tzovaras,Ingo Ebersberger:
  PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles.3041-3043

Gene expression

• 
  Pierre-Louis Cedoz,Marcos Prunello,Kevin Brennan,Olivier Gevaert:
  MethylMix 2.0: an R package for identifying DNA methylation genes.3044-3046

Genetics and Population Analysis

• 
  Kazuki Yoshizoe,Aika Terada,Koji Tsuda:
  MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms.3047-3049

Systems Biology

• 
  Andrea Hornáková,Markus List,Jilles Vreeken,Marcel H. Schulz:
  JAMI: fast computation of conditional mutual information for ceRNA network analysis.3050-3051
• 
  Mahsa Moein,Kamil Grzyb,Teresa Gonçalves Martins,Shinya Komoto,Francesca Peri,Alexander D. Crawford,Aymeric Fouquier d'Hérouël,Alexander Skupin:
  CaSiAn: a Calcium Signaling Analyzer tool.3052-3054

Databases and Ontologies

• 
  Liam Stephenson,Yoshua Wakeham,Nick Seidenman,Jarny Choi:
  Building online genomics applications using BioPyramid.3055-3057
• 
  Douglas Tomachewski,Carolina Weigert Galvão,Arion de Campos Júnior,Alaine Margarete Guimarães,José Carlos Ferreira da Rocha,Rafael Mazer Etto:
  Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins.3058-3060

Volume 34, Number 18, September 2018

Discovery note
Genome Analysis

• 
  Kevin Vervier,Jacob J. Michaelson:
  TiSAn: estimating tissue-specific effects of coding and non-coding variants.3061-3068

Original Papers
Genome Analysis

• 
  Hui Peng,Yi Zheng,Michael Blumenstein,Dacheng Tao,Jinyan Li:
  CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling.3069-3077
• 
  Antti Häkkinen,Amjad Alkodsi,Chiara Facciotto,Kaiyang Zhang,Katja Kaipio,Sirpa Leppä,Olli Carpén,Seija Grénman,Johanna Hynninen,Sakari Hietanen,Rainer Lehtonen,Sampsa Hautaniemi:
  Identifying differentially methylated sites in samples with varying tumor purity.3078-3085
• 
  Bin Liu,Fan Weng,De-Shuang Huang,Kuo-Chen Chou:
  iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC.3086-3093

Sequence Analysis

• 
  Heng Li:
  Minimap2: pairwise alignment for nucleotide sequences.3094-3100
• 
  Alexander Gawronski,Michael Uhl,Yajia Zhang,Yen-Yi Lin,Yashar S. Niknafs,Varune R. Ramnarine,Rohit Malik,Felix Feng,Arul M. Chinnaiyan,Colin C. Collins,Süleyman Cenk Sahinalp,Rolf Backofen:
  MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.3101-3110
• 
  Semmy Wellem Taju,Trinh-Trung-Duong Nguyen,Nguyen-Quoc-Khanh Le,Rosdyana Mangir Irawan Kusuma,Yu-Yen Ou:
  DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters.3111-3117
• 
  Daniele Raimondi,Gabriele Orlando,Yves Moreau,Wim F. Vranken:
  Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping.3118-3125

Structural Bioinformatics

• 
  Julia Varga,Gábor E. Tusnády:
  TMCrys: predict propensity of success for transmembrane protein crystallization.3126-3130
• 
  Kaili Wang,Yiren Jian,Huiwen Wang,Chen Zeng,Yunjie Zhao:
  RBind: computational network method to predict RNA binding sites.3131-3136

Gene expression

• 
  Florian G. Pflug,Arndt von Haeseler:
  TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers.3137-3144
• 
  Dingge Ying,Mulin Jun Li,Pak Chung Sham,Miao-Xin Li:
  A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues.3145-3150
• 
  Xianxiao Zhou,Minghui Wang,Igor Katsyv,Hanna Y. Irie,Bin Zhang:
  EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy.3151-3159

Genetics and Population Analysis

• 
  Sudhir Ghandikota,Gurjit K. Khurana Hershey,Tesfaye B. Mersha:
  GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization.3160-3168

Systems Biology

• 
  Zi Wang,Dali Wang,Chengcheng Li,Yichi Xu,Husheng Li,Zhirong Bao:
  Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis.3169-3177
• 
  Xing Chen,Di Xie,Lei Wang,Qi Zhao,Zhu-Hong You,Hongsheng Liu:
  BNPMDA: Bipartite Network Projection for MiRNA-Disease Association prediction.3178-3186
• 
  Mehmet Emin Bakir,Savas Konur,Marian Gheorghe,Natalio Krasnogor,Mike Stannett:
  Automatic selection of verification tools for efficient analysis of biochemical models.3187-3195

Bioimage Informatics

• 
  Sean Robinson,Michael Courtney:
  Spatial quantification of the synaptic activity phenotype across large populations of neurons with Markov random fields.3196-3204

Applications Notes
Genome Analysis

• 
  Bastian Pfeifer,Martin J. Lercher:
  BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation.3205-3207
• 
  Pau Puigdevall,Robert Castelo:
  GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor.3208-3210
• 
  Yin Tong,Beibei Ru,Jiangwen Zhang:
  miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer.3211-3213

Phylogenetics

• 
  Mukul S. Bansal,Manolis Kellis,Misagh Kordi,Soumya Kundu:
  RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.3214-3216

Gene expression

• 
  Sören Müller,Ara Cho,Siyuan J. Liu,Daniel A. Lim,Aaron Diaz:
  CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones.3217-3219
• 
  Aimin Yan,Yuguang Ban,Zhen Gao,Xi Chen,Lily Wang:
  PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data.3220-3222
• 
  Zhun Miao,Ke Deng,Xiaowo Wang,Xuegong Zhang:
  DEsingle for detecting three types of differential expression in single-cell RNA-seq data.3223-3224

Systems Biology

• 
  Samuel J. Hinshaw,Amy H. Y. Lee,Erin E. Gill,Robert E. W. Hancock:
  MetaBridge: enabling network-based integrative analysis via direct protein interactors of metabolites.3225-3227

Data and Text Mining

• 
  Alba Gutiérrez-Sacristán,Àlex Bravo,Alexia Giannoula,Miguel Angel Mayer,Ferran Sanz,Laura Inés Furlong:
  comoRbidity: an R package for the systematic analysis of disease comorbidities.3228-3230

Databases and Ontologies

• 
  Sophie Zhao,Ian Walsh,Jodie L. Abrahams,Louise Royle,Terry Nguyen-Khuong,Daniel Spencer,Daryl L. Fernandes,Nicolle H. Packer,Pauline M. Rudd,Matthew P. Campbell:
  GlycoStore: a database of retention properties for glycan analysis.3231-3232
• 
  Anthony Nash,Thomas Sewell,Rhys A. Farrer,Alireza Abdolrasouli,Jennifer M. G. Shelton,Matthew C. Fisher,Johanna Rhodes:
  MARDy: Mycology Antifungal Resistance Database.3233-3234
• 
  Carles Hernandez-Ferrer,Juan R. González:
  CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies.3235-3237

Bioimage Informatics

• 
  Anliang Wang,Xiaolong Yan,Zhijun Wei:
  ImagePy: an open-source, Python-based and platform-independent software package for bioimage analysis.3238-3240

Volume 34, Number 19, October 2018

Discovery note
Genome Analysis

• 
  Eli Goz,Zohar Zafrir,Tamir Tuller:
  Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code.3241-3248

Original Papers
Genome Analysis

• 
  Marlena Maziarz,Ruth M. Pfeiffer,Yunhu Wan,Mitchell H. Gail:
  Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation.3249-3257
• 
  Osamu Gotoh:
  Modeling one thousand intron length distributions with fitild.3258-3264
• 
  Laraib Malik,Fatemeh Almodaresi,Rob Patro:
  Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis.3265-3272

Sequence Analysis

• 
  Dilip A. Durai,Marcel H. Schulz:
  In silico read normalization using set multi-cover optimization.3273-3280
• 
  Gleb Filatov,Bruno Bauwens,Attila Kertész-Farkas:
  LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.3281-3288
• 
  Sumaiya Iqbal,Md. Tamjidul Hoque:
  PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence.3289-3299

Structural Bioinformatics

• 
  Aleksandra I. Jarmolinska,Michal Kadlof,Pawel Dabrowski-Tumanski,Joanna I. Sulkowska:
  GapRepairer: a server to model a structural gap and validate it using topological analysis.3300-3307
• 
  David T. Jones,Shaun M. Kandathil:
  High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features.3308-3315
• 
  Jack W. Heal,Gail J. Bartlett,Christopher W. Wood,Andrew R. Thomson,Derek N. Woolfson:
  Applying graph theory to protein structures: an Atlas of coiled coils.3316-3323
• 
  Shintaro Minami,Kengo Sawada,Motonori Ota,George Chikenji:
  MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers.3324-3331

Gene expression

• 
  Amrita Basu,Ritwik Mitra,Han Liu,Stuart L. Schreiber,Paul A. Clemons:
  RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines.3332-3339
• 
  Zhijin Wu,Yi Zhang,Michael L. Stitzel,Hao Wu:
  Two-phase differential expression analysis for single cell RNA-seq.3340-3348
• 
  Siamak Zamani Dadaneh,Mingyuan Zhou,Xiaoning Qian:
  Bayesian negative binomial regression for differential expression with confounding factors.3349-3356

Systems Biology

• 
  Chengqian Lu,Mengyun Yang,Feng Luo,Fang-Xiang Wu,Min Li,Yi Pan,Yaohang Li,Jianxin Wang:
  Prediction of lncRNA-disease associations based on inductive matrix completion.3357-3364

Data and Text Mining

• 
  Konstantinos Sechidis,Konstantinos Papangelou,Paul D. Metcalfe,David Svensson,James Weatherall,Gavin Brown:
  Distinguishing prognostic and predictive biomarkers: an information theoretic approach.3365-3376

Applications Notes
Genome Analysis

• 
  Flavio Pazos Obregón,Pablo Soto,José Luis Lavín,Ana Rosa Cortázar,Rosa Barrio,Ana María Aransay,Rafael Cantera:
  Cluster Locator, online analysis and visualization of gene clustering.3377-3379
• 
  Jayendra Shinde,Quentin Bayard,Sandrine Imbeaud,Théo Z. Hirsch,Feng Liu,Victor Renault,Jessica Zucman-Rossi,Eric Letouzé:
  Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer.3380-3381

Sequence Analysis

• 
  Matthew B. Stocks,Irina Mohorianu,Matthew Beckers,Claudia Paicu,Simon Moxon,Joshua Thody,Tamas Dalmay,Vincent Moulton:
  The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.3382-3384
• 
  Valérie Marot-Lassauzaie,Michael Bernhofer,Burkhard Rost:
  Correcting mistakes in predicting distributions.3385-3386
• 
  Brent S. Pedersen,Aaron R. Quinlan:
  hts-nim: scripting high-performance genomic analyses.3387-3389
• 
  Arnaud Kress,Odile Lecompte,Olivier Poch,Julie Dawn Thompson:
  PROBE: analysis and visualization of protein block-level evolution.3390-3392
• 
  Nirvana Nursimulu,Leon L. Xu,James D. Wasmuth,Ivan Krukov,John Parkinson:
  Improved enzyme annotation with EC-specific cutoffs using DETECT v2.3393-3395
• 
  Waqasuddin Khan,Ganapathi Varma Saripella,Thomas Ludwig,Tania Cuppens,Florian Thibord,Emmanuelle Génin,Jean-Francois Deleuze,David-Alexandre Trégouët:
  MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data.3396-3398

Phylogenetics

• 
  Rudolf Biczok,Peter Bozsoky,Peter Eisenmann,Johannes Ernst,Tobias Ribizel,Fedor Scholz,Axel Trefzer,Florian Weber,Michael Hamann,Alexandros Stamatakis:
  Two C++ libraries for counting trees on a phylogenetic terrace.3399-3401

Structural Bioinformatics

• 
  Julien Dorier,Dimos Goundaroulis,Fabrizio Benedetti,Andrzej Stasiak:
  Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.3402-3404

Gene expression

• 
  Fernando Mora-Márquez,José Luis Vázquez-Poletti,Unai López de Heredia:
  NGScloud: RNA-seq analysis of non-model species using cloud computing.3405-3407

Genetics and Population Analysis

• 
  Gregor Gorjanc,John M. Hickey:
  AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs.3408-3411
• 
  Vincent Laville,Amy R. Bentley,Florian Privé,Xiaofeng Zhu,Jim Gauderman,Thomas W. Winkler,Michael A. Province,D. C. Rao,Hugues Aschard:
  VarExp: estimating variance explained by genome-wide GxE summary statistics.3412-3414

Systems Biology

• 
  Jiajian Zhou,Yile Huang,Yingzhe Ding,Jie Yuan,Huating Wang,Hao Sun:
  lncFunTK: a toolkit for functional annotation of long noncoding RNAs.3415-3416
• 
  Andreas Mock,Rolf Warta,Steffen Dettling,Benedikt Brors,Dirk Jäger,Christel Herold-Mende:
  MetaboDiff: an R package for differential metabolomic analysis.3417-3418
• 
  Baohong Zhang,Shanrong Zhao,Isaac Neuhaus:
  canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit.3419-3420

Volume 34, Number 20, October 2018

Discovery note
Genome Analysis

• 
  Zhi-Kai Yang,Hao Luo,Yanming Zhang,Baijing Wang,Feng Gao:
  Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways.3421-3426

Original Papers
Sequence Analysis

• 
  Xiaoyong Pan,Hong-Bin Shen:
  Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.3427-3436
• 
  René Rahn,Stefan Budach,Pascal Costanza,Marcel Ehrhardt,Jonny Hancox,Knut Reinert:
  Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.3437-3445
• 
  Sirajul Salekin,Jianqiu (Michelle) Zhang,Yufei Huang:
  Base-pair resolution detection of transcription factor binding site by deep deconvolutional network.3446-3453
• 
  Raffaele Giancarlo,Simona E. Rombo,Filippo Utro:
  In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes.3454-3460

Structural Bioinformatics

• 
  Nicholas A. Marze,Shourya S. Roy Burman,William Sheffler,Jeffrey J. Gray:
  Efficient flexible backbone protein-protein docking for challenging targets.3461-3469

Gene expression

• 
  Wenping Deng,Kui Zhang,Sanzhen Liu,Patrick X. Zhao,Shizhong Xu,Hairong Wei:
  JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions.3470-3478
• 
  Wenwen Min,Juan Liu,Shihua Zhang:
  Edge-group sparse PCA for network-guided high dimensional data analysis.3479-3487

Genetics and Population Analysis

• 
  Péter Kómár,Deniz Kural:
  geck: trio-based comparative benchmarking of variant calls.3488-3495
• 
  Peter M. Bourke,Geert van Geest,Roeland E. Voorrips,Johannes Jansen,Twan Kranenburg,Arwa Shahin,Richard G. F. Visser,Paul Arens,Marinus J. M. Smulders,Chris Maliepaard:
  polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.3496-3502

Systems Biology

• 
  Tim Kehl,Lara Schneider,Kathrin Kattler,Daniel Stöckel,Jenny Wegert,Nico Gerstner,Nicole Ludwig,Ute Distler,Markus Schick,Ulrich Keller,Stefan Tenzer,Manfred Gessler,Jörn Walter,Andreas Keller,Norbert M. Graf,Eckart Meese,Hans-Peter Lenhof:
  REGGAE: a novel approach for the identification of key transcriptional regulators.3503-3510
• 
  Joshua Klein,Luis Carvalho,Joseph Zaia:
  Application of network smoothing to glycan LC-MS profiling.3511-3518
• 
  Lixin Cheng,Kwong-Sak Leung:
  Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome.3519-3528

Data and Text Mining

• 
  Han-Ming Wu,Yin-Jing Tien,Meng-Ru Ho,Hai-Gwo Hwu,Wen-Chang Lin,Mi-Hua Tao,Chun-Houh Chen:
  Covariate-adjusted heatmaps for visualizing biological data via correlation decomposition.3529-3538
• 
  Thanh Hai Dang,Hoang-Quynh Le,Trang M. Nguyen,Sinh T. Vu:
  D3NER: biomedical named entity recognition using CRF-biLSTM improved with fine-tuned embeddings of various linguistic information.3539-3546

Databases and Ontologies

• 
  Yang Yang,Xiaofeng Fu,Wenhao Qu,Yiqun Xiao,Hong-Bin Shen:
  MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association.3547-3556
• 
  Rostam M. Razban,Amy I Gilson,Niamh Durfee,Hendrik Strobelt,Kasper Dinkla,Jeong-Mo Choi,Hanspeter Pfister,Eugene I. Shakhnovich:
  ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.3557-3565
• 
  Pallab Bhowmick,Yassene Mohammed,Christoph H. Borchers:
  MRMAssayDB: an integrated resource for validated targeted proteomics assays.3566-3571

Applications Notes
Genome Analysis

• 
  Véronique Geoffroy,Yvan Herenger,Arnaud Kress,Corinne Stoetzel,Amélie Piton,Hélène Dollfus,Jean Muller:
  AnnotSV: an integrated tool for structural variations annotation.3572-3574

Sequence Analysis

• 
  Kathrin M. Seibt,Thomas Schmidt,Tony Heitkam:
  FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses.3575-3577
• 
  Daniel Quang,Yuanfang Guan,Stephen C. J. Parker:
  YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU.3578-3580
• 
  Jiaxing Lin,Jeremy Gresham,Tongrong Wang,So Young Kim,James Alvarez,Jeffrey S. Damrauer,Scott Floyd,Joshua A. Granek,Andrew S. Allen,Cliburn Chan,Jichun Xie,Kouros Owzar:
  bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.3581-3583

Structural Bioinformatics

• 
  Joshua M. A Bullock,Konstantinos Thalassinos,Maya Topf:
  Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry.3584-3585
• 
  Adam Jurcík,David Bednar,Jan Byska,Sérgio M. Marques,Katarína Furmanová,Lukas Daniel,Piia Kokkonen,Jan Brezovsky,Ondrej Strnad,Jan Stourac,Antonín Pavelka,Martin Manak,Jirí Damborský,Barbora Kozlíková:
  CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.3586-3588

Systems Biology

• 
  William M. B. Edmands,Josie Hayes,Stephen M. Rappaport:
  SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis.3589-3590
• 
  Emmanuel Klinger,Dennis Rickert,Jan Hasenauer:
  pyABC: distributed, likelihood-free inference.3591-3593
• 
  Cheng Chang,Kaikun Xu,Chaoping Guo,Jinxia Wang,Qi Yan,Jian Zhang,Fuchu He,Yunping Zhu:
  PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data.3594-3596

Data and Text Mining

• 
  Jonathan D. Tyzack,António J. M. Ribeiro,Neera Borkakoti,Janet M. Thornton:
  Transform-MinER: transforming molecules in enzyme reactions.3597-3599

Corrigendum
Data and Text Mining

• 
  Johannes Köster,Sven Rahmann:
  Snakemake - a scalable bioinformatics workflow engine.3600

Volume 34, Number 21, November 2018

Original Papers
Genome Analysis

• 
  Will P. M. Rowe,Martyn D. Winn:
  Indexed variation graphs for efficient and accurate resistome profiling.3601-3608
• 
  Xinyan Zhang,Bingzong Li,Huiying Han,Sha Song,Hongxia Xu,Zixuan Yi,Yating Hong,Wenzhuo Zhuang,Nengjun Yi:
  Pathway-structured predictive modeling for multi-level drug response in multiple myeloma.3609-3615

Sequence Analysis

• 
  William H. Majoros,Carson Holt,Michael Campbell,Doreen Ware,Mark Yandell,Timothy E. Reddy:
  Predicting gene structure changes resulting from genetic variants via exon definition features.3616-3623
• 
  Le Zhang,Ming Xiao,Jingsong Zhou,Jun Yu:
  Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA).3624-3630
• 
  Anish Man Singh Shrestha,Naruki Yoshikawa,Kiyoshi Asai:
  Combining probabilistic alignments with read pair information improves accuracy of split-alignments.3631-3637

Phylogenetics

• 
  Kris V. Parag,Oliver G. Pybus:
  Exact Bayesian inference for phylogenetic birth-death models.3638-3645
• 
  Wandrille Duchemin,Guillaume Gence,Anne-Muriel Arigon Chifolleau,Lars Arvestad,Mukul S. Bansal,Vincent Berry,Bastien Boussau,François Chevenet,Nicolas Comte,Adrián A. Davín,Christophe Dessimoz,David Dylus,Damir Hasic,Diego Mallo,Rémi Planel,David Posada,Céline Scornavacca,Gergely J. Szöllosi,Louxin Zhang,Eric Tannier,Vincent Daubin:
  RecPhyloXML: a format for reconciled gene trees.3646-3652

Structural Bioinformatics

• 
  Dinara R. Usmanova,Natalya S. Bogatyreva,Joan Ariño Bernad,Aleksandra A. Eremina,Anastasiya A. Gorshkova,German M. Kanevskiy,Lyubov R. Lonishin,Alexander V. Meister,Alisa G. Yakupova,Fyodor A. Kondrashov,Dmitry N. Ivankov:
  Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation.3653-3658
• 
  Fabrizio Pucci,Katrien V. Bernaerts,Jean Marc Kwasigroch,Marianne Rooman:
  Quantification of biases in predictions of protein stability changes upon mutations.3659-3665
• 
  Marta M. Stepniewska-Dziubinska,Piotr Zielenkiewicz,Pawel Siedlecki:
  Development and evaluation of a deep learning model for protein-ligand binding affinity prediction.3666-3674
• 
  Pawel P. Wozniak,J. Pelc,M. Skrzypecki,Gert Vriend,Malgorzata Kotulska:
  Bio-knowledge-based filters improve residue-residue contact prediction accuracy.3675-3683

Gene expression

• 
  Hao Jiang,Lydia L. Sohn,Haiyan Huang,Luonan Chen:
  Single cell clustering based on cell-pair differentiability correlation and variance analysis.3684-3694

Genetics and Population Analysis

• 
  Levent Albayrak,Kamil Khanipov,George Golovko,Yuriy Fofanov:
  Detection of multi-dimensional co-exclusion patterns in microbial communities.3695-3701

Systems Biology

• 
  Ciaran M. Welsh,Nicola Fullard,Carole J. Proctor,Alvaro Martinez-Guimera,Robert J. Isfort,Charles C. Bascom,Ryan Tasseff,Stefan A. Przyborski,Daryl P. Shanley:
  PyCoTools: a Python toolbox for COPASI.3702-3710

Data and Text Mining

• 
  Stefano Nembrini,Inke R. König,Marvin N. Wright:
  The revival of the Gini importance?3711-3718
• 
  Patryk Orzechowski,Moshe Sipper,Xiuzhen Huang,Jason H. Moore:
  EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery.3719-3726
• 
  Yunchuan Kong,Tianwei Yu:
  A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data.3727-3737

Applications Notes
Genome Analysis

• 
  Louis-Marie Bobay,Brian Shin-Hua Ellis,Howard Ochman:
  ConSpeciFix: classifying prokaryotic species based on gene flow.3738-3740
• 
  Donghyun Tae,Junhee Seok:
  mEBT: multiple-matching evidence-based translator of murine genomic responses for human immunity studies.3741-3743

Sequence Analysis

• 
  Huijun Mai,Yifan Zhang,Dinghua Li,Henry Chi-Ming Leung,Ruibang Luo,Chi-Kwong Wong,Hing-Fung Ting,Tak Wah Lam:
  AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.3744-3746
• 
  Jingjing Zhai,Jie Song,Qian Cheng,Yunjia Tang,Chuang Ma:
  PEA: an integrated R toolkit for plant epitranscriptome analysis.3747-3749
• 
  Simon H. Tausch,Benjamin Strauch,Andreas Andrusch,Tobias P. Loka,Martin S. Lindner,Andreas Nitsche,Bernhard Y. Renard:
  LiveKraken--real-time metagenomic classification of illumina data.3750-3752
• 
  Matthieu Leray,Shian-Lei Ho,I-Jeng Lin,Ryuji J. Machida:
  MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database.3753-3754

Structural Bioinformatics

• 
  Alexander S. Rose,Anthony R. Bradley,Yana Valasatava,Jose M. Duarte,Andreas Prlic,Peter W. Rose:
  NGL viewer: web-based molecular graphics for large complexes.3755-3758
• 
  Caroline J. Ross,Bilal Nizami,Michael Glenister,Olivier Sheik Amamuddy,Ali Rana Atilgan,Canan Atilgan,Özlem Tastan Bishop:
  MODE-TASK: large-scale protein motion tools.3759-3763

Systems Biology

• 
  Phit Ling Tan,Yosvany López,Kenta Nakai,Ashwini Patil:
  TimeXNet Web: identifying cellular response networks from diverse omics time-course data.3764-3765
• 
  Guangchuang Yu:
  Using meshes for MeSH term enrichment and semantic analyses.3766-3767

Databases and Ontologies

• 
  Bo Peng,Gao Wang,Jun Ma,Man Chong Leong,Chris Wakefield,James M. Melott,Yulun Chiu,Di Du,John N. Weinstein:
  SoS Notebook: an interactive multi-language data analysis environment.3768-3770
• 
  Chun-Jie Liu,Fei-Fei Hu,Meng-Xuan Xia,Leng Han,Qiong Zhang,An-Yuan Guo:
  GSCALite: a web server for gene set cancer analysis.3771-3772
• 
  Alexandre Borrel,Nicole C. Kleinstreuer,Denis Fourches:
  Exploring drug space with ChemMaps.com.3773-3775

Bioimage Informatics

• 
  Juan José Moreno,Antonio Martínez-Sánchez,José Antonio Martínez,Ester M. Garzón,José-Jesús Fernández:
  TomoEED: fast edge-enhancing denoising of tomographic volumes.3776-3778

Corrigenda
Bioimage Informatics

• 
  Rawan S. Olayan,Haitham Ashoor,Vladimir B. Bajic:
  DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches.3779
• 
  Nikolaos Tsiantis,Eva Balsa-Canto,Julio R. Banga:
  Optimality and identification of dynamic models in systems biology: an inverse optimal control framework.3780

Volume 34, Number 22, November 2018

Original Papers
Genome Analysis

• 
  Ming Wen,Peisheng Cong,Zhimin Zhang,Hongmei Lu,Tonghua Li:
  DeepMirTar: a deep-learning approach for predicting human miRNA targets.3781-3787
• 
  Francisco Abad Navarro,María Eugenia de la Morena-Barrio,Jesualdo Tomás Fernández-Breis,Javier Corral:
  Lost in translation: bioinformatic analysis of variations affecting the translation initiation codon in the human genome.3788-3794
• 
  Panisa Treepong,Christophe Guyeux,Alexandre Meunier,Charlotte Couchoud,Didier Hocquet,Benoit Valot:
  panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.3795-3800
• 
  Zhou Fang,Tianzhou Ma,Gong Tang,Li Zhu,Qi Yan,Ting Wang,Juan C. Celedón,Wei Chen,George C. Tseng:
  Bayesian integrative model for multi-omics data with missingness.3801-3808

Sequence Analysis

• 
  Vitor L. Coelho,Michael Sammeth:
  An automated method for detecting alternatively spliced protein domains.3809-3816
• 
  Kemal Eren,Ben Murrell:
  RIFRAF: a frame-resolving consensus algorithm.3817-3824
• 
  Cheng Yang,Longshu Yang,Man Zhou,Haoling Xie,Chengjiu Zhang,May D. Wang,Huaiqiu Zhu:
  LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning.3825-3834
• 
  Bin Liu,Kai Li,De-Shuang Huang,Kuo-Chen Chou:
  iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach.3835-3842

Phylogenetics

• 
  Nicola F. Müller,David A. Rasmussen,Tanja Stadler:
  MASCOT: parameter and state inference under the marginal structured coalescent approximation.3843-3848

Structural Bioinformatics

• 
  Hosna Jabbari,Ian Wark,Carlo Montemagno,Sebastian Will:
  Knotty: efficient and accurate prediction of complex RNA pseudoknot structures.3849-3856
• 
  Laura Pérez-Benito,Andrew Henry,Minos-Timotheos Matsoukas,Laura Lopez,Daniel Pulido,Miriam Royo,Arnau Cordomí,Gary Tresadern,Leonardo Pardo:
  The size matters? A computational tool to design bivalent ligands.3857-3863

Genetics and Population Analysis

• 
  Ehsan Motazedi,Dick de Ridder,Richard Finkers,Samantha J. Baldwin,Susan Thomson,Katrina Monaghan,Chris Maliepaard:
  TriPoly: haplotype estimation for polyploids using sequencing data of related individuals.3864-3872

Systems Biology

• 
  Vladimir Gligorijevic,Meet Barot,Richard Bonneau:
  deepNF: deep network fusion for protein function prediction.3873-3881
• 
  Mingyuan Tian,Jennifer L. Reed:
  Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis.3882-3888

Data and Text Mining

• 
  Junghwan Baek,Byunghan Lee,Sunyoung Kwon,Sungroh Yoon:
  LncRNAnet: long non-coding RNA identification using deep learning.3889-3897
• 
  Anna M. Schmoker,Heather E. Driscoll,Stefanie R. Geiger,James J. Vincent,Alicia M. Ebert,Bryan A. Ballif:
  An in silico proteomics screen to predict and prioritize protein-protein interactions dependent on post-translationally modified motifs.3898-3906
• 
  Chayaporn Suphavilai,Denis Bertrand,Niranjan Nagarajan:
  Predicting Cancer Drug Response using a Recommender System.3907-3914

Applications Notes
Genome Analysis

• 
  Braulio Valdebenito-Maturana,Gonzalo Riadi:
  TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data.3915-3916
• 
  Liya Wang,Zhenyuan Lu,Peter Van Buren,Doreen Ware:
  SciApps: a cloud-based platform for reproducible bioinformatics workflows.3917-3920
• 
  Massimiliano Volpe,Marco Miralto,Stefano Gustincich,Remo Sanges:
  ClusterScan: simple and generalistic identification of genomic clusters.3921-3923

Sequence Analysis

• 
  Kevin D. Murray,Justin O. Borevitz:
  Axe: rapid, competitive sequence read demultiplexing using a trie.3924-3925
• 
  Elisha D. Roberson:
  Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files.3926-3928
• 
  Simon Whelan,Iker Irisarri,Fabien Burki:
  PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences.3929-3930
• 
  Sandeep Kumar Dhanda,Randi Vita,Brendan Ha,Alba Grifoni,Bjoern Peters,Alessandro Sette:
  ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.3931-3933
• 
  Masahiro Kanai,Yuichi Maeda,Yukinori Okada:
  Grimon: graphical interface to visualize multi-omics networks.3934-3936
• 
  Nicola Bordin,Damien P. Devos:
  ICBdocker: a Docker image for proteome annotation and visualization.3937-3938
• 
  Kodi Collins,Tandy J. Warnow:
  PASTA for proteins.3939-3941

Structural Bioinformatics

• 
  Andrew J. Guy,Vashti Irani,Jack S. Richards,Paul A. Ramsland:
  BioStructMap: a Python tool for integration of protein structure and sequence-based features.3942-3944
• 
  M. Eric Irrgang,Jennifer M. Hays,Peter M. Kasson:
  gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.3945-3947
• 
  Joseph Masison,Paul J. Michalski,Leslie M. Loew,Adam D. Schuyler:
  mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling.3948-3950

Systems Biology

• 
  Phu Van,Wenxin Jiang,Raphael Gottardo,Greg Finak:
  ggCyto: next generation open-source visualization software for cytometry.3951-3953
• 
  Bo Liao,Zhibin Ning,Kai Cheng,Xu Zhang,Leyuan Li,Janice Mayne,Daniel Figeys:
  iMetaLab 1.0: a web platform for metaproteomics data analysis.3954-3956

Data and Text Mining

• 
  Teemu D. Laajala,Mika Murtojärvi,Arho Virkki,Tero Aittokallio:
  ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts.3957-3959

Volume 34, Number 23, December 2018

Discovery note
Structural Bioinformatics

• 
  Joana Pereira,Andrei N. Lupas:
  The ancestral KH peptide at the root of a domain family with three different folds.3961-3965

Original Papers
Genome Analysis

• 
  Ping Chen,Xinyun Jing,Jian Ren,Han Cao,Pei Hao,Xuan Li:
  Modelling BioNano optical data and simulation study of genome map assembly.3966-3974
• 
  Yuanfang Guan,Tingyang Li,Hongjiu Zhang,Fan Zhu,Gilbert S. Omenn:
  Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile.3975-3982
• 
  Josine L. Min,Gibran Hemani,George Davey Smith,Caroline Relton,Matthew Suderman:
  Meffil: efficient normalization and analysis of very large DNA methylation datasets.3983-3989

Sequence Analysis

• 
  Alina Munteanu,Neelanjan Mukherjee,Uwe Ohler:
  SSMART: sequence-structure motif identification for RNA-binding proteins.3990-3998
• 
  Guodong Chen,Man Cao,Kun Luo,Lina Wang,Pingping Wen,Shaoping Shi:
  ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization.3999-4006
• 
  Leyi Wei,Chen Zhou,Huangrong Chen,Jiangning Song,Ran Su:
  ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides.4007-4016
• 
  Sayaka Miura,Karen Gomez,Oscar D. Murillo,Louise A. Huuki,Tracy Vu,Tiffany Buturla,Sudhir Kumar:
  Predicting clone genotypes from tumor bulk sequencing of multiple samples.4017-4026
• 
  Johan Bengtsson-Palme,Rodney T. Richardson,Marco Meola,Christian Wurzbacher,Émilie D. Tremblay,Kaisa Thorell,Kärt Kanger,K. Martin Eriksson,Guillaume J. Bilodeau,Reed M. Johnson,Martin Hartmann,R. Henrik Nilsson:
  Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.4027-4033

Structural Bioinformatics

• 
  Luciano Censoni,Leandro Martínez:
  Prediction of kinetics of protein folding with non-redundant contact information.4034-4038
• 
  Jack Hanson,Kuldip K. Paliwal,Thomas Litfin,Yuedong Yang,Yaoqi Zhou:
  Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.4039-4045
• 
  Georgy Derevyanko,Sergei Grudinin,Yoshua Bengio,Guillaume Lamoureux:
  Deep convolutional networks for quality assessment of protein folds.4046-4053

Gene expression

• 
  Florian Erhard:
  Estimating pseudocounts and fold changes for digital expression measurements.4054-4063
• 
  Pietro Coretto,Angela Serra,Roberto Tagliaferri:
  Robust clustering of noisy high-dimensional gene expression data for patients subtyping.4064-4072

Genetics and Population Analysis

• 
  Weilong Li,Lene Christiansen,Jacob v. B. Hjelmborg,Jan Baumbach,Qihua Tan:
  On the power of epigenome-wide association studies using a disease-discordant twin design.4073-4078

Systems Biology

• 
  Mathurin Dorel,Bertram Klinger,Torsten Gross,Anja Sieber,Anirudh Prahallad,Evert Bosdriesz,Lodewyk F. A. Wessels,Nils Blüthgen:
  Modelling signalling networks from perturbation data.4079-4086

Data and Text Mining

• 
  John M. Giorgi,Gary D. Bader:
  Transfer learning for biomedical named entity recognition with neural networks.4087-4094
• 
  Chen-Hao Chen,Tengfei Xiao,Han Xu,Peng Jiang,Clifford A. Meyer,Wei Li,Myles Brown,Xiaole Shirley Liu:
  Improved design and analysis of CRISPR knockout screens.4095-4101

Bioimage Informatics

• 
  Adela D. Staszowska,Patrick Fox-Roberts,Liisa M. Hirvonen,Christopher J. Peddie,Lucy M. Collinson,Gareth E. Jones,Susan Cox:
  The Rényi divergence enables accurate and precise cluster analysis for localization microscopy.4102-4111

Applications Notes
Genome Analysis

• 
  Kari Nousiainen,Kartiek Kanduri,Isis Ricaño-Ponce,Cisca Wijmenga,Riitta Lahesmaa,Vinod Kumar,Harri Lähdesmäki:
  snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions.4112-4114
• 
  Katarzyna Z. Kedzierska,Livia Gerber,Daniele Cagnazzi,Michael Krützen,Aakrosh Ratan,Logan Kistler:
  SONiCS: PCR stutter noise correction in genome-scale microsatellites.4115-4117
• 
  Blanca Taboada,Karel Estrada,Ricardo Ciria,Enrique Merino:
  Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes.4118-4120

Phylogenetics

• 
  James Hadfield,Colin Megill,Sidney M. Bell,John Huddleston,Barney Potter,Charlton Callender,Pavel Sagulenko,Trevor Bedford,Richard A. Neher:
  Nextstrain: real-time tracking of pathogen evolution.4121-4123

Structural Bioinformatics

• 
  Alejandro A. Icazatti,Osvaldo A. Martin,Myriam Villegas,Igal Szleifer,Jorge A. Vila:
  13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA.4124-4126
• 
  David Hoksza,Piotr Gawron,Marek Ostaszewski,Reinhard Schneider:
  MolArt: a molecular structure annotation and visualization tool.4127-4128

Systems Biology

• 
  Kun Sun,Jiguang Wang,Huating Wang,Hao Sun:
  GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies.4129-4130

Data and Text Mining

• 
  Nima Aghaeepour,Erin F. Simonds,David J. H. F. Knapp,Robert V. Bruggner,Karen Sachs,Anthony Culos,Pier Federico Gherardini,Nikolay Samusik,Gabriela K. Fragiadakis,Sean Bendall,Brice Gaudilliere,Martin S. Angst,Connie J. Eaves,William A. Weiss,Wendy J. Fantl,Garry P. Nolan:
  GateFinder: projection-based gating strategy optimization for flow and mass cytometry.4131-4133
• 
  Andrea S. Martinez-Vernon,Frederick Farrell,Orkun S. Soyer:
  MetQy - an R package to query metabolic functions of genes and genomes.4134-4137

Corrigenda
Data and Text Mining

• 
  Kevin K. Yang,Zachary Wu,Claire N. Bedbrook,Frances H. Arnold:
  Learned protein embeddings for machine learning.4138
• 
  Konstantinos Sechidis,Konstantinos Papangelou,Paul D. Metcalfe,David Svensson,James Weatherall,Gavin Brown:
  Distinguishing prognostic and predictive biomarkers: an information theoretic approach.4139

Erratum
Data and Text Mining

• 
  Rostam M. Razban,Amy I Gilson,Niamh Durfee,Hendrik Strobelt,Kasper Dinkla,Jeong-Mo Choi,Hanspeter Pfister,Eugene I. Shakhnovich:
  ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.4140

Volume 34, Number 24, December 2018

Original Papers
Genome Analysis

• 
  Hui-Yi Lin,Po-Yu Huang,Dung-Tsa Chen,Heng-Yuan Tung,Thomas A. Sellers,Julio M. Pow-Sang,Rosalind A. Eeles,Doug Easton,Zsofia Kote-Jarai,Ali Amin Al Olama,Sara Benlloch,Kenneth Muir,Graham G. Giles,Fredrik Wiklund,Henrik Gronberg,Christopher A. Haiman,Johanna Schleutker,Børge G. Nordestgaard,Ruth C. Travis,Freddie Hamdy,David E. Neal,Nora Pashayan,Kay-Tee Khaw,Janet L. Stanford,William J. Blot,Stephen N. Thibodeau,Christiane Maier,Adam S. Kibel,Cezary Cybulski,Lisa A. Cannon-Albright,Hermann Brenner,Radka Kaneva,Jyotsna Batra,Manuel R. Teixeira,Hardev Pandha,Yong-Jie Lu,PRACTICAL Consortium,Jong Y. Park:
  AA9int: SNP interaction pattern search using non-hierarchical additive model set.4141-4150
• 
  Jungwoo Lee,Sejoon Oh,Lee Sael:
  GIFT: Guided and Interpretable Factorization for Tensors with an application to large-scale multi-platform cancer analysis.4151-4158
• 
  Ibrahim Ahmed,Peter J. Witbooi,Alan Christoffels:
  Prediction of human-Bacillus anthracis protein-protein interactions using multi-layer neural network.4159-4164
• 
  Kay Prüfer:
  snpAD: an ancient DNA genotype caller.4165-4171
• 
  Guoxian Yu,Yuan Jiang,Jun Wang,Hao Zhang,Haiwei Luo:
  BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage.4172-4179

Sequence Analysis

• 
  Jasper Zuallaert,Fréderic Godin,Mijung Kim,Arne Soete,Yvan Saeys,Wesley De Neve:
  SpliceRover: interpretable convolutional neural networks for improved splice site prediction.4180-4188
• 
  Victoria G. Crawford,Alan Kuhnle,Christina Boucher,Rayan Chikhi,Travis Gagie:
  Practical dynamic de Bruijn graphs.4189-4195
• 
  Zhen-Dong Su,Yan Huang,Zhao-Yue Zhang,Ya-Wei Zhao,Dong Wang,Wei Chen,Kuo-Chen Chou,Hao Lin:
  iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC.4196-4204
• 
  Sarah Sandmann,Mohsen Karimi,Aniek O. de Graaf,Christian Rohde,Stefanie Göllner,Julian Varghese,Jan Ernsting,Gunilla Walldin,Bert A. van der Reijden,Carsten Müller-Tidow,Luca Malcovati,Eva Hellström-Lindberg,Joop H. Jansen,Martin Dugas:
  appreci8: a pipeline for precise variant calling integrating 8 tools.4205-4212
• 
  Pierre Morisse,Thierry Lecroq,Arnaud Lefebvre:
  Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph.4213-4222
• 
  Fuyi Li,Chen Li,Tatiana T. Marquez-Lago,André Leier,Tatsuya Akutsu,Anthony W. Purcell,Alexander Ian Smith,Trevor Lithgow,Roger J. Daly,Jiangning Song,Kuo-Chen Chou:
  Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.4223-4231

Gene expression

• 
  Junpeng Zhang,Lin Liu,Jiuyong Li,Thuc Duy Le:
  LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer.4232-4240

Genetics and Population Analysis

• 
  Berke Ç Toptas,Goran Rakocevic,Péter Kómár,Deniz Kural:
  Comparing complex variants in family trios.4241-4247

Systems Biology

• 
  Siu Hung Joshua Chan,Lin Wang,Satyakam Dash,Costas D. Maranas:
  Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints.4248-4255
• 
  Xing Chen,Lei Wang,Jia Qu,Na-Na Guan,Jian-Qiang Li:
  Predicting miRNA-disease association based on inductive matrix completion.4256-4265
• 
  Carolin Loos,Sabrina Krause,Jan Hasenauer:
  Hierarchical optimization for the efficient parametrization of ODE models.4266-4273

Data and Text Mining

• 
  Mehrdad Mansouri,Bowei Yuan,Colin J. D. Ross,Bruce C. Carleton,Martin Ester:
  HUME: large-scale detection of causal genetic factors of adverse drug reactions.4274-4283

Applications Notes
Genome Analysis

• 
  Lewis M. Ward,Patrick M. Shih,Woodward W. Fischer:
  MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes.4284-4286
• 
  Mark A. Walker,Chandra Sekhar Pedamallu,Akinyemi I. Ojesina,Susan Bullman,Ted Sharpe,Christopher W. Whelan,Matthew Meyerson:
  GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts.4287-4289

Sequence Analysis

• 
  Aleksander Cislak,Szymon Grabowski,Jan Holub:
  SOPanG: online text searching over a pan-genome.4290-4292
• 
  Tyler K. Chafin,Marlis R. Douglas,Michael E. Douglas:
  MrBait: universal identification and design of targeted-enrichment capture probes.4293-4296

Structural Bioinformatics

• 
  Jacob S. Lu,Eckart Bindewald,Wojciech Kasprzak,Bruce A. Shapiro:
  RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.4297-4299
• 
  Naohiro Kobayashi,Yoshikazu Hattori,Takashi Nagata,Shoko Shinya,Peter Güntert,Chojiro Kojima,Toshimichi Fujiwara:
  Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks.4300-4301

Gene expression

• 
  Patryk Orzechowski,Artur Panszczyk,Xiuzhen Huang,Jason H. Moore:
  runibic: a Bioconductor package for parallel row-based biclustering of gene expression data.4302-4304
• 
  Mitulkumar V. Patel:
  iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data.4305-4306

Genetics and Population Analysis

• 
  Peng Zhang,Benedetta Bigio,Franck Rapaport,Shen-Ying Zhang,Jean-Laurent Casanova,Laurent Abel,Bertrand Boisson,Yuval Itan:
  PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations.4307-4309
• 
  John A. Lees,Marco Galardini,Stephen D. Bentley,Jeffrey N. Weiser,Jukka Corander:
  pyseer: a comprehensive tool for microbial pangenome-wide association studies.4310-4312

Systems Biology

• 
  Jasmine Chong,Jianguo Xia:
  MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data.4313-4314

Databases and Ontologies

• 
  Sam Q. Sun,R. Jay Mashl,Sohini Sengupta,Adam D. Scott,Weihua Wang,Prag Batra,Liang-Bo Wang,Matthew A. Wyczalkowski,Li Ding:
  Database of evidence for precision oncology portal.4315-4317

Bioimage Informatics

• 
  Leonardo Martins,Ramakanth Neeli-Venkata,Samuel M. D. Oliveira,Antti Häkkinen,Andre S. Ribeiro,José M. Fonseca:
  SCIP: a single-cell image processor toolbox.4318-4320