Bioinformatics, Volume 30

Volume 30, Number 1, January 2014

Hitseq Papers Genome Analysis

• 
  Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna:
  Using Genome Query Language to uncover genetic variation. 1-8

Sequence Analysis

• 
  Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard:
  Specificity control for read alignments using an artificial reference genome-guided false discovery rate. 9-16
• 
  Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente:
  Further Steps in TANGO: improved taxonomic assignment in metagenomics. 17-23
• 
  Lilian Janin, Giovanna Rosone, Anthony J. Cox:
  Adaptive reference-free compression of sequence quality scores. 24-30
• 
  Rayan Chikhi, Paul Medvedev:
  Informed and automated k-mer size selection for genome assembly. 31-37
• 
  Daniel H. Huson, Chao Xie:
  A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA. 38-39

Original Papers Genome Analysis

• 
  David Hernández, Ryan Tewhey, Jean-Baptiste Veyrieras, Laurent Farinelli, Magne Østerås, Patrice François, Jacques Schrenzel:
  De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. 40-49
• 
  Noemi Andor, Julie V. Harness, Sabine Müller, Hans-Werner Mewes, Claudia Petritsch:
  EXPANDS: expanding ploidy and allele frequency on nested subpopulations. 50-60

Structural Bioinformatics

• 
  Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne Birmelé, Michele Borassi, Christophe Junot, Alberto Marchetti-Spaccamela, Andrea Marino, Leen Stougie, Fabien Jourdan, Pierluigi Crescenzi, Vincent Lacroix, Marie-France Sagot:
  Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. 61-70
• 
  Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song:
  Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. 71-80

Systems Biology

• 
  Yijie Wang, Xiaoning Qian:
  Functional module identification in protein interaction networks by interaction patterns. 81-93
• 
  Yungang Xu, Maozu Guo, Xiaoyan Liu, Chun-yu Wang, Yang Liu:
  Inferring the soybean (Glycine max) microRNA functional network based on target gene network. 94-103

Data and Text Mining

• 
  Songhua Xu, Hong-Jun Yoon, Georgia D. Tourassi:
  A user-oriented web crawler for selectively acquiring online content in e-health research. 104-114

Applications Notes Genome Analysis

• 
  Sebastian Bartschat, Stephanie Kehr, Hakim Tafer, Peter F. Stadler, Jana Hertel:
  snoStrip: a snoRNA annotation pipeline. 115-116

Sequence Analysis

• 
  Armando J. Pinho, Diogo Pratas:
  MFCompress: a compression tool for FASTA and multi-FASTA data. 117-118
• 
  André Schumacher, Luca Pireddu, Matti Niemenmaa, Aleksi Kallio, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko:
  SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. 119-120
• 
  Christoph Gille, Birgit Weyand, Andreas Gille:
  Sequence alignment visualization in HTML5 without Java. 121-122

Phylogenetics

• 
  Michael J. Landis, Trevor Bedford:
  Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. 123-124

Structural Bioinformatics

• 
  Shannon L. N. Mayne, Hugh-George Patterton:
  AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes. 125-126

Gene Expression

• 
  Thomas Sandmann, Sarah K. Kummerfeld, Robert Gentleman, Richard Bourgon:
  gCMAP: user-friendly connectivity mapping with R. 127-128

Systems Biology

• 
  Maxwell Lewis Neal, Michal Galdzicki, J. T. Gallimore, Herbert M. Sauro:
  A C library for retrieving specific reactions from the BioModels database. 129-130
• 
  Matthias Bock, Till Scharp, Chaitanya Talnikar, Edda Klipp:
  BooleSim: an interactive Boolean network simulator. 131-132
• 
  Grant Hughes, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina J. Kechris:
  MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. 133-134
• 
  Minji Jeon, Sunwon Lee, Kyubum Lee, Aik Choon Tan, Jaewoo Kang:
  BEReX: Biomedical Entity-Relationship eXplorer. 135-136
• 
  Tomasz Jetka, Agata Charzynska, Anna Gambin, Michael P. H. Stumpf, Michal Komorowski:
  StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. 137-138

Databases and Ontologies

• 
  Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir:
  Pattern search in BioPAX models. 139-140
• 
  Jianfei Hu, Hee-Sool Rho, Robert H. Newman, Jin Zhang, Heng Zhu, Jiang Qian:
  PhosphoNetworks: a database for human phosphorylation networks. 141-142

Message from the ISCB Databases and Ontologies

• 
  Burkhard Rost:
  ISCB: past-present perspective for the International Society for Computational Biology. 143-145
• 
  Andreas W. M. Dress, Michal Linial, Olga G. Troyanskaya, Martin Vingron:
  ISCB/SPRINGER series in computational biology. 146-147
• 
  Jim Cavalcoli, Lonnie R. Welch, Bruce J. Aronow, Sorin Draghici, Daisuke Kihara:
  The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. 148-149

Volume 30, Number 2, January 2014

Genome Analysis

• 
  Laurence O. W. Wilson, Andrew Spriggs, Jennifer M. Taylor, Aude M. Fahrer:
  A novel splicing outcome reveals more than 2000 new mammalian protein isoforms. 151-156
• 
  Dandi Qiao, Michael H. Cho, Heide Loehlein Fier, Per S. Bakke, Amund Gulsvik, Edwin K. Silverman, Christoph Lange:
  On the simultaneous association analysis of large genomic regions: a massive multi-locus association test. 157-164
• 
  Sebastian M. Waszak, Helena Kilpinen, Andreas R. Gschwind, Andrea Orioli, Sunil K. Raghav, Robert M. Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen, Nouria Hernandez, Alexandre Reymond, Emmanouil T. Dermitzakis, Bart Deplancke:
  Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. 165-171
• 
  Longjie Cheng, Yu Zhu:
  A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data. 172-179

Gene Expression

• 
  Ernest Turro, William J. Astle, Simon Tavaré:
  Flexible analysis of RNA-seq data using mixed effects models. 180-188
• 
  Kevin Lim, Limsoon Wong:
  Finding consistent disease subnetworks using PFSNet. 189-196
• 
  Yaqing Si, Peng Liu, Pinghua Li, Thomas P. Brutnell:
  Model-based clustering for RNA-seq data. 197-205

Genetics and Population Analysis

• 
  Buhm Han, Eun Yong Kang, Soumya Raychaudhuri, Paul I. W. de Bakker, Eleazar Eskin:
  Fast pairwise IBD association testing in genome-wide association studies. 206-213

Systems Biology

• 
  Simina M. Boca, Rashmi Sinha, Amanda J. Cross, Steven C. Moore, Joshua N. Sampson:
  Testing multiple biological mediators simultaneously. 214-220
• 
  Mikael Sunnåker, Elías Zamora-Sillero, Adrián López García de Lomana, Florian Rudroff, Uwe Sauer, Jörg Stelling, Andreas Wagner:
  Topological augmentation to infer hidden processes in biological systems. 221-227
• 
  Marianna De Santis, Francesco Rinaldi, Emmanuela Falcone, Stefano Lucidi, Giulia Piaggio, Aymone Gurtner, Lorenzo Farina:
  Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes. 228-233

Data and Text Mining

• 
  Attila Kertész-Farkas, Beáta Reiz, Roberto Vera, Michael P. Myers, Sándor Pongor:
  PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. 234-241
• 
  Mohammad Shahrokh Esfahani, Edward R. Dougherty:
  Effect of separate sampling on classification accuracy. 242-250

Databases and Ontologies

• 
  Mandy L. Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud:
  Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. 251-257
• 
  Álvaro Sebastián, Bruno Contreras-Moreira:
  footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. 258-265

Bioimage Informatics

• 
  Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye:
  Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. 266-273

Sequence Analysis

• 
  Nicolas Terrapon, January 3rd Weiner, Sonja Grath, Andrew D. Moore, Erich Bornberg-Bauer:
  Rapid similarity search of proteins using alignments of domain arrangements. 274-281

Applications Notes - Sequence Analysis

• 
  Andrew D. Moore, Andreas Held, Nicolas Terrapon, January 3rd Weiner, Erich Bornberg-Bauer:
  DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins. 282-283
• 
  Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chavez:
  MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. 284-286
• 
  João F. Matias Rodrigues, Christian von Mering:
  HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. 287-288

Gene Expression

• 
  Toma Tebaldi, Erik Dassi, Galena Kostoska, Gabriella Viero, Alessandro Quattrone:
  tRanslatome: an R/Bioconductor package to portray translational control. 289-291

Systems Biology

• 
  Michael L. Blinov, James C. Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Fei Gao, Frank Morgan, Li Ye, Anuradha Lakshminarayana, Ion I. Moraru, Leslie M. Loew:
  Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. 292-294

Databases and Ontologies

• 
  Luke E. Ulrich, Igor B. Zhulin:
  SeqDepot: streamlined database of biological sequences and precomputed features. 295-297
• 
  Rodrigo Ochoa, Mark Davies, George Papadatos, Francis Atkinson, John P. Overington:
  myChEMBL: a virtual machine implementation of open data and cheminformatics tools. 298-300

Volume 30, Number 3, February 2014

Discovery Notes - Gene Expression

• 
  Yuwen Liu, Jie Zhou, Kevin P. White:
  RNA-seq differential expression studies: more sequence or more replication? 301-304

Systems Biology

• 
  Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-yu Zhang:
  Identification of transcription factors for drug-associated gene modules and biomedical implications. 305-309

Original Papers Genome Analysis

• 
  Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi:
  Spatial regulation dominates gene function in the ganglia chain. 310-316

Sequence Analysis

• 
  Kazunori D. Yamada, Kentaro Tomii:
  Revisiting amino acid substitution matrices for identifying distantly related proteins. 317-325

Structural Bioinformatics

• 
  Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra:
  Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. 326-334
• 
  Douglas E. V. Pires, David B. Ascher, Tom L. Blundell:
  mCSM: predicting the effects of mutations in proteins using graph-based signatures. 335-342
• 
  Luke Day, Ouala Abdelhadi Ep Souki, Andreas Alexander Albrecht, Kathleen Steinhöfel:
  Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs. 343-352
• 
  Hamidreza Khataee, Alan Wee-Chung Liew:
  A mathematical model describing the mechanical kinetics of kinesin stepping. 353-359

Gene Expression

• 
  Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko:
  Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. 360-368
• 
  Chuan Gao, Nicole L. Tignor, Jacqueline Salit, Yael Strulovici-Barel, Neil R. Hackett, Ronald G. Crystal, Jason G. Mezey:
  HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. 369-376
• 
  Hari Krishna Yalamanchili, Bin Yan, Mulin Jun Li, Jing Qin, Zhongying Zhao, Francis Y. L. Chin, Junwen Wang:
  DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment. 377-383

Genetics and Population Analysis

• 
  Barbara Di Camillo, Francesco Sambo, Gianna Toffolo, Claudio Cobelli:
  ABACUS: an entropy-based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. 384-391

Systems Biology

• 
  Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen:
  Protein-driven inference of miRNA-disease associations. 392-397
• 
  Jianlong Peng, Jing Lu, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
  In silico site of metabolism prediction for human UGT-catalyzed reactions. 398-405
• 
  Matan Bodaker, Eran Meshorer, Eduardo Mitrani, Yoram Louzoun:
  Genes related to differentiation are correlated with the gene regulatory network structure. 406-413
• 
  Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch:
  Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. 414-419

Bioimage Informatics

• 
  Violeta N. Kovacheva, Adnan Mujahid Khan, Michael Khan, David B. A. Epstein, Nasir M. Rajpoot:
  DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data. 420-427

Applications Notes - Genome Analysis

• 
  Tiffany J. Morris, Lee M. Butcher, Andrew Feber, Andrew E. Teschendorff, Ankur R. Chakravarthy, Tomasz K. Wojdacz, Stephan Beck:
  ChAMP: 450k Chip Analysis Methylation Pipeline. 428-430
• 
  Bai Zhang, Xuchu Hou, Xiguo Yuan, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Roger R. Wang, Yi Fu, Subha Madhavan, Yue Joseph Wang, Guoqiang Yu:
  AISAIC: a software suite for accurate identification of significant aberrations in cancers. 431-433

Sequence Analysis

• 
  Guan-Zheng Luo, Wei Yang, Ying-Ke Ma, Xiu-Jie Wang:
  ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. 434-436

Structural Bioinformatics

• 
  Esteban López-Camacho, María Jesús García-Godoy, Antonio J. Nebro, José Francisco Aldana Montes:
  jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework. 437-438
• 
  Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel:
  MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. 439-441

Genetics and Population Analysis

• 
  Biao Li, Gao T. Wang, Suzanne M. Leal:
  PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants. 442-444

Data and Text Mining

• 
  Zeliha Görmez, Burcu Bakir-Gungor, Mahmut Samil Sagiroglu:
  HomSI: a homozygous stretch identifier from next-generation sequencing data. 445-447

Volume 30, Number 4, February 2014

Sequence Analysis

• 
  Olga Tanaseichuk, James Borneman, Tao Jiang:
  Phylogeny-based classification of microbial communities. 449-456
• 
  Ruslan A. Soldatov, Svetlana V. Vinogradova, Andrey A. Mironov:
  RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. 457-463
• 
  Francisco Fernandes, Ana T. Freitas:
  slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array. 464-471
• 
  Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou:
  Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. 472-479
• 
  Song Yan, Yun Li:
  BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing. 480-487

Phylogenetics

• 
  Nicolas Lartillot:
  A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data. 488-496

Structural Bioinformatics

• 
  Hua Zhang, Lukasz A. Kurgan:
  Sequence-based Gaussian network model for protein dynamics. 497-505

Gene Expression

• 
  Chen Suo, Stefano Calza, Agus Salim, Yudi Pawitan:
  Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. 506-513
• 
  Hongjie Zhu, Man Luo:
  Chemical structure informing statistical hypothesis testing in metabolomics. 514-522

Systems Biology

• 
  Andreas Krämer, Jeff Green, Jack Pollard Jr., Stuart Tugendreich:
  Causal analysis approaches in Ingenuity Pathway Analysis. 523-530
• 
  Ferhat Alkan, Cesim Erten:
  BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. 531-539
• 
  Jialu Hu, Birte Kehr, Knut Reinert:
  NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. 540-548
• 
  Cong Zhou, Michael J. Walker, Andrew J. K. Williamson, Andrew Pierce, Carlo Berzuini, Caroline Dive, Anthony D. Whetton:
  A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data. 549-558

Data and Text Mining

• 
  Tomaz Hocevar, Janez Demsar:
  A combinatorial approach to graphlet counting. 559-565

Applications Notes - Sequence Analysis

• 
  Richard M. Leggett, Bernardo J. Clavijo, Leah Clissold, Matthew D. Clark, Mario Cáccamo:
  NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. 566-568

Structural Bioinformatics

• 
  José Colmenares, Jesús Ortiz, Walter Rocchia:
  GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. 569-570

Gene Expression

• 
  Nicolas Jung, Frédéric Bertrand, Seiamak Bahram, Laurent Vallat, Myriam Maumy-Bertrand:
  Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network. 571-573
• 
  Raghavendra Hosur, Suzanne Szak, Alice Thai, Norm Allaire, Jadwiga R. Bienkowska:
  ProbeSelect: selecting differentially expressed probes in transcriptional profile data. 574-575

Genetics and Population Analysis

• 
  Darren Kessner, John Novembre:
  forqs: forward-in-time simulation of recombination, quantitative traits and selection. 576-577
• 
  Michel Petitjean, Anne Vanet:
  VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations. 578-580

Systems Biology

• 
  Jiarui Zhou, Ralf J. M. Weber, James William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn, Shan He, Mark R. Viant:
  HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries. 581-583
• 
  Longfei Mao, Wynand S. Verwoerd:
  ORCA: a COBRA toolbox extension for model-driven discovery and analysis. 584-585
• 
  Cheng Chang, Jiyang Zhang, Mingfei Han, Jie Ma, Wei Zhang, Songfeng Wu, Kehui Liu, Hongwei Xie, Fuchu He, Yunping Zhu:
  SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. 586-587

Data and Text Mining

• 
  Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha:
  HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data. 588-589

Databases and Ontologies

• 
  Muhammad A. Shah, Emily Denton, Lihua Liu, Matthieu Schapira:
  ChromoHub V2: cancer genomics. 590-592
• 
  Dennis Bromley, Steven J. Rysavy, Robert Su, Rudesh D. Toofanny, Tom Schmidlin, Valerie Daggett:
  DIVE: a data intensive visualization engine. 593-595

Erratum - 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. 596

Volume 30, Number 5, March 2014

Discovery note - Genome Analysis

• 
  Balamurugan Palanisamy, Rajasekaran Ekambaram, Klaus Heese:
  Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite Plasmodium falciparum 3D7. 597-600

Original Papers - Genome Analysis

• 
  Douglas D. Baumann, Rebecca W. Doerge:
  Robust adjustment of sequence tag abundance. 601-605
• 
  Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard:
  GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. 606-613
• 
  Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis:
  PEAR: a fast and accurate Illumina Paired-End reAd mergeR. 614-620
• 
  Yue Li, Anna Goldenberg, Ka-Chun Wong, Zhaolei Zhang:
  A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. 621-628

Sequence Analysis

• 
  Luis Miguel Rodriguez-Rojas, Konstantinos T. Konstantinidis:
  Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. 629-635
• 
  Matthew Levinson, Qing Zhou:
  A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes. 636-643
• 
  Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp:
  ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. 644-651
• 
  Hongseok Tae, Dong-Yun Kim, John McCormick, Robert E. Settlage, Harold R. Garner:
  Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs. 652-659

Structural Bioinformatics

• 
  Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik:
  FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. 660-667
• 
  Giuseppe Maccari, Giulia L. B. Spampinato, Valentina Tozzini:
  SecStAnT: secondary structure analysis tool for data selection, statistics and models building. 668-674

Gene Expression

• 
  Ben Teng, Ting Huang, Zengyou He:
  Decoy-free protein-level false discovery rate estimation. 675-681
• 
  David A. Liebner, Kun Huang, Jeffrey D. Parvin:
  MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples. 682-689

Genetics and Population Analysis

• 
  Marina Evangelou, Frank Dudbridge, Lorenz Wernisch:
  Two novel pathway analysis methods based on a hierarchical model. 690-697

Data and Text Mining

• 
  Emily Rose Holzinger, Scott M. Dudek, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie:
  ATHENA: the analysis tool for heritable and environmental network associations. 698-705
• 
  Tomomi Ichimiya, Shoko Nishihara, Sayaka Takase-Yoden, Hiroshi Kida, Kiyoko F. Aoki-Kinoshita:
  Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection. 706-711
• 
  Joseph Geraci, Moyez Dharsee, Paulo A. S. Nuin, Alexandria Haslehurst, Madhuri Koti, Harriet E. Feilotter, Kenneth R. Evans:
  Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems. 712-718
• 
  Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier:
  Mouse model phenotypes provide information about human drug targets. 719-725

Bioimage Informatics

• 
  Johannes Stegmaier, Maryam Shahid, Masanari Takamiya, Lixin Yang, Sepand Rastegar, Markus Reischl, Uwe Strähle, Ralf Mikut:
  Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. 726-733

Applications Notes - Sequence Analysis

• 
  Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov:
  orthAgogue: an agile tool for the rapid prediction of orthology relations. 734-736

Systems Biology

• 
  Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu:
  iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. 737-739

Databases and Ontologies

• 
  Sébastien Harispe, Sylvie Ranwez, Stefan Janaqi, Jacky Montmain:
  The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. 740-742

Letter to the Editor - Genetics and Population Analysis

• 
  Eric C. Anderson, Thomas C. Ng:
  Comment on 'Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching'. 743-745

Volume 30, Number 6, March 2014

Discovery note - Data and Text Mining

• 
  Gong-Hua Li, Jing-Fei Huang:
  Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer. 748-752

Original Papers - Genome Analysis

• 
  Chandler Zuo, Sündüz Keles:
  A statistical framework for power calculations in ChIP-seq experiments. 753-760
• 
  Jung-Hsien Chiang, Chan-Hsien Lin:
  NCS: incorporating positioning data to quantify nucleosome stability in yeast. 761-767

Sequence Analysis

• 
  Carson Holt, Bojan Losic, Deepa Pai, Zhen Zhao, Quang Trinh, Sujata Syam, Niloofar Arshadi, Gun Ho Jang, Johar Ali, Tim Beck, John D. McPherson, Lakshmi B. Muthuswamy:
  WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing. 768-774
• 
  Zizhen Yao, Kyle L. MacQuarrie, Abraham P. Fong, Stephen J. Tapscott, Walter L. Ruzzo, Robert Gentleman:
  Discriminative motif analysis of high-throughput dataset. 775-783

Structural Bioinformatics

• 
  Frédéric Guyon, Pierre Tufféry:
  Fast protein fragment similarity scoring using a Binet-Cauchy kernel. 784-791
• 
  Lydia Benkaidali, François André, Boubekeur Maouche, Pridi Siregar, Mohamed Benyettou, François Maurel, Michel Petitjean:
  Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models. 792-800

Gene Expression

• 
  Yufei Xiao, Tzu-Hung Hsiao, Uthra Suresh, Hung-I Harry Chen, Xiaowu Wu, Steven E. Wolf, Yidong Chen:
  A novel significance score for gene selection and ranking. 801-807
• 
  Pengyi Yang, Ellis Patrick, Shi-Xiong Tan, Daniel J. Fazakerley, James G. Burchfield, Christopher Gribben, Matthew J. Prior, David E. James, Yee Hwa Yang:
  Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. 808-814

Genetics and Population Analysis

• 
  Koichiro Doi, Taku Monjo, Pham H. Hoang, Jun Yoshimura, Hideaki Yurino, Jun Mitsui, Hiroyuki Ishiura, Yuji Takahashi, Yaeko Ichikawa, Jun Goto, Shoji Tsuji, Shinichi Morishita:
  Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. 815-822

Systems Biology

• 
  Pengzhan Hu, Zhongchao Shen, Haibo Tu, Li Zhang, Tieliu Shi:
  Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach. 823-830
• 
  Tanya P. Garcia, Samuel Müller, Raymond J. Carroll, Rosemary L. Walzem:
  Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data. 831-837
• 
  José A. Seoane, Ian N. M. Day, Tom R. Gaunt, Colin Campbell:
  A pathway-based data integration framework for prediction of disease progression. 838-845
• 
  Ivan Dimitrov, Lyudmila Naneva, Irini A. Doytchinova, Ivan Bangov:
  AllergenFP: allergenicity prediction by descriptor fingerprints. 846-851
• 
  Xiangtian Yu, Guojun Li, Luonan Chen:
  Prediction and early diagnosis of complex diseases by edge-network. 852-859
• 
  Senol Isci, Haluk Dogan, Cengizhan Ozturk, Hasan H. Otu:
  Bayesian network prior: network analysis of biological data using external knowledge. 860-867

Data and Text Mining

• 
  Sampo Pyysalo, Sophia Ananiadou:
  Anatomical entity mention recognition at literature scale. 868-875

Databases and Ontologies

• 
  Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann:
  The functional therapeutic chemical classification system. 876-883

Applications Notes - Sequence Analysis

• 
  Ulrich Omasits, Christian H. Ahrens, Sebastian Müller, Bernd Wollscheid:
  Protter: interactive protein feature visualization and integration with experimental proteomic data. 884-886
• 
  Sutharzan Sreeskandarajan, Michelle M. Flowers, John E. Karro, Chun Liang:
  A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences. 887-888

Structural Bioinformatics

• 
  Anton A. Polyansky, Anton O. Chugunov, Pavel E. Volynsky, Nikolay A. Krylov, Dmitry E. Nolde, Roman G. Efremov:
  PREDDIMER: a web server for prediction of transmembrane helical dimers. 889-890

Gene Expression

• 
  Xavier Rogé, Xuegong Zhang:
  RNAseqViewer: visualization tool for RNA-Seq data. 891-892

Systems Biology

• 
  Joram M. Posma, Steven L. Robinette, Elaine Holmes, Jeremy K. Nicholson:
  MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. 893-895

Data and Text Mining

• 
  Daniel Jaeger, Johannes Barth, Anna Niehues, Christian Fufezan:
  pyGCluster, a novel hierarchical clustering approach. 896-898

Volume 30, Number 7, April 2014

Discovery note - Structural Bioinformatics

• 
  Kenneth B. Schou, Jens S. Andersen, Lotte B. Pedersen:
  A divergent calponin homology (NN-CH) domain defines a novel family: implications for evolution of ciliary IFT complex B proteins. 899-902

Systems Biology

• 
  Lucian P. Smith, Erik Butterworth, James B. Bassingthwaighte, Herbert M. Sauro:
  SBML and CellML translation in Antimony and JSim. 903-907

Original Papers - Genome Analysis

• 
  Nha Nguyen, An P. N. Vo, Kyoung-Jae Won:
  A wavelet-based method to exploit epigenomic language in the regulatory region. 908-914
• 
  Yu Qian, Brian L. Browning, Sharon R. Browning:
  Efficient clustering of identity-by-descent between multiple individuals. 915-922

Sequence Analysis

• 
  Yang Liao, Gordon K. Smyth, Wei Shi:
  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. 923-930
• 
  Dan Ofer, Michal Linial:
  NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes. 931-940
• 
  Ronak Y. Patel, Gary D. Stormo:
  Discriminative motif optimization based on perceptron training. 941-948

Structural Bioinformatics

• 
  Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li:
  Fingerprinting protein structures effectively and efficiently. 949-955

Gene Expression

• 
  Amit G. Deshwar, Quaid Morris:
  PLIDA: cross-platform gene expression normalization using perturbed topic models. 956-961
• 
  Krzysztof Polanski, Johanna Rhodes, Claire Hill, Peijun Zhang, Dafyd J. Jenkins, Steven J. Kiddle, Aleksey Jironkin, Jim Beynon, Vicky Buchanan-Wollaston, Sascha Ott, Katherine J. Denby:
  Wigwams: identifying gene modules co-regulated across multiple biological conditions. 962-970
• 
  Hadi Jorjani, Mihaela Zavolan:
  TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. 971-974

Systems Biology

• 
  Jon Pey, Francisco J. Planes, John E. Beasley:
  Refining carbon flux paths using atomic trace data. 975-980
• 
  Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa:
  FastPros: screening of reaction knockout strategies for metabolic engineering. 981-987
• 
  Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye:
  BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. 988-995

Bioimage Informatics

• 
  Lin Yang, Xin Qi, Fuyong Xing, Tahsin M. Kurç, Joel H. Saltz, David J. Foran:
  Parallel content-based sub-image retrieval using hierarchical searching. 996-1002

Applications Notes - Genome Analysis

• 
  Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik, W. James Kent:
  Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. 1003-1005
• 
  Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean-Pierre A. Kocher, Liguo Wang:
  CrossMap: a versatile tool for coordinate conversion between genome assemblies. 1006-1007
• 
  Daniel R. Zerbino, Nathan Johnson, Thomas Juettemann, Steven P. Wilder, Paul Flicek:
  WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. 1008-1009

Sequence Analysis

• 
  Jaebum Kim, Jian Ma:
  PSAR-Align: improving multiple sequence alignment using probabilistic sampling. 1010-1012
• 
  Hue Vuong, Robert M. Stephens, Natalia Volfovsky:
  AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations. 1013-1014
• 
  Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl, Li Ding:
  MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. 1015-1016

Phylogenetics

• 
  Sebastián Duchêne, Martyna Molak, Simon Y. W. Ho:
  ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. 1017-1019
• 
  Nicolas Rodrigue, Nicolas Lartillot:
  Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package. 1020-1021

Structural Bioinformatics

• 
  Silvia Caprari, Daniele Toti, Le Viet Hung, Maurizio Di Stefano, Fabio Polticelli:
  ASSIST: a fast versatile local structural comparison tool. 1022-1024

Gene Expression

• 
  Eric Wu, Tracy Nance, Stephen B. Montgomery:
  SplicePlot: a utility for visualizing splicing quantitative trait loci. 1025-1026

Genetics and Population Analysis

• 
  Ida Moltke, Anders Albrechtsen:
  RelateAdmix: a software tool for estimating relatedness between admixed individuals. 1027-1028

Systems Biology

• 
  Charles Winterhalter, Pawel Widera, Natalio Krasnogor:
  JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. 1029-1030
• 
  Xiaoquan Su, Xuetao Wang, Gongchao Jing, Kang Ning:
  GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU. 1031-1033
• 
  Jan Taubert, Keywan Hassani-Pak, Nathalie Castells-Brooke, Christopher J. Rawlings:
  Ondex Web: web-based visualization and exploration of heterogeneous biological networks. 1034-1035
• 
  John T. Sauls, Joerg M. Buescher:
  Assimilating genome-scale metabolic reconstructions with modelBorgifier. 1036-1038

Data and Text Mining

• 
  Anabel Usie, Rui Alves, Francesc Solsona, Miguel Vazquez, Alfonso Valencia:
  CheNER: chemical named entity recognizer. 1039-1040
• 
  Rodrigo Aldecoa, Ignacio Marín:
  SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization. 1041-1042

Databases and Ontologies

• 
  Mengyuan Fan, Hong Sang Low, Hufeng Zhou, Markus R. Wenk, Limsoon Wong:
  LipidGO: database for lipid-related GO terms and applications. 1043-1044
• 
  Changqing Zhang, Guangping Li, Shinong Zhu, Shuo Zhang, Jinggui Fang:
  tasiRNAdb: a database of ta-siRNA regulatory pathways. 1045-1046

Letter to the Editor - Genome Analysis

• 
  Nestoras Karathanasis, Ioannis Tsamardinos, Panayiota Poirazi:
  Don't use a cannon to kill the ... miRNA mosquito. 1047-1048

Volume 30, Number 8, April 2014

Original Papers - Genome Analysis

• 
  Xihao Hu, Thomas K. F. Wong, Zhi John Lu, Ting-Fung Chan, Terrence Chi-Kong Lau, Siu-Ming Yiu, Kevin Y. Yip:
  Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. 1049-1055
• 
  Lei Bao, Minya Pu, Karen Messer:
  AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. 1056-1063
• 
  Jan Schröder, Arthur L. Hsu, Samantha E. Boyle, Geoff MacIntyre, Marek Cmero, Richard W. Tothill, Ricky W. Johnstone, Mark Shackleton, Anthony T. Papenfuss:
  Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. 1064-1072
• 
  Wanding Zhou, Tenghui Chen, Hao Zhao, Agda Karina Eterovic, Funda Meric-Bernstam, Gordon B. Mills, Ken Chen:
  Bias from removing read duplication in ultra-deep sequencing experiments. 1073-1080

Sequence Analysis

• 
  Kamil S. Jaron, Jirí C. Moravec, Natália Martínková:
  SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. 1081-1086
• 
  Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray:
  D-Tailor: automated analysis and design of DNA sequences. 1087-1094
• 
  Atsushi Kurotani, Alexander A. Tokmakov, Yutaka Kuroda, Yasuo Fukami, Kazuo Shinozaki, Tetsuya Sakurai:
  Correlations between predicted protein disorder and post-translational modifications in plants. 1095-1103
• 
  Josep Gregori, Miquel Salicru, Esteban Domingo, Alex Sánchez-Pla, Juan I. Esteban, Francisco Rodríguez-Frías, Josep Quer:
  Inference with viral quasispecies diversity indices: clonal and NGS approaches. 1104-1111
• 
  Ka-Chun Wong, Zhaolei Zhang:
  SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences. 1112-1119
• 
  Ha X. Dang, Christopher B. Lawrence:
  Allerdictor: fast allergen prediction using text classification techniques. 1120-1128

Phylogenetics

• 
  Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin:
  Optimization strategies for fast detection of positive selection on phylogenetic trees. 1129-1137

Structural Bioinformatics

• 
  Derek J. Pitman, Christian D. Schenkelberg, Yao-ming Huang, Frank D. Teets, Daniel J. DiTursi, Christopher Bystroff:
  Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. 1138-1145

Gene Expression

• 
  Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro:
  Estimation of fluorescence-tagged RNA numbers from spot intensities. 1146-1153
• 
  Hans-Ulrich Klein, Martin Schäfer, Bo T. Porse, Marie S. Hasemann, Katja Ickstadt, Martin Dugas:
  Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models. 1154-1162

Systems Biology

• 
  Ming Wu, Christina Chan:
  Prediction of therapeutic microRNA based on the human metabolic network. 1163-1171

Applications Notes - Genome Analysis

• 
  Hamid Younesy, Torsten Möller, Alireza Heravi Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones:
  ALEA: a toolbox for allele-specific epigenomics analysis. 1172-1174
• 
  Jianchao Yao, Kelvin Xi Zhang, Melissa Kramer, Matteo Pellegrini, W. Richard McCombie:
  FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. 1175-1176
• 
  Luis Cebamanos, Alan Gray, I. Stewart, Albert Tenesa:
  Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures. 1177-1179
• 
  An Xiao, Zhenchao Cheng, Lei Kong, Zuoyan Zhu, Shuo Lin, Ge Gao, Bo Zhang:
  CasOT: a genome-wide Cas9/gRNA off-target searching tool. 1180-1182

Gene Expression

• 
  Emmanuel Dimont, Oliver Hofmann, Shannan J. Ho Sui, Alistair R. R. Forrest, Hideya Kawaji, Winston Hide:
  CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. 1183-1184

Genetics and Population Analysis

• 
  Peter J. van der Most, Ahmad Vaez, Bram P. Prins, M. Loretto Munoz, Harold Snieder, Behrooz Z. Alizadeh, Ilja M. Nolte:
  QCGWAS: A flexible R package for automated quality control of genome-wide association results. 1185-1186
• 
  Jean-Marie Cornuet, Pierre Pudlo, Julien Veyssier, Alexandre Dehne-Garcia, Mathieu Gautier, Raphaël Leblois, Jean-Michel Marin, Arnaud Estoup:
  DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. 1187-1189

Systems Biology

• 
  Daogang Guan, Jiaofang Shao, Youping Deng, Panwen Wang, Zhongying Zhao, Yan Liang, Junwen Wang, Bin Yan:
  CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. 1190-1192

Volume 30, Number 9, May 2014

Discovery note - Genome Analysis

• 
  Joseph P. Cornish, Neus Sanchez-Alberola, Patrick K. O'Neill, Ronald O'Keefe, Jameel Gheba, Ivan Erill:
  Characterization of the SOS meta-regulon in the human gut microbiome. 1193-1197

Original Papers - Genome Analysis

• 
  Moritz Gerstung, Elli Papaemmanuil, Peter J. Campbell:
  Subclonal variant calling with multiple samples and prior knowledge. 1198-1204

Sequence Analysis

• 
  Hannes Planatscher, Frederik Weiß, David Eisen, B. H. J. van den Berg, Andreas Zell, Thomas Joos, Oliver Poetz:
  Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting. 1205-1213
• 
  Chengxi Ye, Chiaowen Hsiao, Héctor Corrada Bravo:
  BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution. 1214-1219
• 
  Gorka Prieto, Asier Fullaondo, Jose A. Rodriguez:
  Prediction of nuclear export signals using weighted regular expressions (Wregex). 1220-1227
• 
  Jared T. Simpson:
  Exploring genome characteristics and sequence quality without a reference. 1228-1235
• 
  Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex L. Mitchell, Gift Nuka, Sebastien Pesseat, Antony F. Quinn, Amaia Sangrador-Vegas, Maxim Scheremetjew, Siew-Yit Yong, Rodrigo Lopez, Sarah Hunter:
  InterProScan 5: genome-scale protein function classification. 1236-1240

Phylogenetics

• 
  Linda Dib, Daniele Silvestro, Nicolas Salamin:
  Evolutionary footprint of coevolving positions in genes. 1241-1249

Structural Bioinformatics

• 
  Ali Esmaili-Taheri, Mohammad Ganjtabesh, Morteza Mohammad Noori:
  Evolutionary solution for the RNA design problem. 1250-1258
• 
  Noël Malod-Dognin, Natasa Przulj:
  GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity. 1259-1265

Genetics and Population Analysis

• 
  Richard Durbin:
  Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). 1266-1272

Systems Biology

• 
  Stefan Maetschke, Mark A. Ragan:
  Characterizing cancer subtypes as attractors of Hopfield networks. 1273-1279

Data and Text Mining

• 
  Pierre Mahé, Maud Arsac, Sonia Chatellier, Valérie Monnin, Nadine Perrot, Sandrine Mailler, Victoria Girard, Mahendrasingh Ramjeet, Jérémy Surre, Bruno Lacroix, Alex van Belkum, Jean-Baptiste Veyrieras:
  Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum. 1280-1286

Applications Notes - Genome Analysis

• 
  Burcu Bakir-Gungor, Ece Egemen, Osman Ugur Sezerman:
  PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data. 1287-1289
• 
  David Sims, Nicholas E. Ilott, Stephen N. Sansom, Ian M. Sudbery, Jethro S. Johnson, Katherine A. Fawcett, Antonio J. Berlanga-Taylor, Sebastian Luna-Valero, Chris P. Ponting, Andreas Heger:
  CGAT: computational genomics analysis toolkit. 1290-1291
• 
  Samuel A. Assefa, Mark D. Preston, Susana G. Campino, Harold Ocholla, Colin J. Sutherland, Taane G. Clark:
  estMOI: estimating multiplicity of infection using parasite deep sequencing data. 1292-1294
• 
  Xin Lu, Roman K. Thomas, Martin Peifer:
  CGARS: cancer genome analysis by rank sums. 1295-1296
• 
  Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jing-Fa Xiao:
  PanGP: A tool for quickly analyzing bacterial pan-genome profile. 1297-1299

Sequence Analysis

• 
  Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch:
  Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. 1300-1301
• 
  Michael T. McCarthy, Christopher A. O'Callaghan:
  PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data. 1302-1304
• 
  Glen Stecher, Li Liu, Maxwell D. Sanderford, Daniel Peterson, Koichiro Tamura, Sudhir Kumar:
  MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. 1305-1307

Phylogenetics

• 
  Garry Jolley-Rogers, Temi Varghese, Paul Harvey, Nick dos Remedios, Joseph T. Miller:
  PhyloJIVE: Integrating biodiversity data with the Tree of Life. 1308-1309
• 
  Jose Manuel Santorum, Diego Darriba, Guillermo L. Taboada, David Posada:
  jmodeltest.org: selection of nucleotide substitution models on the cloud. 1310-1311
• 
  Alexandros Stamatakis:
  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. 1312-1313

Structural Bioinformatics

• 
  Alejandro Panjkovich, Xavier Daura:
  PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites. 1314-1315

Gene Expression

• 
  Qiang Fu, Ana Carolina Fierro, Pieter Meysman, Aminael Sánchez-Rodríguez, Klaas Vandepoele, Kathleen Marchal, Kristof Engelen:
  MAGIC: access portal to a cross-platform gene expression compendium for maize. 1316-1318
• 
  Ivan Montiel, Charlotte Konikoff, Bremen L. Braun, Mary Packard, L. Sian Gramates, Qian Sun, Jieping Ye, Sudhir Kumar:
  myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos. 1319-1321
• 
  Laurent Gatto, Lisa M. Breckels, Samuel Wieczorek, Thomas Burger, Kathryn S. Lilley:
  Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. 1322-1324
• 
  Yupeng Cun, Holger Fröhlich:
  netClass: an R-package for network based, integrative biomarker signature discovery. 1325-1326

Systems Biology

• 
  Paul A. Jensen, Jason A. Papin:
  MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. 1327-1328
• 
  Kieran O'Neill, Adrin Jalali, Nima Aghaeepour, Holger H. Hoos, Ryan Remy Brinkman:
  Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data. 1329-1330
• 
  Jörn Starruß, Walter de Back, Lutz Brusch, Andreas Deutsch:
  Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology. 1331-1332
• 
  Jamey D. Young:
  INCA: a computational platform for isotopically non-stationary metabolic flux analysis. 1333-1335
• 
  Ricardo Roberto da Silva, Fabien Jourdan, Diego M. Salvanha, Fabien Létisse, Emilien L. Jamin, Simone Guidetti-Gonzalez, Carlos A. Labate, Ricardo Z. N. Vêncio:
  ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. 1336-1337

Databases and Ontologies

• 
  Simon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. García, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson:
  The EBI RDF platform: linked open data for the life sciences. 1338-1339
• 
  Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
  Ontodog: a web-based ontology community view generation tool. 1340-1342

Volume 30, Number 10, May 2014

Review - Data and Text Mining

• 
  Clara Pizzuti, Simona E. Rombo:
  Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods. 1343-1352

Editorial - Data and Text Mining

• 
  Robert F. Murphy:
  A new era in bioimage informatics. 1353

Original Papers - Genome Analysis

• 
  Yun Heo, Xiaolong Wu, Deming Chen, Jian Ma, Wen-mei W. Hwu:
  BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads. 1354-1362
• 
  Martin J. Aryee, Andrew E. Jaffe, Héctor Corrada Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry:
  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. 1363-1369
• 
  Priyadip Ray, Lingling Zheng, Joseph E. Lucas, Lawrence Carin:
  Bayesian joint analysis of heterogeneous genomics data. 1370-1376

Sequence Analysis

• 
  Xiaowei Wang:
  Composition of seed sequence is a major determinant of microRNA targeting patterns. 1377-1383
• 
  Kaiyong Zhao, Xiaowen Chu:
  G-BLASTN: accelerating nucleotide alignment by graphics processors. 1384-1391

Gene Expression

• 
  Marta Rosikiewicz, Marc Robinson-Rechavi:
  IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. 1392-1399
• 
  Iwona Pawlikowska, Gang Wu, Michael N. Edmonson, Zhifa Liu, Tanja Gruber, Jinghui Zhang, Stan Pounds:
  The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression. 1400-1408
• 
  Bogdan Mirauta, Pierre Nicolas, Hugues Richard:
  Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. 1409-1416
• 
  Martin Vincent, Katharina Perell, Finn Cilius Nielsen, Gedske Daugaard, Niels Richard Hansen:
  Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases. 1417-1423
• 
  Klaus Jung, Hassan Dihazi, Asima Bibi, Gry H. Dihazi, Tim Beißbarth:
  Adaption of the global test idea to proteomics data with missing values. 1424-1430

Genetics and Population Analysis

• 
  Eugene Andres Houseman, John Molitor, Carmen J. Marsit:
  Reference-free cell mixture adjustments in analysis of DNA methylation data. 1431-1439

Systems Biology

• 
  Andreas Raue, Johan Karlsson, Maria Pia Saccomani, Mats Jirstrand, Jens Timmer:
  Comparison of approaches for parameter identifiability analysis of biological systems. 1440-1448
• 
  Dana Silverbush, Roded Sharan:
  Network orientation via shortest paths. 1449-1455
• 
  Kaifang Pang, Ying-Wooi Wan, William T. Choi, Lawrence A. Donehower, Jingchun Sun, Dhruv Pant, Zhandong Liu:
  Combinatorial therapy discovery using mixed integer linear programming. 1456-1463

Applications Notes - Genome Analysis

• 
  Paul Theodor Pyl, Julian Gehring, Bernd Fischer, Wolfgang Huber:
  h5vc: scalable nucleotide tallies with HDF5. 1464-1466
• 
  Alex Chun-Hong Fok, Sunny Siu-Nam Mok, Sau Dan Lee, Kevin Y. Yip:
  ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications. 1467-1468
• 
  Andrey Tovchigrechko, Pratap Venepally, Samuel H. Payne:
  PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. 1469-1470

Sequence Analysis

• 
  Fabian A. Buske, Hugh J. French, Martin A. Smith, Susan J. Clark, Denis C. Bauer:
  NGSANE: a lightweight production informatics framework for high-throughput data analysis. 1471-1472
• 
  Sangsu Bae, Jeongbin Park, Jin-Soo Kim:
  Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. 1473-1475

Phylogenetics

• 
  Fernando Izquierdo-Carrasco, John Cazes, Stephen A. Smith, Alexandros Stamatakis:
  PUmPER: phylogenies updated perpetually. 1476-1477

Structural Bioinformatics

• 
  Ramon Guixà-González, Ismael Rodriguez-Espigares, Juan Manuel Ramírez-Anguita, Pau Carrió-Gaspar, Hector Martinez-Seara, Toni Giorgino, Jana Selent:
  MEMBPLUGIN: studying membrane complexity in VMD. 1478-1480
• 
  Jamel Meslamani, Steven G. Smith, Roberto Sanchez, Ming-Ming Zhou:
  ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. 1481-1483

Gene Expression

• 
  Sander Bollen, Mathias Leddin, Miguel A. Andrade-Navarro, Nancy Mah:
  CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. 1484-1485

Genetics and Population Analysis

• 
  Matteo Fumagalli, Filipe G. Vieira, Tyler Linderoth, Rasmus Nielsen:
  ngsTools: methods for population genetics analyses from next-generation sequencing data. 1486-1487
• 
  James T. Monacell, Ignazio Carbone:
  Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics. 1488-1490

Systems Biology

• 
  Michael Pedersen, Nicolas Oury, Colin Gravill, Andrew Phillips:
  Bio Simulators: a web UI for biological simulation. 1491-1492

Volume 30, Number 11, June 2014

Original Papers - Genome Analysis

• 
  Charles C. Berry, Karen E. Ocwieja, Nirav Malani, Frederic D. Bushman:
  Comparing DNA integration site clusters with scan statistics. 1493-1500
• 
  Jun Hu, Jung-Ying Tzeng:
  Integrative gene set analysis of multi-platform data with sample heterogeneity. 1501-1507
• 
  Megan J. Puckelwartz, Lorenzo L. Pesce, Viswateja Nelakuditi, Lisa Dellefave-Castillo, Jessica R. Golbus, Sharlene M. Day, Thomas P. Cappola, Gerald W. Dorn II, Ian T. Foster, Elizabeth M. McNally:
  Supercomputing for the parallelization of whole genome analysis. 1508-1513

Sequence Analysis

• 
  Eitan Halper-Stromberg, Jared Steranka, Kathleen H. Burns, Sarven Sabunciyan, Rafael A. Irizarry:
  Visualization and probability-based scoring of structural variants within repetitive sequences. 1514-1521
• 
  Shou-Hui Guo, En-Ze Deng, Liqin Xu, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou:
  iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. 1522-1529
• 
  Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt:
  Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. 1530-1538

Gene Expression

• 
  Toby Dylan Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Wilfrid Richer, Franck Bourdeaut, Miyuki Suguro, Masao Seto, Francis R. Bach, Jean-Philippe Vert:
  SegAnnDB: interactive Web-based genomic segmentation. 1539-1546
• 
  Peng Yu, Chad A. Shaw:
  An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function. 1547-1554
• 
  Daniah Trabzuni, Peter C. Thomson:
  Analysis of gene expression data using a linear mixed model/finite mixture model approach: application to regional differences in the human brain. 1555-1561

Genetics and Population Analysis

• 
  David C. Kessler, Jack A. Taylor, David B. Dunson:
  Learning phenotype densities conditional on many interacting predictors. 1562-1568

Systems Biology

• 
  Kristopher A. Hunt, James P. Folsom, Reed L. Taffs, Ross P. Carlson:
  Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. 1569-1578
• 
  Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen:
  Identifying critical transitions of complex diseases based on a single sample. 1579-1586

Data and Text Mining

• 
  Deyu Zhou, Dayou Zhong, Yulan He:
  Event trigger identification for biomedical events extraction using domain knowledge. 1587-1594

Databases and Ontologies

• 
  Clinton J. Mielke, Lawrence J. Mandarino, Valentin Dinu:
  AMASS: a database for investigating protein structures. 1595-1600

Structural Bioinformatics

• 
  Petr Klus, Benedetta Bolognesi, Federico Agostini, Domenica Marchese, Andreas Zanzoni, Gian Gaetano Tartaglia:
  The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. 1601-1608

Bioimage Informatics

• 
  Martin Maska, Vladimír Ulman, David Svoboda, Pavel Matula, Petr Matula, Cristina Ederra, Ainhoa Urbiola, Tomás España, Subramanian Venkatesan, Deepak M. W. Balak, Pavel Karas, Tereza Bolcková, Markéta Streitová, Craig Carthel, Stefano Coraluppi, Nathalie Harder, Karl Rohr, Klas E. G. Magnusson, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Pavel Krízek, Guy M. Hagen, David Pastor-Escuredo, Daniel Jimenez-Carretero, María J. Ledesma-Carbayo, Arrate Muñoz-Barrutia, Erik Meijering, Michal Kozubek, Carlos Ortiz-de-Solorzano:
  A benchmark for comparison of cell tracking algorithms. 1609-1617

Applications Notes - Genome Analysis

• 
  Andy Pohl, Miguel Beato:
  bwtool: a tool for bigWig files. 1618-1619
• 
  Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig:
  HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. 1620-1622
• 
  Jeffrey B. Endelman, Christophe Plomion:
  LPmerge: an R package for merging genetic maps by linear programming. 1623-1624

Sequence Analysis

• 
  Paul C. Lott, Ian Korf:
  StochHMM: a flexible hidden Markov model tool and C++ library. 1625-1626
• 
  Travis M. Drucker, Sarah H. Johnson, Stephen J. Murphy, Kendall W. Cradic, Terry M. Therneau, George Vasmatzis:
  BIMA V3: an aligner customized for mate pair library sequencing. 1627-1629

Gene Expression

• 
  Raúl Aguirre-Gamboa, Victor Trevino:
  SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis. 1630-1632

Systems Biology

• 
  Pete Donnell, Murad Banaji, Anca Marginean, Casian Pantea:
  CoNtRol: an open source framework for the analysis of chemical reaction networks. 1633-1634

Data and Text Mining

• 
  Natalia Novoselova, Cristina Della Beffa, Junxi Wang, Jialiang Li, Frank Pessler, Frank Klawonn:
  HUM calculator and HUM package for R: easy-to-use software tools for multicategory receiver operating characteristic analysis. 1635-1636

Databases and Ontologies

• 
  Mark Maienschein-Cline, Zhengdeng Lei, Vincent Gardeux, Taimur Abbasi, Roberto F. Machado, Victor Gordeuk, Ankit A. Desai, Santosh Saraf, Neil Bahroos, Yves A. Lussier:
  ARTS: automated randomization of multiple traits for study design. 1637-1639
• 
  Chao Li, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, Yixue Li:
  The 3DGD: a database of genome 3D structure. 1640-1642

Volume 30, Number 12, June 2014

ISMB 2014

• 
  Serafim Batzoglou, Russell Schwartz:
  Editorial. 1-2

Original Papers

• 
  Cristina G. Ghiurcuta, Bernard M. E. Moret:
  Evaluating synteny for improved comparative studies. 9-18
• 
  Ya'ara Arkin, Elior Rahmani, Marcus E. Kleber, Reijo Laaksonen, Winfried März, Eran Halperin:
  EPIQ - efficient detection of SNP-SNP epistatic interactions for quantitative traits. 19-25
• 
  Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert:
  A statistical approach for inferring the 3D structure of the genome. 26-33
• 
  Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker:
  Inferring gene ontologies from pairwise similarity data. 34-42
• 
  Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida:
  Automated detection and tracking of many cells by using 4D live-cell imaging data. 43-51
• 
  Anika Oellrich, Julius O. B. Jacobsen, Irene Papatheodorou, Damian Smedley:
  Using association rule mining to determine promising secondary phenotyping hypotheses. 52-59
• 
  Nagarajan Natarajan, Inderjit S. Dhillon:
  Inductive matrix completion for predicting gene-disease associations. 60-68
• 
  Kourosh Zarringhalam, Ahmed Enayetallah, Padmalatha Reddy, Daniel Ziemek:
  Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. 69-77
• 
  Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael:
  A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. 78-86
• 
  Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis:
  Pareto-optimal phylogenetic tree reconciliation. 87-95
• 
  Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci:
  Large scale analysis of signal reachability. 96-104
• 
  Christoph Bernau, Markus Riester, Anne-Laure Boulesteix, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron, Lorenzo Trippa:
  Cross-study validation for the assessment of prediction algorithms. 105-112
• 
  Tarmo Äijö, Vincent Butty, Zhi Jane Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki:
  Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. 113-120
• 
  Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey:
  Deep learning of the tissue-regulated splicing code. 121-129
• 
  Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer:
  Functional association networks as priors for gene regulatory network inference. 130-138
• 
  Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang:
  Graph-regularized dual Lasso for robust eQTL mapping. 139-148
• 
  Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard:
  Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. 149-156
• 
  Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu:
  Metabolite identification through multiple kernel learning on fragmentation trees. 157-164
• 
  Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto:
  Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. 165-174
• 
  A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu:
  MIRA: mutual information-based reporter algorithm for metabolic networks. 175-184
• 
  Richard Leslie, Christopher J. O'Donnell, Andrew D. Johnson:
  GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. 185-194
• 
  Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael:
  Detecting independent and recurrent copy number aberrations using interval graphs. 195-203
• 
  Farhad Hormozdiari, Jong Wha J. Joo, Akshay Wadia, Feng Guan, Rafail Ostrovsky, Amit Sahai, Eleazar Eskin:
  Privacy preserving protocol for detecting genetic relatives using rare variants. 204-211
• 
  Ladislav Rampásek, Aryan Arbabi, Michael Brudno:
  Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. 212-218
• 
  Mengfei Cao, Christopher M. Pietras, Xian Feng, Kathryn J. Doroschak, Thomas Schaffner, Jisoo Park, Hao Zhang, Lenore J. Cowen, Benjamin J. Hescott:
  New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. 219-227
• 
  Lei Huang, Fuhai Li, Jianting Sheng, Xiaofeng Xia, Jinwen Ma, Ming Zhan, Stephen T. C. Wong:
  DrugComboRanker: drug combination discovery based on target network analysis. 228-236
• 
  Marc Hulsman, Christos Dimitrakopoulos, Jeroen de Ridder:
  Scale-space measures for graph topology link protein network architecture to function. 237-245
• 
  Marinka Zitnik, Blaz Zupan:
  Gene network inference by probabilistic scoring of relationships from a factorized model of interactions. 246-254
• 
  Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng:
  An efficient parallel algorithm for accelerating computational protein design. 255-263
• 
  Jing Ren, Qian Liu, John T. Ellis, Jinyan Li:
  Tertiary structure-based prediction of conformational B-cell epitopes through B factors. 264-273
• 
  Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen:
  BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. 274-282
• 
  Zhaojun Zhang, Wei Wang:
  RNA-Skim: a rapid method for RNA-Seq quantification at transcript level. 283-292
• 
  Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey A. Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son K. Pham, Anton I. Korobeynikov, Alla L. Lapidus, Pavel A. Pevzner:
  ExSPAnder: a universal repeat resolver for DNA fragment assembly. 293-301
• 
  Mikhail Kolmogorov, Brian J. Raney, Benedict Paten, Son K. Pham:
  Ragout - a reference-assisted assembly tool for bacterial genomes. 302-309
• 
  Alastair M. Kilpatrick, Bruce Ward, Stuart Aitken:
  Stochastic EM-based TFBS motif discovery with MITSU. 310-318
• 
  Ergude Bao, Tao Jiang, Thomas Girke:
  AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. 319-328
• 
  Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin:
  Accurate viral population assembly from ultra-deep sequencing data. 329-337

Original Papers - Genome Analysis

• 
  Guofeng Meng, Martin Vingron:
  Condition-specific target prediction from motifs and expression. 1643-1650
• 
  Seyed Yahya Anvar, Kristiaan J. van der Gaag, Jaap W. F. van der Heijden, Marcel H. A. M. Veltrop, Rolf H. A. M. Vossen, Rick H. de Leeuw, Cor Breukel, Henk P. J. Buermans, J. Sjef Verbeek, Peter de Knijff, Johan T. den Dunnen, Jeroen F. J. Laros:
  TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes. 1651-1659

Sequence Analysis

• 
  Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li, Xin Zhou, Tak Wah Lam, Yingrui Li, Xun Xu, Gane Ka-Shu Wong, Jun Wang:
  SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. 1660-1666
• 
  Daniel Quang, Xiaohui Xie:
  EXTREME: an online EM algorithm for motif discovery. 1667-1673

Structural Bioinformatics

• 
  Yang Cao, Lei Li:
  Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model. 1674-1680
• 
  Ken Nagata, Arlo Z. Randall, Pierre Baldi:
  Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. 1681-1689

Gene Expression

• 
  Kevin H. Eng, Bret M. Hanlon:
  Discrete mixture modeling to address genetic heterogeneity in time-to-event regression. 1690-1697
• 
  H. Robert Frost, Jason H. Moore:
  Optimization of gene set annotations via entropy minimization over variable clusters (EMVC). 1698-1706

Genetics and Population Analysis

• 
  Anthony Youzhi Cheng, Yik-Ying Teo, Rick Twee-Hee Ong:
  Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals. 1707-1713
• 
  Jin Zhou, Erwin Tantoso, Lai-Ping Wong, Rick Twee-Hee Ong, Jin-Xin Bei, Yi Li, Jianjun Liu, Chiea-Chuen Khor, Yik-Ying Teo:
  iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array. 1714-1720

Systems Biology

• 
  Fazle Elahi Faisal, Tijana Milenkovic:
  Dynamic networks reveal key players in aging. 1721-1729
• 
  Nikhil Prakash Damle, Debasisa Mohanty:
  Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network. 1730-1738

Databases and Ontologies

• 
  Hsiu-Sen Chiang, Dong-Her Shih, Binshan Lin, Ming-Hung Shih:
  An APN model for Arrhythmic beat classification. 1739-1746

Bioimage Informatics

• 
  Eduard Hermann, Stephanie Bleicken, Yamunadevi Subburaj, Ana J. García-Sáez:
  Automated analysis of giant unilamellar vesicles using circular Hough transformation. 1747-1754

Applications Notes - Genome Analysis

• 
  Yeonok Lee, Debashis Ghosh, Ross C. Hardison, Yu Zhang:
  MRHMMs: Multivariate Regression Hidden Markov Models and the variantS. 1755-1756
• 
  Jordi Deu-Pons, Michael P. Schroeder, Núria López-Bigas:
  jHeatmap: an interactive heatmap viewer for the web. 1757-1758
• 
  Ramón Díaz-Uriarte:
  ADaCGH2: parallelized analysis of (big) CNA data. 1759-1761
• 
  Adrian Lärkeryd, Kerstin Myrtennäs, Edvin Karlsson, Chinmay Kumar Dwibedi, Mats Forsman, Pär Larsson, Anders Johansson, Andreas Sjödin:
  CanSNPer: a hierarchical genotype classifier of clonal pathogens. 1762-1764

Sequence Analysis

• 
  Maxim I. Pyatkov, Anton N. Pankratov:
  SBARS: fast creation of dotplots for DNA sequences on different scales using GA-, GC-content. 1765-1766
• 
  Francisco J. López-Domingo, Javier Perez-Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo-Lopez:
  ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing. 1767-1768

Structural Bioinformatics

• 
  Tim Seifert, Andreas Lund, Benny Kneissl, Sabine C. Mueller, Christofer S. Tautermann, Andreas Hildebrandt:
  SKINK: a web server for string kernel based kink prediction in α-helices. 1769-1770
• 
  Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, Zhiping Weng:
  ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. 1771-1773
• 
  Ling-Hong Hung, Ram Samudrala:
  fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. 1774-1776

Gene Expression

• 
  Xi Wang, Murray J. Cairns:
  SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing. 1777-1779
• 
  Mario Huerta, Marc Munyi, David Expósito, Enric Querol, Juan Cedano:
  MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes. 1780-1781
• 
  Matias D. Butti, Hernan Chanfreau, Diego Martínez, Diego García, Ezequiel Lacunza, Martin C. Abba:
  BioPlat: a software for human cancer biomarker discovery. 1782-1784
• 
  Rodrigo Santamaría, Roberto Therón, Luis Quintales:
  BicOverlapper 2.0: visual analysis for gene expression. 1785-1786

Systems Biology

• 
  Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo:
  Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis. 1787-1788
• 
  Emre Guney, Javier García-García, Baldo Oliva:
  GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. 1789-1790

Databases and Ontologies

• 
  Kim M. Rutherford, Midori A. Harris, Antonia Lock, Stephen G. Oliver, Valerie Wood:
  Canto: an online tool for community literature curation. 1791-1792

Volume 30, Number 13, July 2014

Review - Genome Analysis

• 
  Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer:
  Challenges in RNA virus bioinformatics. 1793-1799

Discovery note - Structural Bioinformatics

• 
  Max T. B. Clabbers, René C. L. Olsthoorn, Alexander P. Gultyaev:
  Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region. 1800-1804

Original Papers - Genome Analysis

• 
  Ambarish Biswas, Peter C. Fineran, Chris M. Brown:
  Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. 1805-1813
• 
  Peter A. Stockwell, Aniruddha Chatterjee, Euan J. Rodger, Ian M. Morison:
  DMAP: differential methylation analysis package for RRBS and WGBS data. 1814-1822

Sequence Analysis

• 
  Arief Gusnanto, Charles C. Taylor, Ibrahim Nafisah, Henry M. Wood, Pamela Rabbitts, Stefano Berri:
  Estimating optimal window size for analysis of low-coverage next-generation sequence data. 1823-1829
• 
  Yongzhuang Liu, Bingshan Li, Renjie Tan, Xiaolin Zhu, Yadong Wang:
  A gradient-boosting approach for filtering de novo mutations in parent-offspring trios. 1830-1836
• 
  Christian Otto, Peter F. Stadler, Steve Hoffmann:
  Lacking alignments? The next-generation sequencing mapper segemehl revisited. 1837-1843

Phylogenetics

• 
  Deren A. R. Eaton:
  PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. 1844-1849

Structural Bioinformatics

• 
  Pooya Zakeri, Ben Jeuris, Raf Vandebril, Yves Moreau:
  Protein fold recognition using geometric kernel data fusion. 1850-1857

Gene Expression

• 
  Md. Jamiul Jahid, Tim Hui-Ming Huang, Jianhua Ruan:
  A personalized committee classification approach to improving prediction of breast cancer metastasis. 1858-1866
• 
  Florian Buettner, Victoria Moignard, Berthold Göttgens, Fabian J. Theis:
  Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. 1867-1875

Genetics and Population Analysis

• 
  Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng:
  FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model. 1876-1883

Systems Biology

• 
  Francesco Pappalardo, Marzio Pennisi, Alessia Ricupito, Francesco Topputo, Matteo Bellone:
  Induction of T-cell memory by a dendritic cell vaccine: a computational model. 1884-1891
• 
  Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf:
  Derivative processes for modelling metabolic fluxes. 1892-1898
• 
  Huiming Peng, Tao Peng, Jianguo Wen, David A. Engler, Risë K. Matsunami, Jing Su, Le Zhang, Chung-Che Jeff Chang, Xiaobo Zhou:
  Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach. 1899-1907

Data and Text Mining

• 
  Suh-Yuen Liang, Sz-Wei Wu, Tsung-Hsien Pu, Fang-Yu Chang, Kay-Hooi Khoo:
  An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry. 1908-1916

Applications Notes - Genome Analysis

• 
  Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko:
  Wrangling Galaxy's reference data. 1917-1919
• 
  Jean-Pierre A. Kocher, Daniel J. Quest, Patrick H. Duffy, Michael A. Meiners, Raymond M. Moore, David N. Rider, Asif Hossain, Steven N. Hart, Valentin Dinu:
  The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. 1920-1922

Sequence Analysis

• 
  Chih Lee, Chun-Hsi Huang:
  LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser. 1923-1925
• 
  Florent E. Angly, Christopher J. Fields, Gene W. Tyson:
  The Bio-Community Perl toolkit for microbial ecology. 1926-1927
• 
  Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia:
  Orione, a web-based framework for NGS analysis in microbiology. 1928-1929
• 
  Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N. H. Stern, Kevin C. O'Connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein:
  pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. 1930-1932
• 
  Kemal Akman, Thomas Haaf, Silvia Gravina, Jan Vijg, Achim Tresch:
  Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data. 1933-1934

Structural Bioinformatics

• 
  Jaume Bonet, Joan Segura, Joan Planas-Iglesias, Baldomero Oliva, Narcis Fernandez-Fuentes:
  Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. 1935-1936

Gene Expression

• 
  Francesc Fernández-Albert, Rafael Llorach, Cristina Andres-Lacueva, Alexandre Perera:
  An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). 1937-1939

Genetics and Population Analysis

• 
  Steven Gazal, Mourad Sahbatou, Marie-Claude Babron, Emmanuelle Génin, Anne-Louise Leutenegger:
  FSuite: exploiting inbreeding in dense SNP chip and exome data. 1940-1941

Erratum - Systems Biology

• 
  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. 1942

Volume 30, Number 14, July 2014

Original Papers
Genome Analysis

• 
  Xiaowei Zhou, Jiming Liu, Xiang Wan, Weichuan Yu:
  Piecewise-constant and low-rank approximation for identification of recurrent copy number variations. 1943-1949

Sequence Analysis

• 
  Rajat Shuvro Roy, Debashish Bhattacharya, Alexander Schliep:
  Turtle: Identifying frequent k-mers with cache-efficient algorithms. 1950-1957
• 
  William H. Majoros, Niel Lebeck, Uwe Ohler, Song Li:
  Improved transcript isoform discovery using ORF graphs. 1958-1964
• 
  Emi Tanaka, Timothy L. Bailey, Uri Keich:
  Improving MEME via a two-tiered significance analysis. 1965-1973
• 
  Christophe Charpilloz, Anne-Lise Veuthey, Bastien Chopard, Jean-Luc Falcone:
  Motifs tree: a new method for predicting post-translational modifications. 1974-1982
• 
  A. Mary Thangakani, Sandeep Kumar, Raju Nagarajan, Devadasan Velmurugan, M. Michael Gromiha:
  GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies. 1983-1990
• 
  Chris-André Leimeister, Marcus Boden, Sebastian Horwege, Sebastian Lindner, Burkhard Morgenstern:
  Fast alignment-free sequence comparison using spaced-word frequencies. 1991-1999
• 
  Chris-André Leimeister, Burkhard Morgenstern:
  kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison. 2000-2008

Structural Bioinformatics

• 
  Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
  Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. 2009-2017

Gene Expression

• 
  Yuan-De Tan, Hongyan Xu:
  A general method for accurate estimation of false discovery rates in identification of differentially expressed genes. 2018-2025

Genetics and Population Analysis

• 
  Pekka Marttinen, Matti Pirinen, Antti-Pekka Sarin, Jussi Gillberg, Johannes Kettunen, Ida Surakka, Antti J. Kangas, Pasi Soininen, Paul F. O'Reilly, Marika Kaakinen, Mika Kähönen, Terho Lehtimäki, Mika Ala-Korpela, Olli T. Raitakari, Veikko Salomaa, Marjo-Riitta Järvelin, Samuli Ripatti, Samuel Kaski:
  Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. 2026-2034
• 
  Amir R. Kermany, Laure Segurel, Tiffany R. Oliver, Molly Przeworski:
  TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception. 2035-2042

Systems Biology

• 
  Mario Latendresse, Markus Krummenacker, Peter D. Karp:
  Optimal metabolic route search based on atom mappings. 2043-2050
• 
  Bülent Arman Aksoy, Emek Demir, Özgün Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander:
  Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. 2051-2059

Bioimage Informatics

• 
  Davide Rambaldi, Salvatore Pece, Pier Paolo Di Fiore:
  flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies. 2060-2065

Applications Notes
Genome Analysis

• 
  Uciel Chorostecki, Javier F. Palatnik:
  comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants. 2066-2067
• 
  Torsten Seemann:
  Prokka: rapid prokaryotic genome annotation. 2068-2069

Sequence Analysis

• 
  Peter Audano, Fredrik Vannberg:
  KAnalyze: a fast versatile pipelined K-mer toolkit. 2070-2072
• 
  Zhenpeng Li, Yang Huang, Yabo Ouyang, Yang Jiao, Hui Xing, Lingjie Liao, Shibo Jiang, Yiming Shao, Liying Ma:
  CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure. 2073-2075
• 
  Valerie Obenchain, Michael F. Lawrence, Vincent J. Carey, Stephanie M. Gogarten, Paul Shannon, Martin Morgan:
  VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. 2076-2078

Phylogenetics

• 
  Andreas Sand, Morten Kragelund Holt, Jens Johansen, Gerth Stølting Brodal, Thomas Mailund, Christian N. S. Pedersen:
  tqDist: a library for computing the quartet and triplet distances between binary or general trees. 2079-2080

Structural Bioinformatics

• 
  Dario Ghersi, Mona Singh:
  molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. 2081-2083

Gene Expression

• 
  Sam Buckberry, Stephen J. Bent, Tina Bianco-Miotto, Claire T. Roberts:
  massiR: a method for predicting the sex of samples in gene expression microarray datasets. 2084-2085

Genetics and Population Analysis

• 
  Dale R. Nyholt:
  SECA: SNP effect concordance analysis using genome-wide association summary results. 2086-2088

Message from the ISCB
Genetics and Population Analysis

• 
  So Young Ryu, Samuel H. Payne, Christoph Schaab, Wenzhong Xiao:
  Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013. 2089-2090
• 
  Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg:
  The automated function prediction SIG looks back at 2013 and prepares for 2014. 2091-2092

Volume 30, Number 15, August 2014

Discovery note
Sequence Analysis

• 
  Darius Kazlauskas, Ceslovas Venclovas:
  Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase. 2093-2097

Original Papers
Genome Analysis

• 
  Rong W. Zablocki, Andrew J. Schork, Richard A. Levine, Ole A. Andreassen, Anders M. Dale, Wesley K. Thompson:
  Covariate-modulated local false discovery rate for genome-wide association studies. 2098-2104
• 
  Hervé Marie-Nelly, Martial Marbouty, Axel Cournac, Gianni Liti, Gilles Fischer, Christophe Zimmer, Romain Koszul:
  Filling annotation gaps in yeast genomes using genome-wide contact maps. 2105-2113
• 
  Anthony M. Bolger, Marc Lohse, Björn Usadel:
  Trimmomatic: a flexible trimmer for Illumina sequence data. 2114-2120
• 
  Yi Li, Xiaohui Xie:
  Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. 2121-2129

Sequence Analysis

• 
  Rodrigo Cánovas, Alistair Moffat, Andrew Turpin:
  Lossy compression of quality scores in genomic data. 2130-2136
• 
  Amir Toporik, Itamar Borukhov, Avihay Apatoff, Doron Gerber, Yossef Kliger:
  Computational identification of natural peptides based on analysis of molecular evolution. 2137-2141

Structural Bioinformatics

• 
  Zeyneb Kurt, Nizamettin Aydin, Gökmen Altay:
  A comprehensive comparison of association estimators for gene network inference algorithms. 2142-2149
• 
  Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik:
  CABS-flex predictions of protein flexibility compared with NMR ensembles. 2150-2154

Gene Expression

• 
  Alexandra Jauhiainen, Basetti Madhu, Masako Narita, Masashi Narita, John Griffiths, Simon Tavaré:
  Normalization of metabolomics data with applications to correlation maps. 2155-2161
• 
  Wei Wang, Zhi Wei, Hongzhe Li:
  A change-point model for identifying 3′UTR switching by next-generation RNA sequencing. 2162-2170

Genetics and Population Analysis

• 
  Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor, Kai Yu:
  A fast and powerful tree-based association test for detecting complex joint effects in case-control studies. 2171-2178
• 
  Andriy Derkach, Theodore Chiang, Jiafen Gong, Laura Addis, Sara E. Dobbins, Ian Tomlinson, Richard S. Houlston, Deb K. Pal, Lisa J. Strug:
  Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic. 2179-2188
• 
  Alexandre Bureau, Samuel G. Younkin, Margaret M. Parker, Joan E. Bailey-Wilson, Mary L. Marazita, Jeffrey C. Murray, Elisabeth Mangold, Hasan Albacha-Hejazi, Terri H. Beaty, Ingo Ruczinski:
  Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives. 2189-2196

Systems Biology

• 
  Jon Pey, Francisco J. Planes:
  Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. 2197-2203

Applications Notes
Genome Analysis

• 
  Sylvain Mareschal, Sydney Dubois, Thierry Lecroq, Fabrice Jardin:
  Rgb: a scriptable genome browser for R. 2204-2205
• 
  Xin Zhou, Daofeng Li, Rebecca F. Lowdon, Joseph F. Costello, Ting Wang:
  methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. 2206-2207

Sequence Analysis

• 
  Sung Kyu Robin Park, Aaron Aslanian, Daniel B. McClatchy, Xuemei Han, Harshil Shah, Meha Singh, Navin Rauniyar, James J. Moresco, Antonio F. M. Pinto, Jolene K. Diedrich, Claire Delahunty, John R. Yates III:
  Census 2: isobaric labeling data analysis. 2208-2209
• 
  Ju Xin Chin, Bevan Kai-Sheng Chung, Dong-Yup Lee:
  Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design. 2210-2212
• 
  Lukasz Roguski, Sebastian Deorowicz:
  DSRC 2 - Industry-oriented compression of FASTQ files. 2213-2215

Phylogenetics

• 
  Matthew W. Pennell, Jonathan M. Eastman, Graham J. Slater, Joseph W. Brown, Josef C. Uyeda, Richard G. FitzJohn, Michael E. Alfaro, Luke J. Harmon:
  geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. 2216-2218

Structural Bioinformatics

• 
  Sébastien Morin, Troels E. Linnet, Mathilde Lescanne, Paul Schanda, Gary S. Thompson, Martin Tollinger, Kaare Teilum, Stéphane Gagné, Dominique Marion, Christian Griesinger, Martin Blackledge, Edward J. d'Auvergne:
  relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. 2219-2220
• 
  Björn Wallner:
  ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling. 2221-2223

Gene Expression

• 
  Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G. W. Verhaak:
  PRADA: pipeline for RNA sequencing data analysis. 2224-2226

Genetics and Population Analysis

• 
  Raeece Naeem, Lailatul Hidayah, Mark D. Preston, Taane G. Clark, Arnab Pain:
  SVAMP: sequence variation analysis, maps and phylogeny. 2227-2229

Systems Biology

• 
  Alvin Leung, Gary D. Bader, Jüri Reimand:
  HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. 2230-2232
• 
  Frédéric Fournier, Charles Joly Beauparlant, René Paradis, Arnaud Droit:
  rTANDEM, an R/Bioconductor package for MS/MS protein identification. 2233-2234

Databases and Ontologies

• 
  Horacio Caniza, Alfonso E. Romero, Samuel Heron, Haixuan Yang, Alessandra Devoto, Marco Frasca, Marco Mesiti, Giorgio Valentini, Alberto Paccanaro:
  GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology. 2235-2236
• 
  Dongfang Wang, Jin Gu, Ting Wang, Zijian Ding:
  OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. 2237-2238
• 
  William Duren, Terry E. Weymouth, Tim Hull, Gilbert S. Omenn, Brian D. Athey, Charles F. Burant, Alla Karnovsky:
  MetDisease - connecting metabolites to diseases via literature. 2239-2241

Corrigendum
Databases and Ontologies

• 
  Jinghua Gu, Jianhua Xuan, Rebecca B. Riggins, Li Chen, Yue Joseph Wang, Robert Clarke:
  Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. 2242

Volume 30, Number 16, August 2014

Discovery note
Genome Analysis

• 
  Laurent F. Thomas, Pål Sætrom:
  Circular RNAs are depleted of polymorphisms at microRNA binding sites. 2243-2246

Original Papers
Genome Analysis

• 
  Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann:
  ReadXplorer - visualization and analysis of mapped sequences. 2247-2254

Sequence Analysis

• 
  Andreas Futschik, Thomas Hotz, Axel Munk, Hannes Sieling:
  Multiscale DNA partitioning: statistical evidence for segments. 2255-2262
• 
  Maria Cha, Qing Zhou:
  Detecting clustering and ordering binding patterns among transcription factors via point process models. 2263-2271

Phylogenetics

• 
  Timothy G. Vaughan, Denise Kühnert, Alex Popinga, David Welch, Alexei J. Drummond:
  Efficient Bayesian inference under the structured coalescent. 2272-2279
• 
  Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida:
  kdetrees: non-parametric estimation of phylogenetic tree distributions. 2280-2287

Structural Bioinformatics

• 
  Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M. Deane:
  Improving B-cell epitope prediction and its application to global antibody-antigen docking. 2288-2294
• 
  Chen Yanover, Natalia Vanetik, Michael Levitt, Rachel Kolodny, Chen Keasar:
  Redundancy-weighting for better inference of protein structural features. 2295-2301
• 
  Praveen Nedumpully-Govindan, Lin Li, Emil Alexov, Mark A. Blenner, Feng Ding:
  Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. 2302-2309

Gene Expression

• 
  Matthew N. McCall, Helene R. McMurray, Hartmut Land, Anthony Almudevar:
  On non-detects in qPCR data. 2310-2316

Genetics and Population Analysis

• 
  Hokeun Sun, Shuang Wang:
  A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data. 2317-2323
• 
  Trisevgeni Rapakoulia, Konstantinos A. Theofilatos, Dimitris Kleftogiannis, Spiridon Likothanasis, Athanasios K. Tsakalidis, Seferina Mavroudi:
  EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms. 2324-2333

Systems Biology

• 
  Shibin Mathew, Sankaramanivel Sundararaj, Hikaru Mamiya, Ipsita Banerjee:
  Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway. 2334-2342
• 
  Xiaoke Ma, Long Gao, Kai Tan:
  Modeling disease progression using dynamics of pathway connectivity. 2343-2350
• 
  Connor Clark, Jugal Kalita:
  A comparison of algorithms for the pairwise alignment of biological networks. 2351-2359
• 
  Yinming Jiao, Martin Widschwendter, Andrew E. Teschendorff:
  A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. 2360-2366

Databases and Ontologies

• 
  James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy W. Heiland, James A. Glazier:
  The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. 2367-2374

Applications Notes
Genetics and Population Analysis

• 
  Robert J. Carroll, Lisa Bastarache, Joshua C. Denny:
  R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. 2375-2376
• 
  Gao T. Wang, Biao Li, Regie P. Lyn Santos-Cortez, Bo Peng, Suzanne M. Leal:
  Power analysis and sample size estimation for sequence-based association studies. 2377-2378

Data and Text Mining

• 
  Hiroshi Tsugawa, Mitsuhiro Kanazawa, Atsushi Ogiwara, Masanori Arita:
  MRMPROBS suite for metabolomics using large-scale MRM assays. 2379-2380
• 
  Stephen J. Goodswen, Paul J. Kennedy, John T. Ellis:
  Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology. 2381-2383

Databases and Ontologies

• 
  Matthew Horridge, Tania Tudorache, Csongor Nyulas, Jennifer Vendetti, Natalya Fridman Noy, Mark A. Musen:
  WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. 2384-2385
• 
  Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee, Yu-Ju Chen:
  dbGSH: a database of S-glutathionylation. 2386-2388

Bioimage Informatics

• 
  Martin Ovesný, Pavel Krízek, Josef Borkovec, Zdenek Svindrych, Guy M. Hagen:
  ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. 2389-2390

Volume 30, Number 17, September 2014

ECCB 2014 Proceedings Papers Committee
Editorial

• 
  Marie-Dominique Devignes, Yves Moreau:
  ECCB 2014: The 13^th European Conference on Computational Biology. 345-348

Original Papers

• 
  Hannes Hauswedell, Jochen Singer, Knut Reinert:
  Lambda: the local aligner for massive biological data. 349-355
• 
  Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard:
  Fiona: a parallel and automatic strategy for read error correction. 356-363
• 
  Jocelyn Brayet, Farida Zehraoui, Laurence Jeanson-Leh, David Israeli, Fariza Tahi:
  Towards a piRNA prediction using multiple kernel fusion and support vector machine. 364-370
• 
  Sepideh Mazrouee, Wei Wang:
  FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs. 371-378
• 
  Volodymyr Kuleshov:
  Probabilistic single-individual haplotyping. 379-385
• 
  Céline Lévy-Leduc, Maud Delattre, Tristan Mary-Huard, Stéphane Robin:
  Two-dimensional segmentation for analyzing Hi-C data. 386-392
• 
  Raymond G. Cavalcante, Chee Lee, Ryan P. Welch, Snehal Patil, Terry E. Weymouth, Laura J. Scott, Maureen A. Sartor:
  Broad-Enrich: functional interpretation of large sets of broad genomic regions. 393-400
• 
  Theresa Schacht, Marcus Oswald, Roland Eils, Stefan B. Eichmüller, Rainer König:
  Estimating the activity of transcription factors by the effect on their target genes. 401-407
• 
  John A. Capra, Dennis Kostka:
  Modeling DNA methylation dynamics with approaches from phylogenetics. 408-414
• 
  Thorsten Will, Volkhard Helms:
  Identifying transcription factor complexes and their roles. 415-421
• 
  TaeJin Ahn, Eunjin Lee, Nam Huh, Taesung Park:
  Personalized identification of altered pathways in cancer using accumulated normal tissue data. 422-429
• 
  Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane:
  Alignment-free protein interaction network comparison. 430-437
• 
  Somaye Hashemifar, Jinbo Xu:
  HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks. 438-444
• 
  Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan:
  Experimental design schemes for learning Boolean network models. 445-452
• 
  Yongsoo Kim, Jin-Hyeok Jang, Seungjin Choi, Daehee Hwang:
  TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information. 453-460
• 
  Tommi Suvitaival, Simon Rogers, Samuel Kaski:
  Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations. 461-467
• 
  Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee:
  Causal network inference using biochemical kinetics. 468-474
• 
  Peter Kreyssig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim, Peter Dittrich:
  Effects of small particle numbers on long-term behaviour in discrete biochemical systems. 475-481
• 
  Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson:
  PconsFold: improved contact predictions improve protein models. 482-488
• 
  Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen:
  CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. 489-496
• 
  Suleiman A. Khan, Seppo Virtanen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski:
  Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. 497-504
• 
  Gabriel Studer, Marco Biasini, Torsten Schwede:
  Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). 505-511
• 
  James H. Collier, Lloyd Allison, Arthur M. Lesk, Maria Garcia de la Banda, Arun Siddharth Konagurthu:
  A new statistical framework to assess structural alignment quality using information compression. 512-518
• 
  Manuel Lafond, Cédric Chauve, Riccardo Dondi, Nadia El-Mabrouk:
  Polytomy refinement for the correction of dubious duplications in gene trees. 519-526
• 
  Christina Kratsch, Alice Carolyn McHardy:
  RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees. 527-533
• 
  Philipp Benner, Miroslav Bacák, Pierre-Yves Bourguignon:
  Point estimates in phylogenetic reconstructions. 534-540
• 
  Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow:
  ASTRAL: genome-scale coalescent-based species tree estimation. 541-548
• 
  Michael P. Schroeder, Carlota Rubio-Perez, David Tamborero, Abel Gonzalez-Perez, Núria López-Bigas:
  OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. 549-555
• 
  Mehmet Gönen, Adam A. Margolin:
  Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. 556-563
• 
  Jingwen Yan, Lei Du, Sungeun Kim, Shannon L. Risacher, Heng Huang, Jason H. Moore, Andrew J. Saykin, Li Shen:
  Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm. 564-571
• 
  Rui Tian, Malay Kumar Basu, Emidio Capriotti:
  ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. 572-578
• 
  Xueping Liu, Mónica Campillos:
  Unveiling new biological relationships using shared hits of chemical screening assay pairs. 579-586
• 
  Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone, Giulio Iannello:
  Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images. 587-593
• 
  Vladimir Gligorijevic, Vuk Janjic, Natasa Przulj:
  Integration of molecular network data reconstructs Gene Ontology. 594-600
• 
  Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, Robert Stevens:
  Extracting patterns of database and software usage from the bioinformatics literature. 601-608
• 
  Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac:
  The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. 609-616
• 
  Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Núria López-Bigas, Mathew Garnett, Giuseppe Jurman, Julio Saez-Rodriguez:
  Fast randomization of large genomic datasets while preserving alteration counts. 617-623
• 
  Nadav Rappoport, Amos Stern, Nathan Linial, Michal Linial:
  Entropy-driven partitioning of the hierarchical protein space. 624-630
• 
  Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer:
  Microarray R-based analysis of complex lysate experiments with MIRACLE. 631-638
• 
  Evangelos Bellos, Lachlan J. M. Coin:
  cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. 639-645

Discovery note

• 
  Jihye Kim, Vihas T. Vasu, Rangnath Mishra, Katherine R. Singleton, Minjae Yoo, Sonia M. Leach, Eveline Farias-Hesson, Robert J. Mason, Jaewoo Kang, Preveen Ramamoorthy, Jeffrey A. Kern, Lynn E. Heasley, James H. Finigan, Aik Choon Tan:
  Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. 2393-2398

Original Papers

• 
  Rotem Ben-Hamo, Moriah Gidoni, Sol Efroni:
  PhenoNet: identification of key networks associated with disease phenotype. 2399-2405
• 
  Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher:
  Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. 2406-2413
• 
  Yongseok Park, Maria E. Figueroa, Laura S. Rozek, Maureen A. Sartor:
  MethylSig: a whole genome DNA methylation analysis pipeline. 2414-2422
• 
  Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander:
  SEK: sparsity exploiting k-mer-based estimation of bacterial community composition. 2423-2431
• 
  Walyd Khenoussi, Renaud Vanhoutrève, Olivier Poch, Julie Dawn Thompson:
  SIBIS: a Bayesian model for inconsistent protein sequence estimation. 2432-2439
• 
  Lizong Deng, Aiping Wu, Wentao Dai, Tingrui Song, Ya Cui, Taijiao Jiang:
  Exploring protein domain organization by recognition of secondary structure packing interfaces. 2440-2446
• 
  Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert:
  Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. 2447-2455
• 
  Navodit Misra, Ewa Szczurek, Martin Vingron:
  Inferring the paths of somatic evolution in cancer. 2456-2463
• 
  Mehrab Ghanat Bari, Xuepo Ma, Jianqiu Zhang:
  PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM. 2464-2470
• 
  Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela:
  Exploration and retrieval of whole-metagenome sequencing samples. 2471-2479
• 
  Charny Park, Namhee Yu, Ikjung Choi, Wan Kyu Kim, Sanghyuk Lee:
  lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. 2480-2485
• 
  Florian Gomez, Ralph Lukas Stoop, Ruedi Stoop:
  Universal dynamical properties preclude standard clustering in a large class of biochemical data. 2486-2493

Applications Notes

• 
  Jan De Neve, Joris Meys, Jean-Pierre Ottoy, Lieven Clement, Olivier Thas:
  unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R. 2494-2495
• 
  Kamil Slowikowski, Xinli Hu, Soumya Raychaudhuri:
  SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci. 2496-2497
• 
  Weixin Wang, Panwen Wang, Feng Xu, Ruibang Luo, Maria P. Wong, Tak Wah Lam, Junwen Wang:
  FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data. 2498-2500
• 
  Alex Lancaster, Andrew Nutter-Upham, Susan Lindquist, Oliver D. King:
  PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. 2501-2502
• 
  Gregory G. Faust, Ira M. Hall:
  SAMBLASTER: fast duplicate marking and structural variant read extraction. 2503-2505
• 
  Michael J. Sanderson:
  Ceiba: scalable visualization of phylogenies and 2D/3D image collections. 2506-2507
• 
  Guillermo Rodrigo, Alfonso Jaramillo:
  RiboMaker: computational design of conformation-based riboregulation. 2508-2510
• 
  George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström:
  aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. 2511-2513
• 
  Francesco Russo, Claudia Angelini:
  RNASeqGUI: a GUI for analysing RNA-Seq data. 2514-2516
• 
  Charlotte Soneson:
  compcodeR - an R package for benchmarking differential expression methods for RNA-seq data. 2517-2518
• 
  Thomas Nussbaumer, Karl G. Kugler, Kai Christian Bader, Sapna Sharma, Michael Seidel, Klaus F. X. Mayer:
  RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data. 2519-2520
• 
  Daniel Broudy, Trevor Killeen, Meena Choi, Nicholas Shulman, Deepak R. Mani, Susan E. Abbatiello, Deepak Mani, Rushdy Ahmad, Alexandria K. Sahu, Birgit Schilling, Kaipo Tamura, Yuval Boss, Vagisha Sharma, Bradford W. Gibson, Steven A. Carr, Olga Vitek, Michael J. MacCoss, Brendan MacLean:
  A framework for installable external tools in Skyline. 2521-2523
• 
  Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean, Olga Vitek:
  MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. 2524-2526
• 
  Ken-Chi Yang, Chia-Lang Hsu, Chen-Ching Lin, Hsueh-Fen Juan, Hsuan-Cheng Huang:
  Mirin: identifying microRNA regulatory modules in protein-protein interaction networks. 2527-2528
• 
  Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming:
  fastGapFill: efficient gap filling in metabolic networks. 2529-2531
• 
  Paul Müller, Petra Schwille, Thomas Weidemann:
  PyCorrFit - generic data evaluation for fluorescence correlation spectroscopy. 2532-2533
• 
  Jia-Hong Wang, Ling-Feng Zhao, Pei Lin, Xiao-Rong Su, Shi-Jun Chen, Li-Qiang Huang, Hua-Feng Wang, Hai Zhang, Zhen-Fu Hu, Kai-Tai Yao, Zhong-Xi Huang:
  GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms. 2534-2536
• 
  Jordan Plieskatt, Gabriel Rinaldi, Paul J. Brindley, Xinying Jia, Jeremy Potriquet, Jeffrey Bethony, Jason P. Mulvenna:
  Bioclojure: a functional library for the manipulation of biological sequences. 2537-2539
• 
  Daeun Ryu, SeongBeom Cho, Hun Kim, Sanghyuk Lee, Wan Kyu Kim:
  GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype. 2540-2542

Volume 30, Number 18, September 2014

Original Papers
Genome Analysis

• 
  Huy Hoang Do, Wing-Kin Sung:
  CWig: compressed representation of Wiggle/BedGraph format. 2543-2550
• 
  Israel T. da Silva, Rafael Rosales, Adriano J. Holanda, Michel C. Nussenzweig, Mila Jankovic:
  Identification of chromosomal translocation hotspots via scan statistics. 2551-2558
• 
  Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada:
  Reference-free prediction of rearrangement breakpoint reads. 2559-2567
• 
  Yan-Xiao Zhang, Yu-Hsuan Lin, Timothy D. Johnson, Laura S. Rozek, Maureen A. Sartor:
  PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. 2568-2575

Sequence Analysis

• 
  Zhenhua Yu, Yuanning Liu, Yi Shen, Minghui Wang, Ao Li:
  CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data. 2576-2583

Structural Bioinformatics

• 
  Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger:
  Memory-efficient RNA energy landscape exploration. 2584-2591
• 
  Christophe N. Magnan, Pierre Baldi:
  SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. 2592-2597

Gene Expression

• 
  María José Nueda, Sonia Tarazona, Ana Conesa:
  Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. 2598-2602
• 
  Andrew Quinn, Punita Juneja, Francis M. Jiggins:
  Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data. 2603-2610

Genetics and Population Analysis

• 
  Meng Wang, Shili Lin:
  FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads. 2611-2618

Systems Biology

• 
  Boon-Siew Seah, Sourav S. Bhowmick, C. Forbes Dewey Jr.:
  DualAligner: a dual alignment-based strategy to align protein interaction networks. 2619-2626
• 
  Yue Li, Cheng Liang, Ka-Chun Wong, Jiawei Luo, Zhaolei Zhang:
  Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. 2627-2635

Data and Text Mining

• 
  Christopher J. Conley, Robert Smith, Ralf J. O. Torgrip, Ryan M. Taylor, Ralf Tautenhahn, John T. Prince:
  Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection. 2636-2643

Bioimage Informatics

• 
  Sotiris Dimopoulos, Christian E. Mayer, Fabian Rudolf, Jörg Stelling:
  Accurate cell segmentation in microscopy images using membrane patterns. 2644-2651

Applications Notes
Genome Analysis

• 
  Marek S. Wiewiórka, Antonio Messina, Alicja Pacholewska, Sergio Maffioletti, Piotr Gawrysiak, Michal J. Okoniewski:
  SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision. 2652-2653
• 
  Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak:
  GenomeVISTA - an integrated software package for whole-genome alignment and visualization. 2654-2655
• 
  Matthias Zytnicki, Eduard Akhunov, Hadi Quesneville:
  Tedna: a transposable element de novo assembler. 2656-2658
• 
  Erika Sallet, Jérôme Gouzy, Thomas Schiex:
  EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes. 2659-2661

Sequence Analysis

• 
  Marco Falda, Paolo Fontana, Luisa Barzon, Stefano Toppo, Enrico Lavezzo:
  keeSeek: searching distant non-existing words in genomes for PCR-based applications. 2662-2664
• 
  Peng Jiang, Susanne Meyer, Zhonggang Hou, Nicholas E. Propson, H. Tom Soh, James A. Thomson, Ron M. Stewart:
  MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. 2665-2667
• 
  Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen:
  MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. 2668-2669
• 
  Evan A. Boyle, Brian J. O'Roak, Beth K. Martin, Akash Kumar, Jay Shendure:
  MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. 2670-2672
• 
  Aidan O'Brien, Timothy L. Bailey:
  GT-Scan: identifying unique genomic targets. 2673-2675
• 
  Niko Popitsch:
  CODOC: efficient access, analysis and compression of depth of coverage signals. 2676-2677
• 
  Chen Wang, Jared Evans, Aditya Bhagwate, Naresh Prodduturi, Vivekananda Sarangi, Mridu Middha, Hugues Sicotte, Peter T. Vedell, Steven N. Hart, Gavin R. Oliver, Jean-Pierre A. Kocher, Matthew J. Maurer, Anne J. Novak, Susan L. Slager, James R. Cerhan, Yan W. Asmann:
  PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. 2678-2680

Structural Bioinformatics

• 
  Ahmet Bakan, Anindita Dutta, Wenzhi Mao, Ying Liu, Chakra Chennubhotla, Timothy R. Lezon, Ivet Bahar:
  Evol and ProDy for bridging protein sequence evolution and structural dynamics. 2681-2683
• 
  Barbora Kozlíková, Eva Sebestova, Vilém Sustr, Jan Brezovsky, Ondrej Strnad, Lukas Daniel, David Bednar, Antonín Pavelka, Martin Manak, Martin Bezdeka, Petr Benes, Matus Kotry, Artur Góra, Jirí Damborský, Jiri Sochor:
  CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. 2684-2685

Genetics and Population Analysis

• 
  John M. Hickey, Gregor Gorjanc, Sarah Hearne, Bevan Emma Huang:
  AlphaMPSim: flexible simulation of multi-parent crosses. 2686-2688

Data and Text Mining

• 
  Dimitri Guala, Erik Sjölund, Erik L. L. Sonnhammer:
  MaxLink: network-based prioritization of genes tightly linked to a disease seed set. 2689-2690

Bioimage Informatics

• 
  Stephen Taylor, Roger Noble:
  HTML5 PivotViewer: high-throughput visualization and querying of image data on the web. 2691-2692

Volume 30, Number 19, October 2014

Original Papers
Genome Analysis

• 
  Zi Wang, Edward W. J. Curry, Giovanni Montana:
  Network-guided regression for detecting associations between DNA methylation and gene expression. 2693-2701
• 
  Javier Pérez-Rodríguez, Alexis G. Arroyo-Peña, Nicolás García-Pedrajas:
  Improving translation initiation site and stop codon recognition by using more than two classes. 2702-2708
• 
  Sagar M. Utturkar, Dawn M. Klingeman, Miriam L. Land, Christopher W. Schadt, Mitchel J. Doktycz, Dale A. Pelletier, Steven D. Brown:
  Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. 2709-2716
• 
  Bahlul Haider, Tae-Hyuk Ahn, Brian Bushnell, Juanjuan Chai, Alex Copeland, Chongle Pan:
  Omega: an Overlap-graph de novo Assembler for Metagenomics. 2717-2722

Sequence Analysis

• 
  Paul Greenfield, Konsta Duesing, Alexie Papanicolaou, Denis C. Bauer:
  Blue: correcting sequencing errors using consensus and context. 2723-2732

Structural Bioinformatics

• 
  Mario Abdel Messih, Rosalba Lepore, Paolo Marcatili, Anna Tramontano:
  Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies. 2733-2740

Gene Expression

• 
  So Young Ryu, Wei-Jun Qian, David G. Camp II, Richard D. Smith, Ronald G. Tompkins, Ronald W. Davis, Wenzhong Xiao:
  Detecting differential protein expression in large-scale population proteomics. 2741-2746
• 
  Pashupati P. Mishra, Petri Törönen, Yrjö Leino, Liisa Holm:
  Gene set analysis: limitations in popular existing methods and proposed improvements. 2747-2756
• 
  Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, Elana J. Fertig:
  Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. 2757-2763

Systems Biology

• 
  Rónán Daly, Simon Rogers, Joe Wandy, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling:
  MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach. 2764-2771
• 
  Fan Zhu, Yuanfang Guan:
  Predicting dynamic signaling network response under unseen perturbations. 2772-2778
• 
  Ying Wang, Christopher A. Penfold, David A. Hodgson, Miriam L. Gifford, Nigel J. Burroughs:
  Correcting for link loss in causal network inference caused by regulator interference. 2779-2786

Data and Text Mining

• 
  Ameet Talwalkar, Jesse Liptrap, Julie Newcomb, Christopher Hartl, Jonathan Terhorst, Kristal Curtis, Ma'ayan Bresler, Yun S. Song, Michael I. Jordan, David A. Patterson:
  SMaSH: a benchmarking toolkit for human genome variant calling. 2787-2795
• 
  Lilian Janin, Ole Schulz-Trieglaff, Anthony J. Cox:
  BEETL-fastq: a searchable compressed archive for DNA reads. 2796-2801
• 
  Yinan Zheng, Zhe Fei, Wei Zhang, Justin B. Starren, Lei Liu, Andrea A. Baccarelli, Yi Li, Lifang Hou:
  PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures. 2802-2807

Applications Notes
Genome Analysis

• 
  Douglas H. Phanstiel, Alan P. Boyle, Carlos L. Araya, Michael P. Snyder:
  Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. 2808-2810
• 
  Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors:
  circlize implements and enhances circular visualization in R. 2811-2812

Sequence Analysis

• 
  Lisle E. Mose, Matthew D. Wilkerson, D. Neil Hayes, Charles M. Perou, Joel S. Parker:
  ABRA: improved coding indel detection via assembly-based realignment. 2813-2815
• 
  Simone Leo, Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Nicola Soranzo, Enis Afgan, Gianluigi Zanetti:
  BioBlend.objects: metacomputing with Galaxy. 2816-2817
• 
  James K. Bonfield:
  The Scramble conversion tool. 2818-2819
• 
  Yongkyu Kim, Werner Liesack:
  DAFGA: diversity analysis of functional gene amplicons. 2820-2821

Structural Bioinformatics

• 
  Dariusz Mrozek, Bozena Malysiak-Mrozek, Artur Klapcinski:
  Cloud4Psi: cloud computing for 3D protein structure similarity searching. 2822-2825

Gene Expression

• 
  Jihoon Kim, Eric Levy, Alex Ferbrache, Petra Stepanowsky, Claudiu Farcas, Shuang Wang, Stefan Brunner, Tyler Bath, Yuan Wu, Lucila Ohno-Machado:
  MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. 2826-2827

Genetics and Population Analysis

• 
  Shuang Feng, Dajiang Liu, Xiaowei Zhan, Mary Kate Wing, Gonçalo R. Abecasis:
  RAREMETAL: fast and powerful meta-analysis for rare variants. 2828-2829

Systems Biology

• 
  Max Flöttmann, Jannis Uhlendorf, Till Scharp, Edda Klipp, Thomas W. Spiesser:
  SensA: web-based sensitivity analysis of SBML models. 2830-2831
• 
  Gerard Wong, Jeffrey Chan, Bronwyn A. Kingwell, Christopher Leckie, Peter J. Meikle:
  LICRE: unsupervised feature correlation reduction for lipidomics. 2832-2833
• 
  Shailesh Tripathi, Matthias Dehmer, Frank Emmert-Streib:
  NetBioV: an R package for visualizing large network data in biology and medicine. 2834-2836

Data and Text Mining

• 
  Jikai Lei, Yanni Sun:
  miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data. 2837-2839

Databases and Ontologies

• 
  Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman:
  Literome: PubMed-scale genomic knowledge base in the cloud. 2840-2842

Volume 30, Number 20, October 2014

Review
Sequence Analysis

• 
  Heng Li:
  Toward better understanding of artifacts in variant calling from high-coverage samples. 2843-2851

Original Papers
Genome Analysis

• 
  Alberto Magi, Lorenzo Tattini, Flavia Palombo, Matteo Benelli, Alessandro Gialluisi, Betti Giusti, Rosanna Abbate, Marco Seri, Gian Franco Gensini, Giovanni Romeo, Tommaso Pippucci:
  H³M²: detection of runs of homozygosity from whole-exome sequencing data. 2852-2859
• 
  Qi Zhang, Sündüz Keles:
  CNV-guided multi-read allocation for ChIP-seq. 2860-2867
• 
  Jianling Zhong, Todd Wasson, Alexander J. Hartemink:
  Learning protein-DNA interaction landscapes by integrating experimental data through computational models. 2868-2874

Sequence Analysis

• 
  Javier Arnedo, Rocío Romero-Záliz, Igor Zwir, Coral del Val:
  A multiobjective method for robust identification of bacterial small non-coding RNAs. 2875-2882
• 
  Philip Heller, H. James Tripp, Kendra Turk-Kubo, Jonathan P. Zehr:
  ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank. 2883-2890

Structural Bioinformatics

• 
  Javier Vargas, Ana-Lucia Álvarez-Cabrera, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano:
  Efficient initial volume determination from electron microscopy images of single particles. 2891-2898

Gene Expression

• 
  Francesc Fernández-Albert, Rafael Llorach, Mar Garcia-Aloy, Andrey Ziyatdinov, Cristina Andres-Lacueva, Alexandre Perera-Lluna:
  Intensity drift removal in LC/MS metabolomics by common variance compensation. 2899-2905

Genetics and Population Analysis

• 
  Bogdan Pasaniuc, Noah Zaitlen, Huwenbo Shi, Gaurav Bhatia, Alexander Gusev, Joseph Pickrell, Joel Hirschhorn, David P. Strachan, Nick Patterson, Alkes L. Price:
  Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. 2906-2914
• 
  John Michael Rañola, John Novembre, Kenneth Lange:
  Fast spatial ancestry via flexible allele frequency surfaces. 2915-2922

Systems Biology

• 
  Wenhui Wang, Sen Yang, Xiang Zhang, Jing Li:
  Drug repositioning by integrating target information through a heterogeneous network model. 2923-2930
• 
  Vikram Saraph, Tijana Milenkovic:
  MAGNA: Maximizing Accuracy in Global Network Alignment. 2931-2940

Data and Text Mining

• 
  Tianwei Yu, Dean P. Jones:
  Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach. 2941-2948

Databases and Ontologies

• 
  Ehsan Behnam, Andrew D. Smith:
  The Amordad database engine for metagenomics. 2949-2955

Applications Notes
Genome Analysis

• 
  Erik Gafni, Lovelace J. Luquette, Alex Lancaster, Jared B. Hawkins, Jae-Yoon Jung, Yassine Souilmi, Dennis P. Wall, Peter J. Tonellato:
  COSMOS: Python library for massively parallel workflows. 2956-2958
• 
  Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier:
  GATB: Genome Assembly & Analysis Tool Box. 2959-2961
• 
  Anna-Sapfo Malaspinas, Ole Tange, José Víctor Moreno-Mayar, Morten Rasmussen, Michael Degiorgio, Yong Wang, Cristina E. Valdiosera, Gustavo Politis, Eske Willerslev, Rasmus Nielsen:
  bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). 2962-2964
• 
  Kitty K. Lo, Christopher Boustred, Lyn S. Chitty, Vincent Plagnol:
  RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy. 2965-2967
• 
  Marc Güell, Luhan Yang, George M. Church:
  Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). 2968-2970
• 
  Ruth Heller, Shay Yaacoby, Daniel Yekutieli:
  repfdr: a tool for replicability analysis for genome-wide association studies. 2971-2972

Sequence Analysis

• 
  Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
  TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs. 2973-2974
• 
  Federico Agostini, Davide Cirillo, Carmen Maria Livi, Riccardo Delli Ponti, Gian Gaetano Tartaglia:
  ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli. 2975-2977

Structural Bioinformatics

• 
  Hitesh Patel, Björn A. Grüning, Stefan Günther, Irmgard Merfort:
  PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering. 2978-2980
• 
  Elmar Krieger, Gert Vriend:
  YASARA View - molecular graphics for all devices - from smartphones to workstations. 2981-2982

Systems Biology

• 
  Christopher Pooley, David Ruau, Patrick Lombard, Berthold Göttgens, Anagha Joshi:
  TRES predicts transcription control in embryonic stem cells. 2983-2985
• 
  Gilles Vieira, Marc Carnicer, Jean-Charles Portais, Stéphanie Heux:
  FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. 2986-2988
• 
  Jae-Seong Yang, Eduard Sabidó, Luis Serrano, Christina Kiel:
  TAPAS: tools to assist the targeted protein quantification of human alternative splice variants. 2989-2990
• 
  Andrei Kramer, Vassilios Stathopoulos, Mark A. Girolami, Nicole Radde:
  mcmc_clib-an advanced MCMC sampling package for ode models. 2991-2992

Volume 30, Number 21, November 2014

Editorial
Genome Analysis

• 
  Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium:
  Big data and other challenges in the quest for orthologs. 2993-2998

Discovery note
Systems Biology

• 
  Irene Papatheodorou, Rudolfs Petrovs, Janet M. Thornton:
  Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing. 2999-3003

Original Papers
Sequence Analysis

• 
  Thomas Hackl, Rainer Hedrich, Jörg Schultz, Frank Förster:
  proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. 3004-3011
• 
  Jessen T. Havill, Chinmoy Bhatiya, Steven M. Johnson, Joseph D. Sheets, Jeffrey S. Thompson:
  A new approach for detecting riboswitches in DNA sequences. 3012-3019

Phylogenetics

• 
  Benjamin Horvilleur, Nicolas Lartillot:
  Monte Carlo algorithms for Brownian phylogenetic models. 3020-3028

Structural Bioinformatics

• 
  Christopher W. Wood, Marc Bruning, Amaurys Ávila Ibarra, Gail J. Bartlett, Andrew R. Thomson, Richard B. Sessions, R. Leo Brady, Derek N. Woolfson:
  CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. 3029-3035

Gene Expression

• 
  Aliccia Bollig-Fischer, Luca Marchetti, Cristina Mitrea, Jiusheng Wu, Adéle Kruger, Vincenzo Manca, Sorin Draghici:
  Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion. 3036-3043
• 
  Megan Orr, Peng Liu, Dan Nettleton:
  An improved method for computing q-values when the distribution of effect sizes is asymmetric. 3044-3053
• 
  Chun-Pei Cheng, I-Ying Kuo, Hakan Alakus, Kelly A. Frazer, Olivier Harismendy, Yi-Ching Wang, Vincent S. Tseng:
  Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. 3054-3061
• 
  Sihai Dave Zhao, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron:
  Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. 3062-3069
• 
  Junpeng Zhang, Thuc Duy Le, Lin Liu, Bing Liu, Jianfeng He, Gregory J. Goodall, Jiuyong Li:
  Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data. 3070-3077

Genetics and Population Analysis

• 
  Francesco Sambo, Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli:
  Compression and fast retrieval of SNP data. 3078-3085

Systems Biology

• 
  Mushthofa Mushthofa, Gustavo Torres, Yves Van de Peer, Kathleen Marchal, Martine De Cock:
  ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. 3086-3092
• 
  Ingo Vogt, Jeanette Prinz, Karolina Worf, Mónica Campillos:
  Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations. 3093-3100
• 
  Seunghwa Kang, Simon Kahan, Jason E. McDermott, Nicholas S. Flann, Ilya Shmulevich:
  Biocellion: accelerating computer simulation of multicellular biological system models. 3101-3108
• 
  Eduard Porta-Pardo, Adam Godzik:
  e-Driver: a novel method to identify protein regions driving cancer. 3109-3114

Applications Notes
Genome Analysis

• 
  Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli:
  MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. 3115-3117
• 
  Ezequiel L. Nicolazzi, Daniela Iamartino, John L. Williams:
  AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow. 3118-3119
• 
  Yoli Shavit, Fiona Kathryn Hamey, Pietro Liò:
  FisHiCal: an R package for iterative FISH-based calibration of Hi-C data. 3120-3122
• 
  Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Robert G. Beiko:
  STAMP: statistical analysis of taxonomic and functional profiles. 3123-3124
• 
  Jonathan Crabtree, Sonia Agrawal, Anup Mahurkar, Garry S. A. Myers, David A. Rasko, Owen White:
  Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG. 3125-3127

Sequence Analysis

• 
  Stefan Seemayer, Markus Gruber, Johannes Söding:
  CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations. 3128-3130

Structural Bioinformatics

• 
  Lou Götz, Jodie L. Abrahams, Julien Mariethoz, Pauline M. Rudd, Niclas G. Karlsson, Nicolle H. Packer, Matthew P. Campbell, Frédérique Lisacek:
  GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination. 3131-3133

Genetics and Population Analysis

• 
  Gabriel E. Hoffman, Jason G. Mezey, Eric E. Schadt:
  lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R. 3134-3135

Data and Text Mining

• 
  Bo Wen, Shaohang Xu, Gloria M. Sheynkman, Qiang Feng, Liang Lin, Quanhui Wang, Xun Xu, Jun Wang, Siqi Liu:
  sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. 3136-3138
• 
  Ahmed Mohamed, Timothy Hancock, Canh Hao Nguyen, Hiroshi Mamitsuka:
  NetPathMiner: R/Bioconductor package for network path mining through gene expression. 3139-3141

Corrigendum
Data and Text Mining

• 
  Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng:
  FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model. 3142

Volume 30, Number 22, November 2014

Original Papers
Genome Analysis

• 
  Eduardo G. Gusmão, Christoph Dieterich, Martin Zenke, Ivan G. Costa:
  Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications. 3143-3151
• 
  Ying Ding, Shaowu Tang, Serena G. Liao, Jia Jia, Steffi Oesterreich, Yan Lin, George C. Tseng:
  Bias correction for selecting the minimal-error classifier from many machine learning models. 3152-3158
• 
  Timothy Daley, Andrew D. Smith:
  Modeling genome coverage in single-cell sequencing. 3159-3165

Sequence Analysis

• 
  Joshua Loving, Yözen Hernández, Gary Benson:
  BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm. 3166-3173
• 
  Yeting Zhang, Yazhou Sun:
  A method for de novo nucleic acid diagnostic target discovery. 3174-3180
• 
  Niclas Thomas, Katharine Best, Mattia Cinelli, Shlomit Reich-Zeliger, Hilah Gal, Eric Shifrut, Asaf Madi, Nir Friedman, John Shawe-Taylor, Benny Chain:
  Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. 3181-3188

Structural Bioinformatics

• 
  Daniel Taylor, Gavin C. Cawley, Steven Hayward:
  Quantitative method for the assignment of hinge and shear mechanism in protein domain movements. 3189-3196

Genetics and Population Analysis

• 
  Sungkyoung Choi, Sungyoung Lee, Sven Cichon, Markus M. Nöthen, Christoph Lange, Taesung Park, Sungho Won:
  FARVAT: a family-based rare variant association test. 3197-3205
• 
  Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Myers Kadie, David Heckerman, Jennifer Listgarten:
  Greater power and computational efficiency for kernel-based association testing of sets of genetic variants. 3206-3214
• 
  Damian Smedley, Sebastian Köhler, Johanna Christina Czeschik, Joanna S. Amberger, Carol A. Bocchini, Ada Hamosh, Julian Veldboer, Tomasz Zemojtel, Peter N. Robinson:
  Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. 3215-3222

Systems Biology

• 
  Dapeng Hao, Chuanxing Li, Shaojun Zhang, Jianping Lu, Yongshuai Jiang, Shiyuan Wang, Meng Zhou:
  Network-based analysis of genotype-phenotype correlations between different inheritance modes. 3223-3231
• 
  Siu Hung Joshua Chan, Christian Solem, Peter Ruhdal Jensen, Ping Ji:
  Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property. 3232-3239

Data and Text Mining

• 
  Lana Yeganova, Won Kim, Sun Kim, W. John Wilbur:
  Retro: concept-based clustering of biomedical topical sets. 3240-3248
• 
  Nikolas Papanikolaou, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, Vasilis J. Promponas, Ioannis Iliopoulos:
  BioTextQuest⁺: a knowledge integration platform for literature mining and concept discovery. 3249-3256
• 
  Verena Starke, Andrew Steele:
  Thresher: an improved algorithm for peak height thresholding of microbial community profiles. 3257-3263

Applications Notes
Genome Analysis

• 
  Eun-Cheon Lim, Jonas Müller, Jörg Hagmann, Stefan R. Henz, Sang-Tae Kim, Detlef Weigel:
  Trowel: a fast and accurate error correction module for Illumina sequencing reads. 3264-3265
• 
  David M. Curran, John S. Gilleard, James Wasmuth:
  Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes. 3266-3267

Sequence Analysis

• 
  Carolin Walter, Daniel Schuetzmann, Frank Rosenbauer, Martin Dugas:
  Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data. 3268-3269
• 
  Phi-Vu Nguyen, Chandra Shekhar Verma, Samuel Ken-En Gan:
  DNAApp: a mobile application for sequencing data analysis. 3270-3271
• 
  Michael Olejnik, Michel Steuwer, Sergei Gorlatch, Dominik Heider:
  gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing. 3272-3273
• 
  Heng Li:
  Fast construction of FM-index for long sequence reads. 3274-3275

Phylogenetics

• 
  Anders Larsson:
  AliView: a fast and lightweight alignment viewer and editor for large datasets. 3276-3278

Structural Bioinformatics

• 
  Kazuo Yamashita, Kazuyoshi Ikeda, Karlou Mar Amada, Shide Liang, Yuko Tsuchiya, Haruki Nakamura, Hiroki Shirai, Daron M. Standley:
  Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. 3279-3280
• 
  Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama:
  MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. 3281-3283

Gene Expression

• 
  Seon-Kyu Kim, Jong Hwan Kim, Seok-Joong Yun, Wun-Jae Kim, Seon-Young Kim:
  APPEX: analysis platform for the identification of prognostic gene expression signatures in cancer. 3284-3286

Genetics and Population Analysis

• 
  Michael Nodzenski, Michael J. Muehlbauer, James R. Bain, Anna C. Reisetter, William L. Lowe Jr., Denise M. Scholtens:
  Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data. 3287-3288

Systems Biology

• 
  Qiaonan Duan, Zichen Wang, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan:
  Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. 3289-3290

Bioimage Informatics

• 
  David Breuer, Zoran Nikoloski:
  img2net: automated network-based analysis of imaged phenotypes. 3291-3292

Volume 30, Number 23, December 2014

Original Papers
Genome Analysis

• 
  Ngan Nguyen, Glenn Hickey, Brian J. Raney, Joel Armstrong, Hiram Clawson, Ann S. Zweig, Donna Karolchik, William James Kent, David Haussler, Benedict Paten:
  Comparative assembly hubs: Web-accessible browsers for comparative genomics. 3293-3301

Sequence Analysis

• 
  Naoto Usuyama, Yuichi Shiraishi, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Satoru Miyano, Seiya Imoto:
  HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. 3302-3309
• 
  András Szolek, Benjamin Schubert, Christopher Mohr, Marc Sturm, Magdalena Feldhahn, Oliver Kohlbacher:
  OptiType: precision HLA typing from next-generation sequencing data. 3310-3316

Phylogenetics

• 
  Julia Chifman, Laura Salter Kubatko:
  Quartet Inference from SNP Data Under the Coalescent Model. 3317-3324

Gene Expression

• 
  Fan Zhu, Lihong Shi, Hongdong Li, Ridvan Eksi, James Douglas Engel, Yuanfang Guan:
  Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. 3325-3333

Genetics and Population Analysis

• 
  Wei Xie, Murat Kantarcioglu, William S. Bush, Dana C. Crawford, Joshua C. Denny, Raymond Heatherly, Bradley A. Malin:
  SecureMA: protecting participant privacy in genetic association meta-analysis. 3334-3341
• 
  Oliver S. Burren, Hui Guo, Chris Wallace:
  VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes. 3342-3348

Data and Text Mining

• 
  Ulisses M. Braga-Neto, Amin Zollanvari, Edward R. Dougherty:
  Cross-validation under separate sampling: strong bias and how to correct it. 3349-3355
• 
  Cornelia M. Hooper, Sandra K. Tanz, Ian R. Castleden, Michael A. Vacher, Ian D. Small, A. Harvey Millar:
  SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome. 3356-3364
• 
  Quoc-Chinh Bui, Peter M. A. Sloot, Erik M. van Mulligen, Jan A. Kors:
  A novel feature-based approach to extract drug-drug interactions from biomedical text. 3365-3371
• 
  Kristen Feher, Jenny Kirsch, Andreas Radbruch, Hyun-Dong Chang, Toralf Kaiser:
  Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm. 3372-3378

Databases and Ontologies

• 
  Ming Ni, Fuqiang Ye, Juanjuan Zhu, Zongwei Li, Shuai Yang, Bite Yang, Lu Han, Yongge Wu, Ying Chen, Fei Li, Shengqi Wang, Xiaochen Bo:
  ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO. 3379-3386

Applications Notes
Genome Analysis

• 
  Ian M. Campbell, Regis A. James, Edward S. Chen, Chad A. Shaw:
  NetComm: a network analysis tool based on communicability. 3387-3389

Sequence Analysis

• 
  Aaron M. Newman, Scott V. Bratman, Henning Stehr, Luke J. Lee, Chih Long Liu, Maximilian Diehn, Ash A. Alizadeh:
  FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution. 3390-3393
• 
  Lukas R. Cara, Medina Baitemirova, Franklin Duong, Maia Larios-Sanz, Albert Ribes-Zamora:
  SCDFinder, a Web-based tool for the identification of putative novel ATM and ATR targets. 3394-3395
• 
  Joaquín Tárraga, Vicente Arnau, Héctor Martínez, Raul Moreno, Diego Cazorla, José Salavert Torres, Ignacio Blanquer Espert, Joaquín Dopazo, Ignacio Medina:
  Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. 3396-3398
• 
  Nicholas J. Loman, Aaron R. Quinlan:
  Poretools: a toolkit for analyzing nanopore sequence data. 3399-3401
• 
  Justin Chu, Sara Sadeghi, Anthony Raymond, Shaun D. Jackman, Ka Ming Nip, Richard Mar, Hamid Mohamadi, Yaron S. N. Butterfield, A. Gordon Robertson, Inanç Birol:
  BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. 3402-3404
• 
  Melissa Gymrek:
  PyBamView: a browser-based application for viewing short read alignments. 3405-3407
• 
  Kiran Mukhyala, Alexandre Masselot:
  Visualization of protein sequence features using JavaScript and SVG with pViz.js. 3408-3409
• 
  Christopher Weidner, Cornelius Fischer, Sascha Sauer:
  PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins. 3410-3411
• 
  Carsten Kuenne, Jens Preussner, Mario Herzog, Thomas Braun, Mario Looso:
  MIRPIPE: quantification of microRNAs in niche model organisms. 3412-3413
• 
  Chen Wang, Jaime I. Dávila, Saurabh Baheti, Aditya Bhagwate, Xue Wang, Jean-Pierre A. Kocher, Susan L. Slager, Andrew L. Feldman, Anne J. Novak, James R. Cerhan, E. Aubrey Thompson, Yan W. Asmann:
  RVboost: RNA-seq variants prioritization using a boosting method. 3414-3416

Structural Bioinformatics

• 
  Sanjay Agravat, Joel H. Saltz, Richard D. Cummings, David F. Smith:
  GlycoPattern: a web platform for glycan array mining. 3417-3418

Gene Expression

• 
  Charles Winterhalter, Rémy Nicolle, A. Louis, Cuong To, François Radvanyi, Mohamed Elati:
  Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks. 3419-3420
• 
  Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma:
  READemption - a tool for the computational analysis of deep-sequencing-based transcriptome data. 3421-3423
• 
  David G. Robinson, John D. Storey:
  subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling. 3424-3426

Genetics and Population Analysis

• 
  Ilya Shlyakhter, Pardis C. Sabeti, Stephen F. Schaffner:
  Cosi2: an efficient simulator of exact and approximate coalescent with selection. 3427-3429
• 
  Paula Tataru, Jasmine A. Nirody, Yun S. Song:
  diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. 3430-3431
• 
  Benjamin Voight:
  MR_predictor: a simulation engine for Mendelian Randomization studies. 3432-3434
• 
  Maarten van Iterson, Elmar W. Tobi, Roderick C. Slieker, Wouter den Hollander, René Luijk, P. Eline Slagboom, Bastiaan T. Heijmans:
  MethylAid: visual and interactive quality control of large Illumina 450k datasets. 3435-3437

Databases and Ontologies

• 
  Sean S. Ephraim, Nikhil Anand, Adam P. DeLuca, Kyle R. Taylor, Diana L. Kolbe, Allen C. Simpson, Hela Azaiez, Christina M. Sloan, A. Eliot Shearer, Andrea R. Hallier, Thomas L. Casavant, Todd E. Scheetz, Richard J. H. Smith, Terry A. Braun:
  Cordova: Web-based management of genetic variation data. 3438-3439
• 
  Imtiaz A. Khan, Adam Fraser, Mark-Anthony Bray, Paul J. Smith, Nick S. White, Anne E. Carpenter, Rachel J. Errington:
  ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. 3440-3442

Volume 30, Number 24, December 2014

Hitseq Papers
Genome Analysis

• 
  Valentina Boeva, Tatiana G. Popova, Maxime Lienard, Sebastien Toffoli, Maud Kamal, Christophe Le Tourneau, David Gentien, Nicolas Servant, Pierre Gestraud, Thomas Rio Frio, Philippe Hupé, Emmanuel Barillot, Jean-François Laes:
  Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. 3443-3450
• 
  Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre:
  MindTheGap: integrated detection and assembly of short and long insertions. 3451-3457
• 
  Anna M. Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael:
  Characterization of structural variants with single molecule and hybrid sequencing approaches. 3458-3466
• 
  Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke, Ivan G. Costa:
  Detecting differential peaks in ChIP-seq signals with ODIN. 3467-3475
• 
  Shoshana Marcus, Hayan Lee, Michael C. Schatz:
  SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips. 3476-3483

Sequence Analysis

• 
  Kathrin Trappe, Anne-Katrin Emde, Hans-Christian Ehrlich, Knut Reinert:
  Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. 3484-3490
• 
  Ajay Ummat, Ali Bashir:
  Resolving complex tandem repeats with long reads. 3491-3498
• 
  René Rahn, David Weese, Knut Reinert:
  Journaled string tree - a scalable data structure for analyzing thousands of similar genomes on your laptop. 3499-3505
• 
  Leena Salmela, Eric Rivals:
  LoRDEC: accurate and efficient long read error correction. 3506-3514
• 
  Ilan Ben-Bassat, Benny Chor:
  String graph construction using incremental hashing. 3515-3523
• 
  James Holt, Leonard McMillan:
  Merging of multi-string BWTs with applications. 3524-3531
• 
  Layla Oesper, Gryte Satas, Benjamin J. Raphael:
  Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. 3532-3540
• 
  Páll Melsted, Bjarni V. Halldórsson:
  KmerStream: streaming algorithms for k-mer abundance estimation. 3541-3547
• 
  Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow:
  TIPP: taxonomic identification and phylogenetic profiling. 3548-3555
• 
  Marco Beccuti, Matteo Carrara, Francesca Cordero, Fulvio Lazzarato, Susanna Donatelli, Francesca Nadalin, Alberto Policriti, Raffaele A. Calogero:
  Chimera: a Bioconductor package for secondary analysis of fusion products. 3556-3557

Discovery Notes
Genome Analysis

• 
  Michael Keane, Thomas Craig, Jessica Alföldi, Aaron M. Berlin, Jeremy Johnson, Andrei Seluanov, Vera Gorbunova, Federica Di Palma, Kerstin Lindblad-Toh, George M. Church, João Pedro de Magalhães:
  The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. 3558-3560

Structural Bioinformatics

• 
  Gang Hu, Kui Wang, Jody Groenendyk, Khaled H. Barakat, Marcin J. Mizianty, Jishou Ruan, Marek Michalak, Lukasz A. Kurgan:
  Human structural proteome-wide characterization of Cyclosporine A targets. 3561-3566

Original Papers
Genome Analysis

• 
  David E. Frankhouser, Mark Murphy, James S. Blachly, Jincheol Park, Mike W. Zoller, Javkhlan-Ochir Ganbat, John Curfman, John C. Byrd, Shili Lin, Guido Marcucci, Pearlly Yan, Ralf Bundschuh:
  PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data. 3567-3574

Sequence Analysis

• 
  Sergey L. Sheetlin, Yonil Park, Martin C. Frith, John L. Spouge:
  Frameshift alignment: statistics and post-genomic applications. 3575-3582

Structural Bioinformatics

• 
  K. Yugandhar, M. Michael Gromiha:
  Protein-protein binding affinity prediction from amino acid sequence. 3583-3589

Gene Expression

• 
  Jérôme Ambroise, Yann Deccache, Leonid Irenge, Encho Savov, Annie Robert, Jean-Luc Gala:
  Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping. 3590-3597

Applications note
Databases and Ontologies

• 
  Daniel Lobo, Erica B. Feldman, Michelle Shah, Taylor J. Malone, Michael Levin:
  Limbform: a functional ontology-based database of limb regeneration experiments. 3598-3600