Bioinformatics, Volume 29

Volume 29, Number 1, January 2013

Original Papers - Genome Analysis

• 
  Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan:
  Binary Interval Search: a scalable algorithm for counting interval intersections. 1-7

Sequence Analysis

• 
  Massimo Andreatta, Ole Lund, Morten Nielsen:
  Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. 8-14
• 
  Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras:
  STAR: ultrafast universal RNA-seq aligner. 15-21
• 
  Russell Bonneville, Victor X. Jin:
  A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes. 22-28
• 
  Wenhui Wang, Xiaolin Yin, Yoon Soo Pyon, Matthew Hayes, Jing Li:
  Rare variant discovery and calling by sequencing pooled samples with overlaps. 29-38
• 
  Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén:
  DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. 39-46

Structural Bioinformatics

• 
  Alex W. Slater, Javier I. Castellanos, Manfred J. Sippl, Francisco Melo:
  Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments. 47-53
• 
  Jamie R. Hill, Charlotte M. Deane:
  MP-T: improving membrane protein alignment for structure prediction. 54-61
• 
  Benjamin Merget, David Zilian, Tobias Müller, Christoph A. Sotriffer:
  MycPermCheck: the Mycobacterium tuberculosis permeability prediction tool for small molecules. 62-68
• 
  Thomas L. Vincent, Peter J. Green, Derek N. Woolfson:
  LOGICOIL - multi-state prediction of coiled-coil oligomeric state. 69-76

Gene Expression

• 
  Florian Erhard, Lars Dölken, Ralf Zimmer:
  RIP-chip enrichment analysis. 77-83

Genetics and Population Analysis

• 
  Androniki Menelaou, Jonathan Marchini:
  Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. 84-91

Systems Biology

• 
  Chia Hsin Liu, Ker-Chau Li, Shinsheng Yuan:
  Human protein-protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence. 92-98
• 
  Xi Chen, Hemant Ishwaran:
  Pathway hunting by random survival forests. 99-105
• 
  Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen:
  NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. 106-113

Applications Note - Genome Analysis

• 
  Shiyuyun Tang, Ivan Antonov, Mark Borodovsky:
  MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. 114-116
• 
  Arturo Magana-Mora, Haitham Ashoor, Boris R. Jankovic, Allan Kamau, Karim Awara, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic:
  Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. 117-118
• 
  Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
  PBSIM: PacBio reads simulator - toward accurate genome assembly. 119-121

Sequence Analysis

• 
  Zhengwei Zhu, Beifang Niu, Jing Chen, Sitao Wu, Shulei Sun, Weizhong Li:
  MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. 122-123
• 
  Lu Zhang, Jing Zhang, Jing Yang, Dingge Ying, Yu-Lung Lau, Wanling Yang:
  PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data. 124-125

Structural Bioinformatics

• 
  Dimitrios Vlachakis, Dimosthenis Tsagkrasoulis, Vasileios Megalooikonomou, Sophia Kossida:
  Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit. 126-128

Gene Expression

• 
  Mario Fasold, Hans Binder:
  AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data. 129-131
• 
  Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez:
  DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. 132-134

Genetics and Population Analysis

• 
  Hailiang Huang, Sandeep Tata, Robert J. Prill:
  BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters. 135-136

Systems Biology

• 
  Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano:
  XiP: a computational environment to create, extend and share workflows. 137-139
• 
  Patrick W. Sheppard, Muruhan Rathinam, Mustafa Khammash:
  SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. 140-142
• 
  Michael Weitzel, Katharina Nöh, Tolga Dalman, Sebastian Niedenführ, Birgit Stute, Wolfgang Wiechert:
  13CFLUX2 - high-performance software suite for ¹³C-metabolic flux analysis. 143-145

Databases and Ontologies

• 
  Mark Woodbridge, Christopher D. Tomlinson, Sarah A. Butcher:
  ADAM: automated data management for research datasets. 146-147

Volume 29, Number 2, January 2013

Original Papers - Genome Analysis

• 
  Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju Manyam, Kim-Anh Do:
  iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data. 149-159
• 
  Yang I. Li, Richard R. Copley:
  Scaffolding low quality genomes using orthologous protein sequences. 160-165

Phylogenetics

• 
  Saad I. Sheikh, Tamer Kahveci, Sanjay Ranka, J. Gordon Burleigh:
  Stability analysis of phylogenetic trees. 166-174

Structural Bioinformatics

• 
  Ivan K. Huang, Jimin Pei, Nick V. Grishin:
  Defining and predicting structurally conserved regions in protein superfamilies. 175-181

Gene Expression

• 
  Mehmet Kocak, E. Olusegun George, Saumyadipta Pyne, Stanley Pounds:
  An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data. 182-188
• 
  Andrew E. Teschendorff, Francesco Marabita, Matthias Lechner, Thomas E. Bartlett, Jesper Tegnér, David Gomez-Cabrero, Stephan Beck:
  A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. 189-196

Genetics and Population Analysis

• 
  Mark Silberstein, Omer Weissbrod, Lars Otten, Anna Tzemach, Andrei Anisenia, Oren Shtark, Dvir Tuberg, Eddie Galfrin, Irena Gannon, Adel Shalata, Zvi U. Borochowitz, Rina Dechter, Elizabeth Thompson, Dan Geiger:
  A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees. 197-205
• 
  Barbara Rakitsch, Christoph Lippert, Oliver Stegle, Karsten M. Borgwardt:
  A Lasso multi-marker mixed model for association mapping with population structure correction. 206-214

Systems Biology

• 
  Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Ariston de Carvalho Azevedo, Tobias Wittkop, Jan Baumbach:
  Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. 215-222
• 
  Thomas Sütterlin, Christoph Kolb, Hartmut Dickhaus, Dirk Jäger, Niels Grabe:
  Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. 223-229
• 
  Li C. Xia, Dongmei Ai, Jacob A. Cram, Jed A. Fuhrman, Fengzhu Sun:
  Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. 230-237
• 
  Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng:
  Drug-target interaction prediction by learning from local information and neighbors. 238-245
• 
  Robert J. Flassig, Sandra Heise, Kai Sundmacher, Steffen Klamt:
  An effective framework for reconstructing gene regulatory networks from genetical genomics data. 246-254

Databases and Ontologies

• 
  Frida Belinky, Iris Bahir, Gil Stelzer, Shahar Zimmerman, Naomi Rosen, Noam Nativ, Irina Dalah, Tsippi Iny Stein, Noa Rappaport, Toutai Mituyama, Marilyn Safran, Doron Lancet:
  Non-redundant compendium of human ncRNA genes in GeneCards. 255-261

Applications Note - Genome Analysis

• 
  Jenna L. Butler, Marjorie Elizabeth Osborne Locke, Kathleen A. Hill, Mark Daley:
  HD-CNV: hotspot detector for copy number variants. 262-263
• 
  David R. Powell, Torsten Seemann:
  VAGUE: a graphical user interface for the Velvet assembler. 264-265
• 
  Yunxin Chen, Hui Yao, Erika J. Thompson, Nizar M. Tannir, John N. Weinstein, Xiaoping Su:
  VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. 266-267
• 
  Davide Campagna, Andrea Telatin, Claudio Forcato, Nicola Vitulo, Giorgio Valle:
  PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. 268-270

Structural Bioinformatics

• 
  Michael Golden, Darren Martin:
  DOOSS: a tool for visual analysis of data overlaid on secondary structures. 271-272

Gene Expression

• 
  Dmitri D. Pervouchine, David G. Knowles, Roderic Guigó:
  Intron-centric estimation of alternative splicing from RNA-seq data. 273-274

Genetics and Population Analysis

• 
  Zamin Iqbal, Isaac Turner, Gil McVean:
  High-throughput microbial population genomics using the Cortex variation assembler. 275-276

Systems Biology

• 
  Gerd Zschaler, Thilo Gross:
  Largenet2: an object-oriented programming library for simulating large adaptive networks. 277-278
• 
  Guomin Ren, Zhihua Liu:
  NetCAD: a network analysis tool for coronary artery disease-associated PPI network. 279-280
• 
  Achuthanunni Chokkathukalam, Andris Jankevics, Darren J. Creek, Fiona Achcar, Michael P. Barrett, Rainer Breitling:
  mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. 281-283

Data and Text Mining

• 
  Alexandre P. Blanchard, Graeme S. V. McDowell, Nico Valenzuela, Hongbin Xu, Sarah Gelbard, Martin Bertrand, Gary W. Slater, Daniel Figeys, Stephen Fai, Steffany A. L. Bennett:
  Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass. 284-285
• 
  Ola Spjuth, Valentin Georgiev, Lars Carlsson, Jonathan Alvarsson, Arvid Berg, Egon L. Willighagen, Jarl E. S. Wikberg, Martin Eklund:
  Bioclipse-R: integrating management and visualization of life science data with statistical analysis. 286-289

Databases and Ontologies

• 
  Nozomu Sakurai, Takeshi Ara, Shigehiko Kanaya, Yukiko Nakamura, Yoko Iijima, Mitsuo Enomoto, Takeshi Motegi, Koh Aoki, Hideyuki Suzuki, Daisuke Shibata:
  An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values. 290-291
• 
  Jiayu Gong, Xiaofeng Liu, Xianwen Cao, Yanyan Diao, Daqi Gao, Honglin Li, Xuhong Qian:
  PTID: an integrated web resource and computational tool for agrochemical discovery. 292-294
• 
  Yaping Fang, Hui-Xin Liu, Ning Zhang, Grace L. Guo, Yu-Jui Yvonne Wan, Jianwen Fang:
  NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse. 295-297

Erratum - Databases and Ontologies

• 
  Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld:
  ImgLib2 - generic image processing in Java. 298

Volume 29, Number 3, February 2013

Original Papers - Genome Analysis

• 
  Shengping Yang, Stanley Pounds, Kun Zhang, Zhide Fang:
  PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays. 299-307
• 
  Yongchao Liu, Jan Schröder, Bertil Schmidt:
  Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. 308-315
• 
  Paul M. Gontarz, Jennifer Berger, Chung F. Wong:
  SRmapper: a fast and sensitive genome-hashing alignment tool. 316-321

Structural Bioinformatics

• 
  Takako Takeda, Rosario I. Corona, Jun-tao Guo:
  A knowledge-based orientation potential for transcription factor-DNA docking. 322-330
• 
  Orly Noivirt-Brik, Gershon Hazan, Ron Unger, Yanay Ofran:
  Non-local residue-residue contacts in proteins are more conserved than local ones. 331-337

Systems Biology

• 
  Liming Wang, Xiaodong Wang, Adam P. Arkin, Michael S. Samoilov:
  Inference of gene regulatory networks from genome-wide knockout fitness data. 338-346
• 
  Yuan Shi, Gregory Mellier, Sinong Huang, Jacob K. White, Shazib Pervaiz, Lisa Tucker-Kellogg:
  Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP. 347-354

Data and Text Mining

• 
  Chengwei Lei, Jianhua Ruan:
  A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. 355-364
• 
  Yoshihiko Matsuta, Masahiro Ito, Yukako Tohsato:
  ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine. 365-372

Bioimage Informatics

• 
  Fernando Amat, Eugene W. Myers, Philipp J. Keller:
  Fast and robust optical flow for time-lapse microscopy using super-voxels. 373-380

Applications Notes - Genome Analysis

• 
  Chase A. Miller, Jon S. Anthony, Michelle M. Meyer, Gabor T. Marth:
  Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. 381-383
• 
  Theodore R. Pak, Frederick P. Roth:
  ChromoZoom: a flexible, fluid, web-based genome browser. 384-386
• 
  Connor McCoy, Aaron Gallagher, Noah G. Hoffman, Frederick A. Matsen IV:
  nestly - a framework for running software with nested parameter choices and aggregating results. 387-388
• 
  Thomas M. Keane, Kim Wong, David J. Adams:
  RetroSeq: transposable element discovery from next-generation sequencing data. 389-390

Sequence Analysis

• 
  Raeece Naeem, Mamoon Rashid, Arnab Pain:
  READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation. 391-392

Structural Bioinformatics

• 
  Lane Votapka, Rommie E. Amaro:
  Multistructural hot spot characterization with FTProd. 393-394
• 
  Anna Maria Gallina, Paola Bisignano, Maurizio Bergamino, Domenico Bordo:
  PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures. 395-397
• 
  Mickaël Krzeminski, Joseph A. Marsh, Chris Neale, Wing Yiu Choy, Julie D. Forman-Kay:
  Characterization of disordered proteins with ENSEMBLE. 398-399

Systems Biology

• 
  Brad Reisfeld, Jaime H. Ivy, Michael A. Lyons, Jesse M. Wright, Justin L. Rogers, Arthur N. Mayeno:
  DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction. 400-401
• 
  David M. Reif, Myroslav Sypa, Eric F. Lock, Fred A. Wright, Ander Wilson, Tommy Cathey, Richard S. Judson, Ivan Rusyn:
  ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence. 402-403
• 
  Gang Liu, Apurv Puri, Sriram Neelamegham:
  Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology. 404-406

Data and Text Mining

• 
  Davide Albanese, Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Giuseppe Jurman, Cesare Furlanello:
  minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. 407-408

Databases and Ontologies

• 
  Xinyi Liu, Shuyuan Wang, Fanlin Meng, Jizhe Wang, Yan Zhang, Enyu Dai, Xuexin Yu, Xia Li, Wei Jiang:
  SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression. 409-411

Letter to the Editor Systems Biology

• 
  Oliver Serang:
  Concerning the accuracy of Fido and parameter choice. 412

Volume 29, Number 4, February 2013

Original Papers - Genome Analysis

• 
  Alan Medlar, Dorota Glowacka, Horia Stanescu, Kevin Bryson, Robert Kleta:
  SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU. 413-419
• 
  Jia-Shing Chen, Wei-Shiang Hung, Hsiang-Han Chan, Shaw-Jenq Tsai, Hsiao-Fang Sunny Sun:
  In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma. 420-427
• 
  Nilgun Donmez, Michael Brudno:
  SCARPA: scaffolding reads with practical algorithms. 428-434
• 
  Scott C. Clark, Rob Egan, Peter I. Frazier, Zhong Wang:
  ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. 435-443

Sequence Analysis

• 
  Parameswaran Ramachandran, Gareth A. Palidwor, Christopher J. Porter, Theodore J. Perkins:
  MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. 444-450

Structural Bioinformatics

• 
  Mengjie Chen, Valentina Svicher, Anna Artese, Giosuè Costa, Claudia Alteri, Francesco Ortuso, Lucia Parrotta, Yang Liu, Chang Liu, Carlo-Federico Perno, Stefano Alcaro, Jing Zhang:
  Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. 451-460

Gene Expression

• 
  Andrew McDavid, Greg Finak, Pratip K. Chattopadhyay, Maria Dominguez, Laurie Lamoreaux, Steven S. Ma, Mario Roederer, Raphael Gottardo:
  Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. 461-467

Genetics and Population Analysis

• 
  Rosario M. Piro, Ivan Molineris, Ferdinando Di Cunto, Roland Eils, Rainer König:
  Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. 468-475

Systems Biology

• 
  Jesse A. Gillis, Paul Pavlidis:
  Assessing identity, redundancy and confounds in Gene Ontology annotations over time. 476-482
• 
  Wayne B. Hayes, Kai Sun, Natasa Przulj:
  Graphlet-based measures are suitable for biological network comparison. 483-491

Applications Notes - Genome Analysis

• 
  Jianrong Wang, Victoria V. Lunyak, I. King Jordan:
  BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. 492-493
• 
  Marcus R. Breese, Yunlong Liu:
  NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. 494-496

Structural Bioinformatics

• 
  Jed Zaretzki, Charles Bergeron, Tao-wei Huang, Patrik Rydberg, S. Joshua Swamidass, Curt M. Breneman:
  RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules. 497-498
• 
  Timothy P. Levine, Rachel D. Daniels, Alberto T. Gatta, Louise H. Wong, Matthew J. Hayes:
  The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs. 499-503
• 
  Castrense Savojardo, Piero Fariselli, Rita Casadio:
  BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. 504-505

Gene Expression

• 
  Clemens Wrzodek, Johannes Eichner, Finja Büchel, Andreas Zell:
  InCroMAP: integrated analysis of cross-platform microarray and pathway data. 506-508

Genetics and Population Analysis

• 
  Daniel Bottomly, Beth Wilmot, Jeffrey W. Tyner, Christopher A. Eide, Marc M. Loriaux, Brian J. Druker, Shannon K. McWeeney:
  HitWalker: variant prioritization for personalized functional cancer genomics. 509-510

Systems Biology

• 
  Linnea Järvstråt, Mikael Johansson, Urban Gullberg, Björn Nilsson:
  Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling. 511-512
• 
  Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri:
  GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. 513-514

Data and Text Mining

• 
  Woonghee Lee, Arash Bahrami, John L. Markley:
  ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. 515-517
• 
  Arsen Arakelyan, Lilit Nersisyan:
  KEGGParser: parsing and editing KEGG pathway maps in Matlab. 518-519

Databases and Ontologies

• 
  Frank Kramer, Michaela Bayerlová, Florian Klemm, Annalen Bleckmann, Tim Beißbarth:
  rBiopaxParser - an R package to parse, modify and visualize BioPAX data. 520-522
• 
  Nikolas Fechner, George Papadatos, David A. Evans, John Richard Morphy, Suzanne Clare Brewerton, David A. Thorner, Michael J. Bodkin:
  ChEMBLSpace - a graphical explorer of the chemogenomic space covered by the ChEMBL database. 523-524
• 
  Eamonn Maguire, Alejandra N. González-Beltrán, Patricia L. Whetzel, Susanna-Assunta Sansone, Philippe Rocca-Serra:
  OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets. 525-527
• 
  Qing Duan, Eric Yi Liu, Damien C. Croteau-Chonka, Karen L. Mohlke, Yun Li:
  A comprehensive SNP and indel imputability database. 528-531

Volume 29, Number 5, March 2013

Original Papers - Genome Analysis

• 
  Hyungwon Choi, Damian Fermin, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin:
  Sparsely correlated hidden Markov models with application to genome-wide location studies. 533-541

Sequence Analysis

• 
  Niclas Thomas, James M. Heather, Wilfred Ndifon, John Shawe-Taylor, Benjamin Chain:
  Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. 542-550
• 
  Georg Sauthoff, Mathias Möhl, Stefan Janssen, Robert Giegerich:
  Bellman's GAP - a language and compiler for dynamic programming in sequence analysis. 551-560

Phylogenetics

• 
  François Chevenet, Matthieu Jung, Martine Peeters, Tulio de Oliveira, Olivier Gascuel:
  Searching for virus phylotypes. 561-570
• 
  Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir:
  Systematic inference of highways of horizontal gene transfer in prokaryotes. 571-579

Structural Bioinformatics

• 
  Nikolas S. Burkoff, Csilla Várnai, David L. Wild:
  Predicting protein β-sheet contacts using a maximum entropy-based correlated mutation measure. 580-587
• 
  Tim Wiegels, Stefan Bienert, Andrew E. Torda:
  Fast alignment and comparison of RNA structures. 588-596
• 
  Mu Gao, Jeffrey Skolnick:
  APoc: large-scale identification of similar protein pockets. 597-604

Gene Expression

• 
  Pan Tong, Yong Chen, Xiao Su, Kevin R. Coombes:
  SIBER: systematic identification of bimodally expressed genes using RNAseq data. 605-613
• 
  David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó:
  Grape RNA-Seq analysis pipeline environment. 614-621

Systems Biology

• 
  Christopher L. Poirel, Ahsanur Rahman, Richard R. Rodrigues, Arjun Krishnan, Jacqueline R. Addesa, T. M. Murali:
  Reconciling differential gene expression data with molecular interaction networks. 622-629
• 
  Duc-Hau Le, Yung-Keun Kwon:
  A coherent feedforward loop design principle to sustain robustness of biological networks. 630-637

Data and Text Mining

• 
  Boya Xie, Qin Ding, Hongjin Han, Di Wu:
  miRCancer: a microRNA-cancer association database constructed by text mining on literature. 638-644

Applications Notes - Genome Analysis

• 
  Chengjun Zhang, Jun Wang, Manyuan Long, Chuanzhu Fan:
  gKaKs: the pipeline for genome-level Ka/Ks calculation. 645-646
• 
  Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael C. Ryan, Rachel Karchin:
  CRAVAT: cancer-related analysis of variants toolkit. 647-648

Sequence Analysis

• 
  Jing-Woei Li, Raymond Wan, Chi-Shing Yu, Ngai Na Co, Nathalie Wong, Ting-Fung Chan:
  ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. 649-651
• 
  Guillaume Rizk, Dominique Lavenier, Rayan Chikhi:
  DSK: k-mer counting with very low memory usage. 652-653

Structural Bioinformatics

• 
  Preeti Arunapuram, Ingolfur Edvardsson, Michael Golden, James W. J. Anderson, Ádám Novák, Zsuzsanna Sükösd, Jotun Hein:
  StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction. 654-655

Gene Expression

• 
  Michele A. Busby, Chip Stewart, Chase A. Miller, Krzysztof R. Grzeda, Gabor T. Marth:
  Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. 656-657

Systems Biology

• 
  Zuguang Gu, Jin Wang:
  CePa: an R package for finding significant pathways weighted by multiple network centralities. 658-660
• 
  Gabriela Bindea, Jérôme Galon, Bernhard Mlecnik:
  CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. 661-663
• 
  Richard R. Adams, Allan B. Clark, Azusa Yamaguchi, Neil Hanlon, Nikos Tsorman, Shakir Ali, Galina Lebedeva, Alexey N. Goltsov, Anatoly A. Sorokin, Ozgur E. Akman, Carl Troein, Andrew J. Millar, Igor Goryanin, Stephen Gilmore:
  SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology. 664-665

Databases and Ontologies

• 
  Markus S. Schröder, Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, Benjamin Haibe-Kains:
  RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. 666-668

Erratum - Databases and Ontologies

• 
  Mark Silberstein, Omer Weissbrod, Lars Otten, Anna Tzemach, Andrei Anisenia, Oren Shtark, Dvir Tuberg, Eddie Galfrin, Irena Gannon, Adel Shalata, Zvi U. Borochowitz, Rina Dechter, Elizabeth Thompson, Dan Geiger:
  A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees. 669

Volume 29, Number 6, March 2013

Original Papers - Genome Analysis

• 
  Sebastian Thieme, Philip Groth:
  Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data. 671-677

Sequence Analysis

• 
  Tao Li, Qian-Zhong Li, Shuai Liu, Guoliang Fan, Yongchun Zuo, Yong Peng:
  PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information. 678-685
• 
  Brett Trost, Anthony J. Kusalik:
  Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights. 686-694
• 
  Michael A. DeJesus, Yanjia J. Zhang, Christopher M. Sassetti, Eric J. Rubin, James C. Sacchettini, Thomas R. Ioerger:
  Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. 695-703

Structural Bioinformatics

• 
  James W. J. Anderson, Pierre A. Haas, Leigh-Anne Mathieson, Vladimir Volynkin, Rune B. Lyngsø, Paula Tataru, Jotun Hein:
  Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. 704-710

Gene Expression

• 
  Jérémie Becker, Christopher Yau, John M. Hancock, Christopher C. Holmes:
  NucleoFinder: a statistical approach for the detection of nucleosome positions. 711-716
• 
  Federico M. Giorgi, Cristian Del Fabbro, Francesco Licausi:
  Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana. 717-724

Genetics and Population Analysis

• 
  Mark R. Christie, Jacob A. Tennessen, Michael S. Blouin:
  Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching. 725-732
• 
  Nick Dand, Frauke Sprengel, Volker Ahlers, Thomas Schlitt:
  BioGranat-IG: a network analysis tool to suggest mechanisms of genetic heterogeneity from exome-sequencing data. 733-741

Systems Biology

• 
  Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer:
  Improving the reuse of computational models through version control. 742-748
• 
  Nuno D. Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Grégory Batt, Claudine Chaouiya:
  Composition and abstraction of logical regulatory modules: application to multicellular systems. 749-757

Data and Text Mining

• 
  Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, Hsueh-Wei Chang:
  Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping. 758-764
• 
  Thuc Duy Le, Lin Liu, Anna Tsykin, Gregory J. Goodall, Bing Liu, Bing-Yu Sun, Jiuyong Li:
  Inferring microRNA-mRNA causal regulatory relationships from expression data. 765-771

Bioimage Informatics

• 
  Sorin Pop, Alexandre Dufour, Jean-Francois Le Garrec, Chiara V. Ragni, Clémire Cimper, Sigolene M. Meilhac, Jean-Christophe Olivo-Marin:
  Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart. 772-779
• 
  Songhua Xu, Jianqiang Sheng, Xiaonan Luo:
  A new algorithm for context-based biomedical diagram similarity estimation. 780-789

Applications Notes - Genome Analysis

• 
  Dhwani K. Desai, Harald Schunck, Johannes W. Löser, Julie LaRoche:
  Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes. 790-791
• 
  Petr Novák, Pavel Neumann, Jirí Pech, Jaroslav Steinhaisl, Jirí Macas:
  RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. 792-793
• 
  Xiaohua Douglas Zhang, Zhaozhi Zhang:
  displayHTS: a R package for displaying data and results from high-throughput screening experiments. 794-796

Sequence Analysis

• 
  Christopher S. Oehmen, Douglas J. Baxter:
  ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems. 797-798
• 
  Jian Kang, Kuan-Chieh Huang, Zheng Xu, Yunfei Wang, Gonçalo R. Abecasis, Yun Li:
  AbCD: arbitrary coverage design for sequencing-based genetic studies. 799-801
• 
  Michaël Vyverman, Bernard De Baets, Veerle Fack, Peter Dawyndt:
  essaMEM: finding maximal exact matches using enhanced sparse suffix arrays. 802-804

Structural Bioinformatics

• 
  Marharyta Petukh, Taylor Kimmet, Emil Alexov:
  BION web server: predicting non-specifically bound surface ions. 805-806
• 
  Mieczyslaw Torchala, Iain H. Moal, Raphael A. G. Chaleil, Juan Fernández-Recio, Paul A. Bates:
  SwarmDock: a server for flexible protein-protein docking. 807-809

Gene Expression

• 
  Samuel C. Forster, Alexander M. Finkel, Jodee A. Gould, Paul J. Hertzog:
  RNA-eXpress annotates novel transcript features in RNA-seq data. 810-812
• 
  Andrei Alic, José E. Pérez-Ortín, Joaquín Moreno, Vicente Arnau:
  mRNAStab - a web application for mRNA stability analysis. 813-814

Systems Biology

• 
  Mathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling, Marco Pagni:
  MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. 815-816

Bioimage Informatics

• 
  Raz Shimoni, Kim Pham, Mohammed Yassin, Min Gu, Sarah M. Russell:
  TACTICS, an interactive platform for customized high-content bioimaging analysis. 817-818

Corrigendum - Bioimage Informatics

• 
  Chris J. Oates, Bryan T. J. Hennessy, Yiling Lu, Gordon B. Mills, Sach Mukherjee:
  Network inference using steady-state data and Goldbeter-Koshland kinetics. 819

Volume 29, Number 7, April 2013

Original Papers - Genome Analysis

• 
  Clement Chung, Andrew Emili, Brendan J. Frey:
  Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. 821-829

Sequence Analysis

• 
  Susanne Balzer, Ketil Malde, Markus A. Grohme, Inge Jonassen:
  Filtering duplicate reads from 454 pyrosequencing data. 830-836
• 
  Pierre-Alain Jachiet, Romain Pogorelcnik, Anne Berry, Philippe Lopez, Eric Bapteste:
  MosaicFinder: identification of fused gene families in sequence similarity networks. 837-844

Structural Bioinformatics

• 
  Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl:
  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. 845-854
• 
  Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Frederico F. Campos, Wagner Meira Jr.:
  aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. 855-861

Gene Expression

• 
  Min Chen, Miao Zang, Xinlei Wang, Guanghua Xiao:
  A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies. 862-869
• 
  Jakramate Bootkrajang, Ata Kabán:
  Classification of mislabelled microarrays using robust sparse logistic regression. 870-877

Genetics and Population Analysis

• 
  Yu Zhang:
  A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing. 878-885
• 
  Liina Kamm, Dan Bogdanov, Sven Laur, Jaak Vilo:
  A new way to protect privacy in large-scale genome-wide association studies. 886-893

Systems Biology

• 
  Yonit Hoffman, Dvir Dahary, Debora Rosa Bublik, Moshe Oren, Yitzhak Pilpel:
  The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery. 894-902
• 
  Arne C. Müller, Alexander Bockmayr:
  Fast thermodynamically constrained flux variability analysis. 903-909
• 
  Andrea Ocone, Andrew J. Millar, Guido Sanguinetti:
  Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics. 910-916
• 
  Ahmet Emre Aladag, Cesim Erten:
  SPINAL: scalable protein interaction network alignment. 917-924

Data and Text Mining

• 
  Beáta Reiz, Attila Kertész-Farkas, Sándor Pongor, Michael P. Myers:
  Chemical rule-based filtering of MS/MS spectra. 925-932
• 
  Matthias Zytnicki, YuFei Luo, Hadi Quesneville:
  Efficient comparison of sets of intervals with NC-lists. 933-939

Bioimage Informatics

• 
  Brian E. Ruttenberg, Gabriel Luna, Geoffrey P. Lewis, Steven K. Fisher, Ambuj K. Singh:
  Quantifying spatial relationships from whole retinal images. 940-946

Applications Notes - Genome Analysis

• 
  Gabriel Moreno-Hagelsieb, Zilin Wang, Stephanie Walsh, Aisha ElSherbiny:
  Phylogenomic clustering for selecting non-redundant genomes for comparative genomics. 947-949

Structural Bioinformatics

• 
  Bryce W. Cronkite-Ratcliff, Vijay Pande:
  MSMExplorer: visualizing Markov state models for biomolecule folding simulations. 950-952
• 
  Jan Kosinski, Alessandro Barbato, Anna Tramontano:
  MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. 953-954

Genetics and Population Analysis

• 
  Jerome Kelleher, Nicholas H. Barton, Alison M. Etheridge:
  Coalescent simulation in continuous space. 955-956

Systems Biology

• 
  Safee Ullah Chaudhary, Sung-Young Shin, Daewon Lee, Je-Hoon Song, Kwang-Hyun Cho:
  ELECANS - an integrated model development environment for multiscale cancer systems biology. 957-959
• 
  Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang:
  propy: a tool to generate various modes of Chou's PseAAC. 960-962

Data and Text Mining

• 
  Patrick Kiefer, Uwe Schmitt, Julia A. Vorholt:
  eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. 963-964

Volume 29, Number 8, April 2013

Original Papers - Genome Analysis

• 
  Anish Man Singh Shrestha, Martin C. Frith:
  An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome. 965-972

Sequence Analysis

• 
  Heiner Klingenberg, Kathrin Petra Aßhauer, Thomas Lingner, Peter Meinicke:
  Protein signature-based estimation of metagenomic abundances including all domains of life and viruses. 973-980
• 
  Valentina Indio, Pier Luigi Martelli, Castrense Savojardo, Piero Fariselli, Rita Casadio:
  The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields. 981-988
• 
  Fabian Sievers, David Dineen, Andreas Wilm, Desmond G. Higgins:
  Making automated multiple alignments of very large numbers of protein sequences. 989-995
• 
  Maryam Abbasi, Luís Paquete, Arnaud Liefooghe, Miguel Pinheiro, Pedro Matias:
  Improvements on bicriteria pairwise sequence alignment: algorithms and applications. 996-1003
• 
  Hsueh-Ting Chu, William W. L. Hsiao, Jen-Chih Chen, Tze-Jung Yeh, Mong-Hsun Tsai, Han Lin, Yen-Wenn Liu, Sheng-An Lee, Chaur-Chin Chen, Theresa Tsao, Cheng-Yan Kao:
  EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. 1004-1010

Phylogenetics

• 
  Salvador Capella-Gutiérrez, Toni Gabaldón:
  Measuring guide-tree dependency of inferred gaps in progressive aligners. 1011-1017

Structural Bioinformatics

• 
  Alvaro J. González, Li Liao, Cathy H. Wu:
  Prediction of contact matrix for protein-protein interaction. 1018-1025

Gene Expression

• 
  Can Yang, Lin Wang, Shuqin Zhang, Hongyu Zhao:
  Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. 1026-1034
• 
  Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M. G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, Christina Kendziorski:
  EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. 1035-1043

Systems Biology

• 
  Tri Hieu Nim, Le Luo, Marie-Véronique Clément, Jacob K. White, Lisa Tucker-Kellogg:
  Systematic parameter estimation in data-rich environments for cell signalling dynamics. 1044-1051
• 
  Syed Murtuza Baker, C. Hart Poskar, Falk Schreiber, Björn H. Junker:
  An improved constraint filtering technique for inferring hidden states and parameters of a biological model. 1052-1059
• 
  Alex Greenfield, Christoph Hafemeister, Richard Bonneau:
  Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. 1060-1067

Databases and Ontologies

• 
  Jingjing Jin, Jun Liu, Huan Wang, Limsoon Wong, Nam-Hai Chua:
  PLncDB: plant long non-coding RNA database. 1068-1071

Applications Notes Genome Analysis

• 
  Alexey A. Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler:
  QUAST: quality assessment tool for genome assemblies. 1072-1075

Sequence Analysis

• 
  Sangwoo Kim, Kyowon Jeong, Vineet Bafna:
  Wessim: a whole-exome sequencing simulator based on in silico exome capture. 1076-1077

Structural Bioinformatics

• 
  Hasup Lee, Hahnbeom Park, Junsu Ko, Chaok Seok:
  GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity. 1078-1080

Gene Expression

• 
  Gwenaël G. R. Leday, Mark A. van de Wiel:
  PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data. 1081-1082
• 
  Ting Gong, Joseph D. Szustakowski:
  DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data. 1083-1085

Genetics and Population Analysis

• 
  Stephen W. Hartley, Paola Sebastiani:
  PleioGRiP: genetic risk prediction with pleiotropy. 1086-1088

Systems Biology

• 
  Nils Gehlenborg, Michael S. Noble, Gad Getz, Lynda Chin, Peter J. Park:
  Nozzle: a report generation toolkit for data analysis pipelines. 1089-1091
• 
  Dong-Sheng Cao, Qing-Song Xu, Qian-Nan Hu, Yi-Zeng Liang:
  ChemoPy: freely available python package for computational biology and chemoinformatics. 1092-1094

Data and Text Mining

• 
  Júlio Trevisan, Plamen P. Angelov, Andrew D. Scott, Paul L. Carmichael, Francis L. Martin:
  IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis. 1095-1097

Databases and Ontologies

• 
  Daniel Lobo, Taylor J. Malone, Michael Levin:
  Planform: an application and database of graph-encoded planarian regenerative experiments. 1098-1100
• 
  Bo Peng, Huann-Sheng Chen, Leah E. Mechanic, Ben Racine, John Clarke, Lauren Clarke, Elizabeth Gillanders, Eric J. Feuer:
  Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators. 1101-1102

Bioimage Informatics

• 
  John Gómez, Leyla J. García, Gustavo A. Salazar, Jose M. Villaveces, Swanand P. Gore, Alexander García Castro, Maria Jesus Martin, Guillaume Launay, Rafael Alcántara, Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Sameer Velankar, Henning Hermjakob, Chenggong Zong, Peipei Ping, Manuel Corpas, Rafael C. Jiménez:
  BioJS: an open source JavaScript framework for biological data visualization. 1103-1104

Volume 29, Number 9, May 2013

Original Papers - Sequence Analysis

• 
  Seonjoo Lee, Pauline E. Chugh, Haipeng Shen, R. Eberle, Dirk P. Dittmer:
  Poisson factor models with applications to non-normalized microRNA profiling. 1105-1111
• 
  Carsten Kemena, Giovanni Bussotti, Emidio Capriotti, Marc A. Martí-Renom, Cédric Notredame:
  Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. 1112-1119
• 
  Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields:
  PeptideLocator: prediction of bioactive peptides in protein sequences. 1120-1126

Structural Bioinformatics

• 
  Zhiqiang Yan, Liyong Guo, Liang Hu, Jin Wang:
  Specificity and affinity quantification of protein-protein interactions. 1127-1133
• 
  Robert Schneider, Florian Odronitz, Björn Hammesfahr, Marcel Hellkamp, Martin Kollmar:
  Peakr: simulating solid-state NMR spectra of proteins. 1134-1140

Gene Expression

• 
  Moritz Aschoff, Agnes Hotz-Wagenblatt, Karl-Heinz Glatting, Matthias Fischer, Roland Eils, Rainer König:
  SplicingCompass: differential splicing detection using RNA-Seq data. 1141-1148
• 
  Thierry Rème, Dirk Hose, Charles Theillet, Bernard Klein:
  Modeling risk stratification in human cancer. 1149-1157

Systems Biology

• 
  Dafyd J. Jenkins, Bärbel Finkenstädt, David A. Rand:
  A temporal switch model for estimating transcriptional activity in gene expression. 1158-1165
• 
  Giuseppe Facchetti, Giovanni Iacono, Giovanna De Palo, Claudio Altafini:
  A rate-distortion theory for gene regulatory networks and its application to logic gate consistency. 1166-1173
• 
  Chia-Chin Wu, Kalpana Kannan, Steven Lin, Laising Yen, Aleksandar Milosavljevic:
  Identification of cancer fusion drivers using network fusion centrality. 1174-1181

Data and Text Mining

• 
  George Wu, Jason T. Yustein, Matthew N. McCall, Michael J. Zilliox, Rafael A. Irizarry, Karen Zeller, Chi V. Dang, Hongkai Ji:
  ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. 1182-1189
• 
  Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Dennis E. Shasha, Richard Bonneau:
  Parametric Bayesian priors and better choice of negative examples improve protein function prediction. 1190-1198
• 
  Misook Ha, Soondo Hong, Wen-Hsiung Li:
  Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context. 1199-1205

Applications Notes - Genome Analysis

• 
  Yoli Shavit, Pietro Liò:
  CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks. 1206-1207

Sequence Analysis

• 
  Gabriel Renaud, Martin Kircher, Udo Stenzel, Janet Kelso:
  freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. 1208-1209
• 
  Yan Guo, Jiang Li, Chung-I Li, Yu Shyr, David C. Samuels:
  MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. 1210-1211
• 
  David Weisman, Michie Yasuda, Jennifer L. Bowen:
  FunFrame: functional gene ecological analysis pipeline. 1212-1214
• 
  Thierry Schüpbach, Marco Pagni, Alan J. Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti:
  pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. 1215-1217

Structural Bioinformatics

• 
  Laurie E. Grove, David R. Hall, Dmitri Beglov, Sandor Vajda, Dima Kozakov:
  FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. 1218-1219

Genetics and Population Analysis

• 
  Quan Long, Qingrun Zhang, Bjarni J. Vilhjálmsson, Petar Forai, Ümit Seren, Magnus Nordborg:
  JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models. 1220-1222

Systems Biology

• 
  Xiaoyi Cao, Sheng Zhong:
  Enabling interspecies epigenomic comparison with CEpBrowser. 1223-1225
• 
  Karsten Hiller, André Wegner, Daniel Weindl, Thekla Cordes, Christian M. Metallo, Joanne K. Kelleher, Gregory Stephanopoulos:
  NTFD - a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data. 1226-1228
• 
  Fengkai Zhang, Bastian Robert Angermann, Martin Meier-Schellersheim:
  The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions. 1229-1230

Data and Text Mining

• 
  Olivier Taboureau, Ulrik Plesner Jacobsen, Christian Kalhauge, Daniel Edsgärd, Olga Rigina, Ramneek Gupta, Karine Audouze:
  HExpoChem: a systems biology resource to explore human exposure to chemicals. 1231-1232
• 
  Jelle Scholtalbers, Jasmin Rößler, Patrick Sorn, Jos de Graaf, Valesca Boisguérin, John C. Castle, Ugur Sahin:
  Galaxy LIMS for next-generation sequencing. 1233-1234

Databases and Ontologies

• 
  Fábio C. P. Navarro, Pedro A. F. Galante:
  RCPedia: a database of retrocopied genes. 1235-1237
• 
  Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann:
  Brain: biomedical knowledge manipulation. 1238-1239

Volume 29, Number 10, May 2013

Genome Analysis

• 
  Chen Lu, Jeanne Latourelle, George T. O'Connor, Josée Dupuis, Eric D. Kolaczyk:
  Network-guided sparse regression modeling for detection of gene-by-gene interactions. 1241-1249

Sequence Analysis

• 
  Ergude Bao, Tao Jiang, Thomas Girke:
  BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences. 1250-1259
• 
  Martin S. Lindner, Maximilian Kollock, Franziska Zickmann, Bernhard Y. Renard:
  Analyzing genome coverage profiles with applications to quality control in metagenomics. 1260-1267
• 
  Marco Pagni, Hélène Niculita-Hirzel, Loïc Pellissier, Anne Dubuis, Ioannis Xenarios, Antoine Guisan, Ian R. Sanders, Jérôme Goudet, Nicolas Guex:
  Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. 1268-1274

Gene Expression

• 
  Danni Yu, Wolfgang Huber, Olga Vitek:
  Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. 1275-1282

Systems Biology

• 
  Tarmo Äijö, Kirsi Granberg, Harri Lähdesmäki:
  Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements. 1283-1291
• 
  Bjørn Olav Hald, Morten Garkier Hendriksen, Preben Graae Sørensen:
  Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells. 1292-1298
• 
  Ivan Chang, Pierre Baldi:
  A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions. 1299-1307
• 
  Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal:
  EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. 1308-1316
• 
  Yong-Cui Wang, Shi-Long Chen, Nai-Yang Deng, Yong Wang:
  Network predicting drug's anatomical therapeutic chemical code. 1317-1324

Databases and Ontologies

• 
  Jon C. Ison, Matús Kalas, Inge Jonassen, Dan M. Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer, Peter M. Rice:
  EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. 1325-1332
• 
  David E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik, Jonas S. Almeida:
  A self-updating road map of The Cancer Genome Atlas. 1333-1340

Applications Notes - Genome Analysis

• 
  Glenn Hickey, Benedict Paten, Dent Earl, Daniel R. Zerbino, David Haussler:
  HAL: a hierarchical format for storing and analyzing multiple genome alignments. 1341-1342

Sequence Analysis

• 
  Diogo B. Lima, Yasset Pérez-Riverol, Fabio C. S. Nogueira, Gilberto B. Domont, Jesus Noda, Felipe da Veiga Leprevost, Vladimir Besada, Felipe M. G. França, Valmir Carneiro Barbosa, Aniel Sánchez, Paulo C. Carvalho:
  Effectively addressing complex proteomic search spaces with peptide spectrum matching. 1343-1344

Structural Bioinformatics

• 
  Gerald Weber:
  TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models. 1345-1347

Systems Biology

• 
  Vincent Navratil, Clément Pontoizeau, Elise Billoir, Benjamin J. Blaise:
  SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets. 1348-1349
• 
  Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico:
  Cytoscape App Store. 1350-1351

Data and Text Mining

• 
  Hanfei Sun, Bo Qin, Tao Liu, Qixuan Wang, Jing Liu, Juan Wang, Xueqiu Lin, Yulin Yang, Len Taing, Prakash K. Rao, Myles Brown, Yong Zhang, Henry Long, Xiaole Shirley Liu:
  CistromeFinder for ChIP-seq and DNase-seq data reuse. 1352-1354

Databases and Ontologies

• 
  Amit Zeisel, Assif Yitzhaky, Noa Bossel Ben-Moshe, Eytan Domany:
  An accessible database for mouse and human whole transcriptome qPCR primers. 1355-1356
• 
  Saliha Durmus Tekir, Tunahan Çakir, Emre Ardiç, Ali Semih Sayilirbas, Gökhan Konuk, Mithat Konuk, Hasret Sariyer, Azat Ugurlu, Ilknur Karadeniz, Arzucan Özgür, Fatih Erdogan Sevilgen, Kutlu Ö. Ülgen:
  PHISTO: pathogen-host interaction search tool. 1357-1358

Bioimage Informatics

• 
  Richard J. Giuly, Keun-Young Kim, Mark H. Ellisman:
  DP2: Distributed 3D image segmentation using micro-labor workforce. 1359-1360

Volume 29, Number 11, June 2013

Genome Analysis

• 
  Brendan D. O'Fallon, Whitney Wooderchak-Donahue, David K. Crockett:
  A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data. 1361-1366

Phylogenetics

• 
  Sebastian Höhna:
  Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. 1367-1374

Structural Bioinformatics

• 
  Michail Yu. Lobanov, Masha Yu. Suvorina, Nikita V. Dovidchenko, Igor V. Sokolovskiy, Alexey K. Surin, Oxana V. Galzitskaya:
  A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange. 1375-1381

Gene Expression

• 
  Nicoló Fusi, Christoph Lippert, Karsten M. Borgwardt, Neil D. Lawrence, Oliver Stegle:
  Detecting regulatory gene-environment interactions with unmeasured environmental factors. 1382-1389
• 
  Bo Jiang, Jun S. Liu, Martha L. Bulyk:
  Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. 1390-1398

Genetics and Population Analysis

• 
  Chia-Yen Chen, Samuela Pollack, David J. Hunter, Joel Hirschhorn, Peter Kraft, Alkes L. Price:
  Improved ancestry inference using weights from external reference panels. 1399-1406
• 
  Bogdan Pasaniuc, Sriram Sankararaman, Dara G. Torgerson, Christopher Gignoux, Noah Zaitlen, Celeste Eng, William Rodriguez-Cintron, Rocio Chapela, Jean G. Ford, Pedro C. Avila, Jose Rodriguez-Santana, Gary K. Chen, Loic Le Marchand, Brian E. Henderson, David Reich, Christopher A. Haiman, Esteban Gonzàlez Burchard, Eran Halperin:
  Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation. 1407-1415

System Biology

• 
  Néhémy Lim, Yasin Senbabaoglu, George Michailidis, Florence d'Alché-Buc:
  OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks. 1416-1423

Data and Text Mining

• 
  Zhixia Teng, Maozu Guo, Xiaoyan Liu, Qiguo Dai, Chun-yu Wang, Ping Xuan:
  Measuring gene functional similarity based on group-wise comparison of GO terms. 1424-1432
• 
  Chih-Hsuan Wei, Bethany R. Harris, Hung-Yu Kao, Zhiyong Lu:
  tmVar: a text mining approach for extracting sequence variants in biomedical literature. 1433-1439
• 
  Yufan Guo, Ilona Silins, Ulla Stenius, Anna Korhonen:
  Active learning-based information structure analysis of full scientific articles and two applications for biomedical literature review. 1440-1447

Bioimage Informatics

• 
  Hang Xiao, Hanchuan Peng:
  APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree. 1448-1454

Applications Notes - Genome Analysis

• 
  David H. Silver, Shay Ben-Elazar, Alexei Bogoslavsky, Itai Yanai:
  ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly. 1455-1457
• 
  Yupeng Wang, Jingping Li, Andrew H. Paterson:
  MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans. 1458-1460

Sequence Analysis

• 
  Yuhao Shi, Jacek Majewski:
  FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data. 1461-1462
• 
  Jinyan Huang, Jun Chen, Mark Lathrop, Liming Liang:
  A tool for RNA sequencing sample identity check. 1463-1464

Systems Biology

• 
  Jake Y. Fried, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn, Augustin Luna:
  PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. 1465-1466
• 
  Falko Krause, Marvin Schulz, Ben Ripkens, Max Flöttmann, Marcus Krantz, Edda Klipp, Thomas Handorf:
  Biographer: web-based editing and rendering of SBGN compliant biochemical networks. 1467-1468
• 
  Jens Einloft, Jörg Ackermann, Joachim Nöthen, Ina Koch:
  MonaLisa - visualization and analysis of functional modules in biochemical networks. 1469-1470
• 
  Tim Kacprowski, Nadezhda T. Doncheva, Mario Albrecht:
  NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules. 1471-1473
• 
  Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi, Akira Funahashi:
  LibSBMLSim: a reference implementation of fully functional SBML simulator. 1474-1476

Databases and Ontologies

• 
  Pieter Libin, Gertjan Beheydt, Koen Deforche, Stijn Imbrechts, Fossie Ferreira, Kristel Van Laethem, Kristof Theys, Ana Patricia Carvalho, Joana Cavaco-Silva, Giuseppe Lapadula, Carlo Torti, Matthias Assel, Stefan Wesner, Joke Snoeck, Jean Ruelle, Annelies De Bel, Patrick Lacor, Paul De Munter, Eric Van Wijngaerden, Maurizio Zazzi, Rolf Kaiser, Ahidjo Ayouba, Martine Peeters, Tulio de Oliveira, Luiz Carlos Júnior Alcântara, Zehava Grossman, Peter M. A. Sloot, Dan Otelea, Simona Paraschiv, Charles A. Boucher, Ricardo Camacho, Anne-Mieke Vandamme:
  RegaDB: community-driven data management and analysis for infectious diseases. 1477-1480
• 
  Sanghoon Moon, Kwang Su Jung, Young Jin Kim, Mi Yeong Hwang, Kyungsook Han, Jong-Young Lee, Kiejung Park, Bong-Jo Kim:
  KGVDB: a population-based genomic map of CNVs tagged by SNPs in Koreans. 1481-1483

Letter to the Editor

• 
  Manal Kalkatawi, Farania Rangkuti, Michael Schramm, Boris R. Jankovic, Allan Kamau, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic:
  Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. 1484

Volume 29, Number 12, June 2013

Discovery Notes - Genome Analysis

• 
  Sur Herrera Paredes, Michael F. Melgar, Praveen Sethupathy:
  Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index. 1485-1487

Gene Expression

• 
  Patrick B. F. O'Connor, Gene-Wei Li, Jonathan S. Weissman, John F. Atkins, Pavel V. Baranov:
  rRNA: mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. 1488-1491

Original Papers - Genome Analysis

• 
  Inanç Birol, Anthony Raymond, Shaun D. Jackman, Stephen Pleasance, Robin Coope, Greg A. Taylor, Macaire Man Saint Yuen, Christopher I. Keeling, Dana Brand, Benjamin P. Vandervalk, Heather Kirk, Pawan Pandoh, Richard A. Moore, Yongjun Zhao, Andrew J. Mungall, Barry Jaquish, Alvin Yanchuk, Carol Ritland, Brian Boyle, Jean Bousquet, Kermit Ritland, John MacKay, Jörg Bohlmann, Steven J. M. Jones:
  Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. 1492-1497

Sequence Analysis

• 
  Nancy F. Hansen, Jared J. Gartner, Lan Mei, Yardena Samuels, James C. Mullikin:
  Shimmer: detection of genetic alterations in tumors using next-generation sequence data. 1498-1503
• 
  Hashem A. Shihab, Julian Gough, David N. Cooper, Ian N. M. Day, Tom R. Gaunt:
  Predicting the functional consequences of cancer-associated amino acid substitutions. 1504-1510

Structural Bioinformatics

• 
  Lining Ju, Yijie Dylan Wang, Ying Hung, Chien-Fu Jeff Wu, Cheng Zhu:
  An HMM-based algorithm for evaluating rates of receptor-ligand binding kinetics from thermal fluctuation data. 1511-1518

Gene Expression

• 
  Dan J. Woodcock, Keith W. Vance, Michal Komorowski, Georgy Koentges, Bärbel Finkenstädt, David A. Rand:
  A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number. 1519-1525

Genetics and Population Analysis

• 
  Jennifer Listgarten, Christoph Lippert, Eun Yong Kang, Jing Xiang, Carl Myers Kadie, David Heckerman:
  A powerful and efficient set test for genetic markers that handles confounders. 1526-1533

Systems Biology

• 
  Henrik Failmezger, Paurush Praveen, Achim Tresch, Holger Fröhlich:
  Learning gene network structure from time laps cell imaging in RNAi Knock downs. 1534-1540
• 
  Ming Wu, Li Liu, Hussein Hijazi, Christina Chan:
  A multi-layer inference approach to reconstruct condition-specific genes and their regulation. 1541-1552
• 
  Sriganesh Srihari, Mark A. Ragan:
  Systematic tracking of dysregulated modules identifies novel genes in cancer. 1553-1561

Applications Notes Genome Analysis

• 
  Christopher M. Schroeder, Marc Sturm, Andreas Dufke, Ulrike Mau-Holzmann, Thomas Eggermann, Sven Poths, Olaf Riess, Michael Bonin:
  UPDtool: a tool for detection of iso- and heterodisomy in parent-child trios using SNP microarrays. 1562-1564

Sequence Analysis

• 
  Jia Meng, Xiaodong Cui, Manjeet K. Rao, Yidong Chen, Yufei Huang:
  Exome-based analysis for RNA epigenome sequencing data. 1565-1567

Genetics and Population Analysis

• 
  Kenneth Lange, Jeanette C. Papp, Janet S. Sinsheimer, Ram Sripracha, Hua Zhou, Eric M. Sobel:
  Mendel: the Swiss army knife of genetic analysis programs. 1568-1570

Systems Biology

• 
  Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev:
  OCSANA: optimal combinations of interventions from network analysis. 1571-1573

Databases and Ontologies

• 
  Simone Zorzan, Erika Lorenzetto, Michele Ettorre, Valeria Pontelli, Carlo Laudanna, Mario Buffelli:
  HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration. 1574-1576
• 
  Michael J. Meyer, Jishnu Das, Xiujuan Wang, Haiyuan Yu:
  INstruct: a database of high-quality 3D structurally resolved protein interactome networks. 1577-1579

Bioimage Informatics

• 
  Christoph Sommer, Michael Held, Bernd Fischer, Wolfgang Huber, Daniel Gerlich:
  CellH5: a format for data exchange in high-content screening. 1580-1582

Letter to the Editor Bioimage Informatics

• 
  Robert Smith, Dan Ventura, John T. Prince:
  Novel algorithms and the benefits of comparative validation. 1583-1585

Message from the ISCB Bioimage Informatics

• 
  Christiana N. Fogg, Diane E. Kovats:
  International Society for Computational Biology Honors Goncalo Abecasis with Top Bioinformatics/Computational Biology Award for 2013. 1586-1587

Volume 29, Number 13, July 2013

ISMB/ECCB 2013, July 21-23, 2013, Berlin, Germany

• 
  Nir Ben-Tal:
  Editorial. 1-2
• 
  Saket Navlakha, Joseph Suhan, Alison L. Barth, Ziv Bar-Joseph:
  A high-throughput framework to detect synapses in electron microscopy images. 9-17
• 
  Sarah J. Aerni, Xiao Liu, Chuong B. Do, Samuel S. Gross, Andy Nguyen, Stephen D. Guo, Fuhui Long, Hanchuan Peng, Stuart S. Kim, Serafim Batzoglou:
  Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. 18-26
• 
  Iulian Pruteanu-Malinici, William H. Majoros, Uwe Ohler:
  Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields. 27-35
• 
  Noa Liscovitch, Uri Shalit, Gal Chechik:
  FuncISH: learning a functional representation of neural ISH images. 36-43
• 
  Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou:
  A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. 44-52
• 
  Wyatt T. Clark, Predrag Radivojac:
  Information-theoretic evaluation of predicted ontological annotations. 53-61
• 
  Andrew J. Sedgewick, Stephen C. Benz, Shahrooz Rabizadeh, Patrick Soon-Shiong, Charles J. Vaske:
  Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM. 62-70
• 
  Yaron Orenstein, Ron Shamir:
  Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers. 71-79
• 
  Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens:
  Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. 80-88
• 
  Hai-Son Le, Ziv Bar-Joseph:
  Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. 89-97
• 
  Hiroyuki Kuwahara, Ming Fan, Suojin Wang, Xin Gao:
  A framework for scalable parameter estimation of gene circuit models using structural information. 98-107
• 
  Dina Hafez, Ting Ni, Sayan Mukherjee, Jun Zhu, Uwe Ohler:
  Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. 108-116
• 
  Fantine Mordelet, John Horton, Alexander J. Hartemink, Barbara E. Engelhardt, Raluca Gordân:
  Stability selection for regression-based models of transcription factor-DNA binding specificity. 117-125
• 
  Yuhao Wang, Jianyang Zeng:
  Predicting drug-target interactions using restricted Boltzmann machines. 126-134
• 
  Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Toshiaki Tokimatsu, Susumu Goto:
  Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. 135-144
• 
  Gamze Abaka, Türker Bíyíkoglu, Cesim Erten:
  CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways. 145-153
• 
  Rodrigo Liberal, John W. Pinney:
  Simple topological properties predict functional misannotations in a metabolic network. 154-161
• 
  Dan He:
  IBD-Groupon: an efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships. 162-170
• 
  Chloé-Agathe Azencott, Dominik G. Grimm, Mahito Sugiyama, Yoshinobu Kawahara, Karsten M. Borgwardt:
  Efficient network-guided multi-locus association mapping with graph cuts. 171-179
• 
  Pier Francesco Palamara, Itsik Pe'er:
  Inference of historical migration rates via haplotype sharing. 180-188
• 
  Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
  Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. 189-198
• 
  Carlo Vittorio Cannistraci, Gregorio Alanis-Lobato, Timothy Ravasi:
  Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding. 199-209
• 
  Alexander Lan, Michal Ziv-Ukelson, Esti Yeger Lotem:
  A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. 210-216
• 
  Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman:
  Multitask learning for host-pathogen protein interactions. 217-226
• 
  Anthony Gitter, Ziv Bar-Joseph:
  Identifying proteins controlling key disease signaling pathways. 227-236
• 
  Rob Patro, Carl Kingsford:
  Predicting protein interactions via parsimonious network history inference. 237-246
• 
  Zhidong Xue, Dong Xu, Yan Wang, Yang Zhang:
  ThreaDom: extracting protein domain boundary information from multiple threading alignments. 247-256
• 
  Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu:
  Protein threading using context-specific alignment potential. 257-265
• 
  Zhiyong Wang, Jinbo Xu:
  Predicting protein contact map using evolutionary and physical constraints by integer programming. 266-273
• 
  Min Xu, Frank Alber:
  Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms. 274-282
• 
  Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger:
  Compressive genomics for protein databases. 283-290
• 
  Zhaojun Zhang, Shunping Huang, Jack Wang, Xiang Zhang, Fernando Pardo-Manuel de Villena, Leonard McMillan, Wei Wang:
  GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment. 291-299
• 
  Elmirasadat Forouzmand, Hamidreza Chitsaz:
  The RNA Newton polytope and learnability of energy parameters. 300-307
• 
  Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
  A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. 308-315
• 
  Bo Xie, Boris R. Jankovic, Vladimir B. Bajic, Le Song, Xin Gao:
  Poly(A) motif prediction using spectral latent features from human DNA sequences. 316-325
• 
  Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Ming-Ju Lv, Xin-Guang Zhu, Francis Y. L. Chin:
  IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. 326-334
• 
  Kousik Kundu, Fabrizio Costa, Rolf Backofen:
  A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. 335-343
• 
  David Golan, Paul Medvedev:
  Using state machines to model the Ion Torrent sequencing process and to improve read error rates. 344-351
• 
  Derek Aguiar, Sorin Istrail:
  Haplotype assembly in polyploid genomes and identical by descent shared tracts. 352-360
• 
  Lin Huang, Victoria Popic, Serafim Batzoglou:
  Short read alignment with populations of genomes. 361-370

Discovery Note Structural Bioinformatics

• 
  Mireia Olivella, Angel Gonzalez, Leonardo Pardo, Xavier Deupí:
  Relation between sequence and structure in membrane proteins. 1589-1592

Original Papers Genome Analysis

• 
  Yoonsoo Hahn:
  Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition. 1593-1599

Sequence Analysis

• 
  Matthias Barann, Daniela Esser, Ulrich C. Klostermeier, Tuuli Lappalainen, Anne Luzius, Jan W. P. Kuiper, Ole Ammerpohl, Inga Vater, Reiner Siebert, Vyacheslav Amstislavskiy, Ralf Sudbrak, Hans Lehrach, Stefan Schreiber, Philip Rosenstiel:
  Janus - a comprehensive tool investigating the two faces of transcription. 1600-1606
• 
  Thomas Schnattinger, Uwe Schöning, Hans A. Kestler:
  Structural RNA alignment by multi-objective optimization. 1607-1613
• 
  Xiang Chen, Jian-Ding Qiu, Shao-Ping Shi, Sheng-Bao Suo, Shu-Yun Huang, Ru-Ping Liang:
  Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites. 1614-1622
• 
  Jan Kirrbach, Miriam Krugliak, Christian L. Ried, Philipp Pagel, Isaiah T. Arkin, Dieter Langosch:
  Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins. 1623-1630

Gene Expression

• 
  Adam Roberts, Lorian Schaeffer, Lior Pachter:
  Updating RNA-Seq analyses after re-annotation. 1631-1637
• 
  Martin A. Rijlaarsdam, David J. Rijlaarsdam, Ad J. M. Gillis, Lambert C. J. Dorssers, Leendert H. J. Looijenga:
  miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data. 1638-1646
• 
  Katja Hebestreit, Martin Dugas, Hans-Ulrich Klein:
  Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. 1647-1653

Data and Text Mining

• 
  Behnam Neyshabur, Ahmadreza Khadem, Somaye Hashemifar, Seyed Shahriar Arab:
  NETAL: a new graph-based method for global alignment of protein-protein interaction networks. 1654-1662

Databases and Ontologies

• 
  María Jesús García-Godoy, Esteban López-Camacho, Ismael Navas-Delgado, José Francisco Aldana Montes:
  Sharing and executing linked data queries in a collaborative environment. 1663-1670
• 
  Midori A. Harris, Antonia Lock, Jürg Bähler, Stephen G. Oliver, Valerie Wood:
  FYPO: the fission yeast phenotype ontology. 1671-1678

Applications Notes Genome Analysis

• 
  Christoph Bartenhagen, Martin Dugas:
  RSVSim: an R/Bioconductor package for the simulation of structural variations. 1679-1681

Sequence Analysis

• 
  Hákon Jónsson, Aurelien Ginolhac, Mikkel Schubert, Philip L. F. Johnson, Ludovic Orlando:
  mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. 1682-1684
• 
  Clare Sloggett, Nuwan Goonasekera, Enis Afgan:
  BioBlend: automating pipeline analyses within Galaxy and CloudMan. 1685-1686
• 
  Miriam Rubio-Camarillo, Gonzalo Gómez-López, José María Fernández, Alfonso Valencia, David G. Pisano:
  RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. 1687-1689
• 
  Joseph C. Pearson, Stephen T. Crews:
  Twine: display and analysis of cis-regulatory modules. 1690-1692
• 
  Brett Trost, Ryan Arsenault, Philip J. Griebel, Scott Napper, Anthony J. Kusalik:
  DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites. 1693-1695
• 
  Paul Brown, Laura Baxter, Richard Hickman, Jim Beynon, Jonathan D. Moore, Sascha Ott:
  MEME-LaB: motif analysis in clusters. 1696-1697

Structural Bioinformatics

• 
  Brian Jiménez-García, Carles Pons, Juan Fernández-Recio:
  pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. 1698-1699
• 
  Saskia D. Hiltemann, Elizabeth A. McClellan, Jos van Nijnatten, Sebastiaan Horsman, Ivo Palli, Ines Teles Alves, Thomas Hartjes, Jan Trapman, Peter J. van der Spek, Guido Jenster, Andrew Stubbs:
  iFUSE: integrated fusion gene explorer. 1700-1701

Gene Expression

• 
  Daniel Stöckel, Oliver Müller, Tim Kehl, Andreas Gerasch, Christina Backes, Alexander Rurainski, Andreas Keller, Michael Kaufmann, Hans-Peter Lenhof:
  NetworkTrail - a web service for identifying and visualizing deregulated subnetworks. 1702-1703

Genetics and Population Analysis

• 
  Louis-Philippe Lemieux Perreault, Sylvie Provost, Marc-André Legault, Amina Barhdadi, Marie-Pierre Dubé:
  pyGenClean: efficient tool for genetic data clean up before association testing. 1704-1705

Systems Biology

• 
  Chuan-Yih Yu, Anoop M. Mayampurath, Yunli Hu, Shiyue Zhou, Yehia Mechref, Haixu Tang:
  Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry. 1706-1707
• 
  Antti Häkkinen, Anantha Barathi Muthukrishnan, André Mora, José Manuel Fonseca, Andre S. Ribeiro:
  CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli. 1708-1709

Databases and Ontologies

• 
  Catherine Voegele, Baptiste Bouchereau, Nivonirina Robinot, James McKay, Philippe Damiecki, Lucile Alteyrac:
  A universal open-source Electronic Laboratory Notebook. 1710-1712

Volume 29, Number 14, July 2013

Discovery Note - Genome Analysis

• 
  Che-Yu Lee, Liang Chen:
  Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. 1713-1717

Original Papers - Genome Analysis

• 
  Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg:
  GAGE-B: an evaluation of genome assemblers for bacterial organisms. 1718-1725

Sequence Analysis

• 
  Guilhem Faure, Isabelle Callebaut:
  Identification of hidden relationships from the coupling of Hydrophobic Cluster Analysis and Domain Architecture information. 1726-1733
• 
  Hongseok Tae, Kevin W. McMahon, Robert E. Settlage, Jasmin H. Bavarva, Harold R. Garner:
  ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats. 1734-1741

Structural Bioinformatics

• 
  Jessica Andreani, Guilhem Faure, Raphaël Guérois:
  InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. 1742-1749
• 
  Christoph Wiedemann, Peter Bellstedt, Matthias Görlach:
  CAPITO - a web server-based analysis and plotting tool for circular dichroism data. 1750-1757

Systems Biology

• 
  Mohammadmahdi R. Yousefi, Edward R. Dougherty:
  Intervention in gene regulatory networks with maximal phenotype alteration. 1758-1767
• 
  Hao Lin, Lin He, Bin Ma:
  A combinatorial approach to the peptide feature matching problem for label-free quantification. 1768-1775
• 
  Gennaro Gambardella, Maria Nicoletta Moretti, Rossella de Cegli, Luca Cardone, Adriano Peron, Diego di Bernardo:
  Differential network analysis for the identification of condition-specific pathway activity and regulation. 1776-1785

Data and Text Mining

• 
  Xiaoli Wei, Xue Shi, Imhoi Koo, Seongho Kim, Robin H. Schmidt, Gavin E. Arteel, Walter H. Watson, Craig McClain, Xiang Zhang:
  MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. 1786-1792
• 
  Laura Tolosi, Jessica Theißen, Konstantin Halachev, Barbara Hero, Frank Berthold, Thomas Lengauer:
  A method for finding consensus breakpoints in the cancer genome from copy number data. 1793-1800

Applications Notes - Genome Analysis

• 
  Ryo Sakai, Alejandro Sifrim, Andrew Vande Moere, Jan Aerts:
  TrioVis: a visualization approach for filtering genomic variants of parent-child trios. 1801-1802
• 
  Zheng-Zheng Tang, Dan-Yu Lin:
  MASS: meta-analysis of score statistics for sequencing studies. 1803-1805
• 
  Masahiko Kumagai, Jungsok Kim, Ryutaro Itoh, Takeshi Itoh:
  Tasuke: a web-based visualization program for large-scale resequencing data. 1806-1808

Sequence Analysis

• 
  Michael Piechotta, Christoph Dieterich:
  ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores. 1809-1810
• 
  Daniel Lopez, Florencio Pazos:
  COPRED: prediction of fold, GO molecular function and functional residues at the domain level. 1811-1812
• 
  Ernesto Picardi, Graziano Pesole:
  REDItools: high-throughput RNA editing detection made easy. 1813-1814

Structural Bioinformatics

• 
  Marcin J. Skwark, Abbi Abdel-Rehim, Arne Elofsson:
  PconsC: combination of direct information methods and alignments improves contact prediction. 1815-1816
• 
  Marcin J. Skwark, Arne Elofsson:
  PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. 1817-1818
• 
  Adam Mazur, Björn Hammesfahr, Christian Griesinger, Donghan Lee, Martin Kollmar:
  ShereKhan - calculating exchange parameters in relaxation dispersion data from CPMG experiments. 1819-1820
• 
  Rosalba Lepore, Anna Tramontano, Allegra Via:
  TiPs: a database of therapeutic targets in pathogens and associated tools. 1821-1822

Systems Biology

• 
  Lea A. I. Vaas, Johannes Sikorski, Benjamin Hofner, Anne Fiebig, Nora Buddruhs, Hans-Peter Klenk, Markus Göker:
  opm: an R package for analysing OmniLog^® phenotype microarray data. 1823-1824
• 
  Luca Beltrame, Luca Bianco, Paolo Fontana, Duccio Cavalieri:
  Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data. 1825-1826

Data and Text Mining

• 
  Jiayu Gong, Chaoqian Cai, Xiaofeng Liu, Xin Ku, Hualiang Jiang, Daqi Gao, Honglin Li:
  ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. 1827-1829
• 
  Weijun Luo, Cory Brouwer:
  Pathview: an R/Bioconductor package for pathway-based data integration and visualization. 1830-1831

Databases and Ontologies

• 
  Kun Yang, Ashok Reddy Dinasarapu, Edimara S. Reis, Robert A. DeAngelis, Daniel Ricklin, Shankar Subramaniam, John D. Lambris:
  CMAP: Complement Map Database. 1832-1833
• 
  Changhe Fu, Guangxu Jin, Junfeng Gao, Rui Zhu, Efren Ballesteros-Villagrana, Stephen T. C. Wong:
  DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies. 1834-1836
• 
  Lin Dai, Ming Tian, Jiayan Wu, Jing-Fa Xiao, Xumin Wang, Jeffrey P. Townsend, Zhang Zhang:
  AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. 1837-1839

Bioimage Informatics

• 
  Jean Ollion, Julien Cochennec, François Loll, Christophe Escudé, Thomas Boudier:
  TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. 1840-1841

Volume 29, Number 15, August 2013

Original Papers - Genome Analysis

• 
  Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno:
  Identification of deleterious synonymous variants in human genomes. 1843-1850
• 
  Paul Geeleher, Lori Hartnett, Laurance J. Egan, Aaron Golden, Raja Affendi Raja Ali, Cathal Seoighe:
  Gene-set analysis is severely biased when applied to genome-wide methylation data. 1851-1857
• 
  Michael S. Porter, Robert G. Beiko:
  SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles. 1858-1864

Gene Expression

• 
  Jaeil Ahn, Ying Yuan, Giovanni Parmigiani, Milind B. Suraokar, Lixia Diao, Ignacio I. Wistuba, Wenyi Wang:
  DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. 1865-1871

Systems Biology

• 
  Christopher M. Tan, Edward Y. Chen, Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan:
  Network2Canvas: network visualization on a canvas with enrichment analysis. 1872-1878

Bioimage Informatics

• 
  Ching-Wei Wang, Hsiang-Chou Chen:
  Improved image alignment method in application to X-ray images and biological images. 1879-1887

Applications Notes - Genome Analysis

• 
  Nicholas B. Larson, Brooke L. Fridley:
  PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. 1888-1889
• 
  Graham J. Etherington, Daniel MacLean:
  SVGenes: a library for rendering genomic features in scalable vector graphic format. 1890-1892
• 
  Alexei Nordell-Markovits, Charles Joly Beauparlant, Dominique Toupin, Shengrui Wang, Arnaud Droit, Nicolas Gevry:
  NGS++: a library for rapid prototyping of epigenomics software tools. 1893-1894
• 
  Fabian A. Buske, Denis C. Bauer, John S. Mattick, Timothy L. Bailey:
  Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci. 1895-1897

Sequence Analysis

• 
  Ka-Kyung Kim, Juyoung Ham, Sung Wook Chi:
  miRTCat: a comprehensive map of human and mouse microRNA target sites including non-canonical nucleation bulges. 1898-1899
• 
  Jirí Hon, Tomás Martínek, Kamil Rajdl, Matej Lexa:
  Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. 1900-1901
• 
  Mick Watson, Esther Schnettler, Alain Kohl:
  viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. 1902-1903
• 
  Varun Jaiswal, Sree K. Chanumolu, Pankaj Sharma, Rajinder S. Chauhan, Chittaranjan Rout:
  EpiCombFlu: exploring known influenza epitopes and their combination to design a universal influenza vaccine. 1904-1907
• 
  Shawn E. Yost, Hakan Alakus, Hiroko Matsui, Richard B. Schwab, Kristen Jepsen, Kelly A. Frazer, Olivier Harismendy:
  Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. 1908-1909

Structural Bioinformatics

• 
  Xueping Liu, Ingo Vogt, Tanzeem Haque, Mónica Campillos:
  HitPick: a web server for hit identification and target prediction of chemical screenings. 1910-1912

Gene Expression

• 
  Eduardo P. Costa, Gerben Menschaert, Walter Luyten, Kurt De Grave, Jan Ramon:
  PIUS: peptide identification by unbiased search. 1913-1914

Data and Text Mining

• 
  Tiago Nunes, David Campos, Sérgio Matos, José Luís Oliveira:
  BeCAS: biomedical concept recognition services and visualization. 1915-1916

Databases and Ontologies

• 
  Jindan Zhou, Andrew J. Richardson, Kenneth E. Rudd:
  EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes. 1917-1918
• 
  Rafael C. Jiménez, Juan P. Albar, Jong Bhak, Marie-Claude Blatter, Thomas Blicher, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Marc A. van Driel, Michael J. Dunn, Pedro L. Fernandes, Celia W. G. van Gelder, Henning Hermjakob, Vassilios Ioannidis, David Phillip Judge, Pascal Kahlem, Eija Korpelainen, Hans-Joachim Kraus, Jane E. Loveland, Christine Mayer, Jennifer McDowall, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Gustavo A. Salazar, Reinhard Schneider, Allegra Via, Jose M. Villaveces, Ping Yu, Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas:
  iAnn: an event sharing platform for the life sciences. 1919-1921
• 
  Raymond K. Auerbach, Bin Chen, Atul J. Butte:
  Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. 1922-1924

Volume 29, Number 16, August 2013

Review - Genome Analysis

• 
  Benjamin M. Good, Andrew I. Su:
  Crowdsourcing for bioinformatics. 1925-1933

Discovery Note Systems Biology

• 
  Aurelio A. Moya-García, Juan A. G. Ranea:
  Insights into polypharmacology from drug-domain associations. 1934-1937

Original Papers - Genome Analysis

• 
  Zhi-Zhong Chen, Fei Deng, Lusheng Wang:
  Exact algorithms for haplotype assembly from whole-genome sequence data. 1938-1945

Sequence Analysis

• 
  Dominik Heider, Robin Senge, Weiwei Cheng, Eyke Hüllermeier:
  Multilabel classification for exploiting cross-resistance information in HIV-1 drug resistance prediction. 1946-1952
• 
  Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner:
  UniNovo: a universal tool for de novo peptide sequencing. 1953-1962
• 
  Jérôme Ambroise, Anne-Sophie Piette, Cathy Delcorps, Leen Rigouts, Bouke C. de Jong, Leonid Irenge, Annie Robert, Jean-Luc Gala:
  AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal. 1963-1969

Phylogenetics

• 
  Guy Baele, Philippe Lemey:
  Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. 1970-1979

Structural Bioinformatics

• 
  Pedro Sfriso, Adam Hospital, Agustí Emperador, Modesto Orozco:
  Exploration of conformational transition pathways from coarse-grained simulations. 1980-1986

Gene Expression

• 
  Shandian Zhe, Syed A. Z. Naqvi, Yifan Yang, Yuan Qi:
  Joint network and node selection for pathway-based genomic data analysis. 1987-1996

Genetics and Population Analysis

• 
  Colin D. Veal, Hang Xu, Katherine Reekie, Robert C. Free, Robert J. Hardwick, David McVey, Anthony J. Brookes, Edward J. Hollox, Christopher J. Talbot:
  Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation. 1997-2003

Systems Biology

• 
  Salvatore Alaimo, Alfredo Pulvirenti, Rosalba Giugno, Alfredo Ferro:
  Drug-target interaction prediction through domain-tuned network-based inference. 2004-2008
• 
  Alberto Rezola, Jon Pey, Luis F. de Figueiredo, Adam Podhorski, Stefan Schuster, Angel Rubio, Francisco J. Planes:
  Selection of human tissue-specific elementary flux modes using gene expression data. 2009-2016

Data and Text Mining

• 
  Jinmyung Jung, Doheon Lee:
  Inferring disease association using clinical factors in a combinatorial manner and their use in drug repositioning. 2017-2023

Databases and Ontologies

• 
  Xi Zhou, Pengcheng Chen, Qiang Wei, Xueling Shen, Xin Chen:
  Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets. 2024-2031

Bioimage Informatics

• 
  Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen:
  An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues. 2032-2040

Applications Notes Genome Analysis

• 
  Come Raczy, Roman Petrovski, Christopher T. Saunders, Ilya Chorny, Semyon Kruglyak, Elliott H. Margulies, Han-Yu Chuang, Morten Källberg, Swathi A. Kumar, Arnold Liao, Kristina M. Little, Michael P. Strömberg, Stephen W. Tanner:
  Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. 2041-2043
• 
  Jianlin He, Xinxi Sun, Xiaojian Shao, Liji Liang, Hehuang Xie:
  DMEAS: DNA methylation entropy analysis software. 2044-2045
• 
  Andreas Heger, Caleb Webber, Martin Goodson, Chris P. Ponting, Gerton Lunter:
  GAT: a simulation framework for testing the association of genomic intervals. 2046-2048

Sequence Analysis

• 
  Sangsoon Woo, Xuekui Zhang, Renan Sauteraud, François Robert, Raphael Gottardo:
  PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. 2049-2050

Structural Bioinformatics

• 
  Michal Rostkowski, Ola Spjuth, Patrik Rydberg:
  WhichCyp: prediction of cytochromes P450 inhibition. 2051-2052
• 
  Alessandro Pandini, Arianna Fornili, Franca Fraternali, Jens Kleinjung:
  GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. 2053-2055
• 
  Claudio Mirabello, Gianluca Pollastri:
  Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility. 2056-2058

Gene Expression

• 
  Inna Dubchak, Matthew Munoz, Alexander Poliakov, Nathan Salomonis, Simon Minovitsky, Rolf Bodmer, Alexander C. Zambon:
  Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. 2059-2061
• 
  Alexey Lagunin, Sergey Ivanov, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov:
  DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula. 2062-2063

Systems Biology

• 
  Yingfeng Wang, Tae-Hyuk Ahn, Zhou Li, Chongle Pan:
  Sipros/ProRata: a versatile informatics system for quantitative community proteomics. 2064-2065
• 
  Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico:
  NOA: a cytoscape plugin for network ontology analysis. 2066-2067

Data and Text Mining

• 
  Norbert Dojer, Pawel Bednarz, Agnieszka Podsiadlo, Bartek Wilczynski:
  BNFinder2: Faster Bayesian network learning and Bayesian classification. 2068-2070
• 
  Bülent Arman Aksoy, Jianjiong Gao, Gideon Dresdner, Weiqing Wang, Alex Root, Xiaohong Jing, Ethan G. Cerami, Chris Sander:
  PiHelper: an open source framework for drug-target and antibody-target data. 2071-2072

Corrigendum Data and Text Mining

• 
  Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M. G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, Christina Kendziorski:
  EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. 2073

Volume 29, Number 17, September 2013

Review - Sequence Analysis

• 
  Julie Nocq, Magalie Celton, Patrick Gendron, Sébastien Lemieux, Brian T. Wilhelm:
  Harnessing virtual machines to simplify next-generation DNA sequencing analysis. 2075-2083

Discovery note - Sequence Analysis

• 
  Mikita Suyama:
  Mechanistic insights into mutually exclusive splicing in dynamin 1. 2084-2087

Original Papers - Genome Analysis

• 
  Stan Pounds, Cheng Cheng, Shaoyu Li, Zhifa Liu, Jinghui Zhang, Charles Mullighan:
  A genomic random interval model for statistical analysis of genomic lesion data. 2088-2095

Sequence Analysis

• 
  David Koslicki, Simon Foucart, Gail Rosen:
  Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. 2096-2102
• 
  Yuan Zhang, Yanni Sun, James R. Cole:
  A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. 2103-2111
• 
  Francisco M. Ortuño Guzman, Olga Valenzuela, Fernando Rojas, Héctor Pomares, Javier Perez-Florido, José M. Urquiza, Ignacio Rojas:
  Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns. 2112-2121

Structural Bioinformatics

• 
  Joanna S. G. Slusky, Roland L. Dunbrack Jr.:
  Charge asymmetry in the proteins of the outer membrane. 2122-2128
• 
  Seydou Traoré, David Allouche, Isabelle André, Simon de Givry, George Katsirelos, Thomas Schiex, Sophie Barbe:
  A new framework for computational protein design through cost function network optimization. 2129-2136

Gene Expression

• 
  Xiaowei Chen, Frank J. Slack, Hongyu Zhao:
  Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions. 2137-2145
• 
  Andrea Rau, Mélina Gallopin, Gilles Celeux, Florence Jaffrézic:
  Data-based filtering for replicated high-throughput transcriptome sequencing experiments. 2146-2152
• 
  Ei-Wen Yang, Thomas Girke, Tao Jiang:
  Differential gene expression analysis using coexpression and RNA-Seq data. 2153-2161
• 
  Yuju Lee, Qing Zhou:
  Co-regulation in embryonic stem cells via context-dependent binding of transcription factors. 2162-2168
• 
  Wei Liu, Chunquan Li, Yanjun Xu, Haixiu Yang, Qianlan Yao, Junwei Han, Desi Shang, Chunlong Zhang, Fei Su, Xiaoxi Li, Yun Xiao, Fan Zhang, Meng Dai, Xia Li:
  Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. 2169-2177

Systems Biology

• 
  Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert:
  Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. 2178-2185

Data and Text Mining

• 
  Rong Xu, Li Li, QuanQiu Wang:
  Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature. 2186-2194

Applications Notes - Genome Analysis

• 
  René Snajder, Zlatko Trajanoski, Hubert Hackl:
  GPViz: dynamic visualization of genomic regions and variants affecting protein domains. 2195-2196
• 
  Maxim Barenboim, Thomas Manke:
  ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation. 2197-2198
• 
  Dmitri S. Pavlichin, Tsachy Weissman, Golan Yona:
  The human genome contracts again. 2199-2202
• 
  Martin Triska, David Grocutt, James Southern, Denis J. Murphy, Tatiana V. Tatarinova:
  cisExpress: motif detection in DNA sequences. 2203-2205
• 
  Ryo Sakai, Matthieu Moisse, Joke Reumers, Jan Aerts:
  Pipit: visualizing functional impacts of structural variations. 2206-2207
• 
  Mamunur Rashid, Carla Daniela Robles-Espinoza, Alistair G. Rust, David J. Adams:
  Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes. 2208-2210

Gene Expression

• 
  Renaud Gaujoux, Cathal Seoighe:
  CellMix: a comprehensive toolbox for gene expression deconvolution. 2211-2212

Systems Biology

• 
  John W. May, A. Gordon James, Christoph Steinbeck:
  Metingear: a development environment for annotating genome-scale metabolic models. 2213-2215
• 
  Sebastian Vlaic, Bianca Hoffmann, Peter Kupfer, Michael Weber, Andreas Dräger:
  GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML. 2216-2217

Data and Text Mining

• 
  Rui Zhong, Min Soo Kim, Michael A. White, Yang Xie, Guanghua Xiao:
  SbacHTS: Spatial background noise correction for High-Throughput RNAi Screening. 2218-2220

Databases and Ontologies

• 
  Ke Liu, Zhangming Yan, Yuchao Li, Zhirong Sun:
  Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis. 2221-2222

Volume 29, Number 18, September 2013

Review - Genome Analysis

• 
  Nicola D. Roberts, R. Daniel Kortschak, Wendy T. Parker, Andreas W. Schreiber, Susan Branford, Hamish S. Scott, Garique Glonek, David L. Adelson:
  A comparative analysis of algorithms for somatic SNV detection in cancer. 2223-2230

Original Papers - Genome Analysis

• 
  William K. M. Lai, Michael J. Buck:
  An integrative approach to understanding the combinatorial histone code at functional elements. 2231-2237
• 
  David Tamborero, Abel Gonzalez-Perez, Núria López-Bigas:
  OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. 2238-2244

Sequence Analysis

• 
  Wen-Yun Yang, Farhad Hormozdiari, Zhanyong Wang, Dan He, Bogdan Pasaniuc, Eleazar Eskin:
  Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data. 2245-2252
• 
  Sasha Ames, David A. Hysom, Shea N. Gardner, G. Scott Lloyd, Maya B. Gokhale, Jonathan E. Allen:
  Scalable metagenomic taxonomy classification using a reference genome database. 2253-2260
• 
  Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu:
  An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale. 2261-2268

Phylogenetics

• 
  Juan Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Chun-yu Wang, Linlin Xing, Kai Che:
  Lnetwork: an efficient and effective method for constructing phylogenetic networks. 2269-2276
• 
  Md. Shamsuzzoha Bayzid, Tandy J. Warnow:
  Naive binning improves phylogenomic analyses. 2277-2284

Structural Bioinformatics

• 
  Pier Paolo Olimpieri, Anna Chailyan, Anna Tramontano, Paolo Marcatili:
  Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. 2285-2291

Gene Expression

• 
  Naoki Nariai, Osamu Hirose, Kaname Kojima, Masao Nagasaki:
  TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. 2292-2299
• 
  Laura H. LeGault, Colin N. Dewey:
  Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. 2300-2310

Systems Biology

• 
  Gabriele Lillacci, Mustafa Khammash:
  The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. 2311-2319
• 
  Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez:
  Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. 2320-2326
• 
  Elisenda Feliu, Carsten Wiuf:
  A computational method to preclude multistationarity in networks of interacting species. 2327-2334

Bioimage Informatics

• 
  Theodore Alexandrov, Andreas M. Bartels:
  Testing for presence of known and unknown molecules in imaging mass spectrometry. 2335-2342
• 
  Luís Pedro Coelho, Joshua D. Kangas, Armaghan W. Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, Robert F. Murphy:
  Determining the subcellular location of new proteins from microscope images using local features. 2343-2349

Applications Notes - Genome Analysis

• 
  Joanna L. Sharman, Dietlind L. Gerloff:
  MaGnET: Malaria Genome Exploration Tool. 2350-2352

Sequence Analysis

• 
  Susan K. Rathe, James E. Johnson, Kevin A. T. Silverstein, Jesse J. Erdmann, Adrienne L. Watson, Flavia E. Popescu, John R. Ohlfest, David A. Largaespada:
  MMuFLR: missense mutation and frameshift location reporter. 2353-2354
• 
  Hernán F. Morales, Guillermo Giovambattista:
  BioSmalltalk: a pure object system and library for bioinformatics. 2355-2356

Structural Bioinformatics

• 
  Wenkang Huang, Shaoyong Lu, Zhimin Huang, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang:
  Allosite: a method for predicting allosteric sites. 2357-2359
• 
  Joan Planas-Iglesias, Manuel Alejandro Marín-López, Jaume Bonet, Javier García-García, Baldo Oliva:
  iLoops: a protein-protein interaction prediction server based on structural features. 2360-2362
• 
  Víctor A. Gil, Victor Guallar:
  pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling. 2363-2364

Gene Expression

• 
  Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Nehme Hachem, Gianluca Bontempi, Benjamin Haibe-Kains:
  mRMRe: an R package for parallelized mRMR ensemble feature selection. 2365-2368

Systems Biology

• 
  Wesley Schaal, Ulf Hammerling, Mats G. Gustafsson, Ola Spjuth:
  Automated QuantMap for rapid quantitative molecular network topology analysis. 2369-2370

Volume 29, Number 19, October 2013

Discovery Notes - Sequence Analysis

• 
  Luis Sánchez-Pulido, Chris P. Ponting:
  Tiki, at the head of a new superfamily of enzymes. 2371-2374

Systems Biology

• 
  Zhenpeng Li, Xiuliang Cui, Fei Li, Peng Li, Ming Ni, Shengqi Wang, Xiaochen Bo:
  Exploring the role of human miRNAs in virus-host interactions using systematic overlap analysis. 2375-2379

Original Papers - Genome Analysis

• 
  Robert Schöpflin, Vladimir B. Teif, Oliver Müller, Christin Weinberg, Karsten Rippe, Gero Wedemann:
  Modeling nucleosome position distributions from experimental nucleosome positioning maps. 2380-2386

Sequence Analysis

• 
  Jonathan M. Goldberg, Allison D. Griggs, Janet L. Smith, Brian J. Haas, Jennifer R. Wortman, Qiandong Zeng:
  Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily. 2387-2394
• 
  Zeinab Taghavi, Narjes S. Movahedi, Sorin Draghici, Hamidreza Chitsaz:
  Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities. 2395-2401
• 
  Wenjie Deng, Brandon Maust, Dylan H. Westfall, Lennie Chen, Hong Zhao, Brendan B. Larsen, Shyamala Iyer, Yi Liu, James I. Mullins:
  Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. 2402-2409

Gene Expression

• 
  Amina Noor, Aitzaz Ahmad, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou:
  ROBNCA: robust network component analysis for recovering transcription factor activities. 2410-2418

Genetics and Population Analysis

• 
  Manuel A. Rivas, Matti Pirinen, Matthew J. Neville, Kyle J. Gaulton, Loukas Moutsianas, Cecilia M. Lindgren, Fredrik Karpe, Mark I. McCarthy, Peter Donnelly:
  Assessing association between protein truncating variants and quantitative traits. 2419-2426
• 
  Kui Zhang, Degui Zhi:
  Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads. 2427-2434

Systems Biology

• 
  Wei-Ming Chen, Samuel A. Danziger, Jung-Hsien Chiang, John D. Aitchison:
  PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. 2435-2444

Data and Text Mining

• 
  Robert Smith, Tamil S. Anthonymuthu, Dan Ventura, John T. Prince:
  Statistical agglomeration: peak summarization for direct infusion lipidomics. 2445-2451
• 
  Nikolas Kessler, Heiko Neuweger, Anja Bonte, Georg Langenkämper, Karsten Niehaus, Tim W. Nattkemper, Alexander Goesmann:
  MeltDB 2.0-advances of the metabolomics software system. 2452-2459

Bioimage Informatics

• 
  Vahid Abrishami, Airen Zaldívar-Peraza, José Miguel de la Rosa-Trevín, Javier Vargas, Joaquín Otón, Roberto Marabini, Yoel Shkolnisky, José María Carazo, Carlos Oscar Sánchez Sorzano:
  A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. 2460-2468
• 
  Jijie Wang, Henry Lam:
  Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets. 2469-2476

Applications Notes - Genome Analysis

• 
  Simon J. McGowan, Jim R. Hughes, Zong-Pei Han, Stephen Taylor:
  MIG: Multi-Image Genome viewer. 2477-2478
• 
  Daniel Jost:
  Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA. 2479-2481
• 
  Christopher Yau:
  OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes. 2482-2484
• 
  Alper Küçükural, Hakan Özadam, Guramrit Singh, Melissa J. Moore, Can Cenik:
  ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. 2485-2486

Sequence Analysis

• 
  Travis J. Wheeler, Sean R. Eddy:
  nhmmer: DNA homology search with profile HMMs. 2487-2489
• 
  Lucian Ilie, Michael Molnar:
  RACER: Rapid and accurate correction of errors in reads. 2490-2493
• 
  Matija Korpar, Mile Sikic:
  SW#-GPU-enabled exact alignments on genome scale. 2494-2495
• 
  Josef Maier, Alexei A. Adzhubei, Wolfgang Egge-Jacobsen:
  SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules. 2496-2497
• 
  Chiao-Feng Lin, Otto Valladares, Daniel M. Childress, Egor Klevak, Evan T. Geller, Yih-Chii Hwang, Ellen A. Tsai, Gerard D. Schellenberg, Li-San Wang:
  DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments. 2498-2500

Structural Bioinformatics

• 
  Diana H. P. Low, Efthymios Motakis:
  deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis. 2501-2502

Gene Expression

• 
  Andreas Spitz, Katharina Anna Zweig, Emoke-Ágnes Horvát:
  SICOP: identifying significant co-interaction patterns. 2503-2504

Systems Biology

• 
  Esther Camilo, Luiz A. Bovolenta, Marcio Luis Acencio, José L. Rybarczyk Filho, Mauro A. A. Castro, José C. F. Moreira, Ney Lemke:
  GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks. 2505-2506
• 
  Jennifer E. Dent, Xinyi Yang, Christine Nardini:
  SPNConverter: a new link between static and dynamic complex network analysis. 2507-2508
• 
  Quanwei Zhang, Zhengdong D. Zhang:
  SubNet: a Java application for subnetwork extraction. 2509-2511

Databases and Ontologies

• 
  Alexander Miguel Monzon, Ezequiel I. Juritz, María Silvina Fornasari, Gustavo D. Parisi:
  CoDNaS: a database of conformational diversity in the native state of proteins. 2512-2514
• 
  Mohd Danishuddin, Mohd Hassan Baig, Lalima Kaushal, Asad U. Khan:
  BLAD: A comprehensive database of widely circulated beta-lactamases. 2515-2516
• 
  Foivos Gypas, Georgios N. Tsaousis, Stavros J. Hamodrakas:
  mpMoRFsDB: a database of molecular recognition features in membrane proteins. 2517-2518
• 
  Konika Chawla, Sushil Tripathi, Liv Thommesen, Astrid Lægreid, Martin Kuiper:
  TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. 2519-2520

Volume 29, Number 20, October 2013

Discovery Notes - Sequence Analysis

• 
  Luiz Felipe Valter de Oliveira, Ana Paula Christoff, Rogerio Margis:
  isomiRID: a framework to identify microRNA isoforms. 2521-2523

Structural Bioinformatics

• 
  Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada:
  Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. 2524-2528

Original Papers - Genome Analysis

• 
  Jonas Behr, André Kahles, Yi Zhong, Vipin T. Sreedharan, Philipp Drewe, Gunnar Rätsch:
  MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. 2529-2538
• 
  Mikhail Shugay, Iñigo Ortiz de Mendíbil, José L. Vizmanos, Francisco J. Novo:
  Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions. 2539-2546
• 
  Alessandro Mammana, Martin Vingron, Ho-Ryun Chung:
  Inferring nucleosome positions with their histone mark annotation from ChIP data. 2547-2554
• 
  Christopher Minas, Edward W. J. Curry, Giovanni Montana:
  A distance-based test of association between paired heterogeneous genomic data. 2555-2563

Sequence Analysis

• 
  Sarah Sheppard, Nathan D. Lawson, Lihua Julie Zhu:
  Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier. 2564-2571
• 
  Sebastian Deorowicz, Agnieszka Danek, Szymon Grabowski:
  Genome compression: a novel approach for large collections. 2572-2578

Structural Bioinformatics

• 
  Jing Yang, Richard Jang, Yang Zhang, Hong-Bin Shen:
  High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. 2579-2587
• 
  Jianyi Yang, Ambrish Roy, Yang Zhang:
  Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. 2588-2595

Gene Expression

• 
  Wei Jiang, Yan Zhang, Fanlin Meng, Baofeng Lian, Xiaowen Chen, Xuexin Yu, Enyu Dai, Shuyuan Wang, Xinyi Liu, Xiang Li, Lihong Wang, Xia Li:
  Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease. 2596-2602
• 
  Robert Maier, Ralf Zimmer, Robert Küffner:
  A Turing test for artificial expression data. 2603-2609

Systems Biology

• 
  Eric F. Lock, David B. Dunson:
  Bayesian consensus clustering. 2610-2616
• 
  Xing Chen, Guiying Yan:
  Novel human lncRNA-disease association inference based on lncRNA expression profiles. 2617-2624
• 
  Alberto Giovanni Busetto, Alain Hauser, Gabriel Krummenacher, Mikael Sunnåker, Sotiris Dimopoulos, Cheng Soon Ong, Jörg Stelling, Joachim M. Buhmann:
  Near-optimal experimental design for model selection in systems biology. 2625-2632
• 
  Zixing Wang, Wenlong Xu, F. Anthony San Lucas, Yin Liu:
  Incorporating prior knowledge into Gene Network Study. 2633-2640

Applications Notes - Genome Analysis

• 
  Darren S. Curtis, Aaron R. Phillips, Stephen J. Callister, Sean Conlan, Lee Ann McCue:
  SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes. 2641-2642
• 
  Alexis Allot, Yannick-Noël Anno, Laetitia Poidevin, Raymond Ripp, Olivier Poch, Odile Lecompte:
  PARSEC: PAtteRn SEarch and Contextualization. 2643-2644
• 
  Jianghan Qu, Meng Zhou, Qiang Song, Elizabeth E. Hong, Andrew D. Smith:
  MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation. 2645-2646

Sequence Analysis

• 
  Wenlin Li, Lisa N. Kinch, Nick V. Grishin:
  Pclust: protein network visualization highlighting experimental data. 2647-2648

Structural Bioinformatics

• 
  Tomás Norambuena, Jorge F. Cares, Emidio Capriotti, Francisco Melo:
  WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures. 2649-2650

Gene Expression

• 
  Sören Müller, Lukas Rycak, Peter Winter, Günter Kahl, Ina Koch, Björn Rotter:
  omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. 2651-2652

Systems Biology

• 
  Youyi Fong, Krisztian Sebestyen, Xuesong Yu, Peter Gilbert, Steve Self:
  nCal: an R package for non-linear calibration. 2653-2654

Data and Text Mining

• 
  Matthew K. Matlock, Jed Zaretzki, S. Joshua Swamidass:
  Scaffold network generator: a tool for mining molecular structures. 2655-2656

Databases and Ontologies

• 
  Ganiraju Manyam, Cristina Ivan, George A. Calin, Kevin R. Coombes:
  targetHub: a programmable interface for miRNA-gene interactions. 2657-2658
• 
  Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader:
  The BioPAX Validator. 2659-2660

Bioimage Informatics

• 
  Paola Masuzzo, Niels Hulstaert, Lynn Huyck, Christophe Ampe, Marleen Van Troys, Lennart Martens:
  CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays. 2661-2663

Letter to the Editor - Data and Text Mining

• 
  Anne-Laure Boulesteix:
  On representative and illustrative comparisons with real data in bioinformatics: response to the letter to the editor by Smith et al.. 2664-2666

Corrigendum - Genome Analysis

• 
  Attila Gyenesei, Colin A. M. Semple, Chris S. Haley, Wenhua Wei:
  Corrigendum of 'High throughput analysis of epistasis in genome-wide association studies with BiForce'. 2667-2668

Volume 29, Number 21, November 2013

Original Papers - Genome Analysis

• 
  Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke:
  The MaSuRCA genome assembler. 2669-2677
• 
  Liangcai Zhang, Li Zhang:
  Use of autocorrelation scanning in DNA copy number analysis. 2678-2682
• 
  Gwo-Liang Chen, Yun-Juan Chang, Chun-Hway Hsueh:
  PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes. 2683-2689

Sequence Analysis

• 
  Jie Ren, Kai Song, Fengzhu Sun, Minghua Deng, Gesine Reinert:
  Multiple alignment-free sequence comparison. 2690-2698
• 
  Rafik Amir Salama, Dov J. Stekel:
  A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites. 2699-2704
• 
  Anaïs F. Bardet, Jonas Steinmann, Sangeeta Bafna, Juergen A. Knoblich, Julia Zeitlinger, Alexander Stark:
  Identification of transcription factor binding sites from ChIP-seq data at high resolution. 2705-2713
• 
  Angela D. Wilkins, Eric Venner, David C. Marciano, Serkan Erdin, Benu Atri, Rhonald C. Lua, Olivier Lichtarge:
  Accounting for epistatic interactions improves the functional analysis of protein structures. 2714-2721

Structural Bioinformatics

• 
  Valerio Mariani, Marco Biasini, Alessandro Barbato, Torsten Schwede:
  lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. 2722-2728

Gene Expression

• 
  Sébastien Artigaud, Olivier Gauthier, Vianney Pichereau:
  Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools. 2729-2734
• 
  Ashok Reddy Dinasarapu, Shakti Gupta, Mano Ram Maurya, Eoin Fahy, Jun Min, Manish Sud, Merril J. Gersten, Christopher K. Glass, Shankar Subramaniam:
  A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism. 2735-2743

Genetics and Population Analysis

• 
  Qing Duan, Eric Yi Liu, Paul L. Auer, Guosheng Zhang, Ethan M. Lange, Goo Jun, Chris Bizon, Shuo Jiao, Steven Buyske, Nora Franceschini, Chris S. Carlson, Li Hsu, Alex P. Reiner, Ulrike Peters, Jeffrey Haessler, Keith Curtis, Christina L. Wassel, Jennifer G. Robinson, Lisa W. Martin, Christopher A. Haiman, Loic Le Marchand, Tara Cox Matise, Lucia A. Hindorff, Dana C. Crawford, Themistocles L. Assimes, Hyun Min Kang, Gerardo Heiss, Rebecca D. Jackson, Charles Kooperberg, James G. Wilson, Gonçalo R. Abecasis, Kari E. North, Deborah A. Nickerson, Leslie A. Lange, Yun Li:
  Imputation of coding variants in African Americans: better performance using data from the exome sequencing project. 2744-2749
• 
  James J. Yang, Jia Li, Anne Buu, L. Keoki Williams:
  Efficient inference of local ancestry. 2750-2756

Systems Biology

• 
  Evan O. Paull, Daniel E. Carlin, Mario Niepel, Peter K. Sorger, David Haussler, Joshua M. Stuart:
  Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). 2757-2764
• 
  Leonid Chindelevitch, Cheng-Yu Ma, Chung-Shou Liao, Bonnie Berger:
  Optimizing a global alignment of protein interaction networks. 2765-2773

Data and Text Mining

• 
  Tsung-Heng Tsai, Mahlet G. Tadesse, Cristina Di Poto, Lewis K. Pannell, Yehia Mechref, Yue Joseph Wang, Habtom W. Ressom:
  Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards. 2774-2780

Databases and Ontologies

• 
  João D. Ferreira, Janna Hastings, Francisco M. Couto:
  Exploiting disjointness axioms to improve semantic similarity measures. 2781-2787

Applications Notes - Genome Analysis

• 
  Ben Elsworth, Martin O. Jones, Mark L. Blaxter:
  Badger - an accessible genome exploration environment. 2788-2789

Sequence Analysis

• 
  Fritz J. Sedlazeck, Philipp Rescheneder, Arndt von Haeseler:
  NextGenMap: fast and accurate read mapping in highly polymorphic genomes. 2790-2791

Structural Bioinformatics

• 
  Yan Wang, Tyler W. H. Backman, Kevin Horan, Thomas Girke:
  fmcsR: mismatch tolerant maximum common substructure searching in R. 2792-2794
• 
  Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, Alexander Schug:
  eSBMTools 1.0: enhanced native structure-based modeling tools. 2795-2796

Gene Expression

• 
  Greg C. Imholte, Marie-Pier Scott-Boyer, Aurélie Labbe, Christian F. Deschepper, Raphael Gottardo:
  iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data. 2797-2798
• 
  Amit Kumar Yadav, Puneet Kumar Kadimi, Dhirendra Kumar, Debasis Dash:
  ProteoStats - a library for estimating false discovery rates in proteomics pipelines. 2799-2800

Systems Biology

• 
  Jesse D. Ziebarth, Anindya Bhattacharya, Yan Cui:
  Bayesian Network Webserver: a comprehensive tool for biological network modeling. 2801-2803

Data and Text Mining

• 
  Kevin L. Crowell, Gordon W. Slysz, Erin S. Baker, Brian L. LaMarche, Matthew E. Monroe, Yehia M. Ibrahim, Samuel H. Payne, Gordon A. Anderson, Richard D. Smith:
  LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. 2804-2805

Databases and Ontologies

• 
  Christina M. Bergey, Andrew M. Watkins, Paramjit S. Arora:
  HippDB: a database of readily targeted helical protein-protein interactions. 2806-2807
• 
  Chuming Chen, Zhiwen Li, Hongzhan Huang, Baris E. Suzek, Cathy H. Wu:
  A fast Peptide Match service for UniProt Knowledgebase. 2808-2809
• 
  Cristóbal Fresno, Elmer Andrés Fernández:
  RDAVIDWebService: a versatile R interface to DAVID. 2810-2811

Volume 29, Number 22, November 2013

Original Papers - Genome Analysis

• 
  Caihong Zheng, Xuexia Miao, Yanen Li, Ying Huang, Jue Ruan, Xi Ma, Li Wang, Chung-I Wu, Jun Cai:
  Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing. 2813-2821
• 
  Keiko Sato, Toshihide Hara, Masanori Ohya:
  The code structure of the p53 DNA-binding domain and the prognosis of breast cancer patients. 2822-2825
• 
  Jurgen F. Nijkamp, Mihai Pop, Marcel J. T. Reinders, Dick de Ridder:
  Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. 2826-2834
• 
  Kaname Kojima, Naoki Nariai, Takahiro Mimori, Mamoru Takahashi, Yumi Yamaguchi-Kabata, Yukuto Sato, Masao Nagasaki:
  A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. 2835-2843
• 
  Lauren A. Sugden, Michael R. Tackett, Yiannis A. Savva, William A. Thompson, Charles E. Lawrence:
  Assessing the validity and reproducibility of genome-scale predictions. 2844-2851

Sequence Analysis

• 
  Cristian Oscar Rohr, R. Gonzalo Parra, Patricio Yankilevich, Carolina Perez-Castro:
  INSECT: IN-silico SEarch for Co-occurring Transcription factors. 2852-2858
• 
  Feng Zeng, Rui Jiang, Ting Chen:
  PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data. 2859-2868

Phylogenetics

• 
  Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis, Alexandros Stamatakis:
  A general species delimitation method with applications to phylogenetic placements. 2869-2876

Gene Expression

• 
  Sarah E. Reese, Kellie J. Archer, Terry M. Therneau, Elizabeth J. Atkinson, Celine M. Vachon, Mariza de Andrade, Jean-Pierre A. Kocher, Jeanette E. Eckel-Passow:
  A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. 2877-2883
• 
  Tamar Sofer, Elizabeth D. Schifano, Jane A. Hoppin, Lifang Hou, Andrea A. Baccarelli:
  A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure. 2884-2891

Systems Biology

• 
  Adi L. Tarca, Mario Lauria, Michael Unger, Erhan Bilal, Stéphanie Boué, Kushal Kumar Dey, Julia Hoeng, Heinz Koeppl, Florian Martin, Pablo Meyer, Preetam Nandy, Raquel Norel, Manuel C. Peitsch, John Jeremy Rice, Roberto Romero, Gustavo Stolovitzky, Marja Talikka, Yang Xiang, Christoph Zechner, Improver Dsc Collaborators:
  Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. 2892-2899
• 
  Brian J. Schmidt, Ali Ebrahim, Thomas O. Metz, Joshua N. Adkins, Bernhard Ø. Palsson, Daniel R. Hyduke:
  GIM³E: condition-specific models of cellular metabolism developed from metabolomics and expression data. 2900-2908

Data and Text Mining

• 
  Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu:
  DNorm: disease name normalization with pairwise learning to rank. 2909-2917
• 
  Raul Rodriguez-Esteban, William Loging:
  Quantifying the complexity of medical research. 2918-2924

Applications Notes Genome Analysis

• 
  Donghyung Lee, T. Bernard Bigdeli, Brien P. Riley, Ayman H. Fanous, Silviu-Alin Bacanu:
  DIST: direct imputation of summary statistics for unmeasured SNPs. 2925-2927

Sequence Analysis

• 
  Federico Agostini, Andreas Zanzoni, Petr Klus, Domenica Marchese, Davide Cirillo, Gian Gaetano Tartaglia:
  catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. 2928-2930
• 
  Jan Grau, Jens Boch, Stefan Posch:
  TALENoffer: genome-wide TALEN off-target prediction. 2931-2932
• 
  Eric P. Nawrocki, Sean R. Eddy:
  Infernal 1.1: 100-fold faster RNA homology searches. 2933-2935
• 
  David Gordon, Phil Green:
  Consed: a graphical editor for next-generation sequencing. 2936-2937

Structural Bioinformatics

• 
  Lina Weinbrand, Assaf Avihoo, Danny Barash:
  RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. 2938-2940
• 
  Nikolai Hecker, Tim Wiegels, Andrew E. Torda:
  RNA secondary structure diagrams for very large molecules: RNAfdl. 2941-2942

Gene Expression

• 
  Shintaro Katayama, Virpi Töhönen, Sten Linnarsson, Juha Kere:
  SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. 2943-2945
• 
  Elizabeth A. McClellan, Perry D. Moerland, Peter J. van der Spek, Andrew Stubbs:
  NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data. 2946-2947

Data and Text Mining

• 
  Ryan M. Taylor, Jamison Dance, Russ J. Taylor, John T. Prince:
  Metriculator: quality assessment for mass spectrometry-based proteomics. 2948-2949

Databases and Ontologies

• 
  Hae-Min Park, Ju-Hyeong Park, Yoon-Woo Kim, Kyoung-Jin Kim, Hee-Jin Jeong, Kyoung-Soon Jang, Byung-Gee Kim, Yun-Gon Kim:
  The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire. 2950-2952
• 
  Renkai Ji, Qian Cong, Wenlin Li, Nick V. Grishin:
  M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. 2953-2954
• 
  Ilinca Tudose, Janna Hastings, Venkatesh Muthukrishnan, Gareth I. Owen, Steve Turner, Adriano Dekker, Namrata Kale, Marcus Ennis, Christoph Steinbeck:
  OntoQuery: easy-to-use web-based OWL querying. 2955-2957

Corrigendum

• 
  Christophe Lemetre, Quanwei Zhang, Zhengdong D. Zhang:
  SubNet: a Java application for subnetwork extraction. 2958

Volume 29, Number 23, December 2013

Review - Genome Analysis

• 
  Mark Howison, Felipe Zapata, Casey W. Dunn:
  Toward a statistically explicit understanding of de novo sequence assembly. 2959-2963

Original Papers - Genome Analysis

• 
  Gary K. Chen, Xiao Chang, Christina Curtis, Kai Wang:
  Precise inference of copy number alterations in tumor samples from SNP arrays. 2964-2970
• 
  Jikun Wu, Wenqian Zhang, Songbo Huang, Zengquan He, Yanbing Cheng, Jun Wang, Tak Wah Lam, Zhiyu Peng, Siu-Ming Yiu:
  SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads. 2971-2978
• 
  Haitham Ashoor, Aurélie Hérault, Aurélie Kamoun, François Radvanyi, Vladimir B. Bajic, Emmanuel Barillot, Valentina Boeva:
  HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. 2979-2986
• 
  Ashok Rajaraman, Eric Tannier, Cédric Chauve:
  FPSAC: fast phylogenetic scaffolding of ancient contigs. 2987-2994
• 
  Adam B. Olshen, Andrew C. Hsieh, Craig R. Stumpf, Richard A. Olshen, Davide Ruggero, Barry S. Taylor:
  Assessing gene-level translational control from ribosome profiling. 2995-3002
• 
  Brent S. Pedersen, Ivana V. Yang, Subhajyoti De:
  CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. 3003-3006

Sequence Analysis

• 
  Lauren J. Mills, William R. Pearson:
  Adjusting scoring matrices to correct overextended alignments. 3007-3013
• 
  Henrik Nordberg, Karan Bhatia, Kai Wang, Zhong Wang:
  BioPig: a Hadoop-based analytic toolkit for large-scale sequence data. 3014-3019

Phylogenetics

• 
  Miguel Arenas, Helena G. Dos Santos, David Posada, Ugo Bastolla:
  Protein evolution along phylogenetic histories under structurally constrained substitution models. 3020-3028

Structural Bioinformatics

• 
  Jan-Oliver Janda, Andreas Meier, Rainer Merkl:
  CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data. 3029-3035

Gene Expression

• 
  Young-Suk Lee, Arjun Krishnan, Qian Zhu, Olga G. Troyanskaya:
  Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. 3036-3044

Systems Biology

• 
  Naama Tepper, Tomer Shlomi:
  An integrated computational approach for metabolic flux analysis coupled with inference of tandem-MS collisional fragments. 3045-3052
• 
  David duVerle, Ichiro Takeuchi, Yuko Murakami-Tonami, Kenji Kadomatsu, Koji Tsuda:
  Discovering combinatorial interactions in survival data. 3053-3059
• 
  Yawwani Gunawardana, Mahesan Niranjan:
  Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes. 3060-3066
• 
  Carl Murie, Caroline Barette, Laurence Lafanechère, Robert Nadon:
  Single assay-wide variance experimental (SAVE) design for high-throughput screening. 3067-3072
• 
  David Gfeller, Olivier Michielin, Vincent Zoete:
  Shaping the interaction landscape of bioactive molecules. 3073-3079

Databases and Ontologies

• 
  Johan Nyström-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi:
  Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform. 3080-3086

Bioimage Informatics

• 
  Cemal Çagatay Bilgin, Sun Kim, Elle Leung, Hang Chang, Bahram Parvin:
  Integrated profiling of three dimensional cell culture models and 3D microscopy. 3087-3093

Applications Notes - Sequence Analysis

• 
  Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields, Catherine Mooney:
  CPPpred: prediction of cell penetrating peptides. 3094-3096
• 
  Weichun Huang, Rasiah Loganantharaj, Bryce Schroeder, David Fargo, Leping Li:
  PAVIS: a tool for Peak Annotation and Visualization. 3097-3099
• 
  Charles E. Robertson, J. Kirk Harris, Brandie D. Wagner, David Granger, Kathy Browne, Beth Tatem, Leah M. Feazel, Kristin Park, Norman R. Pace, Daniel N. Frank:
  Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. 3100-3101
• 
  Thomas Schnattinger, Uwe Schöning, Anita Marchfelder, Hans A. Kestler:
  RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments. 3102-3104

Systems Biology

• 
  Oksana Sorokina, Anatoly A. Sorokin, J. Douglas Armstrong, Vincent Danos:
  A simulator for spatially extended kappa models. 3105-3106

Volume 29, Number 24, December 2013

Editorial - Databases and Ontologies

• 
  Christian Theil Have, Lars Juhl Jensen:
  Are graph databases ready for bioinformatics? 3107-3108

Discovery note - Genome Analysis

• 
  Daudi Jjingo, Jianrong Wang, Andrew B. Conley, Victoria V. Lunyak, I. King Jordan:
  Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome. 3109-3112

Original Papers - Genome Analysis

• 
  Elizabeth Purdom, Christine Ho, Catherine S. Grasso, Michael Quist, Raymond J. Cho, Paul T. Spellman:
  Methods and challenges in timing chromosomal abnormalities within cancer samples. 3113-3120
• 
  Bernhard Haubold, Linda Krause, Thomas Horn, Peter Pfaffelhuber:
  An alignment-free test for recombination. 3121-3127
• 
  Pasi Rastas, Lars Paulin, Ilkka Hanski, Rainer Lehtonen, Petri Auvinen:
  Lep-MAP: fast and accurate linkage map construction for large SNP datasets. 3128-3134

Sequence Analysis

• 
  Lingyun Zou, Chonghan Nan, Fuquan Hu:
  Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles. 3135-3142
• 
  Tobias Marschall, Iman Hajirasouliha, Alexander Schönhuth:
  MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. 3143-3150

Structural Bioinformatics

• 
  Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
  BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. 3151-3157
• 
  Guang Qiang Dong, Hao Fan, Dina Schneidman-Duhovny, Ben M. Webb, Andrej Sali:
  Optimized atomic statistical potentials: assessment of protein interfaces and loops. 3158-3166

Gene Expression

• 
  Kourosh Zarringhalam, Ahmed Enayetallah, Alex Gutteridge, Ben Sidders, Daniel Ziemek:
  Molecular causes of transcriptional response: a Bayesian prior knowledge approach. 3167-3173

Systems Biology

• 
  Anastasia Deckard, Ron C. Anafi, John B. Hogenesch, Steven B. Haase, John Harer:
  Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. 3174-3180
• 
  Ciarán P. Fisher, Nicholas J. Plant, J. Bernadette Moore, Andrzej M. Kierzek:
  QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. 3181-3190
• 
  Kai-Cheng Hsu, Feng-Sheng Wang:
  Fuzzy optimization for detecting enzyme targets of human uric acid metabolism. 3191-3198

Data and Text Mining

• 
  Sven Degroeve, Lennart Martens:
  MS²PIP: a tool for MS/MS peak intensity prediction. 3199-3203

Databases and Ontologies

• 
  Tao Wang, Jie Liu, Li Shen, Julian Tonti-Filippini, Yun Zhu, Haiyang Jia, Ryan Lister, John W. Whitaker, Joseph R. Ecker, A. Harvey Millar, Bing Ren, Wei Wang:
  STAR: an integrated solution to management and visualization of sequencing data. 3204-3210
• 
  Magdalena Przydzial, Barun Bhhatarai, Amar Koleti, Uma Vempati, Stephan C. Schürer:
  GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. 3211-3219

Applications Notes - Genome Analysis

• 
  Melanie A. Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker, Michael Lawrence, Jason A. Hackney, Joshua S. Kaminker:
  ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses. 3220-3221
• 
  Yanbo Ye, Bo Wei, Lei Wen, Simon Rayner:
  BlastGraph: a comparative genomics tool based on BLAST and graph algorithms. 3222-3224

Sequence Analysis

• 
  Dadi Gao, Robert Middleton, John E. J. Rasko, William Ritchie:
  miREval 2.0: a web tool for simple microRNA prediction in genome sequences. 3225-3226
• 
  Xueqiu Lin, Deqiang Sun, Benjamin Rodriguez, Qian Zhao, Hanfei Sun, Yong Zhang, Wei Li:
  BSeQC: quality control of bisulfite sequencing experiments. 3227-3229

Structural Bioinformatics

• 
  Rui C. Chaves, Jean-Luc Pellequer:
  DockAFM: benchmarking protein structures by docking under AFM topographs. 3230-3231

Systems Biology

• 
  Jianguo Xia, Ngan H. Lyle, Matthew L. Mayer, Olga M. Pena, Robert E. W. Hancock:
  INVEX - a web-based tool for integrative visualization of expression data. 3232-3234

Data and Text Mining

• 
  Xiaojing Wang, Bing Zhang:
  customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search. 3235-3237
• 
  Wenchao Jiang, Pinghao Li, Shuang Wang, Yuan Wu, Meng Xue, Lucila Ohno-Machado, Xiaoqian Jiang:
  WebGLORE: a Web service for Grid LOgistic REgression. 3238-3240

Databases and Ontologies

• 
  Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach, Julio Saez-Rodriguez:
  BioServices: a common Python package to access biological Web Services programmatically. 3241-3242

Message from the ISCB - Databases and Ontologies

• 
  Burkhard Rost:
  ISCB: past-present perspective for the International Society for Computational Biology. 3243-3245
• 
  ISCB/SPRINGER series in computational biology. 3246-3247