Bioinformatics, Volume 33

Volume 33, Number 1, January 2017

Original Papers
Genome Analysis

• 
  Wei Yang, Saurabh Sinha:
  A novel method for predicting activity of cis-regulatory modules, based on a diverse training set. 1-7
• 
  Rafael Rosales, Rodrigo D. Drummond, Renan Valieris, Emmanuel Dias-Neto, Israel T. da Silva:
  signeR: an empirical Bayesian approach to mutational signature discovery. 8-16
• 
  Sandra L. Taylor, L. Renee Ruhaak, Robert H. Weiss, Karen Kelly, Kyoungmi Kim:
  Multivariate two-part statistics for analysis of correlated mass spectrometry data from multiple biological specimens. 17-25

Sequence Analysis

• 
  Can Kockan, Faraz Hach, Iman Sarrafi, Robert H. Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W. Wyatt, Stanislav Volik, Kim N. Chi, Colin C. Collins, Süleyman Cenk Sahinalp:
  SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. 26-34
• 
  Bin Liu, Shanyi Wang, Ren Long, Kuo-Chen Chou:
  iRSpot-EL: identify recombination spots with an ensemble learning approach. 35-41
• 
  Akinori Awazu:
  Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. 42-48
• 
  Matei David, L. J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson:
  Nanocall: an open source basecaller for Oxford Nanopore sequencing data. 49-55

Structural Bioinformatics

• 
  Lazaros Mavridis, Robert W. Janes:
  PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates. 56-63

Genetics and Population Analysis

• 
  Il-Youp Kwak, Wei Pan:
  Gene- and pathway-based association tests for multiple traits with GWAS summary statistics. 64-71
• 
  Verena Heinrich, Tom Kamphans, Stefan Mundlos, Peter N. Robinson, Peter M. Krawitz:
  A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data. 72-78
• 
  Jie Zheng, Santiago Rodríguez, Charles Laurin, Denis Baird, Lea Trela-Larsen, Mesut A. Erzurumluoglu, Yi Zheng, Jon White, Claudia Giambartolomei, Delilah Zabaneh, Richard Morris, Meena Kumari, Juan P. Casas, Aroon D. Hingorani, David M. Evans, Tom R. Gaunt, Ian N. M. Day:
  HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics. 79-86

Systems Biology

• 
  Minsuk Kim, Gwanggyu Sun, Dong-Yup Lee, Byung-Gee Kim:
  BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals. 87-94
• 
  Igor Marín de Mas, Eric Fanchon, Balázs Papp, Susana G. Kalko, Josep Roca, Marta Cascante:
  Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. 95-103
• 
  Victor Jaravine, Silke Raffegerst, Dolores J. Schendel, Dmitrij Frishman:
  Assessment of cancer and virus antigens for cross-reactivity in human tissues. 104-111

Databases and Ontologies

• 
  Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen:
  LncVar: a database of genetic variation associated with long non-coding genes. 112-118

Application Notes
Genome Analysis

• 
  Anuj Gupta, I. King Jordan, Lavanya Rishishwar:
  stringMLST: a fast k-mer based tool for multilocus sequence typing. 119-121

Sequence Analysis

• 
  Yongchun Zuo, Yuan Li, Yingli Chen, Guangpeng Li, Zhenhe Yan, Lei Yang:
  PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition. 122-124

Phylogenetics

• 
  M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Quinn Snell, Seth M. Bybee:
  The OGCleaner: filtering false-positive homology clusters. 125-127
• 
  Marta Nascimento, Adriano Sousa, Mário Ramirez, Alexandre P. Francisco, João A. Carriço, Cátia Vaz:
  PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. 128-129
• 
  Michael R. McKain, Ryan H. Hartsock, Molly M. Wohl, Elizabeth A. Kellogg:
  Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. 130-132

Structural Bioinformatics

• 
  Sébastien Buchoux:
  FATSLiM: a fast and robust software to analyze MD simulations of membranes. 133-134

Gene expression

• 
  Samuel Wieczorek, Florence Combes, Cosmin Lazar, Quentin Giai Gianetto, Laurent Gatto, Alexia Dorffer, Anne-Marie Hesse, Yohann Couté, Myriam Ferro, Christophe Bruley, Thomas Burger:
  DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. 135-136
• 
  Ilias Georgakopoulos-Soares, Naman Jain, Jesse M. Gray, Martin Hemberg:
  MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. 137-138
• 
  Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch:
  RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints. 139-141

Genetics and Population Analysis

• 
  Rudy Arthur, Ole Schulz-Trieglaff, Anthony J. Cox, Jared O'Connell:
  AKT: ancestry and kinship toolkit. 142-144

Data and Text Mining

• 
  Takaya Saito, Marc Rehmsmeier:
  Precrec: fast and accurate precision-recall and ROC curve calculations in R. 145-147

Databases and Ontologies

• 
  Carlo Ravagli, Francois Pognan, Philippe Marc:
  OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts. 148-149

Corrigendum

• 
  Charlotte Siska, Russell Bowler, Katerina J. Kechris:
  The discordant method: a novel approach for differential correlation. 150

Volume 33, Number 2, January 2017

Discovery Note
Sequence Analysis

• 
  Ahmed Arslan, Vera van Noort:
  Evolutionary conservation of Ebola virus proteins predicts important functions at residue level. 151-154

Original Papers
Genome Analysis

• 
  Niko Popitsch, WGS500 Consortium, Anna Schuh, Jenny C. Taylor:
  ReliableGenome: annotation of genomic regions with high/low variant calling concordance. 155-160
• 
  Xiao Wang, Jinghua Gu, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
  DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. 161-168
• 
  Junwei Luo, Jianxin Wang, Zhen Zhang, Min Li, Fang-Xiang Wu:
  BOSS: a novel scaffolding algorithm based on an optimized scaffold graph. 169-176
• 
  Xi Chen, Xu Shi, Leena Hilakivi-Clarke, Ayesha N. Shajahan-Haq, Robert Clarke, Jianhua Xuan:
  PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification. 177-183

Sequence Analysis

• 
  Ying Liang, Kunlong Qiu, Bo Liao, Wen Zhu, Xuanlin Huang, Lin Li, Xiangtao Chen, Keqin Li:
  Seeksv: an accurate tool for somatic structural variation and virus integration detection. 184-191
• 
  Bo Liu, Yan Gao, Yadong Wang:
  LAMSA: fast split read alignment with long approximate matches. 192-201
• 
  Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu:
  An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. 202-209
• 
  Irene Rodríguez-Luján, Jeff Hasty, Ramón Huerta:
  FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners. 210-218

Gene expression

• 
  Michael Altenbuchinger, Thorsten Rehberg, Helena U. Zacharias, Frank Stämmler, K. Dettmer, D. Weber, Andreas Hiergeist, A. Gessner, E. Holler, Peter J. Oefner, Rainer Spang:
  Reference point insensitive molecular data analysis. 219-226
• 
  Joseph Azofeifa, Robin D. Dowell:
  A generative model for the behavior of RNA polymerase. 227-234
• 
  Chunxuan Shao, Thomas Höfer:
  Robust classification of single-cell transcriptome data by nonnegative matrix factorization. 235-242

Genetics and Population Analysis

• 
  Wenyu Wang, Jingcan Hao, Shuyu Zheng, Qianrui Fan, Awen He, Yan Wen, Xiong Guo, Cuiyan Wu, Sen Wang, Tielin Yang, Hui Shen, Xiangding Chen, Qing Tian, Lijun Tan, Hong-Wen Deng, Feng Zhang:
  Tissue-specific pathway association analysis using genome-wide association study summaries. 243-247
• 
  Gleb Kichaev, Megan Roytman, Ruth Johnson, Eleazar Eskin, Sara Lindström, Peter Kraft, Bogdan Pasaniuc:
  Improved methods for multi-trait fine mapping of pleiotropic risk loci. 248-255

Systems Biology

• 
  Yan Yan, Shangzhao Qiu, Zhuxuan Jin, Sihong Gong, Yun Bai, Jianwei Lu, Tianwei Yu:
  Detecting subnetwork-level dynamic correlations. 256-265

Databases and Ontologies

• 
  Muhammad Shoaib, Adnan Ahmad Ansari, Sung-Min Ahn:
  cMapper: gene-centric connectivity mapper for EBI-RDF platform. 266-271
• 
  Jie Zheng, Mesut A. Erzurumluoglu, Benjamin L. Elsworth, John P. Kemp, Laurence J. Howe, Philip C. Haycock, Gibran Hemani, Katherine Tansey, Charles Laurin, Early Genetics, Lifecourse Epidemiology (EAGLE) Eczema Consortium, Beate St. Pourcain, Nicole M. Warrington, Hilary K. Finucane, Alkes L. Price, Brendan K. Bulik-Sullivan, Verneri Anttila, Lavinia Paternoster, Tom R. Gaunt, David M. Evans, Benjamin M. Neale:
  LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. 272-279

Applications Notes
Genome Analysis

• 
  Sergii Ivakhno, Camilla Colombo, Stephen Tanner, Philip Tedder, Stefano Berri, Anthony J. Cox:
  tHapMix: simulating tumour samples through haplotype mixtures. 280-282
• 
  Val F. Lanza, Fernando Baquero, Fernando de la Cruz, Teresa M. Coque:
  AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks. 283-285

Sequence Analysis

• 
  Jeongbin Park, Kayeong Lim, Jin-Soo Kim, Sangsu Bae:
  Cas-analyzer: an online tool for assessing genome editing results using NGS data. 286-288
• 
  Vladimir Perovic, Neven Sumonja, Branislava Gemovic, Eneda Toska, Stefan G. Roberts, Nevena Veljkovic:
  TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation. 289-291
• 
  Aaron M. Rosenfeld, Wenzhao Meng, Eline T. Luning Prak, Uri Hershberg:
  ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. 292-293

Genetics and Population Analysis

• 
  Rasool Tahmasbi, Matthew C. Keller:
  GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data. 294-296

Systems Biology

• 
  Hasan Baig, Jan Madsen:
  D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits. 297-299

Data and Text Mining

• 
  Ruggero Ferrazza, Julian L. Griffin, Graziano Guella, Pietro Franceschi:
  IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes. 300-302
• 
  Max Klein, Rati Sharma, Christopher Herrick Bohrer, Cameron M. Avelis, Elijah Roberts:
  Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark. 303-305

Databases and Ontologies

• 
  Matthew Norris, Chun Kit Kwok, Jitender Cheema, Matthew Hartley, Richard J. Morris, Sharon Aviran, Yiliang Ding:
  FoldAtlas: a repository for genome-wide RNA structure probing data. 306-308

Corrigendum
Databases and Ontologies

• 
  Andy L. Olivares, Miguel Ángel González Ballester, Jérôme Noailly:
  Virtual exploration of early stage atherosclerosis. 309

Volume 33, Number 3, February 2017

Original Papers
Genome Analysis

• 
  Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok, Kevin Y. Yip, Ting-Fung Chan:
  OMBlast: alignment tool for optical mapping using a seed-and-extend approach. 311-319
• 
  Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat:
  Simulation-based estimation of branching models for LTR retrotransposons. 320-326
• 
  Sufang Wang, Michael Gribskov:
  Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis. 327-333

Sequence Analysis

• 
  Ilham A. Shahmuradov, Rozaimi Mohamad Razali, Salim Bougouffa, Aleksandar Radovanovic, Vladimir B. Bajic:
  bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. 334-340
• 
  Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou:
  iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. 341-346
• 
  Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
  SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. 347-353

Phylogenetics

• 
  Iakov I. Davydov, Marc Robinson-Rechavi, Nicolas Salamin:
  State aggregation for fast likelihood computations in molecular evolution. 354-362

Structural Bioinformatics

• 
  Shuaibing He, Manman Li, Xiaotong Ye, Hongyu Wang, Wenkang Yu, Wenjing He, Yun Wang, Yanjiang Qiao:
  Site of metabolism prediction for oxidation reactions mediated by oxidoreductases based on chemical bond. 363-372
• 
  Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M. Deane:
  Comparing co-evolution methods and their application to template-free protein structure prediction. 373-381
• 
  Christopher L. Barrett, Fenix W. D. Huang, Christian M. Reidys:
  Sequence-structure relations of biopolymers. 382-389
• 
  Dmytro Guzenko, Sergei V. Strelkov:
  Granular clustering of de novo protein models. 390-396

Gene expression

• 
  Roman Hornung, David Causeur, Christoph Bernau, Anne-Laure Boulesteix:
  Improving cross-study prediction through addon batch effect adjustment or addon normalization. 397-404

Systems Biology

• 
  Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen:
  DEF: an automated dead-end filling approach based on quasi-endosymbiosis. 405-413
• 
  Monther Alhamdoosh, Milica Ng, Nicholas J. Wilson, Julie M. Sheridan, Huy Huynh, Michael J. Wilson, Matthew E. Ritchie:
  Combining multiple tools outperforms individual methods in gene set enrichment analyses. 414-424

Applications Notes
Genome Analysis

• 
  Stefan Canzar, Karlynn E. Neu, Qingming Tang, Patrick C. Wilson, Aly A. Khan:
  BASIC: BCR assembly from single cells. 425-427
• 
  Phuc-Loi Luu, Daniela Gerovska, Mikel Arrospide-Elgarresta, Sugoi Retegi-Carrión, Hans R. Schöler, Marcos J. Araúzo-Bravo:
  P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data. 428-431
• 
  Ekaterina A. Khramtsova, Barbara E. Stranger:
  Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. 432-434

Sequence Analysis

• 
  Vojtech Bystrý, Tomas Reigl, Adam Krejci, Martin Demko, Barbora Hanakova, Andrea Grioni, Henrik Knecht, Max Schlitt, Peter Dreger, Leopold Sellner, Dietrich Herrmann, Marine Pingeon, Myriam Boudjoghra, Jos Rijntjes, Christiane Pott, Anton W. Langerak, Patricia J. T. A. Groenen, Frederic Davi, Monika Brüggemann, Nikos Darzentas, EuroClonality-NGS:
  ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data. 435-437

Phylogenetics

• 
  Xingjian Xu, Zhaohua Ji, Zhang Zhang:
  CloudPhylo: a fast and scalable tool for phylogeny reconstruction. 438-440

Structural Bioinformatics

• 
  Krishna Choudhary, Luyao Ruan, Fei Deng, Nathan P. Shih, Sharon Aviran:
  SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. 441-443
• 
  Giacomo Janson, Chengxin Zhang, Maria Giulia Prado, Alessandro Paiardini:
  PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. 444-446

Gene expression

• 
  Jonathan W. Nelson, Jiri Sklenar, Anthony P. Barnes, Jessica Minnier:
  The START App: a web-based RNAseq analysis and visualization resource. 447-449
• 
  Yu Zhang, Juan Xie, Jinyu Yang, Anne Fennell, Chi Zhang, Qin Ma:
  QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. 450-452
• 
  Luca Bianco, Samantha Riccadonna, Enrico Lavezzo, Marco Falda, Elide Formentin, Duccio Cavalieri, Stefano Toppo, Paolo Fontana:
  Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms. 453-455
• 
  Elisa Salviato, Vera Djordjilovic, Monica Chiogna, Chiara Romualdi:
  simPATHy: a new method for simulating data from perturbed biological PATHways. 456-457

Systems Biology

• 
  Wei Lan, Min Li, Kaijie Zhao, Jin Liu, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
  LDAP: a web server for lncRNA-disease association prediction. 458-460

Data and Text Mining

• 
  Thomas Van Parys, Ine Melckenbeeck, Maarten Houbraken, Pieter Audenaert, Didier Colle, Mario Pickavet, Piet Demeester, Yves Van de Peer:
  A Cytoscape app for motif enumeration with ISMAGS. 461-463
• 
  Daniel P. Russo, Marlene T. Kim, Wenyi Wang, Daniel Pinolini, Sunil M. Shende, Judy Strickland, Thomas Hartung, Hao Zhu:
  CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data. 464-466

Databases and Ontologies

• 
  Zhi-Yong Liang, Hong-Yan Lai, Huan Yang, Chang-Jian Zhang, Hui Yang, Huan-Huan Wei, Xin-Xin Chen, Ya-Wei Zhao, Zhen-Dong Su, Wen-Chao Li, En-Ze Deng, Hua Tang, Wei Chen, Hao Lin:
  Pro54DB: a database for experimentally verified sigma-54 promoters. 467-469

Corrigendum
Databases and Ontologies

• 
  Dalia Cohn-Alperovich, Alona Rabner, Ilona Kifer, Yael Mandel-Gutfreund, Zohar Yakhini:
  Mutual enrichment in aggregated ranked lists with applications to gene expression regulation. 470

Volume 33, Number 4, February 2017

Original Papers
Genome Analysis

• 
  João Fadista, Nikolay Oskolkov, Ola Hansson, Leif Groop:
  LoFtool: a gene intolerance score based on loss-of-function variants in 60 706 individuals. 471-474
• 
  Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir:
  Recycler: an algorithm for detecting plasmids from de novo assembly graphs. 475-482
• 
  Hai Yang, Qiang Wei, Xue Zhong, Hushan Yang, Bingshan Li:
  Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework. 483-490
• 
  Toby Dylan Hocking, Patricia Goerner-Potvin, Andreanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque:
  Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. 491-499
• 
  Wei Jiang, Weichuan Yu:
  Controlling the joint local false discovery rate is more powerful than meta-analysis methods in joint analysis of summary statistics from multiple genome-wide association studies. 500-507

Sequence Analysis

• 
  Heydar Maboudi Afkham, Xuanbin Qiu, Matthew The, Lukas Käll:
  Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics. 508-513
• 
  Janne H. Korhonen, Kimmo Palin, Jussi Taipale, Esko Ukkonen:
  Fast motif matching revisited: high-order PWMs, SNPs and indels. 514-521

Gene expression

• 
  Weizhuang Zhou, Lichy Han, Russ B. Altman:
  Imputing gene expression to maximize platform compatibility. 522-528

Systems Biology

• 
  Raphael Petegrosso, Sunho Park, TaeHyun Hwang, Rui Kuang:
  Transfer learning across ontologies for phenome-genome association prediction. 529-536
• 
  Ferhat Alkan, Cesim Erten:
  RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications. 537-544

Applications Notes
Genome Analysis

• 
  Fabian Grandke, Rod Snowdon, Birgit Samans:
  gsrc: an R package for genome structure rearrangement calling. 545-546
• 
  Emanuel Diego S. Penha, Egiebade Iriabho, Alex Dussaq, Diana Magalhaes de Oliveira, Jonas S. Almeida:
  Isomorphic semantic mapping of variant call format (VCF2RDF). 547-548
• 
  Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach:
  Efficient detection of differentially methylated regions using DiMmeR. 549-551
• 
  Blake L. Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C. Schnable, Eric Lyons:
  FractBias: a graphical tool for assessing fractionation bias following polyploidy. 552-554
• 
  Jin Zhang, Elaine R. Mardis, Christopher A. Maher:
  INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. 555-557
• 
  Jean-Philippe Fortin, Timothy Triche, Kasper D. Hansen:
  Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. 558-560
• 
  David C. Qian, Jonathan A. Busam, Xiangjun Xiao, Tracy A. O'Mara, Rosalind A. Eeles, Frederick R. Schumacher, Catherine M. Phelan, Christopher I. Amos:
  seXY: a tool for sex inference from genotype arrays. 561-563

Sequence Analysis

• 
  Diego J. Zea, Diego Anfossi, Morten Nielsen, Cristina Marino Buslje:
  MIToS.jl: mutual information tools for protein sequence analysis in the Julia language. 564-565
• 
  Ankeeta Shah, Yingzhi Qian, Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang:
  CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. 566-567
• 
  Jaroslaw Surkont, Yoan Diekmann, José B. Pereira-Leal:
  Rabifier2: an improved bioinformatic classifier of Rab GTPases. 568-570
• 
  Ahmed Arslan, Vera van Noort:
  yMap: an automated method to map yeast variants to protein modifications and functional regions. 571-573
• 
  Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough, Jonathan Wright, Bernardo J. Clavijo:
  KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. 574-576
• 
  Gabriel Renaud, Kristian Hanghøj, Eske Willerslev, Ludovic Orlando:
  gargammel: a sequence simulator for ancient DNA. 577-579
• 
  Ralf Eggeling, Ivo Grosse, Jan Grau:
  InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. 580-582

Structural Bioinformatics

• 
  Carlos García-Pérez, Rafael Peláez, Roberto Therón, José Luis López-Pérez:
  JADOPPT: java based AutoDock preparing and processing tool. 583-585
• 
  Renzhi Cao, Badri Adhikari, Debswapna Bhattacharya, Miao Sun, Jie Hou, Jianlin Cheng:
  QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. 586-588

Gene expression

• 
  Renana Sabi, Renana Volvovitch Daniel, Tamir Tuller:
  stAIcalc: tRNA adaptation index calculator based on species-specific weights. 589-591
• 
  Stefan J. Haunsberger, Niamh M. C. Connolly, Jochen H. M. Prehn:
  miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions. 592-593

Genetics and Population Analysis

• 
  Joseph H. Marcus, John Novembre:
  Visualizing the geography of genetic variants. 594-595
• 
  Jan Schröder, Vincent Corbin, Anthony T. Papenfuss:
  HYSYS: have you swapped your samples? 596-598
• 
  Arthur Wuster, Diana Chang, Timothy W. Behrens, Tushar Bhangale:
  geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation. 599-600

Systems Biology

• 
  Julian D. Schwab, Andre Burkovski, Lea Siegle, Christoph Müssel, Hans A. Kestler:
  ViSiBooL - visualization and simulation of Boolean networks with temporal constraints. 601-604
• 
  Alberto Noronha, Anna Dröfn Daníelsdóttir, Piotr Gawron, Freyr Jóhannsson, Soffía Jónsdóttir, Sindri Jarlsson, Jón Pétur Gunnarsson, Sigurður Brynjólfsson, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming:
  ReconMap: an interactive visualization of human metabolism. 605-607
• 
  Tolutola Oyetunde, Muhan Zhang, Yixin Chen, Yinjie J. Tang, Cynthia Lo:
  BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods. 608-611
• 
  Sara Ballouz, Melanie Weber, Paul Pavlidis, Jesse A. Gillis:
  EGAD: ultra-fast functional analysis of gene networks. 612-614

Data and Text Mining

• 
  Bhusan K. Kuntal, Sharmila S. Mande:
  Web-igloo: a web based platform for multivariate data visualization. 615-617
• 
  Dayne L. Filer, Parth Kothiya, R. Woodrow Setzer, Richard S. Judson, Matthew T. Martin:
  tcpl: the ToxCast pipeline for high-throughput screening data. 618-620
• 
  Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, David MacIntyre:
  KODAMA: an R package for knowledge discovery and data mining. 621-623

Databases and Ontologies

• 
  Adrian Bickerstaffe, Thilina Ranaweera, Travis Endersby, Christopher Ellis, Sanjaya Maddumarachchi, George E. Gooden, Paul White, Eric K. Moses, Alex W. Hewitt, John L. Hopper:
  The Ark: a customizable web-based data management tool for health and medical research. 624-626
• 
  Nicholas A. Watts, Frank Alex Feltus:
  Big Data Smart Socket (BDSS): a system that abstracts data transfer habits from end users. 627-628

Bioimage Informatics

• 
  Mark C. Hiner, Curtis T. Rueden, Kevin W. Eliceiri:
  ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability. 629-630

Volume 33, Number 5, March 2017

RECOMB-CG 2016
Phylogenetics

• 
  Pranjal Vachaspati, Tandy J. Warnow:
  FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. 631-639
• 
  Charlotte A. Darby, Maureen Stolzer, Patrick J. Ropp, Daniel Barker, Dannie Durand:
  Xenolog classification. 640-649

Original Papers
Genome Analysis

• 
  Denye N. Ogeh, Richard Badge:
  A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data. 650-653

Sequence Analysis

• 
  Agnès Lagnoux, Sabine Mercier, Pierre Vallois:
  Statistical significance based on length and position of the local score in a model of i.i.d. sequences. 654-660
• 
  Jyun-Rong Wang, Wen-Lin Huang, Ming-Ju Tsai, Kai-Ti Hsu, Hui-Ling Huang, Shinn-Ying Ho:
  ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives. 661-668

Phylogenetics

• 
  Xavier Meyer, Bastien Chopard, Nicolas Salamin:
  Accelerating Bayesian inference for evolutionary biology models. 669-676

Structural Bioinformatics

• 
  Tong Wang, Yuedong Yang, Yaoqi Zhou, Haipeng Gong:
  LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. 677-684
• 
  Jack Hanson, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou:
  Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. 685-692

Gene expression

• 
  Cristóbal Fresno, Germán González, Gabriela Alejandra Merino, Ana Georgina Flesia, Osvaldo L. Podhajcer, Andrea S. Llera, Elmer Andrés Fernández:
  A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm. 693-700

Systems Biology

• 
  Frederik Gwinner, Gwénola Boulday, Claire Vandiedonck, Minh Arnould, Cécile Cardoso, Iryna Nikolayeva, Oriol Guitart-Pla, Cécile V. Denis, Olivier D. Christophe, Johann Beghain, Elisabeth Tournier-Lasserve, Benno Schwikowski:
  Network-based analysis of omics data: the LEAN method. 701-709
• 
  Steven S. Andrews:
  Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. 710-717
• 
  Corinna Maier, Carolin Loos, Jan Hasenauer:
  Robust parameter estimation for dynamical systems from outlier-corrupted data. 718-725
• 
  Arya A. Das, T. Ajayakumar Darsana, Elizabeth Jacob:
  Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology. 726-732
• 
  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. 733-739

Applications Notes
Genome Analysis

• 
  Elizabeth Baskin, Rick Farouni, Ewy A. Mathé:
  ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. 740-742
• 
  Hongliang Mao, Hao Wang:
  SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets. 743-745
• 
  Pedro Madrigal:
  fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. 746-748

Sequence Analysis

• 
  Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung:
  FUEL-mLoc: feature-unified prediction and explanation of multi-localization of cellular proteins in multiple organisms. 749-750
• 
  Jeremiah A. Wala, Rameen Beroukhim:
  SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. 751-753

Structural Bioinformatics

• 
  Julia Koehler Leman, Benjamin K. Mueller, Jeffrey J. Gray:
  Expanding the toolkit for membrane protein modeling in Rosetta. 754-756

Gene expression

• 
  Jil Sander, Joachim L. Schultze, Nir Yosef:
  ImpulseDE: detection of differentially expressed genes in time series data using impulse models. 757-759
• 
  Tomas Puelma, Viviana Araus, Javier Canales, Elena A. Vidal, Juan M. Cabello, Alvaro Soto, Rodrigo A. Gutiérrez:
  GENIUS: web server to predict local gene networks and key genes for biological functions. 760-761
• 
  Ethan Bahl, Tanner Koomar, Jacob J. Michaelson:
  cerebroViz: an R package for anatomical visualization of spatiotemporal brain data. 762-763
• 
  Alicia T. Specht, Jun Li:
  LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering. 764-766
• 
  Andrian Yang, Michael Troup, Peijie Lin, Joshua Wing Kei Ho:
  Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud. 767-769

Systems Biology

• 
  Hannes Klarner, Adam Streck, Heike Siebert:
  PyBoolNet: a python package for the generation, analysis and visualization of boolean networks. 770-772
• 
  Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana Luísa Neves, Dominique Gauguier, Jeremy K. Nicholson, Marc-Emmanuel Dumas:
  MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways. 773-775
• 
  B. Muchmore, Marta E. Alarcón-Riquelme:
  CymeR: cytometry analysis using KNIME, docker and R. 776-778
• 
  Guillaume Gautreau, David Pejoski, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon, Nicolas Tchitchek:
  SPADEVizR: an R package for visualization, analysis and integration of SPADE results. 779-781

Data and Text Mining

• 
  Martha Zakrzewski, Carla Proietti, Jonathan J. Ellis, Shihab Hasan, Marie-Jo Brion, Bernard Berger, Lutz Krause:
  Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions. 782-783

Databases and Ontologies

• 
  Daniel A. Russell, Graham F. Hatfull:
  PhagesDB: the actinobacteriophage database. 784-786

Bioimage Informatics

• 
  Sijin He, May Yong, Paul M. Matthews, Yike Guo:
  tranSMART-XNAT Connector tranSMART-XNAT connector - image selection based on clinical phenotypes and genetic profiles. 787-788
• 
  Côme Pasqualin, François Gannier, Angèle Yu, Claire O. Malécot, Pierre Bredeloux, Véronique Maupoil:
  SarConfoCal: simultaneous sarcomere length and cytoplasmic calcium measurements for laser scanning confocal microscopy images. 789-790

Volume 33, Number 6, March 2017

RECOMB-SEQ/RECOMB-CBB 2016
Genome Analysis

• 
  Yang Young Lu, Ting Chen, Jed A. Fuhrman, Fengzhu Sun:
  COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. 791-798

Sequence Analysis

• 
  Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen:
  Accurate self-correction of errors in long reads using de Bruijn graphs. 799-806
• 
  Joaquín Ezpeleta, Flavia J. Krsticevic, Pilar Bulacio, Elizabeth Tapia:
  Designing robust watermark barcodes for multiplex long-read sequencing. 807-813

Systems Biology

• 
  Yoo-Ah Kim, Sanna Madan, Teresa M. Przytycka:
  WeSME: uncovering mutual exclusivity of cancer drivers and beyond. 814-821

Original Papers
Genome Analysis

• 
  Hui-Yi Lin, Dung-Tsa Chen, Po-Yu Huang, Yung-Hsin Liu, Augusto Ochoa, Jovanny Zabaleta, Donald Mercante, Zhide Fang, Thomas A. Sellers, Julio M. Pow-Sang, Chia-Ho Cheng, 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, 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:
  SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns. 822-833

Sequence Analysis

• 
  Linhao Jiang, Yichao Dong, Ning Chen, Ting Chen:
  DACE: a scalable DP-means algorithm for clustering extremely large sequence data. 834-842
• 
  Hang Zhou, Yang Yang, Hong-Bin Shen:
  Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features. 843-853
• 
  Xiaoli Zhang, Shiyong Liu:
  RBPPred: predicting RNA-binding proteins from sequence using SVM. 854-862

Structural Bioinformatics

• 
  Jiaqi Xia, Zhenling Peng, Dawei Qi, Hongbo Mu, Jianyi Yang:
  An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier. 863-870

Genetics and Population Analysis

• 
  Feng Chen, Shuang Wang, Xiaoqian Jiang, Sijie Ding, Yao Lu, Jihoon Kim, Süleyman Cenk Sahinalp, Chisato Shimizu, Jane C. Burns, Victoria J. Wright, Eileen Png, Martin L. Hibberd, David D. Lloyd, Hai Yang, Amalio Telenti, Cinnamon S. Bloss, Dov Fox, Kristin E. Lauter, Lucila Ohno-Machado:
  PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. 871-878
• 
  Anand Bhaskar, Adel Javanmard, Thomas A. Courtade, David Tse:
  Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies. 879-885
• 
  Hon-Cheong So, Pak C. Sham:
  Exploring the predictive power of polygenic scores derived from genome-wide association studies: a study of 10 complex traits. 886-892

Systems Biology

• 
  Matthew R. Long, Jennifer L. Reed:
  Improving flux predictions by integrating data from multiple strains. 893-900
• 
  Zhen Gao, Yang Chen, XiaoShu Cai, Rong Xu:
  Predict drug permeability to blood-brain-barrier from clinical phenotypes: drug side effects and drug indications. 901-908

Data and Text Mining

• 
  Jessica S. Yu, Dante A. Pertusi, Adebola V. Adeniran, Keith E. J. Tyo:
  CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort. 909-916

Applications Notes
Genome Analysis

• 
  Martin S. Lindner, Benjamin Strauch, Jakob M. Schulze, Simon H. Tausch, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard:
  HiLive: real-time mapping of illumina reads while sequencing. 917
• 
  Tilo Buschmann:
  DNABarcodes: an R package for the systematic construction of DNA sample tags. 920-922

Sequence Analysis

• 
  Alexey V. Kochetov, Jens Allmer, Alexandra I. Klimenko, Bulat S. Zuraev, Yury G. Matushkin, Sergey A. Lashin:
  AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs. 923-925
• 
  Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith:
  Training alignment parameters for arbitrary sequencers with LAST-TRAIN. 926-928
• 
  Gauri Shende, Harshala Haldankar, Ram Shankar Barai, Mohammed Husain Bharmal, Vinit Shetty, Susan Idicula-Thomas:
  PBIT: Pipeline Builder for Identification of drug Targets for infectious diseases. 929-931

Phylogenetics

• 
  Bradley R. Jones, Art F. Y. Poon:
  node.dating: dating ancestors in phylogenetic trees in R. 932-934

Structural Bioinformatics

• 
  Justas Dapkunas, Albertas Timinskas, Kliment Olechnovic, Mindaugas Margelevicius, Rytis Diciunas, Ceslovas Venclovas:
  The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures. 935-937

Gene expression

• 
  Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato:
  iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. 938-940
• 
  Zefang Tang, Chenwei Li, Karena Zhang, Mingyu Yang, Xueda Hu:
  GE-mini: a mobile APP for large-scale gene expression visualization. 941-943

Systems Biology

• 
  Chuang Li, Tao Chen, Qiang He, Yunping Zhu, Kenli Li:
  MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework. 944-946
• 
  Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel:
  caspo: a toolbox for automated reasoning on the response of logical signaling networks families. 947-950

Volume 33, Number 7, 2017

Discovery Note
Systems Biology

• 
  Mattia Cinelli, Yuxin Sun, Katharine Best, James M. Heather, Shlomit Reich-Zeliger:
  Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires. 951-955

Original Papers
Genome Analysis

• 
  Bryan Quach, Terrence S. Furey:
  DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter. 956-963
• 
  Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic, Sri Parameswaran:
  Improved VCF normalization for accurate VCF comparison. 964-970

Phylogenetics

• 
  Chris-André Leimeister, Salma Sohrabi-Jahromi, Burkhard Morgenstern:
  Fast and accurate phylogeny reconstruction using filtered spaced-word matches. 971-979
• 
  Edwin Jacox, Mathias Weller, Eric Tannier, Céline Scornavacca:
  Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. 980-987

Structural Bioinformatics

• 
  Sinan Ugur Umu, Paul P. Gardner:
  A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. 988-996
• 
  Frédéric Cazals, Tom Dreyfus:
  The structural bioinformatics library: modeling in biomolecular science and beyond. 997-1004
• 
  James H. Collier, Lloyd Allison, Arthur M. Lesk, Peter J. Stuckey, Maria Garcia de la Banda, Arun Siddharth Konagurthu:
  Statistical inference of protein structural alignments using information and compression. 1005-1013
• 
  Surendra S. Negi, Werner Braun:
  Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity. 1014-1020

Genetics and Population Analysis

• 
  Sajad Mirzaei, Yufeng Wu:
  RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination. 1021-1030

Systems Biology

• 
  Yang Chen, Rong Xu:
  Context-sensitive network-based disease genetics prediction and its implications in drug discovery. 1031-1039
• 
  Itziar Irurzun-Arana, José Martín Pastor, Iñaki F. Trocóniz, José David Gómez-Mantilla:
  Advanced Boolean modeling of biological networks applied to systems pharmacology. 1040-1048
• 
  Fabian Fröhlich, Fabian J. Theis, Joachim O. Rädler, Jan Hasenauer:
  Parameter estimation for dynamical systems with discrete events and logical operations. 1049-1056
• 
  Ehsan Motamedian, Maryam Mohammadi, Seyed Abbas Shojaosadati, Mona Heydari:
  TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data. 1057-1063

Bioimage Informatics

• 
  George Teodoro, Tahsin M. Kurç, Luis F. R. Taveira, Alba C. M. A. Melo, Yi Gao:
  Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines. 1064-1072
• 
  Miroslav Radojevic, Erik Meijering:
  Automated neuron tracing using probability hypothesis density filtering. 1073-1080

Applications Notes
Genome Analysis

• 
  Thomas Lin Pedersen, Intawat Nookaew, David Wayne Ussery, Maria Månsson:
  PanViz: interactive visualization of the structure of functionally annotated pangenomes. 1081-1082
• 
  Liron Ganel, Haley J. Abel, FinMetSeq Consortium, Ira M. Hall:
  SVScore: an impact prediction tool for structural variation. 1083-1085

Sequence Analysis

• 
  Maciej Dlugosz, Sebastian Deorowicz:
  RECKONER: read error corrector based on KMC. 1086-1089
• 
  Wei Zhou, Ruilin Li, Shuo Yuan, ChangChun Liu, Shaowen Yao:
  MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes. 1090-1092
• 
  Luyang Huo, Han Zhang, Xueting Huo, Yasong Yang, Xueqiong Li:
  pHMM-tree: phylogeny of profile hidden Markov models. 1093-1095

Systems Biology

• 
  Irina Balaur, Alexander Mazein, Mansoor A. S. Saqi, Artem Lysenko, Christopher J. Rawlings:
  Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. 1096-1098

Data and Text Mining

• 
  Sudeepta Kumar Panda, Sanjay V. Boddul, Guillermina Yanek Jiménez-Andrade, Long Jiang, Zsolt Kasza:
  Green listed - a CRISPR screen tool. 1099-1100

Databases and Ontologies

• 
  Ravi D. Shankar, Sanchita Bhattacharya, Chethan Jujjavarapu, Sandra Andorf, Jeffrey A. Wiser:
  RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. 1101-1103
• 
  Daniel Greene, Sylvia Richardson, Ernest Turro:
  ontologyX: a suite of R packages for working with ontological data. 1104-1106

Letter to the Editor
Systems Biology

• 
  Ömer Nebil Yaveroglu, Noël Malod-Dognin, Tijana Milenkovic, Natasa Przulj:
  Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods. 1107-1109

Volume 33, Number 8, 2017

Discovery Notes
Sequence Analysis

• 
  Scott D. Brown, Greg Hapgood, Christian Steidl, Andrew P. Weng, Kerry J. Savage:
  Defining the clonality of peripheral T cell lymphomas using RNA-seq. 1111-1115

Structural Bioinformatics

• 
  Kasper Harpsøe, Michael W. Boesgaard, Christian Munk, Hans Bräuner-Osborne, David E. Gloriam:
  Structural insight to mutation effects uncover a common allosteric site in class C GPCRs. 1116-1120

Original Papers
Genome Analysis

• 
  Li Zhu, Ying Ding, Cho-Yi Chen, Lin Wang, Zhiguang Huo:
  MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer. 1121-1129

Sequence Analysis

• 
  Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu:
  H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs. 1130-1138
• 
  Yongjun Piao, Seongkeon Lee, Eun-Joon Lee, Keith D. Robertson, Huidong Shi:
  CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. 1139-1146
• 
  Suyash S. Shringarpure, Rasika A. Mathias, Ryan D. Hernandez, Timothy D. O'Connor, Zachary A. Szpiech:
  Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data. 1147-1153

Phylogenetics

• 
  Mateusz Kaduk, Erik L. L. Sonnhammer:
  Improved orthology inference with Hieranoid 2. 1154-1159
• 
  Ignazio Carbone, James B. White, Jolanta Miadlikowska, A. Elizabeth Arnold, Mark A. Miller:
  T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. 1160-1168

Structural Bioinformatics

• 
  Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang:
  The super-n-motifs model: a novel alignment-free approach for representing and comparing RNA secondary structures. 1169-1178

Gene expression

• 
  Davis J. McCarthy, Kieran R. Campbell, Aaron T. L. Lun, Quin F. Wills:
  Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. 1179-1186

Systems Biology

• 
  Xujun Liang, Pengfei Zhang, Lu Yan, Ying Fu, Fang Peng:
  LRSSL: predict and interpret drug-disease associations based on data integration using sparse subspace learning. 1187-1196
• 
  Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao:
  PhosD: inferring kinase-substrate interactions based on protein domains. 1197-1204

Data and Text Mining

• 
  Andreas Helfenstein, Päivi Tammela:
  Analyzing user-generated online content for drug discovery: development and use of MedCrawler. 1205-1209

Databases and Ontologies

• 
  Xiaoling Chen, Jeffrey T. Chang:
  Planning bioinformatics workflows using an expert system. 1210-1215

Applications Notes
Genome Analysis

• 
  Hajk-Georg Drost, Jerzy Paszkowski:
  Biomartr: genomic data retrieval with R. 1216-1217

Sequence Analysis

• 
  Seung-Hyuk Choi, Hyunwoo Kim, Eunok Paek:
  ACTG: novel peptide mapping onto gene models. 1218-1220
• 
  Pablo Mier, Miguel A. Andrade-Navarro:
  dAPE: a web server to detect homorepeats and follow their evolution. 1221-1223
• 
  Andrzej Zielezinski, Michal Dziubek, Jan Sliski, Wojciech M. Karlowski:
  ORCAN - a web-based meta-server for real-time detection and functional annotation of orthologs. 1224-1226

Phylogenetics

• 
  Ian H. Holmes:
  Historian: accurate reconstruction of ancestral sequences and evolutionary rates. 1227-1229
• 
  Lionel Guy:
  phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics. 1230-1232

Structural Bioinformatics

• 
  Matthew Colledge, B. A. Wallace:
  AnglerFish: a webserver for defining the geometry of α-helices in membrane proteins. 1233-1234
• 
  Ling Wang, Xiaoqian Pang, Yecheng Li, Ziying Zhang, WenAn Tan:
  RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening. 1235-1237
• 
  Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
  SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. 1238-1240

Gene expression

• 
  Kieran R. Campbell, Christopher Yau:
  switchde: inference of switch-like differential expression along single-cell trajectories. 1241-1242

Genetics and Population Analysis

• 
  Peter J. van der Most, Leanne K. Küpers, Harold Snieder, Ilja M. Nolte:
  QCEWAS: automated quality control of results of epigenome-wide association studies. 1243-1245
• 
  Alexandre Fournier-Level, Charles Robin, David J. Balding:
  GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments. 1246-1247
• 
  Gennaro Gambardella, Matteo Cereda, Lorena Benedetti, Francesca D. Ciccarelli:
  MEGA-V: detection of variant gene sets in patient cohorts. 1248-1249

Systems Biology

• 
  Alberto Franzin, Francesco Sambo, Barbara Di Camillo:
  bnstruct: an R package for Bayesian Network structure learning in the presence of missing data. 1250-1252
• 
  Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm:
  SED-ML web tools: generate, modify and export standard-compliant simulation studies. 1253-1254

Data and Text Mining

• 
  Sébastien Carrère, Jérôme Gouzy:
  myGenomeBrowser: building and sharing your own genome browser. 1255-1257

Databases and Ontologies

• 
  Jiewen Du, Xin Yan, Zhihong Liu, Lu Cui, Peng Ding:
  cBinderDB: a covalent binding agent database. 1258-1260

Review
Sequence Analysis

• 
  Justin Chu, Hamid Mohamadi, René L. Warren, Chen Yang, Inanç Birol:
  Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. 1261-1270

Volume 33, Number 9, May 2017

Original Papers
Genome Analysis

• 
  Birgit Debrabant:
  The null hypothesis of GSEA, and a novel statistical model for competitive gene set analysis. 1271-1277
• 
  Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko, Hongzhe Li:
  A general framework for association analysis of microbial communities on a taxonomic tree. 1278-1285
• 
  Dan Luo, Sara Ziebell, Lingling An:
  An informative approach on differential abundance analysis for time-course metagenomic sequencing data. 1286-1292

Sequence Analysis

• 
  Joël Lafond-Lapalme, Marc-Olivier Duceppe, Shengrui Wang, Peter Moffett, Benjamin Mimee:
  A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm. 1293-1300
• 
  Chen Sun, Paul Medvedev:
  VarMatch: robust matching of small variant datasets using flexible scoring schemes. 1301-1308
• 
  Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic, Yunlong Liu, Xiaowen Liu:
  A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. 1309-1316
• 
  Masae Hosoda, Yukie Akune, Kiyoko F. Aoki-Kinoshita:
  Development and application of an algorithm to compute weighted multiple glycan alignments. 1317-1323
• 
  Hamid Mohamadi, Hamza Khan, Inanç Birol:
  ntCard: a streaming algorithm for cardinality estimation in genomics data. 1324-1330
• 
  Quan Le, Fabian Sievers, Desmond G. Higgins:
  Protein multiple sequence alignment benchmarking through secondary structure prediction. 1331-1337

Phylogenetics

• 
  Jeremy Adams, Michael J. Mansfield, Daniel J. Richard, Andrew C. Doxey:
  Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function. 1338-1345

Structural Bioinformatics

• 
  Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M. Deane:
  Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. 1346-1353

Systems Biology

• 
  Sean Maxwell, Mark R. Chance, Mehmet Koyutürk:
  Linearity of network proximity measures: implications for set-based queries and significance testing. 1354-1361
• 
  Olga Nikolova, Russell Moser, Christopher Kemp, Mehmet Gönen, Adam A. Margolin:
  Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies. 1362-1369

Data and Text Mining

• 
  Yifan Yang, Lei Xu, Zheyun Feng, Jeffrey A. Cruz, Linda J. Savage, David M. Kramer, Jin Chen:
  PhenoCurve: capturing dynamic phenotype-environment relationships using phenomics data. 1370-1378

Bioimage Informatics

• 
  Philipp Hanslovsky, John A. Bogovic, Stephan Saalfeld:
  Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy. 1379-1386

Applications Notes
Genome Analysis

• 
  Yan Holtz, Jacques David, Vincent Ranwez:
  The genetic map comparator: a user-friendly application to display and compare genetic maps. 1387-1388
• 
  Audrey Lemaçon, Charles Joly Beauparlant, Penny Soucy, Jamie Allen, Douglas F. Easton, Peter Kraft, Jacques Simard, Arnaud Droit:
  VEXOR: an integrative environment for prioritization of functional variants in fine-mapping analysis. 1389-1391
• 
  Elyashiv Drori, D. Levy, P. Smirin-Yosef, O. Rahimi, Mali Salmon-Divon:
  CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files. 1392-1393

Sequence Analysis

• 
  Martin Sosic, Mile Sikic:
  Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. 1394-1395
• 
  Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln:
  AFS: identification and quantification of species composition by metagenomic sequencing. 1396-1398
• 
  Yong Qian, Thomas J. Butler, Krista Opsahl-Ong, Nicholas S. Giroux, Carlo Sidore, Ramaiah Nagaraja, Francesco Cucca, Luigi Ferrucci, Gonçalo R. Abecasis, David Schlessinger, Jun Ding:
  fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences. 1399-1401

Structural Bioinformatics

• 
  Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Silvio C. E. Tosatto:
  MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. 1402-1404
• 
  Siqi Tian, Rhiju Das:
  Primerize-2D: automated primer design for RNA multidimensional chemical mapping. 1405-1406

Gene expression

• 
  Raziur Rahman, John Otridge, Ranadip Pal:
  IntegratedMRF: random forest-based framework for integrating prediction from different data types. 1407-1410
• 
  Izaskun Mallona, Anna Díez-Villanueva, Berta Martín, Miguel A. Peinado:
  Chainy: an universal tool for standardized relative quantification in real-time PCR. 1411-1413

Genetics and Population Analysis

• 
  Richard H. Adams, Drew R. Schield, Daren C. Card, Heath Blackmon, Todd A. Castoe:
  GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. 1414-1415
• 
  Ivan Krukov, Bianca De Sanctis, A. P. Jason de Koning:
  Wright-Fisher exact solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory. 1416-1417

Systems Biology

• 
  Fotis E. Psomopoulos, Dimitrios M. Vitsios, Shakuntala Baichoo, Christos A. Ouzounis:
  BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution. 1418-1420
• 
  Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming:
  DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. 1421-1423
• 
  Surya Gupta, Veronic De Puysseleyr, José Van der Heyden, Davy Maddelein, Irma Lemmens, Sam Lievens, Sven Degroeve, Jan Tavernier, Lennart Martens:
  MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. 1424-1425

Data and Text Mining

• 
  John Christian Givhan Spainhour, Juho Lim, Peng Qiu:
  GDISC: a web portal for integrative analysis of gene-drug interaction for survival in cancer. 1426-1428

Corrigendum
Data and Text Mining

• 
  Izaskun Mallona, Anna Díez-Villanueva, Berta Martín, Miguel A. Peinado:
  Chainy: an universal tool for standardized relative quantification in real-time PCR. 1429

Volume 33, Number 10, May 2017

Discovery note
Genome Analysis

• 
  Haihua Liu, Xiaoxiao Shang, Hao Zhu:
  LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals. 1431-1436

Original Papers
Genome Analysis

• 
  William H. Majoros, Michael Campbell, Carson Holt, Erin K. DeNardo, Doreen Ware, Andrew S. Allen, Mark Yandell, Timothy E. Reddy:
  High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. 1437-1446
• 
  Feng Zeng, Zicheng Wang, Ying Wang, Jizhong Zhou, Ting Chen:
  Large-scale 16S gene assembly using metagenomics shotgun sequences. 1447-1456

Sequence Analysis

• 
  Li-na Wang, Shaoping Shi, Hao-Dong Xu, Ping-Ping Wen, Jian-Ding Qiu:
  Computational prediction of species-specific malonylation sites via enhanced characteristic strategy. 1457-1463
• 
  Tom Paridaens, Glenn Van Wallendael, Wesley De Neve, Peter Lambert:
  AFRESh: an adaptive framework for compression of reads and assembled sequences with random access functionality. 1464-1472
• 
  Anthony Westbrook, Jordan Ramsdell, Taruna Schuelke, Louisa Normington, R. Daniel Bergeron, W. Kelley Thomas, Matthew D. MacManes:
  PALADIN: protein alignment for functional profiling whole metagenome shotgun data. 1473-1478

Structural Bioinformatics

• 
  Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra:
  Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. 1479-1487
• 
  Anjali Soni, Pooja Khurana, Tanya Singh, Bhyravabhotla Jayaram:
  A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics. 1488-1496
• 
  Pawel P. Wozniak, Gert Vriend, Malgorzata Kotulska:
  Correlated mutations select misfolded from properly folded proteins. 1497-1504

Gene expression

• 
  Malathi S. I. Dona, Luke A. Prendergast, Suresh Mathivanan, Shivakumar Keerthikumar, Agus Salim:
  Powerful differential expression analysis incorporating network topology for next-generation sequencing data. 1505-1513
• 
  Bradley C. Naylor, Michael T. Porter, Elise Wilson, Adam Herring, Spencer Lofthouse, Austin Hannemann, Stephen R. Piccolo, Alan L. Rockwood, John C. Price:
  DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics. 1514-1520

Genetics and Population Analysis

• 
  Niki L. Dimou, Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos:
  GWAR: robust analysis and meta-analysis of genome-wide association studies. 1521-1527

Systems Biology

• 
  Xiao-Tai Huang, Yuan Zhu, Leanne Lai-Hang Chan, Zhongying Zhao, Hong Yan:
  Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification. 1528-1535
• 
  Yuanlong Liu, Myriam Brossard, Damian Roqueiro, Patricia Margaritte-Jeannin, Chloé Sarnowski, Emmanuelle Bouzigon, Florence Demenais:
  SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network. 1536-1544
• 
  Sumanta Basu, William Duren, Charles R. Evans, Charles F. Burant, George Michailidis, Alla Karnovsky:
  Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data. 1545-1553

Databases and Ontologies

• 
  Bharat Panwar, Gilbert S. Omenn, Yuanfang Guan:
  miRmine: a database of human miRNA expression profiles. 1554-1560

Applications Notes
Genome Analysis

• 
  Mariusz Butkiewicz, Jonathan L. Haines, William S. Bush:
  Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants. 1561-1562
• 
  Anthony O. Olarerin-George, Samie R. Jaffrey:
  MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites. 1563-1564
• 
  Maximilian Hastreiter, Tim Jeske, Jonathan Hoser, Michael Kluge, Kaarin Ahomaa, Marie-Sophie Friedl, Sebastian J. Kopetzky, Jan-Dominik Quell, Hans-Werner Mewes, Robert Küffner:
  KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis. 1565-1567
• 
  Dario Beraldi:
  ASCIIGenome: a command line genome browser for console terminals. 1568-1569
• 
  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. 1570-1571

Sequence Analysis

• 
  Putri W. Novianti, Barbara C. Snoek, Saskia M. Wilting, Mark A. van de Wiel:
  Better diagnostic signatures from RNAseq data through use of auxiliary co-data. 1572-1574
• 
  Umberto Ferraro Petrillo, Gianluca Roscigno, Giuseppe Cattaneo, Raffaele Giancarlo:
  FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications. 1575-1577

Structural Bioinformatics

• 
  Karolis Uziela, David Menéndez Hurtado, Nanjiang Shu, Björn Wallner, Arne Elofsson:
  ProQ3D: improved model quality assessments using deep learning. 1578-1580

Genetics and Population Analysis

• 
  Daniel E. Cook, Erik C. Andersen:
  VCF-kit: assorted utilities for the variant call format. 1581-1582

Systems Biology

• 
  Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng:
  NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential. 1583-1585

Data and Text Mining

• 
  Paco Derouault, Béatrice Parfait, Rémi Moulinas, Claire-Cécile Barrot, Franck Sturtz, Stéphane Mérillou, Anne-Sophia Lia:
  'COV'COP' allows to detect CNVs responsible for inherited diseases among amplicons sequencing data. 1586-1588

Databases and Ontologies

• 
  Martin Peters, Johann J. Eicher, David D. van Niekerk, Dagmar Waltemath, Jacky L. Snoep:
  The JWS online simulation database. 1589-1590

Volume 33, Number 11, June 2017

Discovery note
Gene expression

• 
  Shuai Zhang, Chunxia Qin, Guoqiong Cao, Limin Guo, Chengqiang Feng, Wensheng Zhang:
  Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing. 1591-1595

Original Papers
Genome Analysis

• 
  Hernando G. Suarez Duran, Björn E. Langer, Pradnya Ladde, Michael Hiller:
  chainCleaner improves genome alignment specificity and sensitivity. 1596-1603
• 
  Thomas Lin Pedersen:
  Hierarchical sets: analyzing pangenome structure through scalable set visualizations. 1604-1612

Sequence Analysis

• 
  Goro Terai, Satoshi Kamegai, Akito Taneda, Kiyoshi Asai:
  Evolutionary design of multiple genes encoding the same protein. 1613-1620
• 
  Amrita Roy Choudhury, Tiejun Cheng, Lon Phan, Stephen H. Bryant, Yanli Wang:
  Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites. 1621-1629

Phylogenetics

• 
  Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlidis, Alexandros Stamatakis, Tomás Flouri:
  Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. 1630-1638
• 
  Martin Nettling, Hendrik Treutler, Jesús Cerquides, Ivo Grosse:
  Unrealistic phylogenetic trees may improve phylogenetic footprinting. 1639-1646

Structural Bioinformatics

• 
  Chanin Tolson Woods, Alain Laederach:
  Classification of RNA structure change by 'gazing' at experimental data. 1647-1655
• 
  Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
  ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model. 1656-1663
• 
  Wei Tian, Meishan Lin, Hammad Naveed, Jie Liang:
  Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. 1664-1671

Gene expression

• 
  Koji Iwayama, Yuri Aisaka, Natsumaro Kutsuna, Atsushi J. Nagano:
  FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions. 1672-1680

Systems Biology

• 
  Cheng-Yu Ma, Yi-Ping Phoebe Chen, Bonnie Berger, Chung-Shou Liao:
  Identification of protein complexes by integrating multiple alignment of protein interaction networks. 1681-1688
• 
  Hao-Chih Lee, Roman Kosoy, Christine E. Becker, Joel T. Dudley, Brian A. Kidd:
  Automated cell type discovery and classification through knowledge transfer. 1689-1695

Data and Text Mining

• 
  Jiao Zhang, Sam Kwong, Yuheng Jia, Ka-Chun Wong:
  NSSRF: global network similarity search with subgraph signatures and its applications. 1696-1702

Bioimage Informatics

• 
  Ruby Peters, Marta Benthem Muñiz, Juliette Griffié, David J. Williamson, George W. Ashdown, Christian D. Lorenz, Dylan M. Owen:
  Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data. 1703-1711
• 
  Zhiqing Zhang, Nikolay V. Kuzmin, Marie Louise Groot, Jan C. de Munck:
  Extracting morphologies from third harmonic generation images of structurally normal human brain tissue. 1712-1720

Applications Notes
Genome Analysis

• 
  Christopher M. Schroeder, Franz J. Hilke, Markus W. Löffler, Michael Bitzer, Florian Lenz, Marc Sturm:
  A comprehensive quality control workflow for paired tumor-normal NGS experiments. 1721-1722
• 
  Ted Wong, Ira W. Deveson, Simon A. Hardwick, Tim R. Mercer:
  ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing. 1723-1724
• 
  Lauren M. Brinkac, Erin Beck, Jason M. Inman, Pratap Venepally, Derrick E. Fouts, Granger G. Sutton:
  LOCUST: a custom sequence locus typer for classifying microbial isolates. 1725-1726

Sequence Analysis

• 
  Arnald Alonso, Brittany N. Lasseigne, Kelly Williams, Josh Nielsen, Ryne C. Ramaker, Andrew A. Hardigan, Bobbi Johnston, Brian S. Roberts, Sara J. Cooper, Sara Marsal, Richard M. Myers:
  aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments. 1727-1729
• 
  Bruno Fosso, Monica Santamaria, Mattia D'Antonio, Domenica Lovero, Giacomo Corrado, Enrico Vizza, N. Pássaro, Anna Rosa Garbuglia, M. R. Capobianchi, Marco Crescenzi, Gabriel Valiente, Graziano Pesole:
  MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data. 1730-1732
• 
  Charalampos Kyriakopoulos, Pascal Giehr, Verena Wolf:
  H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data. 1733-1734

Gene expression

• 
  Wenzheng Li, Weili Wang, Philip J. Uren, Luiz O. F. Penalva, Andrew D. Smith:
  Riborex: fast and flexible identification of differential translation from Ribo-seq data. 1735-1737

Genetics and Population Analysis

• 
  Kalle Leppälä, Svend V. Nielsen, Thomas Mailund:
  admixturegraph: an R package for admixture graph manipulation and fitting. 1738-1740

Systems Biology

• 
  Hulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh S. Vempala:
  CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models. 1741-1743

Data and Text Mining

• 
  Jennifer E. Kyle, Kevin L. Crowell, Cameron P. Casey, Grant M. Fujimoto, Sangtae Kim, Sydney E. Dautel, Richard D. Smith, Samuel H. Payne, Thomas O. Metz:
  LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. 1744-1746

Databases and Ontologies

• 
  Jan J. Domanski, Oliver Beckstein, Bogdan I. Iorga:
  Ligandbook: an online repository for small and drug-like molecule force field parameters. 1747-1749

Volume 33, Number 12, June 2017

Original Papers
Genome Analysis

• 
  Hashem A. Shihab, Mark F. Rogers, Colin Campbell, Tom R. Gaunt:
  HIPred: an integrative approach to predicting haploinsufficient genes. 1751-1757
• 
  Feng-Biao Guo, Chuan Dong, Hong-Li Hua, Shuo Liu, Hao Luo, Hong-Wan Zhang, Yan-Ting Jin, Kai-Yue Zhang:
  Accurate prediction of human essential genes using only nucleotide composition and association information. 1758-1764
• 
  Hokeun Sun, Ya Wang, Yong Chen, Yun Li, Shuang Wang:
  pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data. 1765-1772

Sequence Analysis

• 
  Ralph Patrick, Bostjan Kobe, Kim-Anh Lê Cao, Mikael Bodén:
  PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. 1773-1781
• 
  Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol:
  Kollector: transcript-informed, targeted de novo assembly of gene loci. 1782-1788

Phylogenetics

• 
  Jingwen Pei, Yufeng Wu:
  STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies. 1789-1797
• 
  Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard:
  Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. 1798-1805

Structural Bioinformatics

• 
  Iain H. Moal, Didier Barradas-Bautista, Brian Jiménez-García, Mieczyslaw Torchala, Arjan van der Velde, Thom Vreven, Zhiping Weng, Paul A. Bates, Juan Fernández-Recio:
  IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. 1806-1813
• 
  Yina Gu, Da-Wei Li, Rafael Brüschweiler:
  Statistical database analysis of the role of loop dynamics for protein-protein complex formation and allostery. 1814-1819

Genetics and Population Analysis

• 
  Felipe Llinares-López, Laetitia Papaxanthos, Dean A. Bodenham, Damian Roqueiro, COPDGene Investigators, Karsten M. Borgwardt:
  Genome-wide genetic heterogeneity discovery with categorical covariates. 1820-1828

Systems Biology

• 
  Biaobin Jiang, Kyle Kloster, David F. Gleich, Michael Gribskov:
  AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs. 1829-1836
• 
  Evi Berchtold, Gergely Csaba, Ralf Zimmer:
  RelExplain - integrating data and networks to explain biological processes. 1837-1844
• 
  Claudia Hernandez-Armenta, David Ochoa, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Pedro Beltrão:
  Benchmarking substrate-based kinase activity inference using phosphoproteomic data. 1845-1851

Data and Text Mining

• 
  Juan Miguel Cejuela, Aleksandar Bojchevski, Carsten Uhlig, Rustem Bekmukhametov, Sanjeev Kumar Karn, Shpend Mahmuti, Ashish Baghudana, Ankit Dubey, Venkata P. Satagopam, Burkhard Rost:
  nala: text mining natural language mutation mentions. 1852-1858

Bioimage Informatics

• 
  Lu Wang, Daniele Durante, Rex E. Jung, David B. Dunson:
  Bayesian network-response regression. 1859-1866

Applications Notes
Genome Analysis

• 
  Brent S. Pedersen, Aaron R. Quinlan:
  cyvcf2: fast, flexible variant analysis with Python. 1867-1869
• 
  Elior Rahmani, Reut Yedidim, Liat Shenhav, Regev Schweiger, Omer Weissbrod, Noah Zaitlen, Eran Halperin:
  GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data. 1870-1872
• 
  Wei-Zhi Song, Torsten Thomas:
  Binning_refiner: improving genome bins through the combination of different binning programs. 1873-1875
• 
  Adam Price, Cynthia Gibas:
  Simulome: a genome sequence and variant simulator. 1876-1878

Sequence Analysis

• 
  Simone Marini, Nelson Nazzicari, Filippo Biscarini, Guang-Zhong Wang:
  Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity. 1879-1880
• 
  Yuanqiang Zou, Zhiqiang Wu, Lizong Deng, Aiping Wu, Fan Wu, Kenli Li, Taijiao Jiang, Yousong Peng:
  cooccurNet: an R package for co-occurrence network construction and analysis. 1881-1882
• 
  André Ramos Fernandes Da Silva, Diogo B. Lima, Alejandro Leyva, Rosario Durán, Carlos Batthyany, Priscila F. Aquino, Juliana C. Leal, Jimmy E. Rodriguez, Gilberto B. Domont, Marlon D. M. Santos, Julia Chamot-Rooke, Valmir C. Barbosa, Paulo C. Carvalho:
  DiagnoProt: a tool for discovery of new molecules by mass spectrometry. 1883-1885

Phylogenetics

• 
  Joseph W. Brown, Joseph F. Walker, Stephen A. Smith:
  Phyx: phylogenetic tools for unix. 1886-1888

Structural Bioinformatics

• 
  Damiano Piovesan, Ian Walsh, Giovanni Minervini, Silvio C. E. Tosatto:
  FELLS: fast estimator of latent local structure. 1889-1891

Gene expression

• 
  Genevieve L. Stein-O'Brien, Jacob L. Carey, Waishing Lee, Michael Considine, Alexander V. Favorov, Emily Flam, Theresa Guo, Sijia Li, Luigi Marchionni, Thomas Sherman, Shawn Sivy, Daria A. Gaykalova, Ronald McKay, Michael F. Ochs, Carlo Colantuoni, Elana J. Fertig:
  PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. 1892-1894

Genetics and Population Analysis

• 
  Alexandre Fort, Nikolaos I. Panousis, Marco Garieri, Stylianos E. Antonarakis, Tuuli Lappalainen, Emmanouil T. Dermitzakis, Olivier Delaneau:
  MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets. 1895-1897
• 
  Ramón Díaz-Uriarte:
  OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations. 1898-1899
• 
  Victor Trevino, José G. Tamez-Peña:
  VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics. 1900-1901

Systems Biology

• 
  Kevin Titeca, Pieter Meysman, Kris Laukens, Lennart Martens, Jan Tavernier, Sven Eyckerman:
  sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets. 1902-1904
• 
  Daniel Cuevas, Robert A. Edwards:
  PMAnalyzer: a new web interface for bacterial growth curve analysis. 1905-1906

Bioimage Informatics

• 
  Ilan Y. Smoly, Eugene Lerman, Michal Ziv-Ukelson, Esti Yeger Lotem:
  MotifNet: a web-server for network motif analysis. 1907-1909

Volume 33, Number 13, July 2017

Discovery Notes
Structural Bioinformatics

• 
  Morena Pappalardo, Ian G. Reddin, Diego Cantoni, Jeremy S. Rossman, Martin Michaelis, Mark N. Wass:
  Changes associated with Ebola virus adaptation to novel species. 1911-1915

Systems Biology

• 
  Pengyi Yang, Andrew J. Oldfield, Taiyun Kim, Andrian Yang, Jean Yee Hwa Yang, Joshua Wing Kei Ho:
  Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. 1916-1920

Original Papers
Sequence Analysis

• 
  Musa Nur Gabere, William Stafford Noble:
  Empirical comparison of web-based antimicrobial peptide prediction tools. 1921-1929
• 
  Bite Yang, Feng Liu, Chao Ren, Zhangyi Ouyang, Ziwei Xie, Xiaochen Bo, Wenjie Shu:
  BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone. 1930-1936
• 
  Yugo Shimizu, Hiroyuki Ogata, Susumu Goto:
  Discriminating the reaction types of plant type III polyketide synthases. 1937-1943

Gene expression

• 
  Yun Zhang, David J. Topham, Juilee Thakar, Xing Qiu:
  FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. 1944-1952
• 
  Sascha Jung, András Hartmann, Antonio del Sol:
  RefBool: a reference-based algorithm for discretizing gene expression data. 1953-1962

Genetics and Population Analysis

• 
  Changshuai Wei, Qing Lu:
  A generalized association test based on U statistics. 1963-1971
• 
  Daniel Schlauch, Heide Loehlein Fier, Christoph Lange:
  Identification of genetic outliers due to sub-structure and cryptic relationships. 1972-1979

Systems Biology

• 
  Sucheendra K. Palaniappan, François Bertaux, Matthieu Pichené, Eric Fabre, Grégory Batt, Blaise Genest:
  Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway. 1980-1986
• 
  Sahar Ansari, Michele Donato, Nafiseh Saberian, Sorin Draghici:
  An approach to infer putative disease-specific mechanisms using neighboring gene networks. 1987-1994
• 
  Yu Chen, Yonghong Wang, Jens Nielsen:
  Systematic inference of functional phosphorylation events in yeast metabolism. 1995-2001

Bioimage Informatics

• 
  Vlad Popovici, Eva Budinska, Ladislav Dusek, Michal Kozubek, Fred Bosman:
  Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. 2002-2009
• 
  William J. Godinez, Imtiaz Hossain, Stanley E. Lazic, John W. Davies, Xian Zhang:
  A multi-scale convolutional neural network for phenotyping high-content cellular images. 2010-2019
• 
  Oliver Hilsenbeck, Michael Schwarzfischer, Dirk Loeffler, Sotiris Dimopoulos, Simon Hastreiter, Carsten Marr, Fabian J. Theis, Timm Schroeder:
  fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. 2020-2028

Applications Notes
Genome Analysis

• 
  Yu Liu, Sha Sun, Timothy Bredy, Marcelo A. Wood, Robert C. Spitale, Pierre Baldi:
  MotifMap-RNA: a genome-wide map of RBP binding sites. 2029-2031
• 
  Jacob E. Munro, Sally L. Dunwoodie, Eleni Giannoulatou:
  SVPV: a structural variant prediction viewer for paired-end sequencing datasets. 2032-2033

Sequence Analysis

• 
  Rogan Magee, Phillipe Loher, Eric Londin, Isidore Rigoutsos:
  Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. 2034-2036
• 
  Petr Danecek, Shane A. McCarthy:
  BCFtools/csq: haplotype-aware variant consequences. 2037-2039
• 
  Xavier Watkins, Leyla J. García, Sangya Pundir, Maria Jesus Martin, The UniProt Consortium:
  ProtVista: visualization of protein sequence annotations. 2040-2041
• 
  Dominik Kopczynski, Harald Barsnes, Pål R. Njølstad, Albert Sickmann, Marc Vaudel, Robert Ahrends:
  PeptideMapper: efficient and versatile amino acid sequence and tag mapping. 2042-2044

Structural Bioinformatics

• 
  Tomasz Magdziarz, Karolina Mitusinska, Sandra Goldowska, Alicja Pluciennik, Michal Stolarczyk, Magdalena Lugowska, Artur Góra:
  AQUA-DUCT: a ligands tracking tool. 2045-2046
• 
  Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E. Bourne, Peter W. Rose:
  BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. 2047-2049

Gene expression

• 
  Shian Su, Charity W. Law, Casey Ah-Cann, Marie-Liesse Asselin-Labat, Marnie E. Blewitt, Matthew E. Ritchie:
  Glimma: interactive graphics for gene expression analysis. 2050-2052
• 
  Michal Sharabi-Schwager, Etti Or, Ron Ophir:
  ctsGE - clustering subgroups of expression data. 2053-2055

Genetics and Population Analysis

• 
  Daniel Taliun, Sonia P. Chothani, Sebastian Schönherr, Lukas Forer, Michael Boehnke, Gonçalo R. Abecasis, Chaolong Wang:
  LASER server: ancestry tracing with genotypes or sequence reads. 2056-2058
• 
  Zachary A. Szpiech, Alexandra Blant, Trevor J. Pemberton:
  GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification. 2059-2062

Data and Text Mining

• 
  Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer:
  DeepBlueR: large-scale epigenomic analysis in R. 2063-2064

Databases and Ontologies

• 
  Qi Liu, Changjun Ding, Yanguang Chu, Weixi Zhang, Ganggang Guo, Jiafei Chen, Xiaohua Su:
  Pln24NT: a web resource for plant 24-nt siRNA producing loci. 2065-2067
• 
  Jungsul Lee, Chulhee Choi:
  Oncopression: gene expression compendium for cancer with matched normal tissues. 2068-2070

Volume 33, Number 14, July 2017

Ismb/ECCB 2017: the 25th Annual Conference Intelligent Systems for molecular Biology held jointly with the 16th Annual European Conference on Computational Biology, Prague, Czech Republic, July 21-25, 2017
ISMB/ECCB 2017 PROCEEDINGS

• 
  Niko Beerenwinkel, Yana Bromberg:
  ISMB/ECCB 2017 proceedings. i1-i2

Ismb/ECCB 2017 Proceedings Papers Committee

• 
  ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE. i3-i4

3DSIG

• 
  Mark A. Hallen, Bruce Randall Donald:
  CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. i5-i12
• 
  Min Xu, Xiaoqi Chai, Hariank Muthakana, Xiaodan Liang, Ge Yang, Tzviya Zeev-Ben-Mordehai, Eric P. Xing:
  Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. i13-i22
• 
  Mirco Michel, David Menéndez Hurtado, Karolis Uziela, Arne Elofsson:
  Large-scale structure prediction by improved contact predictions and model quality assessment. i23-i29
• 
  Michael Estrin, Haim J. Wolfson:
  SnapDock - template-based docking by Geometric Hashing. i30-i36

Bio-Ontologies

• 
  Maryam Habibi, Leon Weber, Mariana L. Neves, David Luis Wiegandt, Ulf Leser:
  Deep learning with word embeddings improves biomedical named entity recognition. i37-i48
• 
  Gizem Sogancioglu, Hakime Öztürk, Arzucan Özgür:
  BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. i49-i58

Camda

• 
  Djork-Arné Clevert, Thomas Unterthiner, Gundula Povysil, Sepp Hochreiter:
  Rectified factor networks for biclustering of omics data. i59-i66
• 
  Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul, Eleazar Eskin:
  Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. i67-i74

Function

• 
  Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz:
  Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. i75-i82
• 
  Ishita K. Khan, Mansurul Bhuiyan, Daisuke Kihara:
  DextMP: deep dive into text for predicting moonlighting proteins. i83-i91

Hitseq

• 
  Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang:
  Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding. i92-i101
• 
  Jing Guo, Jie Zheng:
  HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape. i102-i109
• 
  Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford:
  Improving the performance of minimizers and winnowing schemes. i110-i117
• 
  Yohei Rosen, Jordan Eizenga, Benedict Paten:
  Modelling haplotypes with respect to reference cohort variation graphs. i118-i123
• 
  Martina Fischer, Benjamin Strauch, Bernhard Y. Renard:
  Abundance estimation and differential testing on strain level in metagenomics data. i124-i132
• 
  Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
  deBGR: an efficient and near-exact representation of the weighted de Bruijn graph. i133-i141
• 
  Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro:
  Improved data-driven likelihood factorizations for transcript abundance estimation. i142-i151
• 
  Gryte Satas, Benjamin J. Raphael:
  Tumor phylogeny inference using tree-constrained importance sampling. i152-i160
• 
  Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach:
  Discovery and genotyping of novel sequence insertions in many sequenced individuals. i161-i169

Netbio

• 
  Sean Robinson, Jaakko Nevalainen, Guillaume Pinna, Anna Campalans, J. Pablo Radicella, Laurent Guyon:
  Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields. i170-i179
• 
  Vipin Vijayan, Dominic Critchlow, Tijana Milenkovic:
  Alignment of dynamic networks. i180-i189
• 
  Marinka Zitnik, Jure Leskovec:
  Predicting multicellular function through multi-layer tissue networks. i190-i198
• 
  Francesca Petralia, Vasily N. Aushev, Kalpana Gopalakrishnan, Maya Kappil, Nyan W. Khin, Jia Chen, Susan L. Teitelbaum, Pei Wang:
  A new method to study the change of miRNA-mRNA interactions due to environmental exposures. i199-i207
• 
  Stefan Avey, Subhasis Mohanty, Jean Wilson, Heidi Zapata, Samit R. Joshi, Barbara Siconolfi, Sui Tsang, Albert C. Shaw, Steven H. Kleinstein:
  Multiple network-constrained regressions expand insights into influenza vaccination responses. i208-i216
• 
  Xiongtao Ruan, Christoph Wülfing, Robert F. Murphy:
  Image-based spatiotemporal causality inference for protein signaling networks. i217-i224

Reggen

• 
  Pang Wei Koh, Emma Pierson, Anshul Kundaje:
  Denoising genome-wide histone ChIP-seq with convolutional neural networks. i225-i233
• 
  Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng:
  TITER: predicting translation initiation sites by deep learning. i234-i242
• 
  Lin Zhu, Hong-Bo Zhang, De-Shuang Huang:
  Direct AUC optimization of regulatory motifs. i243-i251
• 
  Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma:
  Exploiting sequence-based features for predicting enhancer-promoter interactions. i252-i260
• 
  Lila Rieber, Shaun Mahony:
  miniMDS: 3D structural inference from high-resolution Hi-C data. i261-i266

Rna

• 
  Mingfu Shao, Jianzhu Ma, Sheng Wang:
  DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. i267-i273
• 
  Anupama Jha, Matthew R. Gazzara, Yoseph Barash:
  Integrative deep models for alternative splicing. i274-i282
• 
  Juraj Michalik, Hélène Touzet, Yann Ponty:
  Efficient approximations of RNA kinetics landscape using non-redundant sampling. i283-i292

Sysmod

• 
  Atefeh Kazeroonian, Fabian J. Theis, Jan Hasenauer:
  A scalable moment-closure approximation for large-scale biochemical reaction networks. i293-i300
• 
  Eugenio Cinquemani, Valérie Laroute, Muriel Cocaign-Bousquet, Hidde de Jong, Delphine Ropers:
  Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. i301-i310
• 
  Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri:
  popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. i311-i318
• 
  Dennis Pischel, Kai Sundmacher, Robert J. Flassig:
  Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems. i319-i324

Transmed

• 
  Omer Weissbrod, Elior Rahmani, Regev Schweiger, Saharon Rosset, Eran Halperin:
  Association testing of bisulfite-sequencing methylation data via a Laplace approximation. i325-i332
• 
  Michael Altenbuchinger, Philipp Schwarzfischer, Thorsten Rehberg, Jörg Reinders, Christian W. Kohler, Wolfram Gronwald, Julia Richter, Monika Szczepanowski, Neus Masqué-Soler, Wolfram Klapper, Peter J. Oefner, Rainer Spang:
  Molecular signatures that can be transferred across different omics platforms. i333-i340
• 
  Xiaoke Hao, Chanxiu Li, Jingwen Yan, Xiaohui Yao, Shannon L. Risacher, Andrew J. Saykin, Li Shen, Daoqiang Zhang:
  Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis. i341-i349
• 
  Lei Ding, Daniel J. McDonald:
  Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression. i350-i358
• 
  Muhammad Ammad-ud-din, Suleiman A. Khan, Krister Wennerberg, Tero Aittokallio:
  Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression. i359-i368

Vari

• 
  Yoichiro Nakatani, Aoife McLysaght:
  Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. i369-i378
• 
  C. H. Lee, Eleazar Eskin, Buhm Han:
  Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects. i379-i388
• 
  Kymberleigh A. Pagel, Vikas Pejaver, Guan Ning Lin, Hyun-Jun Nam, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac:
  When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. i389-i398

Author Index

• 
  Author Index. i399-i400

Original Papers
Genome Analysis

• 
  Erik L. Clarke, Sesh A. Sundararaman, Stephanie N. Seifert, Frederic D. Bushman, Beatrice H. Hahn, Dustin Brisson:
  swga: a primer design toolkit for selective whole genome amplification. 2071-2077
• 
  Shudong Wang, Sicheng He, Fayou Yuan, Xinjie Zhu:
  Tagging SNP-set selection with maximum information based on linkage disequilibrium structure in genome-wide association studies. 2078-2081

Sequence Analysis

• 
  Lorian Schaeffer, Harold Pimentel, Nicolas Bray, Páll Melsted, Lior Pachter:
  Pseudoalignment for metagenomic read assignment. 2082-2088
• 
  Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen:
  RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. 2089-2096
• 
  Zhen Gao, Jianhua Ruan:
  Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning. 2097-2105

Structural Bioinformatics

• 
  Luciano Censoni, Heloisa dos Santos Muniz, Leandro Martínez:
  A network model predicts the intensity of residue-protein thermal coupling. 2106-2113
• 
  Amélie Héliou, Dominik Budday, Rasmus Fonseca, Henry van den Bedem:
  Fast, clash-free RNA conformational morphing using molecular junctions. 2114-2122

Gene expression

• 
  Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei:
  QRank: a novel quantile regression tool for eQTL discovery. 2123-2130
• 
  Musheng Li, Xueying Xie, Jing Zhou, Mengying Sheng, Xiaofeng Yin, Eun-A Ko, Tong Zhou, Wanjun Gu:
  Quantifying circular RNA expression from RNA-seq data using model-based framework. 2131-2139
• 
  Lin Wang, Silvia Liu, Ying Ding, Shin-sheng Yuan, Yen-Yi Ho, George C. Tseng:
  Meta-analytic framework for liquid association. 2140-2147

Genetics and Population Analysis

• 
  Jade Yu Cheng, Thomas Mailund, Rasmus Nielsen:
  Fast admixture analysis and population tree estimation for SNP and NGS data. 2148-2155

Systems Biology

• 
  Nil Mamano, Wayne B. Hayes:
  SANA: simulated annealing far outperforms many other search algorithms for biological network alignment. 2156-2164
• 
  Mojdeh Faraji, Eberhard O. Voit:
  Stepwise inference of likely dynamic flux distributions from metabolic time series data. 2165-2172
• 
  Zengmiao Wang, Huaying Fang, Nelson L. S. Tang, Minghua Deng:
  VCNet: vector-based gene co-expression network construction and its application to RNA-seq data. 2173-2181

Bioimage Informatics

• 
  Murad Megjhani, Pedro Correa de Sampaio, Julienne Leigh Carstens, Raghu Kalluri, Badrinath Roysam:
  Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy. 2182-2190

Applications Notes
Genome Analysis

• 
  Charles Curnin, Assaf Gordon, Yaniv Erlich:
  DNA Compass: a secure, client-side site for navigating personal genetic information. 2191-2193
• 
  Matthias Monfort, Eileen E. M. Furlong, Charles Girardot:
  Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets. 2194-2196
• 
  Asher Haug-Baltzell, Sean A. Stephens, Sean Davey, Carlos Eduardo Scheidegger, Eric Lyons:
  SynMap2 and SynMap3D: web-based whole-genome synteny browsers. 2197-2198
• 
  Koon-Kiu Yan, Galip Gürkan Yardimci, Chengfei Yan, William S. Noble, Mark Gerstein:
  HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. 2199-2201
• 
  Gregory W. Vurture, Fritz J. Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, Michael C. Schatz:
  GenomeScope: fast reference-free genome profiling from short reads. 2202-2204

Sequence Analysis

• 
  Konstantin S. Yarygin, Boris Kovarsky, Tanya Bibikova, Damir Melnikov, Alexander V. Tyakht, Dmitry G. Alexeev:
  ResistoMap - online visualization of human gut microbiota antibiotic resistome. 2205-2206
• 
  Robert D. Stewart, Mick Watson:
  poRe GUIs for parallel and real-time processing of MinION sequence data. 2207-2208
• 
  Felix Simkovic, Jens M. H. Thomas, Daniel J. Rigden:
  ConKit: a python interface to contact predictions. 2209-2211
• 
  Sandrine Perrin, Cyril Firmo, Sophie Lemoine, Stéphane Le Crom, Laurent Jourdren:
  Aozan: an automated post-sequencing data-processing pipeline. 2212-2213

Phylogenetics

• 
  Qi Wu, Zu-Guo Yu, Jianyi Yang:
  DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method. 2214-2215

Gene expression

• 
  Jinkai Wang, Yang Pan, Shihao Shen, Lan Lin, Yi Xing:
  rMATS-DVR: rMATS discovery of differential variants in RNA. 2216-2217
• 
  Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brazma:
  The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data. 2218-2220

Genetics and Population Analysis

• 
  Thomas O. McDonald, Franziska Michor:
  SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. 2221-2223
• 
  Christopher Heffelfinger, Christopher A. Fragoso, Mathias Lorieux:
  Constructing linkage maps in the genomics era with MapDisto 2.0. 2224-2225

Systems Biology

• 
  Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone:
  MaBoSS 2.0: an environment for stochastic Boolean modeling. 2226-2228
• 
  Sascha Herzinger, Wei Gu, Venkata P. Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa-Silva, Reinhard Schneider:
  SmartR: an open-source platform for interactive visual analytics for translational research data. 2229-2231
• 
  Daniel Schlauch, Joseph N. Paulson, Albert Young, Kimberly Glass, John Quackenbush:
  Estimating gene regulatory networks with pandaR. 2232-2234
• 
  Zhiwei Zhou, Xin Xiong, Zheng-Jiang Zhu:
  MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics. 2235-2237
• 
  Istemi Bahceci, Ugur Dogrusoz, Konnor C. La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz:
  PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. 2238-2240

Data and Text Mining

• 
  Clemens Messerschmidt, Manuel Holtgrewe, Dieter Beule:
  HLA-MA: simple yet powerful matching of samples using HLA typing results. 2241-2242

Message from the ISCB
Data and Text Mining

• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev. 2243-2244
• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner. 2245-2246
• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock. 2247-2248
• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter. 2249-2250

Volume 33, Number 15, August 2017

Original Papers
Genome Analysis

• 
  Xiuwen Zheng, Stephanie M. Gogarten, Michael F. Lawrence, Adrienne Stilp, Matthew P. Conomos, Bruce S. Weir, Cathy C. Laurie, David Levine:
  SeqArray - a storage-efficient high-performance data format for WGS variant calls. 2251-2257
• 
  Georg Stricker, Alexander Engelhardt, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur:
  GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. 2258-2265
• 
  Maximilian Knoll, Jürgen Debus, Amir Abdollahi:
  cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data. 2266-2272
• 
  Zhicong Huang, Huang Lin, Jacques Fellay, Zoltán Kutalik, Jean-Pierre Hubaux:
  SQC: secure quality control for meta-analysis of genome-wide association studies. 2273-2280

Sequence Analysis

• 
  Hsin-Nan Lin, Wen-Lian Hsu:
  Kart: a divide-and-conquer algorithm for NGS read alignment. 2281-2287
• 
  Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo:
  BEESEM: estimation of binding energy models using HT-SELEX data. 2288-2295

Structural Bioinformatics

• 
  Baoji He, S. M. Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang:
  NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers. 2296-2306

Gene expression

• 
  Robert Brown, Gleb Kichaev, Nicholas Mancuso, James Boocock, Bogdan Pasaniuc:
  Enhanced methods to detect haplotypic effects on gene expression. 2307-2313
• 
  Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S. H. Ko, Shigeru B. H. Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido:
  SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. 2314-2321

Genetics and Population Analysis

• 
  Steven H. Wu, Rachel Schwartz, David J. Winter, Donald F. Conrad, Reed A. Cartwright:
  Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions. 2322-2329
• 
  Maggie Haitian Wang, Haoyi Weng, Rui Sun, Jack Lee, William Ka Kei Wu, Ka Chun Chong, Benny Zee:
  A Zoom-Focus algorithm (ZFA) to locate the optimal testing region for rare variant association tests. 2330-2336

Systems Biology

• 
  Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy:
  Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. 2337-2344
• 
  Hyun-Seob Song, Noam Goldberg, Ashutosh Mahajan, Doraiswami Ramkrishna:
  Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming. 2345-2353

Data and Text Mining

• 
  Cheng-Hong Yang, Li-Yeh Chuang, Yu-Da Lin:
  CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies. 2354-2362
• 
  Yinxia Lou, Yue Zhang, Tao Qian, Fei Li, Shufeng Xiong, Donghong Ji:
  A transition-based joint model for disease named entity recognition and normalization. 2363-2371
• 
  Weijia Zhang, Thuc Duy Le, Lin Liu, Zhi-Hua Zhou, Jiuyong Li:
  Mining heterogeneous causal effects for personalized cancer treatment. 2372-2378

Applications Notes
Genome Analysis

• 
  Yosuke Nishimura, Takashi Yoshida, Megumi Kuronishi, Hideya Uehara, Hiroyuki Ogata, Susumu Goto:
  ViPTree: the viral proteomic tree server. 2379-2380
• 
  Raymond G. Cavalcante, Maureen A. Sartor:
  annotatr: genomic regions in context. 2381-2383
• 
  Feifei Xiao, Yue Niu, Ning Hao, Yanxun Xu, Zhilin Jin, Heping Zhang:
  modSaRa: a computationally efficient R package for CNV identification. 2384-2385

Sequence Analysis

• 
  Andrew J. Gartland, Nicholas D. Kullman, Allan C. deCamp, Graham Clenaghan, Wayne Yang, Craig A. Magaret, Paul Thatcher Edlefsen, Peter B. Gilbert:
  SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials. 2386-2388
• 
  Pedro J. Torres, Robert A. Edwards, Katelyn McNair:
  PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive. 2389-2391

Phylogenetics

• 
  Timothy G. Vaughan:
  IcyTree: rapid browser-based visualization for phylogenetic trees and networks. 2392-2394

Structural Bioinformatics

• 
  Inanc Soylu, Stefano M. Marino:
  Cpipe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues. 2395-2396

Gene expression

• 
  Noé Fernández-Pozo, Yi Zheng, Stephen I. Snyder, Philippe Nicolas, Yoshihito Shinozaki, Zhangjun Fei, Carmen Catala, James J. Giovannoni, Jocelyn K. C. Rose, Lukas A. Mueller:
  The Tomato Expression Atlas. 2397-2398

Genetics and Population Analysis

• 
  Jing Wang, David C. Samuels, Yu Shyr, Yan Guo:
  StrandScript: evaluation of Illumina genotyping array design and strand correction. 2399-2401
• 
  Alessandro Romanel, Tuo Zhang, Olivier Elemento, Francesca Demichelis:
  EthSEQ: ethnicity annotation from whole exome sequencing data. 2402-2404
• 
  Matti Pirinen, Christian Benner, Pekka Marttinen, Marjo-Riitta Järvelin, Manuel A. Rivas, Samuli Ripatti:
  biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements. 2405-2407
• 
  Zhiqiang Hu, Chen Sun, Kuang-Chen Lu, Xixia Chu, Yue Zhao, Jinyuan Lu, Jianxin Shi, Chaochun Wei:
  EUPAN enables pan-genome studies of a large number of eukaryotic genomes. 2408-2409

Systems Biology

• 
  Åsmund Flobak, Miguel Vazquez, Astrid Lægreid, Alfonso Valencia:
  CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. 2410-2412
• 
  Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang:
  SynergyFinder: a web application for analyzing drug combination dose-response matrix data. 2413-2415
• 
  Michael B. Mundy, Helena Mendes-Soares, Nicholas Chia:
  Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models. 2416-2418

Data and Text Mining

• 
  Thomas Naake, Emmanuel Gaquerel:
  MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data. 2419-2420

Databases and Ontologies

• 
  Nikolas Pontikos, Jing Yu, Ismail Moghul, Lucy Withington, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun Ernest Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene, Julius O. B. Jacobsen, Tristan Clark, David S. Gregory, Andrea M. Nemeth, Stephanie Halford, Chris F. Inglehearn, Susan M. Downes, Graeme C. M. Black, Andrew R. Webster, Alison J. Hardcastle, Ukirdc, Vincent Plagnol:
  Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data. 2421-2423

Bioimage Informatics

• 
  Ignacio Arganda-Carreras, Verena Kaynig, Curtis Rueden, Kevin W. Eliceiri, Johannes E. Schindelin, Albert Cardona, H. Sebastian Seung:
  Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. 2424-2426
• 
  Pere Ràfols, Sonia Torres, Noelia Ramírez, Esteban del Castillo, Oscar Yanes, Jesús Brezmes, Xavier Correig:
  rMSI: an R package for MS imaging data handling and visualization. 2427-2428

Message from the ISCB
Bioimage Informatics

• 
  Kieran O'Neill, Vivek Rai, Alastair M. Kilpatrick:
  The International Society for Computational Biology and WikiProject Computational Biology: celebrating 10 years of collaboration towards open access. 2429-2430

Volume 33, Number 16, August 2017

Discovery note
Sequence Analysis

• 
  Donald W. Lee, Gary R. Whittaker:
  Use of AAScatterPlot tool for monitoring the evolution of the hemagglutinin cleavage site in H9 avian influenza viruses. 2431-2435

Original Papers
Genome Analysis

• 
  Xiao-Fei Zhang, Le Ou-Yang, Hong Yan:
  Incorporating prior information into differential network analysis using non-paranormal graphical models. 2436-2445
• 
  Claudia Paicu, Irina Mohorianu, Matthew B. Stocks, Ping Xu, Aurore Coince, Martina Billmeier, Tamas Dalmay, Vincent Moulton, Simon Moxon:
  miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. 2446-2454

Sequence Analysis

• 
  Sivan Leviyang, Igor Griva, Sergio Ita, Welkin E. Johnson:
  A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection. 2455-2463
• 
  Marco Salvatore, Per Warholm, Nanjiang Shu, Walter Basile, Arne Elofsson:
  SubCons: a new ensemble method for improved human subcellular localization predictions. 2464-2470
• 
  Alejandro Ochoa, Mona Singh:
  Domain prediction with probabilistic directional context. 2471-2478

Structural Bioinformatics

• 
  Mélanie Boudard, Dominique Barth, Julie Bernauer, Alain Denise, Johanne Cohen:
  GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization. 2479-2486
• 
  Anand Sastry, Jonathan Monk, Hanna Tegel, Mathias Uhlen, Bernhard O. Palsson, Johan Rockberg, Elizabeth Brunk:
  Machine learning in computational biology to accelerate high-throughput protein expression. 2487-2495
• 
  Balachandran Manavalan, Jooyoung Lee:
  SVMQA: support-vector-machine-based protein single-model quality assessment. 2496-2503

Gene expression

• 
  Sabrina Rashid, Darrell N. Kotton, Ziv Bar-Joseph:
  TASIC: determining branching models from time series single cell data. 2504-2512

Genetics and Population Analysis

• 
  Keelin Greenlaw, Elena Szefer, Jinko Graham, Mary Lesperance, Farouk S. Nathoo:
  A Bayesian group sparse multi-task regression model for imaging genetics. 2513-2522

Systems Biology

• 
  Majed Alzahrani, Hiroyuki Kuwahara, Wei Wang, Xin Gao:
  Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. 2523-2531
• 
  Xiaoyuan Zhou, Guofeng Meng, Christine Nardini, Hongkang Mei:
  Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc. 2532-2538

Data and Text Mining

• 
  Uri Shaham, Kelly P. Stanton, Jun Zhao, Huamin Li, Khadir Raddassi, Ruth R. Montgomery, Yuval Kluger:
  Removal of batch effects using distribution-matching residual networks. 2539-2546

Databases and Ontologies

• 
  Matthias Hörtenhuber, Enrique M. Toledo, Erik Smedler, Ernest Arenas, Seth Malmersjö, Lauri Louhivuori, Per Uhlén:
  Mapping genes for calcium signaling and their associated human genetic disorders. 2547-2554

Bioimage Informatics

• 
  Tao Zeng, Bian Wu, Shuiwang Ji:
  DeepEM3D: approaching human-level performance on 3D anisotropic EM image segmentation. 2555-2562
• 
  Corinna Blasse, Stephan Saalfeld, Raphaël Etournay, Andreas Sagner, Suzanne Eaton, Eugene W. Myers:
  PreMosa: extracting 2D surfaces from 3D microscopy mosaics. 2563-2569

Applications Notes
Genome Analysis

• 
  Alice C. L. Parodi, Laura M. Sangalli, Simone Vantini, Bruno Amati, Piercesare Secchi, Marco J. Morelli:
  FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. 2570-2572
• 
  Patrick Czeczko, Steven C. Greenway, A. P. Jason de Koning:
  EzMap: a simple pipeline for reproducible analysis of the human virome. 2573-2574
• 
  Renato Augusto Corrêa dos Santos, Gustavo H. Goldman, Diego Mauricio Riaño-Pachón:
  ploidyNGS: visually exploring ploidy with Next Generation Sequencing data. 2575-2576
• 
  Shengfeng Huang, Mingjing Kang, Anlong Xu:
  HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. 2577-2579

Sequence Analysis

• 
  Felipe da Veiga Leprevost, Björn A. Grüning, Saulo Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo A. Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jiménez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Pérez-Riverol:
  BioContainers: an open-source and community-driven framework for software standardization. 2580-2582
• 
  Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher:
  MISA-web: a web server for microsatellite prediction. 2583-2585
• 
  Jinyu Yang, Xin Chen, Adam McDermaid, Qin Ma:
  DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. 2586-2588

Structural Bioinformatics

• 
  Hitesh Patel, Tobias Brinkjost, Oliver Koch:
  PyGOLD: a python based API for docking based virtual screening workflow generation. 2589-2590

Gene expression

• 
  José Fernández Navarro, Joel Sjöstrand, Fredrik Salmén, Joakim Lundeberg, Patrik L. Ståhl:
  ST Pipeline: an automated pipeline for spatial mapping of unique transcripts. 2591-2593

Genetics and Population Analysis

• 
  Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand:
  RTK: efficient rarefaction analysis of large datasets. 2594-2595

Systems Biology

• 
  James J. Kelley, Shay Maor, Min Kyung Kim, Anatoliy Lane, Desmond S. Lun:
  MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks. 2596-2597

Data and Text Mining

• 
  Martin Larralde, Thomas N. Lawson, Ralf J. M. Weber, Pablo A. Moreno, Kenneth Haug, Philippe Rocca-Serra, Mark R. Viant, Christoph Steinbeck, Reza M. Salek:
  mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data. 2598-2600
• 
  Daniel Cannon, Jeremy J. Yang, Stephen L. Mathias, Oleg Ursu, Subramani Mani, Anna Waller, Stephan C. Schürer, Lars Juhl Jensen, Larry A. Sklar, Cristian Bologa, Tudor I. Oprea:
  TIN-X: target importance and novelty explorer. 2601-2603

Databases and Ontologies

• 
  David Weichselbaum, Bojan Zagrovic, Anton A. Polyansky:
  Fuento: functional enrichment for bioinformatics. 2604-2606
• 
  Carlos Horro, Martin Cook, Teresa K. Attwood, Michelle D. Brazas, John M. Hancock, Patricia M. Palagi, Manuel Corpas, Rafael C. Jiménez:
  BioCIDER: a Contextualisation InDEx for biological Resources discovery. 2607-2608

Corrigenda
Databases and Ontologies

• 
  Elizabeth Baskin, Rick Farouni, Ewy A. Mathé:
  ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data. 2609
• 
  Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou:
  iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. 2610

Volume 33, Number 17, September 2017

Discovery note
Genome Analysis

• 
  Hebing Chen, Shuai Jiang, Zhuo Zhang, Hao Li, Yiming Lu, Xiaochen Bo:
  Exploring spatially adjacent TFBS-clustered regions with Hi-C data. 2611-2614

Original Papers
Genome Analysis

• 
  Jens Lichtenberg, Laura Elnitski, David M. Bodine:
  SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures. 2615-2621
• 
  Keqin Liu, Dominik Beck, Julie A. I. Thoms, Liang Liu, Weiling Zhao, John E. Pimanda, Xiaobo Zhou:
  Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. 2622-2630
• 
  Xinjie Hui, Yueming Hu, Ming-An Sun, Xingsheng Shu, Rongfei Han, Qinggang Ge, Yejun Wang:
  EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons. 2631-2641
• 
  Nicolò Navarin, Fabrizio Costa:
  An efficient graph kernel method for non-coding RNA functional prediction. 2642-2650
• 
  Weiwei Zhang, Hao Feng, Hao Wu, Xiaoqi Zheng:
  Accounting for tumor purity improves cancer subtype classification from DNA methylation data. 2651-2657

Sequence Analysis

• 
  Yeeleng Scott Vang, Xiaohui Xie:
  HLA class I binding prediction via convolutional neural networks. 2658-2665
• 
  Tsukasa Fukunaga, Michiaki Hamada:
  RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. 2666-2674

Structural Bioinformatics

• 
  Dapeng Xiong, Jianyang Zeng, Haipeng Gong:
  A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy. 2675-2683
• 
  Daniel W. A. Buchan, David T. Jones:
  EigenTHREADER: analogous protein fold recognition by efficient contact map threading. 2684-2690

Gene expression

• 
  Hongfu Liu, Rui Zhao, Hongsheng Fang, Feixiong Cheng, Yun Fu, Yang-Yu Liu:
  Entropy-based consensus clustering for patient stratification. 2691-2698
• 
  Mingli Lei, Jia Xu, Li-Ching Huang, Lily Wang, Jing Li:
  Network module-based model in the differential expression analysis for RNA-seq. 2699-2705

Systems Biology

• 
  Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen:
  Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. 2706-2714

Data and Text Mining

• 
  Jian Ma, Cameron P. Casey, Xueyun Zheng, Yehia M. Ibrahim, Christopher S. Wilkins, Ryan S. Renslow, Dennis G. Thomas, Samuel H. Payne, Matthew E. Monroe, Richard D. Smith, Justin G. Teeguarden, Erin S. Baker, Thomas O. Metz:
  PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. 2715-2722

Databases and Ontologies

• 
  Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf:
  Neuro-symbolic representation learning on biological knowledge graphs. 2723-2730
• 
  Michael J. Bell, Phillip W. Lord:
  On patterns and re-use in bioinformatics databases. 2731-2736

Applications Notes
Genome Analysis

• 
  Kieran O'Neill, Mark Hills, Mike Gottlieb, Matthew Borkowski, Aly Karsan, Peter M. Lansdorp:
  Assembling draft genomes using contiBAIT. 2737-2739
• 
  Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier:
  OMSim: a simulator for optical map data. 2740-2742
• 
  Anthony Chiu, Mahmood Ayub, Caroline Dive, Ged Brady, Crispin J. Miller:
  twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. 2743-2745

Sequence Analysis

• 
  Alice Héliou, Solon P. Pissis, Simon J. Puglisi:
  emMAW: computing minimal absent words in external memory. 2746-2749
• 
  Bo Liu, Tao Jiang, Siu-Ming Yiu, Junyi Li, Yadong Wang:
  rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering. 2750-2752
• 
  Alex T. Müller, Gisela Gabernet, Jan A. Hiss, Gisbert Schneider:
  modlAMP: Python for antimicrobial peptides. 2753-2755
• 
  Jiawei Wang, Bingjiao Yang, Jerico Nico De Leon Revote, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Jiangning Song, Kuo-Chen Chou, Trevor Lithgow:
  POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. 2756-2758
• 
  Marek Kokot, Maciej Dlugosz, Sebastian Deorowicz:
  KMC 3: counting and manipulating k-mer statistics. 2759-2761
• 
  Roberto R. Expósito, Jorge Veiga, Jorge González-Domínguez, Juan Touriño:
  MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud. 2762-2764

Structural Bioinformatics

• 
  Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B. Siegel, Firas Khatib, Seth Cooper:
  Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. 2765-2767
• 
  David K. Brown, David L. Penkler, Olivier Sheik Amamuddy, Caroline J. Ross, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop:
  MD-TASK: a software suite for analyzing molecular dynamics trajectories. 2768-2771

Gene expression

• 
  Andrew Anand Brown:
  veqtl-mapper: variance association mapping for molecular phenotypes. 2772-2773
• 
  Francesco Del Carratore, Andris Jankevics, Rob Eisinga, Tom Heskes, Fangxin Hong, Rainer Breitling:
  RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. 2774-2775

Genetics and Population Analysis

• 
  Gad Abraham, Yixuan Qiu, Michael Inouye:
  FlashPCA2: principal component analysis of Biobank-scale genotype datasets. 2776-2778
• 
  Sergi Hervas, Esteve Sanz, Sònia Casillas, John E. Pool, Antonio Barbadilla:
  PopFly: the Drosophila population genomics browser. 2779-2780

Systems Biology

• 
  Katherine Maia McCoy, Margaret L. Antonio, Tim van Opijnen:
  MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization. 2781-2783

Databases and Ontologies

• 
  Judong Shen, Kijoung Song, Andrew J. Slater, Enrico Ferrero, Matthew R. Nelson:
  STOPGAP: a database for systematic target opportunity assessment by genetic association predictions. 2784-2786
• 
  Sherlyn Jemimah, K. Yugandhar, M. Michael Gromiha:
  PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics. 2787-2788

Corrigendum
Databases and Ontologies

• 
  Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol:
  Kollector: transcript-informed, targeted de novo assembly of gene loci. 2789

Erratum
Databases and Ontologies

• 
  Michael Altenbuchinger, Philipp Schwarzfischer, Thorsten Rehberg, Jörg Reinders, Christian W. Kohler, Wolfram Gronwald, Julia Richter, Monika Szczepanowski, Neus Masqué-Soler, Wolfram Klapper, Peter J. Oefner, Rainer Spang:
  Molecular signatures that can be transferred across different omics platforms. 2790

Volume 33, Number 18, September 2017

Original Papers
Genome Analysis

• 
  Nora Rieber, Regina Bohnert, Ulrike Ziehm, Gunther Jansen:
  Reliability of algorithmic somatic copy number alteration detection from targeted capture data. 2791-2798
• 
  Zaixiang Tang, Yueping Shen, Xinyan Zhang, Nengjun Yi:
  The spike-and-slab lasso Cox model for survival prediction and associated genes detection. 2799-2807
• 
  Ferdinando Montecuollo, Giovanni Schmid, Roberto Tagliaferri:
  E2FM: an encrypted and compressed full-text index for collections of genomic sequences. 2808-2817
• 
  Burçak Otlu, Can Firtina, Sündüz Keles, Öznur Tastan:
  GLANET: genomic loci annotation and enrichment tool. 2818-2828
• 
  Xiong Li:
  A fast and exhaustive method for heterogeneity and epistasis analysis based on multi-objective optimization. 2829-2836

Sequence Analysis

• 
  Loris Nanni, Sheryl Brahnam:
  Multi-label classifier based on histogram of gradients for predicting the anatomical therapeutic chemical class/classes of a given compound. 2837-2841

Structural Bioinformatics

• 
  Rhys Heffernan, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou:
  Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility. 2842-2849
• 
  Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß:
  RNAblueprint: flexible multiple target nucleic acid sequence design. 2850-2858
• 
  Mirco Michel, Marcin J. Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson:
  Predicting accurate contacts in thousands of Pfam domain families using PconsC3. 2859-2866

Gene expression

• 
  Bahjat F. Qaqish, Jonathon J. O'Brien, Jonathan C. Hibbard, Katie J. Clowers:
  Accelerating high-dimensional clustering with lossless data reduction. 2867-2872

Genetics and Population Analysis

• 
  Jian Xiao, Hongyuan Cao, Jun Chen:
  False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing. 2873-2881
• 
  Mingwei Dai, Jingsi Ming, Mingxuan Cai, Jin Liu, Can Yang, Xiang Wan, Zongben Xu:
  IGESS: a statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies. 2882-2889

Systems Biology

• 
  Nicolas Städler, Frank Dondelinger, Steven M. Hill, Rehan Akbani, Yiling Lu, Gordon B. Mills, Sach Mukherjee:
  Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study. 2890-2896

Data and Text Mining

• 
  Kristen A. Severson, Brinda Monian, J. Christopher Love, Richard D. Braatz:
  A method for learning a sparse classifier in the presence of missing data for high-dimensional biological datasets. 2897-2905
• 
  Trang T. Le, W. Kyle Simmons, Masaya Misaki, Jerzy Bodurka, Bill C. White, Jonathan Savitz, Brett A. McKinney:
  Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests. 2906-2913
• 
  Matthew Bernstein, AnHai Doan, Colin N. Dewey:
  MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. 2914-2923

Databases and Ontologies

• 
  Nili Tickotsky, Tal Sagiv, Jaime Prilusky, Eric Shifrut, Nir Friedman:
  McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences. 2924-2929

Applications Notes
Genome Analysis

• 
  Zhicheng Ji, Weiqiang Zhou, Hongkai Ji:
  Single-cell regulome data analysis by SCRAT. 2930-2932
• 
  Alden King-Yung Leung, Nana Jin, Kevin Y. Yip, Ting-Fung Chan:
  OMTools: a software package for visualizing and processing optical mapping data. 2933-2935
• 
  Byoungnam Min, Igor V. Grigoriev, In-Geol Choi:
  FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation. 2936-2937
• 
  Jake R. Conway, Alexander Lex, Nils Gehlenborg:
  UpSetR: an R package for the visualization of intersecting sets and their properties. 2938-2940

Sequence Analysis

• 
  Johannes T. Roehr, Christoph Dieterich, Knut Reinert:
  Flexbar 3.0 - SIMD and multicore parallelization. 2941-2942
• 
  Kamil Jan Cygan, Clayton Hendrick Sanford, William G. Fairbrother:
  Spliceman2: a computational web server that predicts defects in pre-mRNA splicing. 2943-2945

Phylogenetics

• 
  Lukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele, Michiel Van Bel:
  PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. 2946-2947
• 
  José Manuel Abuín, Tomás F. Pena, Juan Carlos Pichel:
  PASTASpark: multiple sequence alignment meets Big Data. 2948-2950

Gene expression

• 
  Jiannong Li, Inna Smalley, Michael J. Schell, Keiran S. M. Smalley, Yian Ann Chen:
  SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer. 2951-2953
• 
  Stian Lågstad, Sen Zhao, Andreas M. Hoff, Bjarne Johannessen, Ole Christian Lingjærde, Rolf I. Skotheim:
  chimeraviz: a tool for visualizing chimeric RNA. 2954-2956
• 
  Jinghua Gu, Xuan Wang, Jinyan Chan, Nicole E. Baldwin, Jacob A. Turner:
  Phantom: investigating heterogeneous gene sets in time-course data. 2957-2959

Systems Biology

• 
  Christian Scheeder, Florian Heigwer, Michael Boutros:
  HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens. 2960-2962
• 
  Hyun-hwan Jeong, Seon Young Kim, Maxime W. C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu:
  CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution. 2963-2965
• 
  Atis Elsts, Agris Pentjuss, Egils Stalidzans:
  SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. 2966-2967

Message from the ISCB
Systems Biology

• 
  Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
  ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. 2968
• 
  Alastair M. Kilpatrick:
  Message from the ISCB: The 5th ISCB Wikipedia competition: coming to a classroom near you? 2969

Volume 33, Number 19, October 2017

Discovery note
Structural Bioinformatics

• 
  Minh N. Nguyen, Mohan R. Pradhan, Chandra S. Verma, Pingyu Zhong:
  The interfacial character of antibody paratopes: analysis of antibody-antigen structures. 2971-2976

Original Papers
Genome Analysis

• 
  Sylvain Mareschal, Philippe Ruminy, Marion Alcantara, Céline Villenet, Martin Figeac, Sydney Dubois, Philippe Bertrand, Abdelilah Bouzelfen, Pierre-Julien Viailly, Dominique Penther, Hervé Tilly, Christian Bastard, Fabrice Jardin:
  Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma. 2977-2985
• 
  Milos Pavlovic, Pradipta Ray, Kristina Pavlovic, Aaron Kotamarti, Min Chen, Michael Q. Zhang:
  DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. 2986-2994
• 
  Jacquiline W. Mugo, Ephifania Geza, Joel Defo, Samar S. M. Elsheikh, Gaston K. Mazandu, Nicola J. Mulder, Emile R. Chimusa:
  A multi-scenario genome-wide medical population genetics simulation framework. 2995-3002

Sequence Analysis

• 
  Wenxiu Ma, Lin Yang, Remo Rohs, William Stafford Noble:
  DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. 3003-3010
• 
  Cristian Zambrano-Vega, Antonio J. Nebro, José García-Nieto, José Francisco Aldana Montes:
  M2Align: parallel multiple sequence alignment with a multi-objective metaheuristic. 3011-3017
• 
  Hao Peng, Yifan Yang, Shandian Zhe, Jian Wang, Michael Gribskov, Yuan Qi:
  DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates. 3018-3027
• 
  Ka-Chun Wong:
  MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences. 3028-3035

Structural Bioinformatics

• 
  José Jiménez, Stefan Doerr, Gerard Martínez-Rosell, Alexander S. Rose, Gianni De Fabritiis:
  DeepSite: protein-binding site predictor using 3D-convolutional neural networks. 3036-3042
• 
  Christopher W. Wood, Jack W. Heal, Andrew R. Thomson, Gail J. Bartlett, Amaurys Ávila Ibarra, R. Leo Brady, Richard B. Sessions, Derek N. Woolfson:
  ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. 3043-3050
• 
  Sang-Jun Park, Jumin Lee, Dhilon S. Patel, Hongjing Ma, Hui Sun Lee, Sunhwan Jo, Wonpil Im:
  Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank. 3051-3057

Gene expression

• 
  Dimitrios V. Vavoulis, Jenny C. Taylor, Anna Schuh:
  Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data. 3058-3064

Systems Biology

• 
  Alice Madonia, Cristiano Melchiorri, Simone Bonamano, Marco Marcelli, Chiara Bulfon, Filippo Castiglione, Marco Galeotti, Donatella Volpatti, Francesco Mosca, Pietro-Giorgio Tiscar, Nicla Romano:
  Computational modeling of immune system of the fish for a more effective vaccination in aquaculture. 3065-3071
• 
  Christoph Schmal, Jihwan Myung, Hanspeter Herzel, Grigory V. Bordyugov:
  Moran's I quantifies spatio-temporal pattern formation in neural imaging data. 3072-3079
• 
  Jiadong Ji, Di He, Yang Feng, Yong He, Fuzhong Xue, Lei Xie:
  JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. 3080-3087

Applications Notes
Genome Analysis

• 
  Bernat Gel, Eduard Serra:
  karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. 3088-3090
• 
  Rallis Karamichalis, Lila Kari:
  MoDMaps3D: an interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences. 3091-3093
• 
  Giorgio Gonnella, Stefan Kurtz:
  GfaPy: a flexible and extensible software library for handling sequence graphs in Python. 3094-3095

Sequence Analysis

• 
  William L. Miller, W. David Walter:
  CWDPRNP: a tool for cervid prion sequence analysis in program R. 3096-3097
• 
  Max Hebditch, M. Alejandro Carballo-Amador, Spyros Charonis, Robin Curtis, Jim Warwicker:
  Protein-Sol: a web tool for predicting protein solubility from sequence. 3098-3100
• 
  Andrew Low, Nicolas Rodrigue, Alex Wong:
  COMPASS: the COMPletely Arbitrary Sequence Simulator. 3101-3103
• 
  Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia:
  omiXcore: a web server for prediction of protein interactions with large RNA. 3104-3106
• 
  Yuxuan Yuan, Philipp E. Bayer, Huey-Tyng Lee, David Edwards:
  runBNG: a software package for BioNano genomic analysis on the command line. 3107-3109
• 
  Preeti Bais, Sandeep Namburi, Daniel M. Gatti, Xinyu Zhang, Jeffrey H. Chuang:
  CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens. 3110-3112
• 
  Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding:
  WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. 3113-3114
• 
  Jochen Kruppa, Erhard van der Vries, Wendy K. Jo, Alexander Postel, Paul Becher, Albert Osterhaus, Klaus Jung:
  kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies. 3115-3116

Structural Bioinformatics

• 
  Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang:
  Structurexplor: a platform for the exploration of structural features of RNA secondary structures. 3117-3120
• 
  Matthew A. Wyczalkowski, Kristine M. Wylie, Song Cao, Michael D. McLellan, Jennifer Flynn, Mo Huang, Kai Ye, Xian Fan, Ken Chen, Michael C. Wendl, Li Ding:
  BreakPoint Surveyor: a pipeline for structural variant visualization. 3121-3122

Gene expression

• 
  Vincent Gardeux, Fabrice P. A. David, Adrian Shajkofci, Petra C. Schwalie, Bart Deplancke:
  ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. 3123-3125
• 
  Jason T. Serviss, Jesper Gådin, Per Eriksson, Lasse Folkersen, Dan Grandér:
  ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data. 3126-3128

Genetics and Population Analysis

• 
  Ilya Y. Zhbannikov, Konstantin G. Arbeev, Anatoliy I. Yashin:
  rqt: an R package for gene-level meta-analysis. 3129-3130

Systems Biology

• 
  Taosheng Xu, Thuc Duy Le, Lin Liu, Ning Su, Rujing Wang, Bing-Yu Sun, Antonio Colaprico, Gianluca Bontempi, Jiuyong Li:
  CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization. 3131-3133
• 
  Aditya Bharadwaj, Divit P. Singh, Anna M. Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel K. Brazhnik, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson, T. M. Murali:
  GraphSpace: stimulating interdisciplinary collaborations in network biology. 3134-3136

Data and Text Mining

• 
  Joseph W. Brown, Meg Pirrung, Lee Ann McCue:
  FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. 3137-3139
• 
  Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski:
  TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. 3140-3141
• 
  Kylie A. Bemis, Olga Vitek:
  matter: an R package for rapid prototyping with larger-than-memory datasets on disk. 3142-3144

Bioimage Informatics

• 
  Chris Churas, Alex J. Perez, Hiroyuki Hakozaki, Willy Wong, David Lee, Steven Peltier, Mark H. Ellisman:
  Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections. 3145-3147

Population genetics

• 
  Emil Jørsboe, Kristian Hanghøj, Anders Albrechtsen:
  fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample. 3148-3150

Volume 33, Number 20, October 2017

Original Papers
Genome Analysis

• 
  Yu-Jia Shiah, Michael Fraser, Robert G. Bristow, Paul C. Boutros:
  Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array. 3151-3157
• 
  Elena D. Stavrovskaya, Tejasvi Niranjan, Elana J. Fertig, Sarah J. Wheelan, Alexander V. Favorov, Andrey A. Mironov:
  StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data. 3158-3165
• 
  Qing Zhang, Xiaodan Fan, Yejun Wang, Ming-an Sun, Jianlin Shao, Dianjing Guo:
  BPP: a sequence-based algorithm for branch point prediction. 3166-3172
• 
  Moritz Hess, Stefan Lenz, Tamara J. Blätte, Lars Bullinger, Harald Binder:
  Partitioned learning of deep Boltzmann machines for SNP data. 3173-3180

Sequence Analysis

• 
  Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher:
  Succinct colored de Bruijn graphs. 3181-3187
• 
  Antoine Recanati, Thomas Brüls, Alexandre d'Aspremont:
  A spectral algorithm for fast de novo layout of uncorrected long nanopore reads. 3188-3194
• 
  Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang:
  Matrix completion with side information and its applications in predicting the antigenicity of influenza viruses. 3195-3201
• 
  Marc G. Chevrette, Fabian Aicheler, Oliver Kohlbacher, Cameron R. Currie, Marnix H. Medema:
  SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria. 3202-3210

Gene expression

• 
  Nikolaos-Kosmas Chlis, F. Alexander Wolf, Fabian J. Theis:
  Model-based branching point detection in single-cell data by K-branches clustering. 3211-3219
• 
  Martin Schäfer, Hans-Ulrich Klein, Holger Schwender:
  Integrative analysis of multiple genomic variables using a hierarchical Bayesian model. 3220-3227
• 
  Attila Csala, Frans Voorbraak, Aeilko H. Zwinderman, Michel H. Hof:
  Sparse redundancy analysis of high-dimensional genetic and genomic data. 3228-3234
• 
  Arief Gusnanto, John Paul Gosling, Christopher Pope:
  Identification of transcript regulatory patterns in cell differentiation. 3235-3242

Genetics and Population Analysis

• 
  Paul Vauterin, Ben Jeffery, Alistair Miles, Roberto Amato, Lee Hart, Ian Wright, Dominic Kwiatkowski:
  Panoptes: web-based exploration of large scale genome variation data. 3243-3249

Systems Biology

• 
  Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen:
  Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. 3250-3257

Data and Text Mining

• 
  Iurie Caraus, Bogdan Mazoure, Robert Nadon, Vladimir Makarenkov:
  Detecting and removing multiplicative spatial bias in high-throughput screening technologies. 3258-3267
• 
  Yu He, Ting Wang:
  EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. 3268-3275

Databases and Ontologies

• 
  Xian Zeng, Lin Tao, Peng Zhang, Chu Qin, Shangying Chen, Weidong He, Ying Tan, Hong Xia Liu, Sheng-Yong Yang, Zhe Chen, Yu Yang Jiang, Yuzong Chen:
  HEROD: a human ethnic and regional specific omics database. 3276-3282

Applications Notes
Genome Analysis

• 
  Ludovic Mallet, Tristan Bitard-Feildel, Franck Cerutti, Hélène Chiapello:
  PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies. 3283-3285
• 
  Li Yao, Heming Wang, Yuanyuan Song, Guangchao Sui:
  BioQueue: a novel pipeline framework to accelerate bioinformatics analysis. 3286-3288

Sequence Analysis

• 
  Changlin Wan, Jianing Gao, Huan Zhang, Xiaohua Jiang, Qiguang Zang, Rongjun Ban, Yuanwei Zhang, Qinghua Shi:
  CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data. 3289-3291
• 
  Philipp C. Münch, Bärbel Stecher, Alice C. McHardy:
  EDEN: evolutionary dynamics within environments. 3292-3295
• 
  Minji Kim, Yeonsung Kim, Lei Qian, Jun S. Song:
  TeachEnG: a Teaching Engine for Genomics. 3296-3298

Structural Bioinformatics

• 
  Kathryn A. Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov:
  ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. 3299-3301

Gene expression

• 
  Igor Mandric, Yvette Temate-Tiagueu, Tatiana Shcheglova, Sahar Al Seesi, Alex Zelikovsky, Ion I. Mandoiu:
  Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data. 3302-3304
• 
  Alexey Uvarovskii, Christoph Dieterich:
  pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments. 3305-3307
• 
  Wenbin Guo, Cristiane P. G. Calixto, John W. S. Brown, Runxuan Zhang:
  TSIS: an R package to infer alternative splicing isoform switches for time-series data. 3308-3310

Genetics and Population Analysis

• 
  Michael F. Lawrence, Robert Gentleman:
  VariantTools: an extensible framework for developing and testing variant callers. 3311-3313

Data and Text Mining

• 
  Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen:
  CircPro: an integrated tool for the identification of circRNAs with protein-coding potential. 3314-3316

Databases and Ontologies

• 
  Sajid Mughal, Ismail Moghul, Jing Yu, Ukirdc, Tristan Clark, David S. Gregory, Nikolas Pontikos:
  Pheno4J: a gene to phenotype graph database. 3317-3319

Bioimage Informatics

• 
  Sam Cooper, Alexis R. Barr, Robert Glen, Chris Bakal:
  NucliTrack: an integrated nuclei tracking application. 3320-3322

Review
Genome Analysis

• 
  Mikhail G. Dozmorov:
  Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning. 3323-3330

Volume 33, Number 21, November 2017

Original Papers
Genome Analysis

• 
  Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, B. Franz Lang, Nadia El-Mabrouk:
  CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. 3331-3339
• 
  Zhiqun Xie, Haixu Tang:
  ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. 3340-3347
• 
  Yuchao Xia, Yun Liu, Minghua Deng, Ruibin Xi:
  SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms. 3348-3354

Sequence Analysis

• 
  Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan:
  GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. 3355-3363
• 
  Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li:
  High-speed and high-ratio referential genome compression. 3364-3372
• 
  Jirí Hon, Tomás Martínek, Jaroslav Zendulka, Matej Lexa:
  pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. 3373-3379
• 
  Hirak Sarkar, Rob Patro:
  Quark enables semi-reference-based compression of RNA-seq data. 3380-3386
• 
  José Juan Almagro Armenteros, Casper Kaae Sønderby, Søren Kaae Sønderby, Henrik Nielsen, Ole Winther:
  DeepLoc: prediction of protein subcellular localization using deep learning. 3387-3395

Phylogenetics

• 
  Jan P. Meier-Kolthoff, Markus Göker:
  VICTOR: genome-based phylogeny and classification of prokaryotic viruses. 3396-3404

Structural Bioinformatics

• 
  Pawel P. Wozniak, Bogumil Konopka, J. Xu, Gert Vriend, Malgorzata Kotulska:
  Forecasting residue-residue contact prediction accuracy. 3405-3414
• 
  Fabrizio Pucci, Jean Marc Kwasigroch, Marianne Rooman:
  SCooP: an accurate and fast predictor of protein stability curves as a function of temperature. 3415-3422

Gene expression

• 
  Huamin Li, Uri Shaham, Kelly P. Stanton, Yi Yao, Ruth R. Montgomery, Yuval Kluger:
  Gating mass cytometry data by deep learning. 3423-3430

Systems Biology

• 
  Sébastien De Landtsheer, Panuwat Trairatphisan, Philippe Lucarelli, Thomas Sauter:
  FALCON: a toolbox for the fast contextualization of logical networks. 3431-3436
• 
  Giorgos Minas, Dafyd J. Jenkins, David A. Rand, Bärbel Finkenstädt:
  Inferring transcriptional logic from multiple dynamic experiments. 3437-3444
• 
  Satya Swarup Samal, Ovidiu Radulescu, Andreas Weber, Holger Fröhlich:
  Linking metabolic network features to phenotypes using sparse group lasso. 3445-3453

Databases and Ontologies

• 
  Sylvain Poux, Cecilia N. Arighi, Michele Magrane, Alex Bateman, Chih-Hsuan Wei, Zhiyong Lu, Emmanuel Boutet, Hema Bye-A-Jee, Maria Livia Famiglietti, Bernd Roechert, The UniProt Consortium:
  On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. 3454-3460
• 
  Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steven Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews, Heeyeon Song, Lincoln Stein, Robin Haw, Peter D'Eustachio, Peipei Ping, Henning Hermjakob, Antonio Fabregat:
  Reactome enhanced pathway visualization. 3461-3467

Applications Notes
Genome Analysis

• 
  Mete Akgün, Hüseyin Demirci:
  VCF-Explorer: filtering and analysing whole genome VCF files. 3468-3470

Sequence Analysis

• 
  Mathieu Schaeffer, Alain Gateau, Daniel Dinis Teixeira, Pierre-André Michel, Monique Zahn-Zabal, Lydie Lane:
  The neXtProt peptide uniqueness checker: a tool for the proteomics community. 3471-3472
• 
  Junjie Chen, Mingyue Guo, Shumin Li, Bin Liu:
  ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank. 3473-3476
• 
  Jun Ding, Ziv Bar-Joseph:
  MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. 3477-3479

Structural Bioinformatics

• 
  Jinling Shang, Xi Dai, Yecheng Li, Marco Pistolozzi, Ling Wang:
  HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques. 3480-3481
• 
  Anna Laddach, Mathias Gautel, Franca Fraternali:
  TITINdb - a computational tool to assess titin's role as a disease gene. 3482-3485

Gene expression

• 
  Beate Vieth, Christoph Ziegenhain, Swati Parekh, Wolfgang Enard, Ines Hellmann:
  powsimR: power analysis for bulk and single cell RNA-seq experiments. 3486-3488

Systems Biology

• 
  Danica Wiredja, Mehmet Koyutürk, Mark R. Chance:
  The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. 3489-3491
• 
  Leonard A. Harris, Marco S. Nobile, James C. Pino, Alexander L. R. Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F. Lopez:
  GPU-powered model analysis with PySB/cupSODA. 3492-3494
• 
  Kun Sun, Fiona F. M. Lun, Peiyong Jiang, Hao Sun:
  BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data. 3495-3496

Data and Text Mining

• 
  Ahmed Allam, Michael Krauthammer:
  PySeqLab: an open source Python package for sequence labeling and segmentation. 3497-3499
• 
  Katja Koeppen, Bruce A. Stanton, Thomas H. Hampton:
  ScanGEO: parallel mining of high-throughput gene expression data. 3500-3501

Databases and Ontologies

• 
  Ian H. Holmes, Christopher J. Mungall:
  BioMake: a GNU make-compatible utility for declarative workflow management. 3502-3504
• 
  Meng-Pin Weng, Ben-Yang Liao:
  modPhEA: model organism Phenotype Enrichment Analysis of eukaryotic gene sets. 3505-3507

Bioimage Informatics

• 
  Rory Nolan, Luis A. J. Alvarez, Jonathan Elegheert, Maro Iliopoulou, G. Maria Jakobsdottir, Marina Rodriguez-Muñoz, A. Radu Aricescu, Sergi Padilla-Parra:
  nandb - number and brightness in R with a novel automatic detrending algorithm. 3508-3510

Volume 33, Number 22, November 2017

Original Papers
Genome Analysis

• 
  José Carbonell-Caballero, Alicia Amadoz, Roberto Alonso, Marta R. Hidalgo, Cankut Çubuk, David V. Conesa, Antonio López-Quílez, Joaquín Dopazo:
  Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. 3511-3517

Sequence Analysis

• 
  Wei Chen, Hui Yang, Peng-Mian Feng, Hui Ding, Hao Lin:
  iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties. 3518-3523
• 
  Xiang Cheng, Shu-Guang Zhao, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou:
  pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites. 3524-3531
• 
  Jean-Michel Garant, Jean-Pierre Perreault, Michelle S. Scott:
  Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. 3532-3537
• 
  Feng Zhang, Yulan Lu, Sijia Yan, Qinghe Xing, Weidong Tian:
  SPRINT: an SNP-free toolkit for identifying RNA editing sites. 3538-3548

Structural Bioinformatics

• 
  Zixuan Cang, Guo-Wei Wei:
  Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology. 3549-3557

Gene expression

• 
  Ashar Ahmad, Holger Fröhlich:
  Towards clinically more relevant dissection of patient heterogeneity via survival-based Bayesian clustering. 3558-3566
• 
  Carl Brunius, Anders Pedersen, Daniel Malmodin, B. Göran Karlsson, Lars Andersson, Gunnel Tybring, Rikard Landberg:
  Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data. 3567-3574
• 
  Hanjun Dai, Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Le Song, Xin Gao:
  Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. 3575-3583

Genetics and Population Analysis

• 
  Vanda M. Lourenço, Paulo C. Rodrigues, Ana M. Pires, Hans-Peter Piepho:
  A robust DF-REML framework for variance components estimation in genetic studies. 3584-3594
• 
  Yao-Hwei Fang, Jie-Huei Wang, Chao A. Hsiung:
  TSGSIS: a high-dimensional grouped variable selection approach for detection of whole-genome SNP-SNP interactions. 3595-3602

Systems Biology

• 
  Siu Hung Joshua Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas:
  Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. 3603-3609
• 
  Dana Ferranti, David Krane, David Craft:
  The value of prior knowledge in machine learning of complex network systems. 3610-3618
• 
  Jonghwan Choi, Sanghyun Park, Youngmi Yoon, Jaegyoon Ahn:
  Improved prediction of breast cancer outcome by identifying heterogeneous biomarkers. 3619-3626

Databases and Ontologies

• 
  Chao Pang, Fleur D. L. Kelpin, David van Enckevort, Niina Eklund, Kaisa Silander, Dennis Hendriksen, Mark de Haan, Jonathan Jetten, Tommy de Boer, Bart Charbon, Petr Holub, Hans L. Hillege, Morris A. Swertz:
  BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. 3627-3634

Applications Notes
Genome Analysis

• 
  Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku:
  gVolante for standardizing completeness assessment of genome and transcriptome assemblies. 3635-3637
• 
  Matthew D. Whiteside, Victor P. J. Gannon, Chad R. Laing:
  Phylotyper: in silico predictor of gene subtypes. 3638-3641
• 
  Yuanyan Xiong, Xiaowei Xie, Yanzhi Wang, Wenbin Ma, Puping Liang, Songyang Zhou, Zhiming Dai:
  pgRNAFinder: a web-based tool to design distance independent paired-gRNA. 3642-3644

Sequence Analysis

• 
  Omar Wagih:
  ggseqlogo: a versatile R package for drawing sequence logos. 3645-3647
• 
  Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca:
  CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. 3648-3651
• 
  Sean La, Ehsan Haghshenas, Cédric Chauve:
  LRCstats, a tool for evaluating long reads correction methods. 3652-3654

Structural Bioinformatics

• 
  Joan Segura, Rubén Sánchez García, Marta Martínez, Jesús Cuenca Alba, Daniel Tabas-Madrid, Carlos Oscar Sánchez Sorzano, José María Carazo:
  3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures. 3655-3657
• 
  David Lagorce, Lina Bouslama, Jérôme Bécot, Maria A. Miteva, Bruno O. Villoutreix:
  FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery. 3658-3660
• 
  Lin Li, Zhe Jia, Yunhui Peng, Arghya Chakravorty, Lexuan Sun, Emil Alexov:
  DelPhiForce web server: electrostatic forces and energy calculations and visualization. 3661-3663

Systems Biology

• 
  Chia-Lang Hsu, Jiankai Wang, Pei-Chun Lu, Hsuan-Cheng Huang, Hsueh-Fen Juan:
  DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics. 3664-3666
• 
  Marek Kochanczyk, William S. Hlavacek, Tomasz Lipniacki:
  SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. 3667-3669
• 
  Glyn Bradley, Steven J. Barrett:
  CausalR: extracting mechanistic sense from genome scale data. 3670-3672
• 
  Colin W. Combe, Marine Sivade, Henning Hermjakob, Joshua Heimbach, Birgit H. M. Meldal, Gos Micklem, Sandra E. Orchard, Juri Rappsilber:
  ComplexViewer: visualization of curated macromolecular complexes. 3673-3675

Data and Text Mining

• 
  Alessandro Pietrelli, Luca Valenti:
  myVCF: a desktop application for high-throughput mutations data management. 3676-3678

Databases and Ontologies

• 
  Daniel Domingo-Fernández, Alpha Tom Kodamullil, Anandhi Iyappan, Mufassra Naz, Mohammad Asif Emon, Tamara Raschka, Reagon Karki, Stephan Springstubbe, Christian Ebeling, Martin Hofmann-Apitius:
  Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment. 3679-3681
• 
  Erzsébet Fichó, István Reményi, István Simon, Bálint Mészáros:
  MFIB: a repository of protein complexes with mutual folding induced by binding. 3682-3684

Review
Sequence Analysis

• 
  Vanessa Isabell Jurtz, Alexander Rosenberg Johansen, Morten Nielsen, José Juan Almagro Armenteros, Henrik Nielsen, Casper Kaae Sønderby, Ole Winther, Søren Kaae Sønderby:
  An introduction to deep learning on biological sequence data: examples and solutions. 3685-3690

Volume 33, Number 23, December 2017

Discovery Notes
Gene expression

• 
  Pedro Carmona-Saez, Nieves Varela, María José Luque, Daniel Toro-Domínguez, Jordi Martorell-Marugan, Marta E. Alarcón-Riquelme, Concepción Marañón:
  Metagene projection characterizes GEN2.2 and CAL-1 as relevant human plasmacytoid dendritic cell models. 3691-3695
• 
  Trisevgeni Rapakoulia, Xin Gao, Yi Huang, Michiel J. L. de Hoon, Mariko Okada-Hatakeyama, Harukazu Suzuki, Erik Arner:
  Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. 3696-3700

Original Papers
Genome Analysis

• 
  Linghao Shen, Jun Zhu, Shuo-Yen Robert Li, Xiaodan Fan:
  Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data. 3701-3708
• 
  Cuiping Pan, Gregory McInnes, Nicole Deflaux, Michael Snyder, Jonathan Bingham, Somalee Datta, Philip S. Tsao:
  Cloud-based interactive analytics for terabytes of genomic variants data. 3709-3715
• 
  Meng Wang, Zhanglong Ji, Shuang Wang, Jihoon Kim, Hai Yang, Xiaoqian Jiang, Lucila Ohno-Machado:
  Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. 3716-3725
• 
  Pasi Rastas:
  Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. 3726-3732
• 
  Kai Wang:
  Conditional asymptotic inference for the kernel association test. 3733-3739
• 
  André Müller, Christian Hundt, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt:
  MetaCache: context-aware classification of metagenomic reads using minhashing. 3740-3748

Structural Bioinformatics

• 
  Jianwei Zhu, Haicang Zhang, Shuai Cheng Li, Chao Wang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
  Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. 3749-3757
• 
  Tushar Jain, Todd Boland, Asparouh Lilov, Irina Burnina, Michael Brown, Yingda Xu, Maximiliano Vásquez:
  Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning. 3758-3766

Gene expression

• 
  Alexis Delabrière, Ulli M. Hohenester, Benoit Colsch, Christophe Junot, François Fenaille, Etienne A. Thévenot:
  proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry. 3767-3775

Systems Biology

• 
  Zhenwen Dai, Mudassar Iqbal, Neil D. Lawrence, Magnus Rattray:
  Efficient inference for sparse latent variable models of transcriptional regulation. 3776-3783

Data and Text Mining

• 
  Chrysoula Zerva, Riza Batista-Navarro, Philip Day, Sophia Ananiadou:
  Using uncertainty to link and rank evidence from biomedical literature for model curation. 3784-3792

Applications Notes
Genome Analysis

• 
  Joshua S. Martin, Zheng Xu, Alex P. Reiner, Karen L. Mohlke, Patrick F. Sullivan, Bing Ren, Ming Hu, Yun Li:
  HUGIn: Hi-C Unifying Genomic Interrogator. 3793-3795
• 
  Luis Vielva, María de Toro, Val F. Lanza, Fernando de la Cruz:
  PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes. 3796-3798
• 
  Steven M. Foltz, Wen-Wei Liang, Mingchao Xie, Li Ding:
  MIRMMR: binary classification of microsatellite instability using methylation and mutations. 3799-3801

Sequence Analysis

• 
  Karol Pal, Vojtech Bystrý, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova, Nikos Darzentas:
  GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data. 3802-3804
• 
  Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti:
  wft4galaxy: a workflow testing tool for galaxy. 3805-3807
• 
  João F. Matias Rodrigues, Thomas S. B. Schmidt, Janko Tackmann, Christian von Mering:
  MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. 3808-3810
• 
  Xuning Wang, Charles Tilford, Isaac Neuhaus, Gabe Mintier, Qi Guo, John N. Feder, Stefan Kirov:
  CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline. 3811-3812

Structural Bioinformatics

• 
  Ignacio Faustino, Siewert J. Marrink:
  cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. 3813-3815
• 
  Alexandre Borrel, Denis Fourches:
  RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality. 3816-3818
• 
  Aleksandra Maria Gierut, Wanda Niemyska, Pawel Dabrowski-Tumanski, Piotr Sulkowski, Joanna I. Sulkowska:
  PyLasso: a PyMOL plugin to identify lassos. 3819-3821

Systems Biology

• 
  Marcin Radom, Agnieszka Rybarczyk, Bartlomiej Szawulak, Hubert Andrzejewski, Piotr Chabelski, Adam Kozak, Piotr Formanowicz:
  Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems. 3822-3823

Bioimage Informatics

• 
  Zachary Berndsen, Charles Bowman, Haerin Jang, Andrew B. Ward:
  EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing. 3824-3826

Special Issue Papers: GIW 2016
Gene expression

• 
  Inuk Jung, Kyuri Jo, Hyejin Kang, Hongryul Ahn, Youngjae Yu, Sun Kim:
  TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. 3827-3835

Structural Bioinformatics

• 
  Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama:
  Spresso: an ultrafast compound pre-screening method based on compound decomposition. 3836-3843

Sequence Analysis

• 
  Liang Zhao, Qingfeng Chen, Wencui Li, Peng Jiang, Limsoon Wong, Jinyan Li:
  MapReduce for accurate error correction of next-generation sequencing data. 3844-3851

Gene expression

• 
  Yinglei Lai, Fanni Zhang, Tapan K. Nayak, Reza Modarres, Norman H. Lee, Timothy A. McCaffrey:
  An efficient concordant integrative analysis of multiple large-scale two-sample expression data sets. 3852-3860

Special Issue Paper: APBC 2016
Structural Bioinformatics

• 
  Yi Liu, Weiping Sun, Baozhen Shan, Kaizhong Zhang:
  DISC: DISulfide linkage Characterization from tandem mass spectra. 3861-3870

Volume 33, Number 24, December 2017

Original Papers
Genome Analysis

• 
  Mehmet Tekman, Alan Medlar, Monika Mozere, Robert Kleta, Horia Stanescu:
  HaploForge: a comprehensive pedigree drawing and haplotype visualization web application. 3871-3877
• 
  Jin Liu, Xiang Wan, Chaolong Wang, Chao Yang, Xiaowei Zhou, Can Yang:
  LLR: a latent low-rank approach to colocalizing genetic risk variants in multiple GWAS. 3878-3886
• 
  Minli Bao, Kai Wang:
  Genome-wide association studies using a penalized moving-window regression. 3887-3894
• 
  Nilah M. Ioannidis, Joe R. Davis, Marianne K. DeGorter, Nicholas B. Larson, Shannon K. McDonnell, Amy J. French, Alexis J. Battle, Trevor J. Hastie, Stephen N. Thibodeau, Stephen B. Montgomery, Carlos D. Bustamante, Weiva Sieh, Alice S. Whittemore:
  FIRE: functional inference of genetic variants that regulate gene expression. 3895-3901

Sequence Analysis

• 
  Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim F. Vranken:
  SVM-dependent pairwise HMM: an application to protein pairwise alignments. 3902-3908
• 
  Duolin Wang, Shuai Zeng, Chunhui Xu, Wangren Qiu, Yanchun Liang, Trupti Joshi, Dong Xu:
  MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. 3909-3916
• 
  Martin Christen Frølund Thomsen, Henrik Hasman, Henrik Westh, Hülya Kaya, Ole Lund:
  RUCS: rapid identification of PCR primers for unique core sequences. 3917-3921
• 
  Brandon D. Pickett, Justin Miller, Perry G. Ridge:
  Kmer-SSR: a fast and exhaustive SSR search algorithm. 3922-3928
• 
  Wolfgang Kopp, Martin Vingron:
  An improved compound Poisson model for the number of motif hits in DNA sequences. 3929-3937

Phylogenetics

• 
  Alexander Yermanos, Victor Greiff, Nike Julia Krautler, Ulrike Menzel, Andreas Dounas, Enkelejda Miho, Annette Oxenius, Tanja Stadler, Sai T. Reddy:
  Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). 3938-3946

Genetics and Population Analysis

• 
  Emma E. Kim, Seunghoon Lee, Cue Hyunkyu Lee, Hyunjung Oh, Kyuyoung Song, Buhm Han:
  FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects. 3947-3954

Systems Biology

• 
  Aravind Sankar, Sayan Ranu, Karthik Raman:
  Predicting novel metabolic pathways through subgraph mining. 3955-3963
• 
  Yue Deng, Hector Zenil, Jesper Tegnér, Narsis Aftab Kiani:
  HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation. 3964-3972

Data and Text Mining

• 
  Simon Baker, Imran Ali, Ilona Silins, Sampo Pyysalo, Yufan Guo, Johan Högberg, Ulla Stenius, Anna Korhonen:
  Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. 3973-3981

Applications Notes
Genome Analysis

• 
  Yuan Tian, Tiffany J. Morris, Amy P. Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E. Teschendorff:
  ChAMP: updated methylation analysis pipeline for Illumina BeadChips. 3982-3984
• 
  Virag Sharma, Peter Schwede, Michael Hiller:
  CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation. 3985-3987
• 
  Son Hoang Nguyen, Tania P. S. Duarte, Lachlan J. M. Coin, Minh Duc Cao:
  Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode. 3988-3990

Sequence Analysis

• 
  Gilbert Deléage:
  ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments. 3991-3992

Phylogenetics

• 
  Pieter Libin, Ewout Vanden Eynden, Francesca Incardona, Ann Nowé, Antonia Bezenchek, EucoHIV Study Group, Anders Sönnerborg, Anne-Mieke Vandamme, Kristof Theys, Guy Baele:
  PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context. 3993-3995

Structural Bioinformatics

• 
  Enrico Guarnera, Zhen Wah Tan, Zejun Zheng, Igor N. Berezovsky:
  AlloSigMA: allosteric signaling and mutation analysis server. 3996-3998
• 
  Massimiliano Bonomi, Carlo Camilloni:
  Integrative structural and dynamical biology with PLUMED-ISDB. 3999-4000

Gene expression

• 
  Aurora Torrente, Alvis Brazma:
  clustComp, a bioconductor package for the comparison of clustering results. 4001-4003

Data and Text Mining

• 
  Alba Gutiérrez-Sacristán, Carles Hernandez-Ferrer, Juan R. González, Laura Inés Furlong:
  psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes. 4004-4006

Databases and Ontologies

• 
  Yoann Gloaguen, Fraser R. Morton, Rónán Daly, Ross Gurden, Simon Rogers, Joe Wandy, David Wilson, Michael P. Barrett, Karl E. V. Burgess:
  PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data. 4007-4009
• 
  Enyu Dai, Feng Yang, Jing Wang, Xu Zhou, Qian Song, Weiwei An, Lihong Wang, Wei Jiang:
  ncDR: a comprehensive resource of non-coding RNAs involved in drug resistance. 4010-4011
• 
  Stefan Rödiger, Michal Burdukiewicz, Andrej-Nikolai Spiess, Konstantin Blagodatskikh:
  Enabling reproducible real-time quantitative PCR research: the RDML package. 4012-4014

Special Issue: Hitseq
Genome Analysis

• 
  Jana Ebler, Alexander Schönhuth, Tobias Marschall:
  Genotyping inversions and tandem duplications. 4015-4023

Sequence Analysis

• 
  Ilya Minkin, Son K. Pham, Paul Medvedev:
  TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes. 4024-4032
• 
  Abhinav Nellore, Leonardo Collado-Torres, Andrew E. Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T. Leek, Ben Langmead:
  Rail-RNA: scalable analysis of RNA-seq splicing and coverage. 4033-4040
• 
  Snædís Kristmundsdóttir, Brynja D. Sigurpálsdóttir, Birte Kehr, Bjarni V. Halldórsson:
  popSTR: population-scale detection of STR variants. 4041-4048

Corrigenda
Sequence Analysis

• 
  José Juan Almagro Armenteros, Casper Kaae Sønderby, Søren Kaae Sønderby, Henrik Nielsen, Ole Winther:
  DeepLoc: prediction of protein subcellular localization using deep learning. 4049
• 
  Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato:
  iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. 4050