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, The 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, The 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 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, The 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