Bioinformatics, Volume 28

Volume 28, Number 1, January 2012

Discovery Note - Systems Biology

• 
  Yang Chen,Jin Gu,Dan Li,Shao Li:
  Time-course network analysis reveals TNF-α can promote G₁/S transition of cell cycle in vascular endothelial cells.1-4

Original Papers - Genome Analysis

• 
  Minzhu Xie,Jing Li,Tao Jiang:
  Detecting genome-wide epistases based on the clustering of relatively frequent items.5-12

Sequence Analysis

• 
  Guohui Yao,Liang Ye,Hongyu Gao,Patrick Minx,Wesley C. Warren,George M. Weinstock:
  Graph accordance of next-generation sequence assemblies.13-16
• 
  David Langenberger,Sachin Pundhir,Claus Thorn Ekstrøm,Peter F. Stadler,Steve Hoffmann,Jan Gorodkin:
  deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.17-24
• 
  Natsuhiro Ichinose,Tetsushi Yada,Osamu Gotoh:
  Large-scale motif discovery using DNA Gray code and equiprobable oligomers.25-31
• 
  Dapeng Li,Tonghua Li,Peisheng Cong,Wenwei Xiong,Jiangming Sun:
  A novel structural position-specific scoring matrix for the prediction of protein secondary structures.32-39
• 
  Arief Gusnanto,Henry M. Wood,Yudi Pawitan,Pamela Rabbitts,Stefano Berri:
  Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.40-47

Phylogenetics

• 
  Ryan M. Ames,Daniel Money,Vikramsinh P. Ghatge,Simon Whelan,Simon C. Lovell:
  Determining the evolutionary history of gene families.48-55

Gene Expression

• 
  Gabriel Cuéllar-Partida,Fabian A. Buske,Robert C. McLeay,Tom Whitington,William Stafford Noble,Timothy L. Bailey:
  Epigenetic priors for identifying active transcription factor binding sites.56-62
• 
  Ming Hu,Yu Zhu,Jeremy M. G. Taylor,Jun S. Liu,Zhaohui S. Qin:
  Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.63-68

Systems Biology

• 
  Stefan Maetschke,Martin Simonsen,Melissa J. Davis,Mark A. Ragan:
  Gene Ontology-driven inference of protein-protein interactions using inducers.69-75
• 
  Nicola Soranzo,Fahimeh Ramezani,Giovanni Iacono,Claudio Altafini:
  Decompositions of large-scale biological systems based on dynamical properties.76-83
• 
  Emmanuelle Becker,Benoît Robisson,Charles E. Chapple,Alain Guénoche,Marie-Christine Brun:
  Multifunctional proteins revealed by overlapping clustering in protein interaction network.84-90
• 
  Muhammad Tahir,Asifullah Khan,Abdul Majid:
  Protein subcellular localization of fluorescence imagery using spatial and transform domain features.91-97
• 
  Xiujun Zhang,Xing-Ming Zhao,Kun He,Le Lu,Yongwei Cao,Jingdong Liu,Jin-Kao Hao,Zhi-Ping Liu,Luonan Chen:
  Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information.98-104
• 
  Edward Y. Chen,Huilei Xu,Simon Gordonov,Maribel P. Lim,Matthew H. Perkins,Avi Ma'ayan:
  Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.105-111

Data and Text Mining

• 
  Daniel J. Stekhoven,Peter Bühlmann:
  MissForest - non-parametric missing value imputation for mixed-type data.112-118

Applications Note - Genome Analysis

• 
  Xavier Rafael Palou,Michael P. Schroeder,Núria López-Bigas:
  SVGMap: configurable image browser for experimental data.119-120
• 
  Kun Liang,Sündüz Keles:
  Detecting differential binding of transcription factors with ChIP-seq.121-122
• 
  Francesco Vezzi,Cristian Del Fabbro,Alexandru I. Tomescu,Alberto Policriti:
  rNA: a fast and accurate short reads numerical aligner.123-124

Sequence Analysis

• 
  Yongan Zhao,Haixu Tang,Yuzhen Ye:
  RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.125-126
• 
  Manal Kalkatawi,Farania Rangkuti,Michael Schramm,Boris R. Jankovic,Allan Kamau,Rajesh Chowdhary,John A. C. Archer,Vladimir B. Bajic:
  Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences.127-129
• 
  Marc Torrent,Paolo Di Tommaso,David Pulido,Victòria M. Nogués,Cédric Notredame,Ester Boix,David Andreu:
  AMPA: an automated web server for prediction of protein antimicrobial regions.130-131
• 
  Mattia C. F. Prosperi,Marco Salemi:
  QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.132-133

Genetics and Population Analysis

• 
  Céline Bellenguez,Amy Strange,Colin Freeman,Peter Donnelly,Chris C. A. Spencer:
  A robust clustering algorithm for identifying problematic samples in genome-wide association studies.134-135

Systems Biology

• 
  Brian Pratt,J. Jeffry Howbert,Natalie I. Tasman,Erik J. Nilsson:
  MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.136-137
• 
  Walter Georgescu,John P. Wikswo,Vito Quaranta:
  CellAnimation: an open source MATLAB framework for microscopy assays.138-139

Data and Text Mining

• 
  Stephanie A. Canny,Yasel Cruz,Mark R. Southern,Patrick R. Griffin:
  PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem.140-141

Databases and Ontologies

• 
  Erik Dassi,A. Malossini,Angela Re,Tommaso Mazza,Toma Tebaldi,Luigi Caputi,Alessandro Quattrone:
  AURA: Atlas of UTR Regulatory Activity.142-144

Letters to the Editor - Genome Analysis

• 
  Xiang Wan,Can Yang,Weichuan Yu:
  Comments on 'An empirical comparison of several recent epistatic interaction detection methods'.145-146

Genetics and Population Analysis

• 
  Yue Wang,Guimei Liu,Mengling Feng,Limsoon Wong:
  Response: an empirical comparison of several recent epistatic interaction detection methods.147-148

Corrigenda - Genetics and Population Analysis

• 
  Marie Brown,David C. Wedge,Royston Goodacre,Douglas B. Kell,Philip N. Baker,Louise C. Kenny,Mamas A. Mamas,Ludwig Neyses,Warwick B. Dunn:
  Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets.149
• 
  Farhad Hormozdiari,Faraz Hach,Süleyman Cenk Sahinalp,Evan E. Eichler,Can Alkan:
  Sensitive and fast mapping of di-base encoded reads.150

Volume 28, Number 2, January 2012

Original Papers - Genome Analysis

• 
  Gerard Wong,Christopher Leckie,Adam Kowalczyk:
  FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number.151-159
• 
  David R. Riley,Samuel V. Angiuoli,Jonathan Crabtree,Julie C. Dunning Hotopp,Hervé Tettelin:
  Using Sybil for interactive comparative genomics of microbes on the web.160-166

Sequence Analysis

• 
  Jiarui Ding,Ali Bashashati,Andrew Roth,Arusha Oloumi,Kane Tse,Thomas Zeng,Gholamreza Haffari,Martin Hirst,Marco A. Marra,Anne Condon,Sam Aparicio,Sohrab P. Shah:
  Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.167-175
• 
  Yi-Fei Huang,Geoffrey Brian Golding:
  Inferring sequence regions under functional divergence in duplicate genes.176-183
• 
  David T. Jones,Daniel W. A. Buchan,Domenico Cozzetto,Massimiliano Pontil:
  PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments.184-190

Phylogenetics

• 
  Benjamin Albrecht,Céline Scornavacca,Alberto Cenci,Daniel H. Huson:
  Fast computation of minimum hybridization networks.191-197

Structural Bioinformatics

• 
  Anna Philips,Kaja Milanowska,Grzegorz Lach,Michal J. Boniecki,Kristian Rother,Janusz M. Bujnicki:
  MetalionRNA: computational predictor of metal-binding sites in RNA structures.198-205

Gene Expression

• 
  Mark Maienschein-Cline,Jie Zhou,Kevin P. White,Roger Sciammas,Aaron R. Dinner:
  Discovering transcription factor regulatory targets using gene expression and binding data.206-213
• 
  Geert Geeven,Ronald E. van Kesteren,August B. Smit,Mathisca C. M. de Gunst:
  Identification of context-specific gene regulatory networks with GEMULA - gene expression modeling using LAsso.214-221
• 
  Bettina Grün,Theresa Scharl,Friedrich Leisch:
  Modelling time course gene expression data with finite mixtures of linear additive models.222-228

Genetics and Population Analysis

• 
  Hua Wang,Feiping Nie,Heng Huang,Sungeun Kim,Kwangsik Nho,Shannon L. Risacher,Andrew J. Saykin,Li Shen:
  Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort.229-237

Systems Biology

• 
  Jose L. Rubio-Guivernau,Vasily Gurchenkov,Miguel A. Luengo-Oroz,Louise Duloquin,Paul Bourgine,Andrés Santos,Nadine Peyriéras,María J. Ledesma-Carbayo:
  Wavelet-based image fusion in multi-view three-dimensional microscopy.238-245

Data and Text Mining

• 
  José Caldas,Nils Gehlenborg,Eeva Kettunen,Ali Faisal,Mikko Rönty,Andrew G. Nicholson,Sakari Knuutila,Alvis Brazma,Samuel Kaski:
  Data-driven information retrieval in heterogeneous collections of transcriptomics data linksSIM2s to malignant pleural mesothelioma.246-253
• 
  Nathan Harmston,Wendy Filsell,Michael P. H. Stumpf:
  Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices.254-260
• 
  Jean-Philippe Carralot,Arnaud Ogier,Annette Boese,Auguste Genovesio,Priscille Brodin,Peter Sommer,Thierry Dorval:
  A novel specific edge effect correction method for RNA interference screenings.261-268

Databases and Ontologies

• 
  Fidel Ramírez,Glenn Lawyer,Mario Albrecht:
  Novel search method for the discovery of functional relationships.269-276

Applications Note - Genome Analysis

• 
  Yan W. Asmann,Sumit Middha,Asif Hossain,Saurabh Baheti,Ying Li,High-Seng Chai,Zhifu Sun,Patrick H. Duffy,Ahmed A. Hadad,Asha A. Nair,Xiaoyu Liu,Yuji Zhang,Eric W. Klee,Krishna R. Kalari,Jean-Pierre A. Kocher:
  TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.277-278
• 
  Pablo Librado,Filipe G. Vieira,Julio Rozas:
  BadiRate: estimating family turnover rates by likelihood-based methods.279-281
• 
  Aristotelis Tsirigos,Niina Haiminen,Erhan Bilal,Filippo Utro:
  GenomicTools: a computational platform for developing high-throughput analytics in genomics.282-283

Sequence Analysis

• 
  R. W. W. Brouwer,M. C. G. N. van den Hout,Frank G. Grosveld,Wilfred F. J. van IJcken:
  NARWHAL, a primary analysis pipeline for NGS data.284-285

Structural Bioinformatics

• 
  Chi-Ho Ngan,David R. Hall,Brandon S. Zerbe,Laurie E. Grove,Dima Kozakov,Sandor Vajda:
  FTSite: high accuracy detection of ligand binding sites on unbound protein structures.286-287

Gene Expression

• 
  Laurent Gatto,Kathryn S. Lilley:
  MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.288-289

Systems Biology

• 
  Christopher W. Whelan,M. Kemal Sönmez:
  Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter.290-291
• 
  Dominique F. Chu,Nicolae Radu Zabet,Tobias von der Haar:
  A novel and versatile computational tool to model translation.292-293
• 
  Lu Zhang,Shengchang Gu,Yuan Liu,Bingqiang Wang,Francisco Azuaje:
  Gene set analysis in the cloud.294-295

Data and Text Mining

• 
  Nigel F. Reuel,Peter Bojo,Jingqing Zhang,Ardemis A. Boghossian,Jin-Ho Ahn,Jong-Ho Kim,Michael S. Strano:
  NoRSE: noise reduction and state evaluator for high-frequency single event traces.296-297
• 
  Heidi E. L. Lischer,Laurent Excoffier:
  PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.298-299

Letter to the Editor - Structural Bioinformatics

• 
  Christian M. Reidys,Fenix W. D. Huang,Jørgen E. Andersen,Robert C. Penner,Peter F. Stadler,Markus E. Nebel:
  Addendum: topology and prediction of RNA pseudoknots.300

Volume 28, Number 3, February 2012

Discovery Note - Systems Biology

• 
  Xin Wei,Ann F. Hoffman,Shannon M. Hamilton,Qing Xiang,Yang He,W. Venus So,Sung-Sau So,David Mark:
  A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens.301-305

Original Papers - Genome Analysis

• 
  Olga Shevchuk,Louisa Roselius,Gabriele Günther,Johannes Klein,Dieter Jahn,Michael Steinert,Richard Münch:
  InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes.306-310

Sequence Analysis

• 
  David E. Larson,Christopher C. Harris,Ken Chen,Daniel C. Koboldt,Travis E. Abbott,David J. Dooling,Timothy J. Ley,Elaine R. Mardis,Richard K. Wilson,Li Ding:
  SomaticSniper: identification of somatic point mutations in whole genome sequencing data.311-317
• 
  Antonio Marco,Sam Griffiths-Jones:
  Detection of microRNAs in color space.318-323

Structural Bioinformatics

• 
  Ryotaro Koike,Motonori Ota:
  SCPC: a method to structurally compare protein complexes.324-330
• 
  Ke Chen,Marcin J. Mizianty,Lukasz A. Kurgan:
  Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors.331-341
• 
  Valdete M. Gonçalves-Almeida,Douglas E. V. Pires,Raquel Cardoso de Melo Minardi,Carlos Henrique da Silveira,Wagner Meira Jr.,Marcelo M. Santoro:
  HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids.342-349
• 
  J. W. Heal,J. E. Jimenez-Roldan,Stephen A. Wells,R. B. Freedman,Rudolf A. Römer:
  Inhibition of HIV-1 protease: the rigidity perspective.350-357

Genetics and Population Analysis

• 
  Gengxin Li,Joel Gelernter,Henry R. Kranzler,Hongyu Zhao:
  M³: an improved SNP calling algorithm for Illumina BeadArray data.358-365

Systems Biology

• 
  Wei Liu,Mahesan Niranjan:
  Gaussian process modelling forbicoid mRNA regulation in spatio-temporal Bicoid profile.366-372
• 
  Alla Karnovsky,Terry E. Weymouth,Tim Hull,V. Glenn Tarcea,Giovanni Scardoni,Carlo Laudanna,Maureen A. Sartor,Kathleen A. Stringer,H. V. Jagadish,Charles F. Burant,Brian D. Athey,Gilbert S. Omenn:
  Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.373-380
• 
  Kathrin Ballerstein,Axel von Kamp,Steffen Klamt,Utz-Uwe Haus:
  Minimal cut sets in a metabolic network are elementary modes in a dual network.381-387
• 
  Mario Latendresse,Markus Krummenacker,Miles Trupp,Peter D. Karp:
  Construction and completion of flux balance models from pathway databases.388-396

Databases and Ontologies

• 
  Natalia Jiménez-Lozano,Joan Segura,José Ramón Macías,Juanjo Vega,José María Carazo:
  Integrating human and murine anatomical gene expression data for improved comparisons.397-402
• 
  Yupeng Wang,Sandeep J. Joseph,Xinyu Liu,Michael Kelley,Romdhane Rekaya:
  SNPxGE²: a database for human SNP-coexpression associations.403-410
• 
  Nestor Milyaev,David Osumi-Sutherland,Simon Reeve,Nicholas Burton,Richard A. Baldock,J. Douglas Armstrong:
  The Virtual Fly Brain browser and query interface.411-415

Applications Note - Genome Analysis

• 
  Yongbing Zhao,Jiayan Wu,Junhui Yang,Shixiang Sun,Jing-Fa Xiao,Jun Yu:
  PGAP: pan-genomes analysis pipeline.416-418
• 
  Mikhail G. Dozmorov,Lukas R. Cara,Cory B. Giles,Jonathan D. Wren:
  GenomeRunner: automating genome exploration.419-420
• 
  F. Anthony San Lucas,Gao T. Wang,Paul Scheet,Bo Peng:
  Integrated annotation and analysis of genetic variants from next-generation sequencing studies withvariant tools.421-422
• 
  Valentina Boeva,Tatiana G. Popova,Kevin Bleakley,Pierre Chiche,Julie Cappo,Gudrun Schleiermacher,Isabelle Janoueix-Lerosey,Olivier Delattre,Emmanuel Barillot:
  Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.423-425

Sequence Analysis

• 
  Carlos Prieto,Carlos García-Estrada,Diego Lorenzana,Juan Francisco Martín:
  NRPSsp: non-ribosomal peptide synthase substrate predictor.426-427
• 
  Benjamin Kreck,George Marnellos,Julia Richter,Felix Krueger,Reiner Siebert,Andre Franke:
  B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data.428-429
• 
  Yuanxin Xi,Christoph Bock,Fabian Müller,Deqiang Sun,Alexander Meissner,Wei Li:
  RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.430-432
• 
  Robert Schmieder,Yan Wei Lim,Robert A. Edwards:
  Identification and removal of ribosomal RNA sequences from metatranscriptomes.433-435
• 
  Antonio González,Jesse Stombaugh,Christian L. Lauber,Noah Fierer,Rob Knight:
  SitePainter: a tool for exploring biogeographical patterns.436-438

Structural Bioinformatics

• 
  Conan K. Wang,Saroja K. Weeratunga,Chris M. Pacheco,Andreas Hofmann:
  DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments.439-440
• 
  Julia T. Philip,Charles H. Pence,Holly V. Goodson:
  MTBindingSim: simulate protein binding to microtubules.441-443

Genetics and Population Analysis

• 
  Christian Fuchsberger,Daniel Taliun,Peter P. Pramstaller,Cristian Pattaro:
  GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data.444-445

Systems Biology

• 
  Enrico Glaab,Reinhard Schneider:
  PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data.446-447

Databases and Ontologies

• 
  Sarala M. Wimalaratne,Pierre Grenon,Robert Hoehndorf,Georgios V. Gkoutos,Bernard de Bono:
  An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.448-450
• 
  Kai Xia,Andrey A. Shabalin,Shunping Huang,Vered Madar,Yi-Hui Zhou,Wei Wang,Fei Zou,Wei Sun,Patrick F. Sullivan,Fred A. Wright:
  seeQTL: a searchable database for human eQTLs.451-452

Volume 28, Number 4, February 2012

Discovery Note - Genome Analysis

• 
  Wilson Wen Bin Goh,Hirotaka Oikawa,Judy Chia Ghee Sng,Marek J. Sergot,Limsoon Wong:
  The role of miRNAs in complex formation and control.453-456

Original Papers Genome Analysis

• 
  Thomas J. Hardcastle,Krystyna A. Kelly,David C. Baulcombe:
  Identifying small interfering RNA loci from high-throughput sequencing data.457-463
• 
  Tim Carver,Simon R. Harris,Matthew Berriman,Julian Parkhill,Jacqueline A. McQuillan:
  Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.464-469
• 
  Alberto Magi,Lorenzo Tattini,Tommaso Pippucci,Francesca Torricelli,Matteo Benelli:
  Read count approach for DNA copy number variants detection.470-478

Sequence Analysis

• 
  Yanju Zhang,Eric-Wubbo Lameijer,Peter A. C. 't Hoen,Zemin Ning,P. Eline Slagboom,Kai Ye:
  PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.479-486
• 
  Phil Arnold,Ionas Erb,Mikhail Pachkov,Nacho Molina,Erik van Nimwegen:
  MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.487-494
• 
  Benjamin P. Blackburne,Simon Whelan:
  Measuring the distance between multiple sequence alignments.495-502

Structural Bioinformatics

• 
  Ian Walsh,Alberto J. M. Martin,Tomás Di Domenico,Silvio C. E. Tosatto:
  ESpritz: accurate and fast prediction of protein disorder.503-509
• 
  Tim Harder,Mikael Borg,Wouter Boomsma,Peter Røgen,Thomas Hamelryck:
  Fast large-scale clustering of protein structures using Gauss integrals.510-515
• 
  Sikander Hayat,Arne Elofsson:
  BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.516-522
• 
  Sudhakar Sahoo,Andreas Alexander Albrecht:
  Approximating the set of local minima in partial RNA folding landscapes.523-530

Gene Expression

• 
  Tiejun Tong,Liang Chen,Hongyu Zhao:
  Improved mean estimation and its application to diagonal discriminant analysis.531-537
• 
  Isaac S. Kohane,Vladimir I. Valtchinov:
  Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome.538-545

Systems Biology

• 
  Lipi R. Acharya,Thair Judeh,Guangdi Wang,Dongxiao Zhu:
  Optimal structural inference of signaling pathways from unordered and overlapping gene sets.546-556
• 
  Thomas Handorf,Edda Klipp:
  Modeling mechanistic biological networks: An advanced Boolean approach.557-563

Data and Text Mining

• 
  Youting Sun,Jianqiu Zhang,Ulisses M. Braga-Neto,Edward R. Dougherty:
  BPDA2d - a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.564-572
• 
  Raivo Kolde,Sven Laur,Priit Adler,Jaak Vilo:
  Robust rank aggregation for gene list integration and meta-analysis.573-580

Applications Note - Genome Analysis

• 
  Leila Taher,Leelavati Narlikar,Ivan Ovcharenko:
  CLARE: Cracking the LAnguage of Regulatory Elements.581-583

Sequence Analysis

• 
  Thilo Muth,Juan A. García-Martín,Antonio Rausell,David de Juan,Alfonso Valencia,Florencio Pazos:
  JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.584-586
• 
  Jinyan Huang,Victor Renault,J. Sengenès,Nizar Touleimat,Sven Michel,Mark G. Lathrop,Jorg Tost:
  MeQA: a pipeline for MeDIP-seq data quality assessment and analysis.587-588
• 
  Evarist Planet,Camille Stephan-Otto Attolini,Oscar Reina,Oscar Flores,David Rossell:
  htSeqTools: high-throughput sequencing quality control, processing and visualization in R.589-590
• 
  Athina Theodosiou,Vasilis J. Promponas:
  LaTcOm: a web server for visualizing rare codon clusters in coding sequences.591-592
• 
  Weichun Huang,Leping Li,Jason R. Myers,Gabor T. Marth:
  ART: a next-generation sequencing read simulator.593-594

Genetics and Population Analysis

• 
  Miquel Ràmia,Pablo Librado,Sònia Casillas,Julio Rozas,Antonio Barbadilla:
  PopDrowser: the Population Drosophila Browser.595-596

Data and Text Mining

• 
  Sun Kim,Dongseop Kwon,Soo-Yong Shin,W. John Wilbur:
  PIEthe search: searching PubMed literature for protein interaction information.597-598
• 
  Jamie K. Teer,Eric D. Green,James C. Mullikin,Leslie G. Biesecker:
  VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer.599-600

Databases and Ontologies

• 
  Christian Schaefer,Alice Meier,Burkhard Rost,Yana Bromberg:
  SNPdbe: constructing an nsSNP functional impacts database.601-602

Volume 28, Number 5, March 2012

Discovery Note - Phylogenetics

• 
  Natasha Latysheva,Vivien L. Junker,William J. Palmer,Geoffrey A. Codd,Daniel Barker:
  The evolution of nitrogen fixation in cyanobacteria.603-606

Original Papers - Genome Analysis

• 
  Maria D. Chikina,Olga G. Troyanskaya:
  An effective statistical evaluation of ChIPseq dataset similarity.607-613
• 
  Katelyn McNair,Barbara A. Bailey,Robert A. Edwards:
  PHACTS, a computational approach to classifying the lifestyle of phages.614-618
• 
  Anne-Katrin Emde,Marcel H. Schulz,David Weese,Ruping Sun,Martin Vingron,Vera M. Kalscheuer,Stefan A. Haas,Knut Reinert:
  Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.619-627

Sequence Analysis

• 
  Raymond Wan,Vo Ngoc Anh,Kiyoshi Asai:
  Transformations for the compression of FASTQ quality scores of next-generation sequencing data.628-635
• 
  Søren Mørk,Ian H. Holmes:
  Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.636-642
• 
  Na You,Gabriel H. Murillo,Xiaoquan Su,Xiaowei Zeng,Jian Xu,Kang Ning,Shoudong Zhang,Jiankang Zhu,Xinping Cui:
  SNP calling using genotype model selection on high-throughput sequencing data.643-650
• 
  Ergun Gumus,Olcay Kursun,Ahmet Sertbas,Duran Üstek:
  Application of canonical correlation analysis for identifying viral integration preferences.651-655
• 
  Jonathan Göke,Marcel H. Schulz,Julia Lasserre,Martin Vingron:
  Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.656-663

Structural Bioinformatics

• 
  Zhe Zhang,Lin Wang,Yang Gao,Jie Zhang,Maxim Zhenirovskyy,Emil Alexov:
  Predicting folding free energy changes upon single point mutations.664-671

Gene Expression

• 
  Maxime Garcia,Raphaelle Millat-Carus,François Bertucci,Pascal Finetti,Daniel Birnbaum,Ghislain Bidaut:
  Interactome-transcriptome integration for predicting distant metastasis in breast cancer.672-678

Genetics and Population Analysis

• 
  Alex L. B. Leach,James P. J. Chong,Kelly R. Redeker:
  SSuMMo: rapid analysis, comparison and visualization of microbial communities.679-686

Systems Biology

• 
  Serguei Sokol,Pierre Millard,Jean-Charles Portais:
  influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments.687-693
• 
  Kakajan Komurov:
  Modeling community-wide molecular networks of multicellular systems.694-700
• 
  Mei-Ju May Chen,Lih-Ching Chou,Tsung-Ting Hsieh,Ding-Dar Lee,Kai-Wei Liu,Chi-Yuan Yu,Yen-Jen Oyang,Huai-Kuang Tsai,Chien-Yu Chen:
  De novo motif discovery facilitates identification of interactions between transcription factors inSaccharomyces cerevisiae.701-708

Data and Text Mining

• 
  Christian Senger,Björn A. Grüning,Anika Erxleben,Kersten Döring,Hitesh Patel,Stephan Flemming,Irmgard Merfort,Stefan Günther:
  Mining and evaluation of molecular relationships in literature.709-714

Applications Note - Genome Analysis

• 
  Todd F. DeLuca,Jike Cui,Jae-Yoon Jung,Kristian Che St. Gabriel,Dennis P. Wall:
  Roundup 2.0: enabling comparative genomics for over 1800 genomes.715-716
• 
  Thomas Hentrich,Julia M. Schulze,Eldon Emberly,Michael S. Kobor:
  CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures.717-718
• 
  Gary K. Chen:
  A scalable and portable framework for massively parallel variable selection in genetic association studies.719-720
• 
  Dongwan Hong,Arang Rhie,Sung-Soo Park,Jongkeun Lee,Young Seok Ju,Sujung Kim,Saet-Byeol Yu,Thomas Bleazard,Hyun Seok Park,Hwanseok Rhee,Hyonyong Chong,Kap-Seok Yang,Yeon-Su Lee,In-Hoo Kim,Jin Soo Lee,Jong-Il Kim,Jeong-Sun Seo:
  FX: an RNA-Seq analysis tool on the cloud.721-723
• 
  Vladimir Makarov,Tina O'Grady,Guiqing Cai,Jayon Lihm,Joseph D. Buxbaum,Seungtai Yoon:
  AnnTools: a comprehensive and versatile annotation toolkit for genomic variants.724-725

Gene Expression

• 
  Thomas W. Chittenden,Eleanor Howe,Jennifer M. Taylor,Jessica Cara Mar,Martin J. Aryee,Harold Gómez,Razvan Sultana,John C. Braisted,Sarita J. Nair,John Quackenbush,Chris Holmes:
  nEASE: a method for gene ontology subclassification of high-throughput gene expression data.726-728
• 
  Dan Wang,Li Yan,Qiang Hu,Lara E. Sucheston,Michael J. Higgins,Christine B. Ambrosone,Candace S. Johnson,Dominic J. Smiraglia,Song Liu:
  IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data.729-730

Systems Biology

• 
  Michal Komorowski,Justina Zurauskiene,Michael P. H. Stumpf:
  StochSens - matlab package for sensitivity analysis of stochastic chemical systems.731-733
• 
  Rogan Carr,Elhanan Borenstein:
  NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.734-735
• 
  Christoph Bueschl,Bernhard Kluger,Franz Berthiller,Gerald Lirk,Stephan Winkler,Rudolf Krska,Rainer Schuhmacher:
  MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research.736-738

Data and Text Mining

• 
  Sergey Kozhenkov,Michael Baitaluk:
  Mining and integration of pathway diagrams from imaging data.739-742
• 
  Adrian Benton,John H. Holmes,Shawndra Hill,Annie Chung,Lyle H. Ungar:
  medpie: an information extraction package for medical message board posts.743-744
• 
  Yasubumi Sakakibara,Tsuyoshi Hachiya,Miho Uchida,Nobuyoshi Nagamine,Yohei Sugawara,Masahiro Yokota,Masaomi Nakamura,Kris Popendorf,Takashi Komori,Kengo Sato:
  COPICAT: a software system for predicting interactions between proteins and chemical compounds.745-746

Databases and Ontologies

• 
  Sentil Balaji,Charles Mcclendon,Rajesh Chowdhary,Jun S. Liu,Jinfeng Zhang:
  IMID: integrated molecular interaction database.747-749
• 
  Mustafa H. Syed,Tatiana V. Karpinets,Morey Parang,Michael R. Leuze,Byung-Hoon Park,Doug Hyatt,Steven D. Brown,Steve Moulton,Michael D. Galloway,Edward C. Uberbacher:
  BESC knowledgebase public portal.750-751
• 
  David van der Spoel,Paul J. van Maaren,Carl Caleman:
  GROMACS molecule & liquid database.752-753

Volume 28, Number 6, March 2012

Original Papers - Genome Analysis

• 
  Charles C. Berry,Nicolas A. Gillet,Anat Melamed,Niall A. Gormley,Charles R. M. Bangham,Frederic D. Bushman:
  Estimating abundances of retroviral insertion sites from DNA fragment length data.755-762
• 
  Santi González,Bàrbara Montserrat-Sentís,Friman Sánchez,Montserrat Puiggròs,Enrique Blanco,Alex Ramírez,David Torrents:
  ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.763-770

Sequence Analysis

• 
  Martin Reczko,Manolis Maragkakis,Panagiotis Alexiou,Ivo Grosse,Artemis G. Hatzigeorgiou:
  Functional microRNA targets in protein coding sequences.771-776
• 
  Eva E. R. Philipp,Lars Kraemer,D. Mountfort,M. Schilhabel,Stefan Schreiber,Philip Rosenstiel:
  The Transcriptome Analysis and Comparison Explorer - T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.777-783

Structural Bioinformatics

• 
  David Ryan Koes,Carlos J. Camacho:
  Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure.784-791
• 
  Matthew G. Seetin,David H. Mathews:
  TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.792-798

Gene Expression

• 
  Sutirtha Chakraborty,Somnath Datta,Susmita Datta:
  Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies.799-806
• 
  Yihan Li,Debashis Ghosh:
  Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data.807-814
• 
  Kyungpil Kim,Keni Jiang,Siew Leng Teng,Lewis J. Feldman,Haiyan Huang:
  Using biologically interrelated experiments to identify pathway genes inArabidopsis.815-822
• 
  Ka Yee Yeung,T. A. Gooley,A. Zhang,Adrian E. Raftery,J. P. Radich,V. G. Oehler:
  Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data.823-830

Genetics and Population Analysis

• 
  Christopher J. R. Illingworth,Ville Mustonen:
  A method to infer positive selection from marker dynamics in an asexual population.831-837
• 
  Chul Joo Kang,Paul Marjoram:
  Exact coalescent simulation of new haplotype data from existing reference haplotypes.838-844
• 
  Clara S. Tang,Manuel A. R. Ferreira:
  A gene-based test of association using canonical correlation analysis.845-850

Systems Biology

• 
  Martin Simonsen,Stefan Maetschke,Mark A. Ragan:
  Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling.851-857
• 
  Alfredo Rodríguez,David Sosa,Leda Torres,Bertha Molina,Sara Frías,Luis Mendoza:
  A Boolean network model of the FA/BRCA pathway.858-866

Data and Text Mining

• 
  Thanh Thieu,Sneha Joshi,Samantha Warren,Dmitry Korkin:
  Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches.867-875

Applications Note Sequence Analysis

• 
  Matti Niemenmaa,Aleksi Kallio,André Schumacher,Petri Klemelä,Eija Korpelainen,Keijo Heljanko:
  Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.876-877
• 
  Chi-Man Liu,Thomas K. F. Wong,Edward Wu,Ruibang Luo,Siu-Ming Yiu,Yingrui Li,Bingqiang Wang,Chang Yu,Xiaowen Chu,Kaiyong Zhao,Ruiqiang Li,Tak Wah Lam:
  SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.878-879

Structural Bioinformatics

• 
  Grzegorz Chojnowski,Janusz M. Bujnicki,Matthias Bochtler:
  RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes.880-881

Gene Expression

• 
  Jeffrey T. Leek,W. Evan Johnson,Hilary S. Parker,Andrew E. Jaffe,John D. Storey:
  The sva package for removing batch effects and other unwanted variation in high-throughput experiments.882-883
• 
  Björn Schwalb,Daniel Schulz,Mai Sun,Benedikt Zacher,Sebastian Dümcke,Dietmar E. Martin,Patrick Cramer,Achim Tresch:
  Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA).884-885

Genetics and Population Analysis

• 
  Michael C. Turchin,Joel Hirschhorn:
  Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples.886-888

Systems Biology

• 
  Kumar Chandan,Martijn P. van Iersel,Mirit I. Aladjem,Kurt W. Kohn,Augustin Luna:
  PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.889-890
• 
  Matthew DeJongh,Benjamin Bockstege,Paul Frybarger,Nicholas L. Hazekamp,Joshua Kammeraad,Travis McGeehan:
  CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.891-892
• 
  Aleksandar Stojmirovic,Alexander Bliskovsky,Yi-Kuo Yu:
  CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores.893-894

Databases and Ontologies

• 
  Michael Hartung,Anika Groß,Erhard Rahm:
  CODEX: exploration of semantic changes between ontology versions.895-896
• 
  Mehdi Pirooznia,Tao Wang,Dimitrios Avramopoulos,David Valle,Gareth Thomas,Richard L. Huganir,Fernando S. Goes,James B. Potash,Peter P. Zandi:
  SynaptomeDB: an ontology-based knowledgebase for synaptic genes.897-899

Letter to the Editor Genome Analysis

• 
  Christophe Dessimoz,Toni Gabaldón,David S. Roos,Erik L. L. Sonnhammer,Javier Herrero:
  Toward community standards in the quest for orthologs.900-904

Corrigendum Genome Analysis

• 
  Isaac S. Kohane,Vladimir I. Valtchinov:
  Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome.905

Volume 28, Number 7, April 2012

Original Papers - Sequence Analysis

• 
  Andrew Roth,Jiarui Ding,Ryan D. Morin,Anamaria Crisan,Gavin Ha,Ryan Giuliany,Ali Bashashati,Martin Hirst,Gulisa Turashvili,Arusha Oloumi,Marco A. Marra,Sam Aparicio,Sohrab P. Shah:
  JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.907-913

Structural Bioinformatics

• 
  Zhi Liu,Ahmed Abbas,Bing-Yi Jing,Xin Gao:
  WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering.914-920

Gene Expression

• 
  Daniel C. Jones,Walter L. Ruzzo,Xinxia Peng,Michael G. Katze:
  A new approach to bias correction in RNA-Seq.921-928
• 
  Shuji Kawaguchi,Kei Iida,Erimi Harada,Kousuke Hanada,Akihiro Matsui,Masanori Okamoto,Kazuo Shinozaki,Motoaki Seki,Tetsuro Toyoda:
  Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads.929-937

Genetics and Population Analysis

• 
  Degui Zhi,Jihua Wu,Nianjun Liu,Kui Zhang:
  Genotype calling from next-generation sequencing data using haplotype information of reads.938-946

Systems Biology

• 
  John L. Van Hemert,Julie A. Dickerson:
  Discriminating response groups in metabolic and regulatory pathway networks.947-954
• 
  Shiwen Zhao,Shao Li:
  A co-module approach for elucidating drug-disease associations and revealing their molecular basis.955-961
• 
  Andy C. W. Lai,Alex N. Nguyen Ba,Alan M. Moses:
  Predicting kinase substrates using conservation of local motif density.962-969
• 
  Feng He,Jie Ren,Wei Wang,Jun Ma:
  Evaluating theDrosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts.970-975
• 
  Robert J. Weatheritt,Katja Luck,Evangelia Petsalaki,Norman E. Davey,Toby J. Gibson:
  The identification of short linear motif-mediated interfaces within the human interactome.976-982
• 
  Guy Naamati,Yitzhak Friedman,Ohad Balaga,Michal Linial:
  Susceptibility of the human pathways graphs to fragmentation by small sets of microRNAs.983-990

Data and Text Mining

• 
  Maria Liakata,Shyamasree Saha,Simon Dobnik,Colin R. Batchelor,Dietrich Rebholz-Schuhmann:
  Automatic recognition of conceptualization zones in scientific articles and two life science applications.991-1000
• 
  Theofanis Karaletsos,Oliver Stegle,Christine Dreyer,John M. Winn,Karsten M. Borgwardt:
  ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.1001-1008
• 
  Nima Aghaeepour,Pratip K. Chattopadhyay,Anuradha Ganesan,Kieran O'Neill,Habil Zare,Adrin Jalali,Holger H. Hoos,Mario Roederer,Ryan Remy Brinkman:
  Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.1009-1016

Databases and Ontologies

• 
  Anne Niknejad,Aurélie Comte,Gilles Parmentier,Julien Roux,Frederic B. Bastian,Marc Robinson-Rechavi:
  vHOG, a multispecies vertebrate ontology of homologous organs groups.1017-1020

Applications Note Genome Analysis

• 
  William K. M. Lai,Jonathan E. Bard,Michael J. Buck:
  ArchTEx: accurate extraction and visualization of next-generation sequence data.1021-1023
• 
  Ruping Sun,Michael I. Love,Tomasz Zemojtel,Anne-Katrin Emde,Ho-Ryun Chung,Martin Vingron,Stefan A. Haas:
  Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.1024-1025

Sequence Analysis

• 
  Conan K. Wang,Ursula Broder,Saroja K. Weeratunga,Robin B. Gasser,Alex Loukas,Andreas Hofmann:
  SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.1026-1027
• 
  Sang-Mun Chi,Dougu Nam:
  WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms.1028-1030
• 
  Kian Huat Lim,William G. Fairbrother:
  Spliceman - a computational web server that predicts sequence variations in pre-mRNA splicing.1031-1032
• 
  Martin Wu,Alexandra J. Scott:
  Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.1033-1034
• 
  Raoul Jean Pierre Bonnal,Jan Aerts,George Githinji,Naohisa Goto,Daniel MacLean,Chase A. Miller,Hiroyuki Mishima,Massimiliano Pagani,Ricardo Ramirez-Gonzalez,Geert Smant,Francesco Strozzi,Rob Syme,Rutger A. Vos,Trevor J. Wennblom,Ben J. Woodcroft,Toshiaki Katayama,Pjotr Prins:
  Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.1035-1037

Structural Bioinformatics

• 
  Alessandro Barbato,Pascal Benkert,Torsten Schwede,Anna Tramontano,Jan Kosinski:
  Improving your target-template alignment with MODalign.1038-1039
• 
  Franck Samson,Richard Shrager,Chin-Hsien Tai,Vichetra Sam,Byungkook Lee,Peter J. Munson,Jean-François Gibrat,Jean Garnier:
  DOMIRE: a web server for identifying structural domains and their neighbors in proteins.1040-1041

Genetics and Population Analysis

• 
  Danny Arends,K. Joeri van der Velde,Pjotr Prins,Karl W. Broman,Steffen Möller,Ritsert C. Jansen,Morris A. Swertz:
  xQTL workbench: a scalable web environment for multi-level QTL analysis.1042-1044
• 
  John Bunge,Linda Woodard,Dankmar Böhning,James A. Foster,Sean Connolly,Heather K. Allen:
  Estimating population diversity with CatchAll.1045-1047

Systems Biology

• 
  Darren J. Creek,Andris Jankevics,Karl E. V. Burgess,Rainer Breitling,Michael P. Barrett:
  IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data.1048-1049
• 
  Eero Lihavainen,Jarno Mäkelä,Johannes N. Spelbrink,Andre S. Ribeiro:
  Mytoe: automatic analysis of mitochondrial dynamics.1050-1051

Data and Text Mining

• 
  Till Bald,Johannes Barth,Anna Niehues,Michael Specht,Michael Hippler,Christian Fufezan:
  pymzML - Python module for high-throughput bioinformatics on mass spectrometry data.1052-1053

Databases and Ontologies

• 
  Valentin Guignon,Gaëtan Droc,Michael Alaux,Franc-Christophe Baurens,Olivier Garsmeur,Claire Poiron,Tim Carver,Mathieu Rouard,Stéphanie Bocs:
  Chado Controller: advanced annotation management with a community annotation system.1054-1056

Volume 28, Number 8, April 2012

Editorial

• 
  Hanchuan Peng,Alex Bateman,Alfonso Valencia,Jonathan D. Wren:
  Bioimage informatics: a new category inBioinformatics.1057

Discovery Note - Genome Analysis

• 
  William Ritchie,Dadi Gao,John E. J. Rasko:
  Defining and providing robust controls for microRNA prediction.1058-1061

Original Papers - Genome Analysis

• 
  Dominik Beck,Miriam Brandl,Lies Boelen,Ashwin Unnikrishnan,John E. Pimanda,Jason W. H. Wong:
  Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq.1062-1069

Sequence Analysis

• 
  Vitaly L. Galinsky:
  YOABS: yet other aligner of biological sequences - an efficient linearly scaling nucleotide aligner.1070-1077
• 
  Vincent Miele,Simon Penel,Vincent Daubin,Franck Picard,Daniel Kahn,Laurent Duret:
  High-quality sequence clustering guided by network topology and multiple alignment likelihood.1078-1085
• 
  Marcel H. Schulz,Daniel R. Zerbino,Martin Vingron,Ewan Birney:
  Oases: robustde novo RNA-seq assembly across the dynamic range of expression levels.1086-1092

Structural Bioinformatics

• 
  Hisanori Kiryu,Kiyoshi Asai:
  Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.1093-1101

Gene Expression

• 
  Ruijie Liu,Ana-Teresa Maia,Roslin Russell,Carlos Caldas,Bruce A. Ponder,Matthew E. Ritchie:
  Allele-specific expression analysis methods for high-density SNP microarray data.1102-1108
• 
  Zhongxue Chen,Qingzhong Liu,Saralees Nadarajah:
  A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data.1109-1113
• 
  Leonid Chindelevitch,Daniel Ziemek,Ahmed Enayetallah,Ranjit Randhawa,Ben Sidders,Christoph Brockel,Enoch S. Huang:
  Causal reasoning on biological networks: interpreting transcriptional changes.1114-1121
• 
  Jeffrey T. Chang:
  Deriving transcriptional programs and functional processes from gene expression databases.1122-1129

Systems Biology

• 
  Joep Vanlier,Christian A. Tiemann,Peter A. J. Hilbers,Natal A. W. van Riel:
  An integrated strategy for prediction uncertainty analysis.1130-1135
• 
  Joep Vanlier,Christian A. Tiemann,Peter A. J. Hilbers,Natal A. W. van Riel:
  A Bayesian approach to targeted experiment design.1136-1142

Data and Text Mining

• 
  Jan Kölling,Daniel Langenkämper,Sylvie Abouna,Michael Khan,Tim W. Nattkemper:
  WHIDE - a web tool for visual data mining colocation patterns in multivariate bioimages.1143-1150
• 
  Loris Nanni,Sheryl Brahnam,Alessandra Lumini:
  Combining multiple approaches for gene microarray classification.1151-1157
• 
  Seongho Kim,Imhoi Koo,Xiaoli Wei,Xiang Zhang:
  A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry.1158-1163

Applications Note - Genome Analysis

• 
  Xiaobei Zhao,Albin Sandelin:
  GMD: measuring the distance between histograms with applications on high-throughput sequencing reads.1164-1165
• 
  Konstantin Okonechnikov,Olga Golosova,Mikhail Fursov:
  Unipro UGENE: a unified bioinformatics toolkit.1166-1167
• 
  Volker Steiß,Thomas Letschert,Helmut Schäfer,Roman Pahl:
  PERMORY-MPI: a program for high-speed parallel permutation testing in genome-wide association studies.1168-1169

Phylogenetics

• 
  Oscar Westesson,Lars Barquist,Ian H. Holmes:
  HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.1170-1171

Structural Bioinformatics

• 
  Yingjie Lin,Seungyeul Yoo,Roberto Sanchez:
  SiteComp: a server for ligand binding site analysis in protein structures.1172-1173

Gene Expression

• 
  Aparna Bhaduri,Kun Qu,Carolyn S. Lee,Alexander Ungewickell,Paul A. Khavari:
  Rapid identification of non-human sequences in high-throughput sequencing datasets.1174-1175

Genetics and Population Analysis

• 
  Mathieu Gautier,Renaud Vitalis:
  rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.1176-1177

Systems Biology

• 
  Johannes Gräßler,Dirk Koschützki,Falk Schreiber:
  CentiLib: comprehensive analysis and exploration of network centralities.1178-1179
• 
  Richard R. Adams:
  SED-ED, a workflow editor for computational biology experiments written in SED-ML.1180-1181

Data and Text Mining

• 
  Hanwen Huang,Xiaosun Lu,Yufeng Liu,Perry Haaland,J. S. Marron:
  R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment.1182-1183

Databases and Ontologies

• 
  Markus Krupp,Jens U. Marquardt,Ugur Sahin,Peter R. Galle,John C. Castle,Andreas Teufel:
  RNA-Seq Atlas - a reference database for gene expression profiling in normal tissue by next-generation sequencing.1184-1185
• 
  Nigel Collier,Son Doan:
  GENI-DB: a database of global events for epidemic intelligence.1186-1188
• 
  Scott F. Saccone,Jiaxi Quan,Peter L. Jones:
  BioQ: tracing experimental origins in public genomic databases using a novel data provenance model.1189-1191

Volume 28, Number 9, May 2012

Review - Systems Biology

• 
  Pablo Meyer,Julia Hoeng,John Jeremy Rice,Raquel Norel,Jörg Sprengel,Katrin Stolle,Thomas Bonk,Stephanie Corthesy,Ajay K. Royyuru,Manuel C. Peitsch,Gustavo Stolovitzky:
  Industrial methodology for process verification in research (IMPROVER): toward systems biology verification.1193-1201

Original Papers - Phylogenetics

• 
  Iman Hajirasouliha,Alexander Schönhuth,David de Juan,Alfonso Valencia,Süleyman Cenk Sahinalp:
  Mirroring co-evolving trees in the light of their topologies.1202-1208

Structural Bioinformatics

• 
  Michael I. Sadowski,William R. Taylor:
  Evolutionary inaccuracy of pairwise structural alignments.1209-1215
• 
  Noah M. Daniels,Raghavendra Hosur,Bonnie Berger,Lenore J. Cowen:
  SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.1216-1222
• 
  Bin Li,Feng Liang,Jianhua Hu,Xuming He:
  Reno: regularized non-parametric analysis of protein lysate array data.1223-1229

Genetics and Population Analysis

• 
  William H. Mather,Jeff Hasty,Lev S. Tsimring:
  Fast stochastic algorithm for simulating evolutionary population dynamics.1230-1238

Systems Biology

• 
  Hang T. T. Phan,Michael J. E. Sternberg:
  PINALOG: a novel approach to align protein interaction networks - implications for complex detection and function prediction.1239-1245
• 
  Yuan Yuan,Yanxun Xu,Jianfeng Xu,Robyn L. Ball,Han Liang:
  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data.1246-1252

Data and Text Mining

• 
  David Campos,Sérgio Matos,Ian Lewin,José Luís Oliveira,Dietrich Rebholz-Schuhmann:
  Harmonization of gene/protein annotations: towards a gold standard MEDLINE.1253-1261

Databases and Ontologies

• 
  David Osumi-Sutherland,Simon Reeve,Christopher J. Mungall,Fabian Neuhaus,Alan Ruttenberg,Gregory S. X. E. Jefferis,J. Douglas Armstrong:
  A strategy for building neuroanatomy ontologies.1262-1269

Applications Note - Genome Analysis

• 
  Sabine Ménigaud,Ludovic Mallet,Géraldine Picord,Cécile Churlaud,Alexandre Borrel,Patrick Deschavanne:
  GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'.1270-1271
• 
  Jing-Woei Li,Robert Schmieder,R. Matthew Ward,Joann Delenick,Eric C. Olivares,David Mittelman:
  SEQanswers: an open access community for collaboratively decoding genomes.1272-1273
• 
  Junhee Seok,Weihong Xu,Hong Gao,Ronald W. Davis,Wenzhong Xiao:
  JETTA: junction and exon toolkits for transcriptome analysis.1274-1275

Sequence Analysis

• 
  Kris Popendorf,Yasubumi Sakakibara:
  SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.1276-1277

Structural Bioinformatics

• 
  Adam Hospital,Pau Andrio,Carlos Fenollosa,Damjan Cicin-Sain,Modesto Orozco,Josep Lluis Gelpí:
  MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.1278-1279

Genetics and Population Analysis

• 
  Richard T. Barfield,Varun Kilaru,Alicia K. Smith,Karen N. Conneely:
  CpGassoc: an R function for analysis of DNA methylation microarray data.1280-1281
• 
  Mark Reppell,Michael Boehnke,Sebastian Zöllner:
  FTEC: a coalescent simulator for modeling faster than exponential growth.1282-1283

Systems Biology

• 
  Florian Gnad,Javier Estrada,Jeremy Gunawardena:
  Proteus: a web-based, context-specific modelling tool for molecular networks.1284-1286
• 
  Nicolae Radu Zabet,Boris Adryan:
  GRiP: a computational tool to simulate transcription factor binding in prokaryotes.1287-1289
• 
  Stefan Streif,Anton Savchenko,Philipp Rumschinski,Steffen Borchers,Rolf Findeisen:
  ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling.1290-1291

Data and Text Mining

• 
  J. Lamar Barnett,Jialiang Yang,Zhipeng Cai,Tong Zhang,Xiu-Feng Wan:
  AntigenMap 3D: an online antigenic cartography resource.1292-1293
• 
  Pierre Millard,Fabien Létisse,Serguei Sokol,Jean-Charles Portais:
  IsoCor: correcting MS data in isotope labeling experiments.1294-1296

Corrigendum - Data and Text Mining

• 
  Catherine Stamoulis,Rebecca A. Betensky:
  A novel signal processing approach for the detection of copy number variations in the human genome.1297

Volume 28, Number 10, May 2012

Discovery Notes - Structural Bioinformatics

• 
  Cyril F. Reboul,Khalid Mahmood,James C. Whisstock,Michelle A. Dunstone:
  Predicting giant transmembrane β-barrel architecture.1299-1302

Databases and Ontologies

• 
  Hiren J. Joshi,Katy M. Christiansen,Joffrey Fitz,Jun Cao,Anna Lipzen,Joel Martin,A. Michelle Smith-Moritz,Len A. Pennacchio,Wendy S. Schackwitz,Detlef Weigel,Joshua L. Heazlewood:
  1001 Proteomes: a functional proteomics portal for the analysis ofArabidopsis thaliana accessions.1303-1306

Original Papers - Genome Analysis

• 
  Jason Li,Richard Lupat,Kaushalya C. Amarasinghe,Ella R. Thompson,Maria A. Doyle,Georgina L. Ryland,Richard W. Tothill,Saman K. Halgamuge,Ian G. Campbell,Kylie L. Gorringe:
  CONTRA: copy number analysis for targeted resequencing.1307-1313

Sequence Analysis

• 
  Jie Lin,Donald A. Adjeroh,Bing-Hua Jiang:
  Probabilistic suffix array: efficient modeling and prediction of protein families.1314-1323
• 
  Matthew S. Burriesci,Erik M. Lehnert,John R. Pringle:
  Fulcrum: condensing redundant reads from high-throughput sequencing studies.1324-1327
• 
  Erola Pairo,Joan Maynou,Santiago Marco,Alexandre Perera:
  A subspace method for the detection of transcription factor binding sites.1328-1335
• 
  Hongtao Sun,Jeremy D. Buhler:
  PhyLAT: a phylogenetic local alignment tool.1336-1344

Structural Bioinformatics

• 
  Bin Pang,Nan Zhao,Dmitry Korkin,Chi-Ren Shyu:
  Fast protein binding site comparisons using visual words representation.1345-1352

Gene Expression

• 
  Andrey A. Shabalin:
  Matrix eQTL: ultra fast eQTL analysis via large matrix operations.1353-1358

Genetics and Population Analysis

• 
  Yael Baran,Bogdan Pasaniuc,Sriram Sankararaman,Dara G. Torgerson,Christopher Gignoux,Celeste Eng,William Rodriguez-Cintron,Rocio Chapela,Jean G. Ford,Pedro C. Avila,Jose Rodriguez-Santana,Esteban Gonzàlez Burchard,Eran Halperin:
  Fast and accurate inference of local ancestry in Latino populations.1359-1367
• 
  Hokeun Sun,Shuang Wang:
  Penalized logistic regression for high-dimensional DNA methylation data with case-control studies.1368-1375

Systems Biology

• 
  Robert Küffner,Tobias Petri,Pegah Tavakkolkhah,Lukas Windhager,Ralf Zimmer:
  Inferring gene regulatory networks by ANOVA.1376-1382

Databases and Ontologies

• 
  Haixuan Yang,Tamás Nepusz,Alberto Paccanaro:
  Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty.1383-1389
• 
  Andrew Sparkes,Amanda Clare:
  AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory.1390-1397

Applications Note - Genome Analysis

• 
  Nizar Fawal,Bruno Savelli,Christophe Dunand,Catherine Mathé:
  GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families.1398-1399

Structural Bioinformatics

• 
  Federico Comoglio,Maurizio Rinaldi:
  Rknots: topological analysis of knotted biopolymers with R.1400-1401

Data and Text Mining

• 
  Vincent Xue,Tony Burdett,Margus Lukk,Julie Taylor,Alvis Brazma,Helen E. Parkinson:
  MageComet - web application for harmonizing existing large-scale experiment descriptions.1402-1403
• 
  Penghao Wang,Pengyi Yang,Jean Yee Hwa Yang:
  OCAP: an open comprehensive analysis pipeline for iTRAQ.1404-1405

Databases and Ontologies

• 
  Mario Novkovic,Juraj Simunic,Viktor Bojovic,Alessandro Tossi,Davor Juretic:
  DADP: the database of anuran defense peptides.1406-1407
• 
  Maureen A. Sartor,Alexander S. Ade,Zach Wright,David J. States,Gilbert S. Omenn,Brian D. Athey,Alla Karnovsky:
  Metab2MeSH: annotating compounds with medical subject headings.1408-1410
• 
  Bo Qin,Meng Zhou,Ying Ge,Len Taing,Tao Liu,Qian Wang,Su Wang,Junsheng Chen,Lingling Shen,Xikun Duan,Sheng'en Hu,Wei Li,Henry Long,Yong Zhang,Xiaole Shirley Liu:
  CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.1411-1412

Corrigendum - Databases and Ontologies

• 
  Feng Feng,Ana Paula Sales,Thomas B. Kepler:
  A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays.1413

Volume 28, Number 11, June 2012

Hitseq Papers - Genome Analysis

• 
  Anthony J. Cox,Markus J. Bauer,Tobias Jakobi,Giovanna Rosone:
  Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform.1415-1419

Sequence Analysis

• 
  Yu Peng,Henry C. M. Leung,Siu-Ming Yiu,Francis Y. L. Chin:
  IDBA-UD: ade novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.1420-1428
• 
  Alexey A. Gritsenko,Jurgen F. Nijkamp,Marcel J. T. Reinders,Dick de Ridder:
  GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.1429-1437

Original Papers - Genome Analysis

• 
  Matthieu Chartier,Francis Gaudreault,Rafael Najmanovich:
  Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.1438-1445
• 
  Anton Aboukhalil,Martha L. Bulyk:
  LOESS correction for length variation in gene set-based genomic sequence analysis.1446-1454
• 
  Binbin Lai,Ruogu Ding,Yang Li,Liping Duan,Huaiqiu Zhu:
  Ade novo metagenomic assembly program for shotgun DNA reads.1455-1462

Structural Bioinformatics

• 
  Valéry Ozenne,Frédéric Bauer,Loïc Salmon,Jie-rong Huang,Malene Ringkjøbing Jensen,Stéphane Segard,Pau Bernadó,Céline Charavay,Martin Blackledge:
  Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables.1463-1470

Gene Expression

• 
  Christian Otto,Kristin Reiche,Jörg Hackermüller:
  Detection of differentially expressed segments in tiling array data.1471-1479
• 
  Haroon Naeem,Ralf Zimmer,Pegah Tavakkolkhah,Robert Küffner:
  Rigorous assessment of gene set enrichment tests.1480-1486
• 
  Andrew E. Teschendorff,Martin Widschwendter:
  Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions.1487-1494

Systems Biology

• 
  Jochen Weile,Katherine James,Jennifer Hallinan,Simon J. Cockell,Phillip W. Lord,Anil Wipat,Darren J. Wilkinson:
  Bayesian integration of networks without gold standards.1495-1500
• 
  Xin Liu,Mahesan Niranjan:
  State and parameter estimation of the heat shock response system using Kalman and particle filters.1501-1507
• 
  Bing Liu,Andrei Hagiescu,Sucheendra K. Palaniappan,Bipasa Chattopadhyay,Zheng Cui,Weng-Fai Wong,P. S. Thiagarajan:
  Approximate probabilistic analysis of biopathway dynamics.1508-1516
• 
  Nicolae Radu Zabet,Boris Adryan:
  A comprehensive computational model of facilitated diffusion in prokaryotes.1517-1524

Applications Note - Genome Analysis

• 
  Simon P. Sadedin,Bernard J. Pope,Alicia Oshlack:
  Bpipe: a tool for running and managing bioinformatics pipelines.1525-1526
• 
  Vikas Rao Pejaver,Jaehyun An,SungMin Rhee,Ankita Bhan,Jeong-Hyeon Choi,Boshu Liu,Heewook Lee,Pamela J. Brown,David Kysela,Yves V. Brun,Sun Kim:
  GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis.1527-1529
• 
  David S. DeLuca,Joshua Z. Levin,Andrey Sivachenko,Tim Fennell,Marc-Danie Nazaire,Chris Williams,Michael Reich,Wendy Winckler,Gad Getz:
  RNA-SeQC: RNA-seq metrics for quality control and process optimization.1530-1532

Sequence Analysis

• 
  Xuesong Hu,Jianying Yuan,Yujian Shi,Jianliang Lu,Binghang Liu,Zhenyu Li,Yanxiang Chen,Desheng Mu,Hao Zhang,Nan Li,Zhen Yue,Fan Bai,Heng Li,Wei Fan:
  pIRS: Profile-based Illumina pair-end reads simulator.1533-1535

Phylogenetics

• 
  Andrei-Alin Popescu,Katharina T. Huber,Emmanuel Paradis:
  ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.1536-1537

Structural Bioinformatics

• 
  Osvaldo A. Martin,Jorge A. Vila,Harold A. Scheraga:
  CheShift-2: graphic validation of protein structures.1538-1539
• 
  Emilie Pihan,Lionel Colliandre,Jean-François Guichou,Dominique Douguet:
  e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design.1540-1541

Gene Expression

• 
  Laurent Jourdren,Maria Bernard,Marie-Agnès Dillies,Stéphane Le Crom:
  Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses.1542-1543
• 
  Jian-Bo Pan,Shi-chang Hu,Hao Wang,Quan Zou,Zhi-Liang Ji:
  PaGeFinder: quantitative identification of spatiotemporal pattern genes.1544-1545
• 
  Daryl Waggott,Kenneth C. Chu,Shaoming Yin,Bradly G. Wouters,Fei-Fei Liu,Paul C. Boutros:
  NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data.1546-1548

Systems Biology

• 
  Gábor Szederkényi,Julio R. Banga,Antonio A. Alonso:
  CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks.1549-1550

Databases and Ontologies

• 
  Feng Gao,Hao Luo,Chun-Ting Zhang:
  DeOri: a database of eukaryotic DNA replication origins.1551-1552

Genetics and Population Analysis

• 
  Stephen A. Stanhope,Mark Abney:
  GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations.1553-1554

Volume 28, Number 12, June 2012

ISMB 2012

• 
  Bonnie Berger:
  Editorial.1
• 
  ISMB 2012 Committee.2-6
• 
  Alexander Herbig,Günter Jäger,Florian Battke,Kay Nieselt:
  GenomeRing: alignment visualization based on SuperGenome coordinates.7-15
• 
  Xiao Cai,Hua Wang,Heng Huang,Chris H. Q. Ding:
  Joint stage recognition and anatomical annotation ofdrosophila gene expression patterns.16-24
• 
  Linqing Feng,Ting Zhao,Jinhyun Kim:
  Improved synapse detection for mGRASP-assisted brain connectivity mapping.25-31
• 
  Jieyue Li,Liang Xiong,Jeff G. Schneider,Robert F. Murphy:
  Protein subcellular location pattern classification in cellular images using latent discriminative models.32-39
• 
  Yongjin Park,Joel S. Bader:
  How networks change with time.40-48
• 
  Yu-Keng Shih,Srinivasan Parthasarathy:
  A single sourcek-shortest paths algorithm to infer regulatory pathways in a gene network.49-58
• 
  Jianzhu Ma,Jian Peng,Sheng Wang,Jinbo Xu:
  A conditional neural fields model for protein threading.59-66
• 
  Milana Frenkel-Morgenstern,Alfonso Valencia:
  Novel domain combinations in proteins encoded by chimeric transcripts.67-74
• 
  Fatemeh Miri Disfani,Wei-Lun Hsu,Marcin J. Mizianty,Christopher J. Oldfield,Bin Xue,A. Keith Dunker,Vladimir N. Uversky,Lukasz A. Kurgan:
  MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins.75-83
• 
  Ryan G. Christensen,Metewo Selase Enuameh,Marcus B. Noyes,Michael H. Brodsky,Scot A. Wolfe,Gary D. Stormo:
  Recognition models to predict DNA-binding specificities of homeodomain proteins.84-89
• 
  Sikander Hayat,Arne Elofsson:
  Ranking models of transmembraneβ-barrel proteins using Z-coordinate predictions.90-96
• 
  Arun Siddharth Konagurthu,Arthur M. Lesk,Lloyd Allison:
  Minimum message length inference of secondary structure from protein coordinate data.97-105
• 
  Dorit S. Hochbaum,Chun-Nan Hsu,Yan T. Yang:
  Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores.106-114
• 
  Atsushi Niida,Seiya Imoto,Teppei Shimamura,Satoru Miyano:
  Statistical model-based testing to evaluate the recurrence of genomic aberrations.115-120
• 
  Chirag J. Patel,Rong Chen,Atul J. Butte:
  Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.121-126
• 
  Hua Wang,Feiping Nie,Heng Huang,Shannon L. Risacher,Andrew J. Saykin,Li Shen:
  Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning.127-136
• 
  Seunghak Lee,Eric P. Xing:
  Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs.137-146
• 
  Gregory Darnell,Dat Duong,Buhm Han,Eleazar Eskin:
  Incorporating prior information into association studies.147-153
• 
  Derek Aguiar,Bjarni V. Halldórsson,Eric M. Morrow,Sorin Istrail:
  DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism.154-162
• 
  Qian Peng,Joseph R. Ecker:
  Detection of allele-specific methylation through a generalized heterogeneous epigenome model.163-171
• 
  Thomas C. Conway,Jeremy Wazny,Andrew J. Bromage,Martin Tymms,Dhanya Sooraj,Elizabeth D. Williams,Bryan Beresford-Smith:
  Xenome - a tool for classifying reads from xenograft samples.172-178
• 
  Deniz Yörükoglu,Faraz Hach,Lucas Swanson,Colin C. Collins,Inanç Birol,Süleyman Cenk Sahinalp:
  Dissect: detection and characterization of novel structural alterations in transcribed sequences.179-187
• 
  Roy Ronen,Christina Boucher,Hamidreza Chitsaz,Pavel A. Pevzner:
  SEQuel: improving the accuracy of genome assemblies.188-196
• 
  David Golan,Yaniv Erlich,Saharon Rosset:
  Weighted pooling - practical and cost-effective techniques for pooled high-throughput sequencing.197-206
• 
  Vladimir Reinharz,François Major,Jérôme Waldispühl:
  Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.207-214
• 
  Jan Hoinka,Elena Zotenko,Adam Friedman,Zuben E. Sauna,Teresa M. Przytycka:
  Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.215-223
• 
  Steffen Heyne,Fabrizio Costa,Dominic Rose,Rolf Backofen:
  GraphClust: alignment-free structural clustering of local RNA secondary structures.224-232
• 
  Christopher A. Penfold,Vicky Buchanan-Wollaston,Katherine J. Denby,David L. Wild:
  Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks.233-241
• 
  Anton Polishko,Nadia Ponts,Karine G. Le Roch,Stefano Lonardi:
  NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model.242-249
• 
  Tatsunori B. Hashimoto,Tommi S. Jaakkola,Richard Sherwood,Esteban O. Mazzoni,Hynek Wichterle,David K. Gifford:
  Lineage-based identification of cellular states and expression programs.250-257
• 
  Aaron Wise,Zoltán N. Oltvai,Ziv Bar-Joseph:
  Matching experiments across species using expression values and textual information.258-264
• 
  Franziska Hufsky,Kai Dührkop,Florian Rasche,Markus Chimani,Sebastian Böcker:
  Fast alignment of fragmentation trees.265-273
• 
  Serita M. Nelesen,Kevin Liu,Li-San Wang,C. Randal Linder,Tandy J. Warnow:
  DACTAL: divide-and-conquer trees (almost) without alignments.274-282
• 
  Mukul S. Bansal,Eric J. Alm,Manolis Kellis:
  Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.283-291
• 
  Götz Fabian,Thomas Wächter,Michael Schroeder:
  Extending ontologies by finding siblings using set expansion techniques.292-300

Regular Papers

• 
  Ahrim Youn,Richard Simon:
  Estimating the order of mutations during tumorigenesis from tumor genome sequencing data.1555-1561
• 
  Tuobin Wang,Arminja N. Kettenbach,Scott A. Gerber,Chris Bailey-Kellogg:
  MMFPh: a maximal motif finder for phosphoproteomics datasets.1562-1570
• 
  Axel Bernal,Koby Crammer,Fernando Pereira:
  Automated gene-model curation using global discriminative learning.1571-1578
• 
  Zhong-Ru Xie,Ming-Jing Hwang:
  Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles.1579-1585
• 
  Xuan Wang,Gordon A. Anderson,Richard D. Smith,Alan R. Dabney:
  A hybrid approach to protein differential expression in mass spectrometry-based proteomics.1586-1591
• 
  Ovidiu D. Iancu,Sunita Kawane,Daniel Bottomly,Robert P. Searles,Robert Hitzemann,Shannon K. McWeeney:
  Utilizing RNA-Seq data forde novo coexpression network inference.1592-1597
• 
  T. S. Shah,Jimmy Zhenli Liu,J. A. B. Floyd,James A. Morris,N. Wirth,Jeffrey C. Barrett,Carl A. Anderson:
  optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.1598-1603
• 
  Bor-Sen Chen,Chia-Chou Wu:
  On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach.1604-1611
• 
  Juliane Siebourg,Gunter Merdes,Benjamin Misselwitz,Wolf-Dietrich Hardt,Niko Beerenwinkel:
  Stability of gene rankings from RNAi screens.1612-1618
• 
  Dennis Egen,Desmond S. Lun:
  Truncated branch and bound achieves efficient constraint-based genetic design.1619-1623
• 
  Tavis K. Anderson,William W. Laegreid,Francesco Cerutti,Fernando A. Osorio,Eric A. Nelson,Jane Christopher-Hennings,Tony L. Goldberg:
  Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development.1624-1632
• 
  Tim Rocktäschel,Michael Weidlich,Ulf Leser:
  ChemSpot: a hybrid system for chemical named entity recognition.1633-1640

Applications Note

• 
  Clemens Kreutz,J. S. Gehring,Daniel Lang,Ralf Reski,Jens Timmer,Stefan A. Rensing:
  TSSi - an R package for transcription start site identification from 5′ mRNA tag data.1641-1642
• 
  Vittore F. Scolari,Mina Zarei,Matteo Osella,Marco Cosentino Lagomarsino:
  NuST: analysis of the interplay between nucleoid organization and gene expression.1643-1644
• 
  Joshua Tan,Durga Kuchibhatla,Fernanda L. Sirota,Westley A. Sherman,Tobias Gattermayer,Chia Yee Kwoh,Frank Eisenhaber,Georg Schneider,Sebastian Maurer-Stroh:
  Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.1645-1646
• 
  Matthew Kearse,Richard Moir,Amy Wilson,Steven Stones-Havas,Matthew Cheung,Shane S. Sturrock,Simon Buxton,Alex Cooper,Sidney Markowitz,Chris Duran,Tobias Thierer,Bruce Ashton,Peter L. Meintjes,Alexei J. Drummond:
  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data.1647-1649
• 
  Weizhong Li,Hamish McWilliam,Mickael Goujon,Andrew Peter Cowley,Rodrigo Lopez,William R. Pearson:
  PSI-Search: iterative HOE-reduced profile SSEARCH searching.1650-1651
• 
  Paulo C. Carvalho,John R. Yates III,Valmir Carneiro Barbosa:
  Improving the TFold test for differential shotgun proteomics.1652-1654
• 
  Nicholas Smith,Shawn Witham,Subhra Sarkar,Jie Zhang,Lin Li,Chuan Li,Emil Alexov:
  DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.1655-1657
• 
  Claudia Andreini,Gabriele Cavallaro,Serena Lorenzini:
  FindGeo: a tool for determining metal coordination geometry.1658-1660
• 
  Adrià Cereto-Massagué,Laura Guasch,Cristina Valls,Miquel Mulero,Gerard Pujadas,Santiago Garcia-Vallvé:
  DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.1661-1662
• 
  Hadas Zur,Tamir Tuller:
  RFMapp: ribosome flow model application.1663-1664
• 
  Marco Brandizi,Natalja Kurbatova,Ugis Sarkans,Philippe Rocca-Serra:
  graph2tab, a library to convert experimental workflow graphs into tabular formats.1665-1667

Volume 28, Number 13, July 2012

Original Papers - Genome Analysis

• 
  Catherine A. Hayes,Szilárd Nemes,Niclas G. Karlsson:
  Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state.1669-1676
• 
  Shreepriya Das,Haris Vikalo:
  OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.1677-1683

Sequence Analysis

• 
  Ari Löytynoja,Albert J. Vilella,Nick Goldman:
  Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.1684-1691
• 
  Xiaowen Liu,Alessandro Mammana,Vineet Bafna:
  Speeding up tandem mass spectral identification using indexes.1692-1697
• 
  Christian Otto,Peter F. Stadler,Steve Hoffmann:
  Fast and sensitive mapping of bisulfite-treated sequencing data.1698-1704

Structural Bioinformatics

• 
  Lars J. Kangas,Thomas O. Metz,Giorgis Isaac,Brian T. Schrom,Bojana Ginovska-Pangovska,Luning Wang,Li Tan,Robert R. Lewis,John H. Miller:
  In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids.1705-1713

Gene Expression

• 
  Benedikt Zacher,Khalid Abnaof,Stephan Gade,Erfan Younesi,Achim Tresch,Holger Fröhlich:
  Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.1714-1720
• 
  Peter Glaus,Antti Honkela,Magnus Rattray:
  Identifying differentially expressed transcripts from RNA-seq data with biological variation.1721-1728

Genetics and Population Analysis

• 
  Noah Zaitlen,Bogdan Pasaniuc,Nick Patterson,Samuela Pollack,Benjamin Voight,Leif Groop,David Altshuler,Brian E. Henderson,Laurence N. Kolonel,Loic Le Marchand,Kevin Waters,Christopher A. Haiman,Barbara E. Stranger,Emmanouil T. Dermitzakis,Peter Kraft,Alkes L. Price:
  Analysis of case-control association studies with known risk variants.1729-1737
• 
  Benjamin A. Logsdon,Cara L. Carty,Alexander P. Reiner,James Y. Dai,Charles L. Kooperberg:
  A novel variational Bayes multiple locusZ-statistic for genome-wide association studies with Bayesian model averaging.1738-1744
• 
  Dajiang J. Liu,Suzanne M. Leal:
  SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations.1745-1751

Systems Biology

• 
  Yu-Chieh Liao,Ming-Hsin Tsai,Feng-Chi Chen,Chao A. Hsiung:
  GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.1752-1758

Data and Text Mining

• 
  Makoto Miwa,Paul Thompson,Sophia Ananiadou:
  Boosting automatic event extraction from the literature using domain adaptation and coreference resolution.1759-1765
• 
  Vân Anh Huynh-Thu,Yvan Saeys,Louis Wehenkel,Pierre Geurts:
  Statistical interpretation of machine learning-based feature importance scores for biomarker discovery.1766-1774
• 
  Plamen Dragiev,Robert Nadon,Vladimir Makarenkov:
  Two effective methods for correcting experimental high-throughput screening data.1775-1782

Databases and Ontologies

• 
  Robert Hoehndorf,Midori A. Harris,Heinrich Herre,Gabriella Rustici,Georgios V. Gkoutos:
  Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.1783-1789

Applications Note - Genome Analysis

• 
  Ji-Hong Kim,Hae-Jin Hu,Seon-Hee Yim,Joon Seol Bae,Seon-Young Kim,Yeun-Jun Chung:
  CNVRuler: a copy number variation-based case-control association analysis tool.1790-1792
• 
  Maria Ortiz-Estevez,Ander Aramburu,Henrik Bengtsson,Pierre Neuvial,Angel Rubio:
  CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.1793-1794

Sequence Analysis

• 
  Elena Yavorska Harris,Nadia Ponts,Karine G. Le Roch,Stefano Lonardi:
  BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.1795-1796

Genetics and Population Analysis

• 
  Phil H. Lee,Colm O'Dushlaine,Brett Thomas,Shaun Purcell:
  INRICH: interval-based enrichment analysis for genome-wide association studies.1797-1799

Systems Biology

• 
  Maria Anna Rapsomaniki,Panagiotis Kotsantis,Ioanna-Eleni Symeonidou,Nickolaos-Nikiforos Giakoumakis,Stavros L. Taraviras,Zoi Lygerou:
  easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data.1800-1801

Data and Text Mining

• 
  Noppadon Khiripet,Wongarnet Khantuwan,John R. Jungck:
  Ka-me: a Voronoi image analyzer.1802-1804

Databases and Ontologies

• 
  Xiaoli Jiao,Brad T. Sherman,Da Wei Huang,Robert M. Stephens,Michael W. Baseler,H. Clifford Lane,Richard A. Lempicki:
  DAVID-WS: a stateful web service to facilitate gene/protein list analysis.1805-1806

Volume 28, Number 14, July 2012

Discovery Note - Data and Text Mining

• 
  Terry Bertozzi,Kate L. Sanders,Mark J. Sistrom,Michael G. Gardner:
  Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys.1807-1810

Original Papers - Genome Analysis

• 
  Christopher T. Saunders,Wendy S. W. Wong,Sajani Swamy,Jennifer Becq,Lisa J. Murray,R. Keira Cheetham:
  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.1811-1817
• 
  Arend Voorman,Ken Rice,Thomas Lumley:
  Fast computation for genome-wide association studies using boosted one-step statistics.1818-1822

Sequence Analysis

• 
  Elmar Pruesse,Jörg Peplies,Frank Oliver Glöckner:
  SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes.1823-1829
• 
  Yongchao Liu,Bertil Schmidt,Douglas L. Maskell:
  CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.1830-1837
• 
  Heng Li:
  Exploring single-sample SNP and INDEL calling with whole-genomede novo assembly.1838-1844

Structural Bioinformatics

• 
  Joan Segura,Pamela F. Jones,Narcis Fernandez-Fuentes:
  A holisticin silico approach to predict functional sites in protein structures.1845-1850
• 
  Maria T. Buenavista,Daniel B. Roche,Liam J. McGuffin:
  Improvement of 3D protein models using multiple templates guided by single-template model quality assessment.1851-1857
• 
  David Hoksza,Daniel Svozil:
  Efficient RNA pairwise structure comparison by SETTER method.1858-1864

Gene Expression

• 
  Barbara Piasecka,Marc Robinson-Rechavi,Sven Bergmann:
  Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.1865-1872
• 
  Jishnu Das,Jaaved Mohammed,Haiyuan Yu:
  Genome-scale analysis of interaction dynamics reveals organization of biological networks.1873-1878

Genetics and Population Analysis

• 
  Mingxiang Teng,Shoji Ichikawa,Leah R. Padgett,Yadong Wang,Matthew E. Mort,David N. Cooper,Daniel L. Koller,Tatiana Foroud,Howard J. Edenberg,Michael J. Econs,Yunlong Liu:
  regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions.1879-1886

Systems Biology

• 
  Daniela Beisser,Stefan Brunkhorst,Thomas Dandekar,Gunnar W. Klau,Marcus T. Dittrich,Tobias Müller:
  Robustness and accuracy of functional modules in integrated network analysis.1887-1894
• 
  Doug Hyatt,Chongle Pan:
  Exhaustive database searching for amino acid mutations in proteomes.1895-1901
• 
  Chen Zhao,Jianping Hua,Michael L. Bittner,Ivan Ivanov,Edward R. Dougherty:
  Identifying mechanistic similarities in drug responses.1902-1910

Data and Text Mining

• 
  Haisu Ma,Hongyu Zhao:
  iFad: an integrative factor analysis model for drug-pathway association inference.1911-1918

Applications Note - Genome Analysis

• 
  Shane J. Neph,Scott Kuehn,Alex P. Reynolds,Eric Haugen,Robert E. Thurman,Audra K. Johnson,Eric Rynes,Matthew T. Maurano,Jeff Vierstra,Sean Thomas,Richard S. Sandstrom,Richard Humbert,John A. Stamatoyannopoulos:
  BEDOPS: high-performance genomic feature operations.1919-1920
• 
  Pierre-Yves Chibon,Heiko Schoof,Richard G. F. Visser,Richard Finkers:
  Marker2sequence, mine your QTL regions for candidate genes.1921-1922

Sequence Analysis

• 
  Ken Chen,John W. Wallis,Cyriac Kandoth,Joelle M. Kalicki-Veizer,Karen L. Mungall,Andrew J. Mungall,Steven J. M. Jones,Marco A. Marra,Timothy J. Ley,Elaine R. Mardis,Richard K. Wilson,John N. Weinstein,Li Ding:
  BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.1923-1924
• 
  Yuanwei Zhang,Bo Xu,Yifan Yang,Rongjun Ban,Huan Zhang,Xiaohua Jiang,Howard J. Cooke,Yu Xue,Qinghua Shi:
  CPSS: a computational platform for the analysis of small RNA deep sequencing data.1925-1927
• 
  Nianxiang Zhang,Yan Xu,Martin O'Hely,Terence P. Speed,Curt Scharfe,Wenyi Wang:
  SRMA: an R package for resequencing array data analysis.1928-1930
• 
  Marleen Claeys,Valerie Storms,Hong Sun,Tom Michoel,Kathleen Marchal:
  MotifSuite: workflow for probabilistic motif detection and assessment.1931-1932
• 
  Jun Hu,Huanying Ge,Matthew Newman,Kejun Liu:
  OSA: a fast and accurate alignment tool for RNA-Seq.1933-1934
• 
  Virag Sharma,David P. Murphy,Gregory M. Provan,Pavel V. Baranov:
  CodonLogo: a sequence logo-based viewer for codon patterns.1935-1936
• 
  Thomas C. Conway,Jeremy Wazny,Andrew J. Bromage,Justin Zobel,Bryan Beresford-Smith:
  Gossamer - a resource-efficientde novo assembler.1937-1938

Gene Expression

• 
  John A. Dawson,Shuyun Ye,Christina Kendziorski:
  R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression.1939-1940
• 
  Regis A. James,Mitchell M. Rao,Edward S. Chen,Margaret A. Goodell,Chad A. Shaw:
  The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool.1941-1942

Systems Biology

• 
  Chao Zhang,Kristina Hanspers,Allan Kuchinsky,Nathan Salomonis,Dong Xu,Alexander R. Pico:
  Mosaic: making biological sense of complex networks.1943-1944

Data and Text Mining

• 
  Arnaud Ogier,Thierry Dorval:
  HCS-Analyzer: open source software for high-content screening data correction and analysis.1945-1946

Databases and Ontologies

• 
  Morgan G. I. Langille,Matthew R. Laird,William W. L. Hsiao,Terry A. Chiu,Jonathan A. Eisen,Fiona S. L. Brinkman:
  MicrobeDB: a locally maintainable database of microbial genomic sequences.1947-1948
• 
  Shigeo Fujimori,Naoya Hirai,Kazuyo Masuoka,Tomohiro Oshikubo,Tatsuhiro Yamashita,Takanori Washio,Ayumu Saito,Masao Nagasaki,Satoru Miyano,Etsuko Miyamoto-Sato:
  IRView: a database and viewer for protein interacting regions.1949-1950

Corrigendum - Databases and Ontologies

• 
  David Ryan Koes,Carlos J. Camacho:
  Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure.1951

Volume 28, Number 15, August 2012

Discovery Note - Sequence Analysis

• 
  Luis Sánchez-Pulido,Lesheng Kong,Chris P. Ponting:
  A common ancestry for BAP1 and Uch37 regulators.1953-1956

Original Papers - Genome Analysis

• 
  Attila Gyenesei,Jonathan Moody,Colin A. M. Semple,Chris S. Haley,Wenhua Wei:
  High-throughput analysis of epistasis in genome-wide association studies with BiForce.1957-1964
• 
  Kai Fu,Qianzi Tang,Jianxing Feng,Xiaole Shirley Liu,Yong Zhang:
  DiNuP: a systematic approach to identify regions of differential nucleosome positioning.1965-1971

Structural Bioinformatics

• 
  Douglas L. Theobald,Phillip A. Steindel:
  Optimal simultaneous superpositioning of multiple structures with missing data.1972-1979
• 
  Ernst Wit,David J. Bakewell:
  Borrowing strength: a likelihood ratio test for related sparse signals.1980-1989

Gene Expression

• 
  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.1990-1997
• 
  Carmen D. Tekwe,Raymond J. Carroll,Alan R. Dabney:
  Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data.1998-2003
• 
  Moysés Nascimento,Thelma Sáfadi,Fabyano Fonseca e Silva,Ana Carolina C. Nascimento:
  Bayesian model-based clustering of temporal gene expression using autoregressive panel data approach.2004-2007

Genetics and Population Analysis

• 
  Joshua S. Paul,Yun S. Song:
  Blockwise HMM computation for large-scale population genomic inference.2008-2015

Systems Biology

• 
  Martijn P. van Iersel,Alice Villéger,Tobias Czauderna,Sarah E. Boyd,Frank T. Bergmann,Augustin Luna,Emek Demir,Anatoly A. Sorokin,Ugur Dogrusöz,Yukiko Matsuoka,Akira Funahashi,Mirit I. Aladjem,Huaiyu Mi,Stuart L. Moodie,Hiroaki Kitano,Nicolas Le Novère,Falk Schreiber:
  Software support for SBGN maps: SBGN-ML and LibSBGN.2016-2021
• 
  Yaki Setty:
  Multi-scale computational modeling of developmental biology.2022-2028
• 
  Rami Mahdi,Abishek S. Madduri,Guoqing Wang,Yael Strulovici-Barel,Jacqueline Salit,Neil R. Hackett,Ronald G. Crystal,Jason G. Mezey:
  Empirical Bayes conditional independence graphs for regulatory network recovery.2029-2036
• 
  Elad Noor,Arren Bar-Even,Avi I. Flamholz,Yaniv Lubling,Dan Davidi,Ron Milo:
  An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.2037-2044
• 
  Chihyun Park,Jaegyoon Ahn,Youngmi Yoon,Sanghyun Park:
  Identification of functional CNV region networks using a CNV-gene mapping algorithm in a genome-wide scale.2045-2051

Data and Text Mining

• 
  Yongchao Ge,Stuart C. Sealfon:
  flowPeaks: a fast unsupervised clustering for flow cytometry data viaK-means and density peak finding.2052-2058

Applications Note - Sequence Analysis

• 
  Matthew B. Stocks,Simon Moxon,Daniel Mapleson,Hugh C. Woolfenden,Irina Mohorianu,Leighton Folkes,Frank Schwach,Tamas Dalmay,Vincent Moulton:
  The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets.2059-2061
• 
  Ashwini Jeggari,Debora S. Marks,Erik Larsson:
  miRcode: a map of putative microRNA target sites in the long non-coding transcriptome.2062-2063

Phylogenetics

• 
  Alexandros Stamatakis,Andre J. Aberer,Christian Goll,Stephen A. Smith,Simon A. Berger,Fernando Izquierdo-Carrasco:
  RAxML-Light: a tool for computing terabyte phylogenies.2064-2066
• 
  Vanderlei J. Debastiani,Valério D. Pillar:
  SYNCSA - R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.2067-2068

Structural Bioinformatics

• 
  Rhonald C. Lua:
  PyKnot: a PyMOL tool for the discovery and analysis of knots in proteins.2069-2071
• 
  Hannes Braberg,Benjamin M. Webb,Elina Tjioe,Ursula Pieper,Andrej Sali,Mallur S. Madhusudhan:
  SALIGN: a web server for alignment of multiple protein sequences and structures.2072-2073
• 
  Andrea Volkamer,Daniel Kuhn,Friedrich Rippmann,Matthias Rarey:
  DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment.2074-2075
• 
  Masafumi Shionyu,Ken-ichi Takahashi,Mitiko Go:
  AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts.2076-2077
• 
  Srinivas Somarowthu,Mary Jo Ondrechen:
  POOL server: machine learning application for functional site prediction in proteins.2078-2079
• 
  Tomás Di Domenico,Ian Walsh,Alberto J. M. Martin,Silvio C. E. Tosatto:
  MobiDB: a comprehensive database of intrinsic protein disorder annotations.2080-2081

Genetic and Population Analysis

• 
  Olivier Sosnowski,Alain Charcosset,Johann Joets:
  BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms.2082-2083
• 
  Robert Kofler,Christian Schlötterer:
  Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.2084-2085
• 
  Valentin Wimmer,Theresa Albrecht,Hans-Jürgen Auinger,Chris-Carolin Schön:
  synbreed: a framework for the analysis of genomic prediction data using R.2086-2087

Systems Biology

• 
  Jie Hao,William J. Astle,Maria De Iorio,Timothy M. D. Ebbels:
  BATMAN - an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model.2088-2090

Corrigendum - Systems Biology

• 
  David Osumi-Sutherland,Simon Reeve,Christopher J. Mungall,Fabian Neuhaus,Alan Ruttenberg,Gregory S. X. E. Jefferis,J. Douglas Armstrong:
  A strategy for building neuroanatomy ontologies.2091

Volume 28, Number 16, August 2012

Discovery Note - Genetics and Population Analysis

• 
  Vanessa E. Gray,Kimberly R. Kukurba,Sudhir Kumar:
  Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations.2093-2096

Genome Analysis

• 
  Hayan Lee,Michael C. Schatz:
  Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.2097-2105
• 
  Jun Chen,Kyle Bittinger,Emily S. Charlson,Christian Hoffmann,James D. Lewis,Gary D. Wu,Ronald G. Collman,Frederic D. Bushman,Hongzhe Li:
  Associating microbiome composition with environmental covariates using generalized UniFrac distances.2106-2113

Sequence Analysis

• 
  Francesco Abate,Andrea Acquaviva,Giulia Paciello,Carmelo Foti,Elisa Ficarra,Alberto Ferrarini,Massimo Delledonne,Ilaria Iacobucci,Simona Soverini,Giovanni Martinelli,Enrico Macii:
  Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.2114-2121
• 
  Chandana Tennakoon,Rikky W. Purbojati,Wing-Kin Sung:
  BatMis: a fast algorithm fork-mismatch mapping.2122-2128

Systems Biology

• 
  Sayed Mohammad Ebrahim Sahraeian,Byung-Jun Yoon:
  RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks.2129-2136
• 
  Ömer Sinan Saraç,Vera Pancaldi,Jürg Bähler,Andreas Beyer:
  Topology of functional networks predicts physical binding of proteins.2137-2145
• 
  Chao-Yi Dong,Dongkwan Shin,Sunghoon Joo,Yoonkey Nam,Kwang-Hyun Cho:
  Identification of feedback loops in neural networks based on multi-step Granger causality.2146-2153

Data and Text Mining

• 
  Martin Gerner,Farzaneh Sarafraz,Casey M. Bergman,Goran Nenadic:
  BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.2154-2161
• 
  Darby Tien-Hao Chang,Chao-Hsuan Ke,Jung-Hsin Lin,Jung-Hsien Chiang:
  AutoBind: automatic extraction of protein-ligand-binding affinity data from biological literature.2162-2168

Databases and Ontologies

• 
  Robert Hoehndorf,Michel Dumontier,Georgios V. Gkoutos:
  Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.2169-2175

Applications Note - Genome Analysis

• 
  Taemin Song,Kyu Baek Hwang,Michael Hsing,Kyungjoon Lee,Justin Bohn,Sek Won Kong:
  gSearch: a fast and flexible general search tool for whole-genome sequencing.2176-2177

Sequence Analysis

• 
  Lida Zhang,Yuyi Huang,Zehong Zou,Ying He,Ximo Chen,Ailin Tao:
  SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides.2178-2179
• 
  Zhifu Sun,Saurabh Baheti,Sumit Middha,Rahul Kanwar,Yuji Zhang,Xing Li,Andreas S. Beutler,Eric W. Klee,Yan W. Asmann,E. Aubrey Thompson,Jean-Pierre A. Kocher:
  SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.2180-2181
• 
  Zejun Zheng,Stefan Kramer,Bertil Schmidt:
  DySC: software for greedy clustering of 16S rRNA reads.2182-2183
• 
  Liguo Wang,Shengqin Wang,Wei Li:
  RSeQC: quality control of RNA-seq experiments.2184-2185

Structural Bioinformatics

• 
  Benjamin J. Bachman,Eric Venner,Rhonald C. Lua,Serkan Erdin,Olivier Lichtarge:
  ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.2186-2188
• 
  Ian Walsh,Giovanni Minervini,Alessandra Corazza,Gennaro Esposito,Silvio C. E. Tosatto,Federico Fogolari:
  Bluues server: electrostatic properties of wild-type and mutated protein structures.2189-2190
• 
  Ling-Hong Hung,Ram Samudrala:
  Accelerated protein structure comparison using TM-score-GPU.2191-2192
• 
  Anna Caroline E. Dahl,Matthieu Chavent,Mark S. P. Sansom:
  Bendix: intuitive helix geometry analysis and abstraction.2193-2194

Systems Biology

• 
  Anat Kreimer,Adi Doron-Faigenboim,Elhanan Borenstein,Shiri Freilich:
  NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species.2195-2197

Data and Text Mining

• 
  Wade K. Copeland,Vandhana Krishnan,Daniel Beck,Matt Settles,James A. Foster,Kyu-Chul Cho,Mitch Day,Roxana Hickey,Ursel M. E. Schütte,Xia Zhou,Christopher J. Williams,Larry J. Forney,Zaid Abdo:
  mcaGUI: microbial community analysis R-Graphical User Interface (GUI).2198-2199
• 
  Jan Wildenhain,Nicholas FitzGerald,Mike Tyers:
  MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models.2200-2201
• 
  Máté Szalay-Beko,Robin Palotai,Balázs Szappanos,István A. Kovács,Balázs Papp,Peter Csermely:
  ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality.2202-2204

Databases and Ontologies

• 
  Lihua Liu,Xi Ting Zhen,Emily Denton,Brian D. Marsden,Matthieu Schapira:
  ChromoHub: a data hub for navigators of chromatin-mediated signalling.2205-2206
• 
  Javier Otegui,Arturo H. Ariño:
  BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network.2207-2208
• 
  Alexander C. Zambon,Stan Gaj,Isaac Ho,Kristina Hanspers,Karen Vranizan,Chris T. A. Evelo,Bruce R. Conklin,Alexander R. Pico,Nathan Salomonis:
  GO-Elite: a flexible solution for pathway and ontology over-representation.2209-2210

Letter to the Editor - Databases and Ontologies

• 
  Zengyou He,Haipeng Gong:
  Comments on 'MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets'.2211-2212
• 
  Tuobin Wang,Arminja N. Kettenbach,Scott A. Gerber,Chris Bailey-Kellogg:
  Response to 'Comments on "MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets"'.2213

Volume 28, Number 17, September 2012

Original Papers - Genome Analysis

• 
  Kristoffer Sahlin,Nathaniel Street,Joakim Lundeberg,Lars Arvestad:
  Improved gap size estimation for scaffolding algorithms.2215-2222
• 
  Doug Hyatt,Philip F. LoCascio,Loren J. Hauser,Edward C. Uberbacher:
  Gene and translation initiation site prediction in metagenomic sequences.2223-2230

Sequence Analysis

• 
  Hiro Takahashi,Anna Takahashi,Satoshi Naito,Hitoshi Onouchi:
  BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to theArabidopsis thaliana genome.2231-2241

Structural Bioinformatics

• 
  Gero Doose,Dirk Metzler:
  Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.2242-2248
• 
  Gwo-Yu Chuang,Jeffrey C. Boyington,M. Gordon Joyce,Jiang Zhu,Gary J. Nabel,Peter D. Kwong,Ivelin Georgiev:
  Computational prediction of N-linked glycosylation incorporating structural properties and patterns.2249-2255

Gene Expression

• 
  Tomas Puelma,Rodrigo A. Gutiérrez,Alvaro Soto:
  Discriminative local subspaces in gene expression data for effective gene function prediction.2256-2264

Applications Note - Genome Analysis

• 
  Xiaoping Su,Li Zhang,Jianping Zhang,Funda Meric-Bernstam,John N. Weinstein:
  PurityEst: estimating purity of human tumor samples using next-generation sequencing data.2265-2266
• 
  Lukas Habegger,Suganthi Balasubramanian,David Z. Chen,Ekta Khurana,Andrea Sboner,Arif Ozgun Harmanci,Joel S. Rozowsky,Declan Clarke,Michael Snyder,Mark Gerstein:
  VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.2267-2269
• 
  Sebastian Gibb,Korbinian Strimmer:
  MALDIquant: a versatile R package for the analysis of mass spectrometry data.2270-2271

Gene Expression

• 
  Anton Zoubarev,Kelsey M. Hamer,Kiran Keshav,E. Luke McCarthy,Joseph Roy C. Santos,Thea Van Rossum,Cameron McDonald,Adam Hall,Xiang Wan,Raymond Lim,Jesse A. Gillis,Paul Pavlidis:
  Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data.2272-2273

Genetics and Population Analysis

• 
  Nikolaos Alachiotis,Alexandros Stamatakis,Pavlos Pavlidis:
  OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.2274-2275

Systems Biology

• 
  Johannes Klein,Stefan Leupold,Ilona Biegler,Rebekka Biedendieck,Richard Münch,Dieter Jahn:
  TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies.2276-2277
• 
  Florence Nicolè,Yann Guitton,Elodie A. Courtois,Sandrine Moja,Laurent Legendre,Martine Hossaert-McKey:
  MSeasy: unsupervised and untargeted GC-MS data processing.2278-2280
• 
  Rodrigo Santamaría,Philippe Pierre:
  Voronto: mapper for expression data to ontologies.2281-2282
• 
  Peter M. Krempl,Jürgen Mairhofer,Gerald Striedner,Gerhard G. Thallinger:
  A sequence comparison and gene expression data integration add-on for the Pathway Tools software.2283-2284

Data and Text Mining

• 
  David Salgado,Martin Krallinger,Marc Depaule,Elodie Drula,Ashish V. Tendulkar,Florian Leitner,Alfonso Valencia,Christophe Marcelle:
  MyMiner: a web application for computer-assisted biocuration and text annotation.2285-2287
• 
  Dmitry Grapov,John W. Newman:
  imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.2288-2290

Databases and Ontologies

• 
  Liming Lai,Arthur Liberzon,Jason Hennessey,Gaixin Jiang,Jianli Qi,Jill P. Mesirov,Steven X. Ge:
  AraPath: a knowledgebase for pathway analysis in Arabidopsis.2291-2292
• 
  Tzong-Yi Lee,Yi-Ju Chen,Cheng-Tsung Lu,Wei-Chieh Ching,Yu-Chuan Teng,Hsien-Da Huang,Yu-Ju Chen:
  dbSNO: a database of cysteineS-nitrosylation.2293-2295

Volume 28, Number 18, September 2012

Editorial

• 
  Torsten Schwede,Dagmar Iber:
  ECCB 2012: The 11^th European Conference on Computational Biology.303-305
• 
  Ma'ayan Bresler,Sara Sheehan,Andrew H. Chan,Yun S. Song:
  Telescoper:de novo assembly of highly repetitive regions.311-317
• 
  Yongchao Liu,Bertil Schmidt:
  Long read alignment based on maximal exact match seeds.318-324
• 
  Md Pavel Mahmud,John Wiedenhoeft,Alexander Schliep:
  Indel-tolerant read mapping with trinucleotide frequencies using cache-obliviouskd-trees.325-332
• 
  Tobias Rausch,Thomas Zichner,Andreas Schlattl,Adrian M. Stütz,Vladimir Benes,Jan O. Korbel:
  DELLY: structural variant discovery by integrated paired-end and split-read analysis.333-339
• 
  Alexander C. J. Roth:
  Decoding properties of tRNA leave a detectable signal in codon usage bias.340-348
• 
  Matthew Ruffalo,Mehmet Koyutürk,Soumya Ray,Thomas LaFramboise:
  Accurate estimation of short read mapping quality for next-generation genome sequencing.349-355
• 
  Yi Wang,Henry C. M. Leung,Siu-Ming Yiu,Francis Y. L. Chin:
  MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample.356-362
• 
  Yu-Wei Wu,Mina Rho,Thomas G. Doak,Yuzhen Ye:
  Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.363-369

Mutations, Variations, and Population genomics

• 
  Lachlan James M. Coin,Dandan Cao,Jingjing Ren,Xianbo Zuo,Liangdan Sun,Sen Yang,Xuejun Zhang,Yong Cui,Yingrui Li,Xin Jin,Jun Wang:
  An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis.370-374
• 
  Hongjie Zhu,Lexin Li,Hua Zhou:
  Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping.375-381

Evolution, Phylogeny, and Comparative genomics

• 
  Sèverine Bérard,Coralie Gallien,Bastien Boussau,Gergely J. Szöllosi,Vincent Daubin,Eric Tannier:
  Evolution of gene neighborhoods within reconciled phylogenies.382-388
• 
  Ofir Cohen,Haim Ashkenazy,David Burstein,Tal Pupko:
  Uncovering the co-evolutionary network among prokaryotic genes.389-394
• 
  Slavica Dimitrieva,Philipp Bucher:
  Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements.395-401
• 
  David Sankoff,Chunfang Zheng:
  Fractionation, rearrangement and subgenome dominance.402-408
• 
  Maureen Stolzer,Han Lai,Minli Xu,Deepa Sathaye,Benjamin Vernot,Dannie Durand:
  Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.409-415

Macromolecular Structure, Dynamics and Function

• 
  Fayyaz ul Amir Afsar Minhas,Asa Ben-Hur:
  Multiple instance learning of Calmodulin binding sites.416-422
• 
  Francis Gaudreault,Matthieu Chartier,Rafael Najmanovich:
  Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding.423-430
• 
  Morten Källberg,Nitin Bhardwaj,Robert E. Langlois,Hui Lu:
  A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains.431-437
• 
  Patrik Koskinen,Liisa Holm:
  SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.438-443
• 
  Mario Abdel Messih,Meghana Chitale,Vladimir B. Bajic,Daisuke Kihara,Xin Gao:
  Protein domain recurrence and order can enhance prediction of protein functions.444-450

Protein Interactions, molecular Networks, and proteomics

• 
  Enrico Glaab,Anaïs Baudot,Natalio Krasnogor,Reinhard Schneider,Alfonso Valencia:
  EnrichNet: network-based gene set enrichment analysis.451-457
• 
  Tatyana Goldberg,Tobias Hamp,Burkhard Rost:
  LocTree2 predicts localization for all domains of life.458-465
• 
  Meghana Kshirsagar,Jaime G. Carbonell,Judith Klein-Seetharaman:
  Techniques to cope with missing data in host-pathogen protein interaction prediction.466-472
• 
  Yu-Keng Shih,Srinivasan Parthasarathy:
  Identifying functional modules in interaction networks through overlapping Markov clustering.473-479
• 
  Ryan W. Solava,Ryan P. Michaels,Tijana Milenkovic:
  Graphlet-based edge clustering reveals pathogen-interacting proteins.480-486
• 
  Yasuo Tabei,Edouard Pauwels,Véronique Stoven,Kazuhiro Takemoto,Yoshihiro Yamanishi:
  Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers.487-494

Regulation, pathways, and Systems Biology

• 
  Amit Singh,Juliana M. Nascimento,Silke Kowar,Hauke Busch,Melanie Boerries:
  Boolean approach to signalling pathway modelling in HGF-induced keratinocyte migration.495-501
• 
  Abdelhalim Larhlimi,Georg Basler,Sergio Grimbs,Joachim Selbig,Zoran Nikoloski:
  Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks.502-508
• 
  Jie Li,Xu Hua,Martin Haubrock,Jin Wang,Edgar Wingender:
  The architecture of the gene regulatory networks of different tissues.509-514
• 
  Daniel Machado,Zita Soons,Kiran Raosaheb Patil,Eugénio C. Ferreira,Isabel Rocha:
  Random sampling of elementary flux modes in large-scale metabolic networks.515-521
• 
  Sayaka Mizutani,Edouard Pauwels,Véronique Stoven,Susumu Goto,Yoshihiro Yamanishi:
  Relating drug-protein interaction network with drug side effects.522-528
• 
  Max Schelker,Andreas Raue,Jens Timmer,Clemens Kreutz:
  Comprehensive estimation of input signals and dynamics in biochemical reaction networks.529-534
• 
  Patrick Weber,Andrei Kramer,Clemens Dingler,Nicole Radde:
  Trajectory-oriented Bayesian experiment design versus Fisher A-optimal design: an in depth comparison study.535-541

Bioimaging, Spatial-Temporal Modeling and Data Visualization

• 
  Günter Jäger,Florian Battke,Kay Nieselt:
  Reveal - visual eQTL analytics.542-548
• 
  Michael Klann,Arnab Ganguly,Heinz Koeppl:
  Hybrid spatial Gillespie and particle tracking simulation.549-555
• 
  Nico Scherf,Maria Herberg,Konstantin Thierbach,Thomas Zerjatke,Tuzer Kalkan,Peter Humphreys,Austin Smith,Ingmar Glauche,Ingo Roeder:
  Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions.556-561

Databases, Ontologies, and Text Mining

• 
  Michael J. Bell,Colin S. Gillespie,Daniel Swan,Phillip W. Lord:
  An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB.562-568
• 
  Ernesto Iacucci,Léon-Charles Tranchevent,Dusan Popovic,Georgios A. Pavlopoulos,Bart De Moor,Reinhard Schneider,Yves Moreau:
  ReLiance: a machine learning and literature-based prioritization of receptor - ligand pairings.569-574
• 
  Sampo Pyysalo,Tomoko Ohta,Makoto Miwa,Han-Cheol Cho,Junichi Tsujii,Sophia Ananiadou:
  Event extraction across multiple levels of biological organization.575-581

Bioinformatics of Health and Disease, Biomarkers and Personalized Medicine

• 
  Seungyeoun Lee,Min-Seok Kwon,Jung Mi Oh,Taesung Park:
  Gene-gene interaction analysis for the survival phenotype based on the Cox model.582-588
• 
  Nico Pfeifer,Thomas Lengauer:
  Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.589-595
• 
  Thang V. Pham,Connie R. Jimenez:
  An accurate paired sample test for count data.596-602
• 
  Peter Sykacek:
  Bayesian assignment of gene ontology terms to gene expression experiments.603-610
• 
  Masataka Takarabe,Masaaki Kotera,Yosuke Nishimura,Susumu Goto,Yoshihiro Yamanishi:
  Drug target prediction using adverse event report systems: a pharmacogenomic approach.611-618
• 
  Hua Wang,Feiping Nie,Heng Huang,Jingwen Yan,Sungeun Kim,Kwangsik Nho,Shannon L. Risacher,Andrew J. Saykin,Li Shen:
  From phenotype to genotype: an association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs.619-625

Applied and Translational Bioinformatics

• 
  Florian Buettner,Fabian J. Theis:
  A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst.626-632
• 
  Hiroshi Hatsuda:
  Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model.633-639
• 
  Sam Ng,Eric A. Collisson,Artem Sokolov,Theodore Goldstein,Abel Gonzalez-Perez,Núria López-Bigas,Christopher Benz,David Haussler,Joshua M. Stuart:
  PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.640-646

Author Index Applied and Translational Bioinformatics

• 
  Thaís Gaudencio do Rêgo,Helge G. Roider,Francisco de A. T. de Carvalho,Ivan G. Costa:
  Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models.2297-2303

Systems Biology

• 
  Mehmet Gönen:
  Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization.2304-2310
• 
  Federica Eduati,Javier De Las Rivas,Barbara Di Camillo,Gianna Toffolo,Julio Saez-Rodriguez:
  Integrating literature-constrained and data-driven inference of signalling networks.2311-2317
• 
  Thomas Sakoparnig,Niko Beerenwinkel:
  Efficient sampling for Bayesian inference of conjunctive Bayesian networks.2318-2324
• 
  Jianlong Qi,Tom Michoel:
  Context-specific transcriptional regulatory network inference from global gene expression maps using double two-wayt-tests.2325-2332
• 
  Markus Heinonen,Huibin Shen,Nicola Zamboni,Juho Rousu:
  Metabolite identification and molecular fingerprint prediction through machine learning.2333-2341
• 
  Chris J. Oates,Bryan T. J. Hennessy,Yiling Lu,Gordon B. Mills,Sach Mukherjee:
  Network inference using steady-state data and Goldbeter-koshland kinetics.2342-2348

Data and Text Mining

• 
  Elisabeth Georgii,Jarkko Salojärvi,Mikael Brosché,Jaakko Kangasjärvi,Samuel Kaski:
  Targeted retrieval of gene expression measurements using regulatory models.2349-2356

Original Papers Genome Analysis

• 
  Guillem Rigaill,Sidney Cadot,Roelof J. C. Kluin,Zheng Xue,René Bernards,Ian J. Majewski,Lodewyk F. A. Wessels:
  A regression model for estimating DNA copy number applied to capture sequencing data.2357-2365

Sequence Analysis

• 
  John C. Mu,Hui Jiang,Amirhossein Kiani,Marghoob Mohiyuddin,Narges Bani Asadi,Wing Hung Wong:
  Fast and accurate read alignment for resequencing.2366-2373

Bioimage Informatics

• 
  Boguslaw Obara,Vicente Grau,Mark D. Fricker:
  A bioimage informatics approach to automatically extract complex fungal networks.2374-2381

Applications Note Sequence Analysis

• 
  Pei Li,Guoli Ji,Min Dong,Emily Schmidt,Douglas Lenox,Liangliang Chen,Qi Liu,Lin Liu,Jie Zhang,Chun Liang:
  CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.2382-2384
• 
  Michael C. Ryan,James A. Cleland,RyangGuk Kim,Wing Chung Wong,John N. Weinstein:
  SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.2385-2387

Phylogenetics

• 
  Bradley R. Jones,Ashok Rajaraman,Eric Tannier,Cédric Chauve:
  ANGES: reconstructing ANcestral GEnomeS maps.2388-2390

Structural Bioinformatics

• 
  Arun Prasad Pandurangan,Maya Topf:
  RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps.2391-2393
• 
  Carles Pons,Daniel Jiménez-González,Cecilia González-Alvarez,Harald Servat,Daniel Cabrera-Benitez,Xavier Aguilar,Juan Fernández-Recio:
  Cell-Dock: high-performance protein-protein docking.2394-2396

Genetics and Population Analysis

• 
  Alexander E. Lipka,Feng Tian,Qishan Wang,Jason Peiffer,Meng Li,Peter J. Bradbury,Michael A. Gore,Edward S. Buckler,Zhiwu Zhang:
  GAPIT: genome association and prediction integrated tool.2397-2399

Systems Biology

• 
  Michael D. Linderman,Zach Bjornson,Erin F. Simonds,Peng Qiu,Robert V. Bruggner,Ketaki Sheode,Teresa H. Meng,Sylvia K. Plevritis,Garry P. Nolan:
  CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.2400-2401
• 
  Matthias König,Andreas Dräger,Hermann-Georg Holzhütter:
  CySBML: a Cytoscape plugin for SBML.2402-2403

Data and Text Mining

• 
  Thomas Taverner,Yuliya V. Karpievitch,Ashoka D. Polpitiya,Joseph N. Brown,Alan R. Dabney,Gordon A. Anderson,Richard D. Smith:
  DanteR: an extensible R-based tool for quantitative analysis of -omics data.2404-2406

Volume 28, Number 19, October 2012

Discovery Note - Sequence Analysis

• 
  Dapeng Zhang,Lakshminarayan M. Iyer,L. Aravind:
  Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms.2407-2411

Original Papers - Genome Analysis

• 
  Toshiro K. Ohsumi,Mark L. Borowsky:
  MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks.2412-2416

Sequence Analysis

• 
  Gregory G. Faust,Ira M. Hall:
  YAHA: fast and flexible long-read alignment with optimal breakpoint detection.2417-2424
• 
  Thomas C. Freeman Jr.,William C. Wimley:
  TMBB-DB: a transmembrane β-barrel proteome database.2425-2430

Structural Bioinformatics

• 
  Edvin Fuglebakk,Julian Echave,Nathalie Reuter:
  Measuring and comparing structural fluctuation patterns in large protein datasets.2431-2440
• 
  Jaume Bacardit,Pawel Widera,Alfonso E. Márquez Chamorro,Federico Divina,Jesús S. Aguilar-Ruiz,Natalio Krasnogor:
  Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features.2441-2448
• 
  Pietro di Lena,Ken Nagata,Pierre Baldi:
  Deep architectures for protein contact map prediction.2449-2457

Gene Expression

• 
  Wenyuan Li,Shi-Hua Zhang,Chun-Chi Liu,Xianghong Jasmine Zhou:
  Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.2458-2466

Genetics and Population Analysis

• 
  Z. Zhang,François Guillaume,A. Sartelet,Carole Charlier,Michel Georges,Frédéric Farnir,Tom Druet:
  Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification.2467-2473

Systems Biology

• 
  Vicente Acuña,Paulo Vieira Milreu,Ludovic Cottret,Alberto Marchetti-Spaccamela,Leen Stougie,Marie-France Sagot:
  Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.2474-2483
• 
  Daniel Gusenleitner,Eleanor Howe,Stefan Bentink,John Quackenbush,Aedín C. Culhane:
  iBBiG: iterative binary bi-clustering of gene sets.2484-2492
• 
  Xiaoquan Su,Jian Xu,Kang Ning:
  Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.2493-2501

Databases and Ontologies

• 
  Sebastian Bauer,Sebastian Köhler,Marcel H. Schulz,Peter N. Robinson:
  Bayesian ontology querying for accurate and noise-tolerant semantic searches.2502-2508

Applications Notes - Genome Analysis

• 
  Rolf Hilker,Corinna Sickinger,Christian N. S. Pedersen,Jens Stoye:
  UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ.2509-2511
• 
  Sandro Morganella,Michele Ceccarelli:
  VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets.2512-2514
• 
  Tom Kamphans,Peter M. Krawitz:
  GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes.2515-2516
• 
  Valentina Boeva,Alban Lermine,Camille Barette,Christel Guillouf,Emmanuel Barillot:
  Nebula - a web-server for advanced ChIP-seq data analysis.2517-2519
• 
  Johannes Köster,Sven Rahmann:
  Snakemake - a scalable bioinformatics workflow engine.2520-2522

Sequence Analysis

• 
  Peter Menzel,Stefan E. Seemann,Jan Gorodkin:
  RILogo: visualizing RNA-RNA interactions.2523-2526
• 
  Monzoorul Haque Mohammed,Anirban Dutta,Tungadri Bose,Sudha Chadaram,Sharmila S. Mande:
  DELIMINATE - a fast and efficient method for loss-less compression of genomic sequences: Sequence analysis.2527-2529

Structural Bioinformatics

• 
  Ronny Lorenz,Ivo L. Hofacker,Stephan H. Bernhart:
  Folding RNA/DNA hybrid duplexes.2530-2531

Gene Expression

• 
  Nicolas Delhomme,Ismaël Padioleau,Eileen E. M. Furlong,Lars M. Steinmetz:
  easyRNASeq: a bioconductor package for processing RNA-Seq data.2532-2533
• 
  Xingbin Wang,Dongwan D. Kang,Kui Shen,Chi Song,Shuya Lu,Lun-Ching Chang,Serena G. Liao,Zhiguang Huo,Shaowu Tang,Ying Ding,Naftali Kaminski,Etienne Sibille,Yan Lin,Jia Li,George C. Tseng:
  An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection.2534-2536

Genetics and Population Analysis

• 
  Rod Peakall,Peter E. Smouse:
  GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update.2537-2539
• 
  Sang Hong Lee,Jian Yang,M. E. Goddard,Peter M. Visscher,Naomi R. Wray:
  Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood.2540-2542
• 
  Jacqueline I. Goldstein,Andrew Crenshaw,Jason P. Carey,George B. Grant,Jared Maguire,Menachem Fromer,Colm O'Dushlaine,Jennifer L. Moran,Kimberly Chambert,Christine Stevens,Pamela Sklar,Christina M. Hultman,Shaun Purcell,Steven A. McCarroll,Patrick F. Sullivan,Mark J. Daly,Benjamin M. Neale:
  zCall: a rare variant caller for array-based genotyping: Genetics and population analysis.2543-2545

Systems Biology

• 
  Dorothee Girbig,Joachim Selbig,Sergio Grimbs:
  A MATLAB toolbox for structural kinetic modeling.2546-2547

Data and Text Mining

• 
  Wenzhou Li,Heather A. O'Neill,Vicki H. Wysocki:
  SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification.2548-2550

Databases and Ontologies

• 
  Ming-an Sun,Yejun Wang,Han Cheng,Qing Zhang,Wei Ge,Dianjing Guo:
  RedoxDB - a curated database for experimentally verified protein oxidative modification.2551-2552
• 
  Sonu Kumar,Thomas Lütteke,Reinhard Schwartz-Albiez:
  GlycoCD: a repository for carbohydrate-related CD antigens.2553-2555

ISCB News - Databases and Ontologies

• 
  Burkhard Rost,Terry Gaasterland,Thomas Lengauer,Michal Linial,Scott Markel,B. J. Morrison McKay,Reinhard Schneider,Paul Horton,Janet Kelso:
  Paving the future: finding suitable ISMB venues.2556-2559

Corrigendum - Databases and Ontologies

• 
  Anat Kreimer,Adi Doron-Faigenboim,Elhanan Borenstein,Shiri Freilich:
  NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species.2560

Volume 28, Number 20, October 2012

Original Papers - Genome Analysis

• 
  Changqing Zhang,Guangping Li,Jin Wang,Jinggui Fang:
  Identification oftrans-acting siRNAs and their regulatory cascades in grapevine.2561-2568
• 
  Baiyu Zhou:
  An empirical Bayes mixture model for SNP detection in pooled sequencing data.2569-2575

Sequence Analysis

• 
  Yue Jiang,Yadong Wang,Michael Brudno:
  PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.2576-2583
• 
  Zhaonan Sun,Yu Zhu:
  Systematic comparison of RNA-Seq normalization methods using measurement error models.2584-2591
• 
  David Weese,Manuel Holtgrewe,Knut Reinert:
  RazerS 3: Faster, fully sensitive read mapping.2592-2599

Structural Bioinformatics

• 
  Iain H. Moal,Juan Fernández-Recio:
  SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.2600-2607
• 
  Ryan Brenke,David R. Hall,Gwo-Yu Chuang,Stephen R. Comeau,Tanggis Bohnuud,Dmitri Beglov,Ora Schueler-Furman,Sandor Vajda,Dima Kozakov:
  Application of asymmetric statistical potentials to antibody-protein docking.2608-2614

Genetics and Population Analysis

• 
  Raymond Walters,Charles Laurin,Gitta H. Lubke:
  An integrated approach to reduce the impact of minor allele frequency and linkage disequilibrium on variable importance measures for genome-wide data.2615-2623

Systems Biology

• 
  Boon-Siew Seah,Sourav S. Bhowmick,C. Forbes Dewey Jr.:
  FACETS: multi-faceted functional decomposition of protein interaction networks.2624-2631
• 
  Ernest Lo,Emmanuelle Soleilhac,Anne Martinez,Laurence Lafanechère,Robert Nadon:
  Intensity quantile estimation and mapping - a novel algorithm for the correction of image non-uniformity bias in HCS data.2632-2639
• 
  Peng Yang,Xiaoli Li,Jian-Ping Mei,Chee Keong Kwoh,See-Kiong Ng:
  Positive-unlabeled learning for disease gene identification.2640-2647
• 
  Finja Büchel,Clemens Wrzodek,Florian Mittag,Andreas Dräger,Johannes Eichner,Nicolas Rodriguez,Nicolas Le Novère,Andreas Zell:
  Qualitative translation of relations from BioPAX to SBML qual.2648-2653

Data and Text Mining

• 
  Quoc-Chinh Bui,Peter M. A. Sloot:
  A robust approach to extract biomedical events from literature.2654-2661
• 
  Haisu Ma,Hongyu Zhao:
  FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment.2662-2670

Databases and Ontologies

• 
  Anika Groß,Michael Hartung,Kay Prüfer,Janet Kelso,Erhard Rahm:
  Impact of ontology evolution on functional analyses.2671-2677

Applications Note - Genome Analysis

• 
  Fernando García-Alcalde,Konstantin Okonechnikov,José Carbonell,Luis M. Cruz,Stefan Götz,Sonia Tarazona,Joaquín Dopazo,Thomas F. Meyer,Ana Conesa:
  Qualimap: evaluating next-generation sequencing alignment data.2678-2679

Sequence Analysis

• 
  Valerie Hower,Richard Starfield,Adam Roberts,Lior Pachter:
  Quantifying uniformity of mapped reads.2680-2682
• 
  Paulo Gaspar,José Luís Oliveira,Jörg Frommlet,Manuel A. S. Santos,Gabriela R. Moura:
  EuGene: maximizing synthetic gene design for heterologous expression.2683-2684
• 
  Sudhir Kumar,Glen Stecher,Daniel Peterson,Koichiro Tamura:
  MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.2685-2686
• 
  Narendra Kumar,Jeffrey Skolnick:
  EFICAz^2.5: application of a high-precision enzyme function predictor to 396 proteomes.2687-2688

Phylogenetics

• 
  Stephen A. Smith,Brian C. O'Meara:
  treePL: divergence time estimation using penalized likelihood for large phylogenies.2689-2690

Structural Bioinformatics

• 
  Zsuzsanna Sükösd,Bjarne Knudsen,Jørgen Kjems,Christian N. S. Pedersen:
  PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.2691-2692
• 
  Andreas Prlic,Andrew D. Yates,Spencer Bliven,Peter W. Rose,Julius O. B. Jacobsen,Peter V. Troshin,Mark Chapman,Jianjiong Gao,Chuan Hock Koh,Sylvain Foisy,Richard C. G. Holland,Gediminas Rimsa,Michael L. Heuer,Hannes Brandstätter-Müller,Philip E. Bourne,Scooter Willis:
  BioJava: an open-source framework for bioinformatics in 2012.2693-2695
• 
  Dong Zhang,Xingran Xue,Russell L. Malmberg,Liming Cai:
  TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.2696-2697

Gene Expression

• 
  Vikas Gupta,Katharina Markmann,Christian N. S. Pedersen,Jens Stougaard,Stig U. Andersen:
  shortran: a pipeline for small RNA-seq data analysis.2698-2700
• 
  Roberto-Rafael Ramos-Rodriguez,Raquel Cuevas-Diaz-Duran,Francesco Falciani,José Gerardo Tamez-Peña,Victor Trevino:
  COMPADRE: an R and web resource for pathway activity analysis by component decompositions.2701-2702

Genetics and Population Analysis

• 
  Biao Li,Gao T. Wang,Suzanne M. Leal:
  SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits.2703-2704

Systems Biology

• 
  Leslie Aïchaoui,Matthieu Jules,Ludovic Le Chat,Stéphane Aymerich,Vincent Fromion,Anne Goelzer:
  BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array.2705-2706

Databases and Ontologies

• 
  Miguel Rojas-Chertó,Michael van Vliet,Julio E. Peironcely,Ronnie van Doorn,Maarten Kooyman,Tim te Beek,Marc A. van Driel,Thomas Hankemeier,Theo H. Reijmers:
  MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data.2707-2709

Volume 28, Number 21, November 2012

Review - Sequence Analysis

• 
  Teo Shu Mei,Yudi Pawitan,Ku Chee Seng,Kee Seng Chia,Agus Salim:
  Statistical challenges associated with detecting copy number variations with next-generation sequencing.2711-2718

Discovery Note - Genome Analysis

• 
  Zhiming Dai,Xianhua Dai:
  Antisense transcription is coupled to nucleosome occupancy in sense promoters.2719-2723

Original Papers - Genome Analysis

• 
  Trevor Paterson,Andy Law:
  JEnsembl: a version-aware Java API to Ensembl data systems.2724-2731

Sequence Analysis

• 
  Zechen Chong,Jue Ruan,Chung-I Wu:
  Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.2732-2737
• 
  Anne Wenzel,Erdinç Akbasli,Jan Gorodkin:
  RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.2738-2746
• 
  Vincent Plagnol,James Curtis,Michael Epstein,Kin Y. Mok,Emma Stebbings,Sofia Grigoriadou,Nicholas W. Wood,Sophie Hambleton,Siobhan O. Burns,Adrian J. Thrasher,Dinakantha Kumararatne,Rainer Doffinger,Sergey Nejentsev:
  A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.2747-2754

Structural Bioinformatics

• 
  Juliana R. Rocha,Marx G. van der Linden,Diogo C. Ferreira,Paulo H. Azevêdo,Antônio F. Pereira de Araújo:
  Information-theoretic analysis and prediction of protein atomic burials: on the search for an informational intermediate between sequence and structure.2755-2762
• 
  Qifang Xu,Roland L. Dunbrack Jr.:
  Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.2763-2772

Gene Expression

• 
  Bruce A. Rosa,Ji Zhang,Ian T. Major,Wensheng Qin,Jin Chen:
  Optimal timepoint sampling in high-throughput gene expression experiments.2773-2781
• 
  Jianxing Feng,Clifford A. Meyer,Qian Wang,Jun S. Liu,Xiaole Shirley Liu,Yong Zhang:
  GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.2782-2788
• 
  Robert C. McLeay,Tom Lesluyes,Gabriel Cuéllar-Partida,Timothy L. Bailey:
  Genome-widein silico prediction of gene expression.2789-2796

Genetics and Population Analysis

• 
  Alexander G. Churbanov,Rachael Ryan,Nabeeh Hasan,Donovan Bailey,Haofeng Chen,Brook Milligan,Peter Houde:
  HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.2797-2803

Systems Biology

• 
  Steven M. Hill,Yiling Lu,Jennifer Molina,Laura Heiser,Paul T. Spellman,Terence P. Speed,Joe W. Gray,Gordon B. Mills,Sach Mukherjee:
  Bayesian Inference of Signaling Network Topology in a Cancer Cell Line.2804-2810
• 
  Ariel Feiglin,Adar Hacohen,Avital Sarusi,Jasmin Fisher,Ron Unger,Yanay Ofran:
  Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks.2811-2818
• 
  Daniel J. Stekhoven,Izabel Moraes,Gardar Sveinbjörnsson,Lars Hennig,Marloes H. Maathuis,Peter Bühlmann:
  Causal stability ranking.2819-2823

Data and Text Mining

• 
  Mohammadmahdi R. Yousefi,Edward R. Dougherty:
  Performance reproducibility index for classification.2824-2833
• 
  Haitian Wang,Shaw-Hwa Lo,Tian Zheng,Inchi Hu:
  Interaction-based feature selection and classification for high-dimensional biological data.2834-2842

Applications Note - Sequence Analysis

• 
  Nicolas Servant,Bryan R. Lajoie,Elphège P. Nora,Luca Giorgetti,Chong-Jian Chen,Edith Heard,Job Dekker,Emmanuel Barillot:
  HiTC: exploration of high-throughput 'C' experiments.2843-2844
• 
  Alan E. Barber II,Patricia C. Babbitt:
  Pythoscape: a framework for generation of large protein similarity networks.2845-2846

Gene Expression

• 
  Sudhir Kumar,Kelly Boccia,Michael McCutchan,Jieping Ye:
  Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone.2847-2848

Systems Biology

• 
  Yoshitsugu Konishi,Kiyoko F. Aoki-Kinoshita:
  The GlycomeAtlas tool for visualizing and querying glycome data.2849-2850

Data and Text Mining

• 
  Tiejun Cheng,Yanli Wang,Stephen H. Bryant:
  FSelector: a Ruby gem for feature selection.2851-2852

Databases and Ontologies

• 
  Ratheesh Kumar R.,Nagarajan N. S.,Arunraj S. P.,Devanjan Sinha,Vinoth Babu Veedin Rajan,Vinoth Kumar Esthaki,Patrick D'Silva:
  HSPIR: a manually annotated heat shock protein information resource.2853-2855
• 
  Ralf J. M. Weber,Eva Li,Jonathan Bruty,Shan He,Mark R. Viant:
  MaConDa: a publicly accessible mass spectrometry contaminants database.2856-2857
• 
  William Speier,Michael F. Ochs:
  Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.2858-2859

Volume 28, Number 22, November 2012

Original Papers - Genome Analysis

• 
  Pan Tong,Kevin R. Coombes:
  integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory.2861-2869
• 
  Binghang Liu,Jianying Yuan,Siu-Ming Yiu,Zhenyu Li,Yinlong Xie,Yanxiang Chen,Yujian Shi,Hao Zhang,Yingrui Li,Tak Wah Lam,Ruibang Luo:
  COPE: an accuratek-mer-based pair-end reads connection tool to facilitate genome assembly.2870-2874
• 
  Tobias Marschall,Ivan G. Costa,Stefan Canzar,Markus Bauer,Gunnar W. Klau,Alexander Schliep,Alexander Schönhuth:
  CLEVER: clique-enumerating variant finder.2875-2882

Sequence Analysis

• 
  Peiyong Jiang,K. C. Allen Chan,Gary J. W. Liao,Yama W. L. Zheng,Tak Y. Leung,Rossa W. K. Chiu,Yuk Ming Dennis Lo,Hao Sun:
  FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma.2883-2890
• 
  Marc J. Bonder,Sanne Abeln,Egija Zaura,Bernd W. Brandt:
  Comparing clustering and pre-processing in taxonomy analysis.2891-2897
• 
  Xin Yang,John A. Todd,David Clayton,Chris Wallace:
  Extra-binomial variation approach for analysis of pooled DNA sequencing data.2898-2904

Structural Bioinformatics

• 
  Fuxiao Xin,Predrag Radivojac:
  Post-translational modifications induce significant yet not extreme changes to protein structure.2905-2913

Gene Expression

• 
  Wei Li,Tao Jiang:
  Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.2914-2921
• 
  Adam F. Allred,Hilary Renshaw,Scott Weaver,Robert B. Tesh,David Wang:
  VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays.2922-2929
• 
  Michael Seifert,Sandra Cortijo,Maria Colomé-Tatché,Frank Johannes,François Roudier,Vincent Colot:
  MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays.2930-2939
• 
  Junfei Zhao,Shi-Hua Zhang,Ling-Yun Wu,Xiang-Sun Zhang:
  Efficient methods for identifying mutated driver pathways in cancer.2940-2947

Systems Biology

• 
  Hua Tan,Jiguang Bao,Xiaobo Zhou:
  A novel missense-mutation-related feature extraction scheme for 'driver' mutation identification.2948-2955

Data and Text Mining

• 
  Ting Huang,Zengyou He:
  A linear programming model for protein inference problem in shotgun proteomics.2956-2962
• 
  Leon French,Suzanne Lane,Lydia Xu,Celia Siu,Cathy Kwok,Yiqi Chen,Claudia Krebs,Paul Pavlidis:
  Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text.2963-2970

Databases and Ontologies

• 
  Tomasz Kalwarczyk,Marcin Tabaka,Robert Holyst:
  Biologistics - Diffusion coefficients for complete proteome ofEscherichia coli.2971-2978

Applications Note - Genome Analysis

• 
  Gary K. Chen,Kai Wang,Alex H. Stram,Eric M. Sobel,Kenneth Lange:
  Mendel-GPU: haplotyping and genotype imputation on graphics processing units.2979-2980
• 
  Jean-Baptiste Cazier,Christopher C. Holmes,John Broxholme:
  GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples.2981-2982
• 
  Mark D. Preston,Magnus Manske,Neil R. Horner,Samuel A. Assefa,Susana G. Campino,Sarah Auburn,Issaka Zongo,Jean-Bosco Ouedraogo,Francois Nosten,Timothy J. C. Anderson,Taane G. Clark:
  VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.2983-2985

Sequence Analysis

• 
  Brent S. Pedersen,David A. Schwartz,Ivana V. Yang,Katerina J. Kechris:
  Comb-p: software for combining, analyzing, grouping and correcting spatially correlatedP-values.2986-2988
• 
  A. P. Jason de Koning,Wanjun Gu,Todd A. Castoe,David D. Pollock:
  Phylogenetics, likelihood, evolution and complexity.2989-2990
• 
  Francesc Coll,Kim Mallard,Mark D. Preston,Stephen D. Bentley,Julian Parkhill,Ruth McNerney,Nigel J. Martin,Taane G. Clark:
  SpolPred: rapid and accurate prediction ofMycobacterium tuberculosis spoligotypes from short genomic sequences.2991-2993

Phylogenetics

• 
  Joel Sjöstrand,Bengt Sennblad,Lars Arvestad,Jens Lagergren:
  DLRS: gene tree evolution in light of a species tree.2994-2995

Structural Bioinformatics

• 
  Ivan Kalev,Martin Mechelke,Klaus O. Kopec,Thomas Holder,Simeon Carstens,Michael Habeck:
  CSB: a Python framework for structural bioinformatics.2996-2997
• 
  Jae-Seong Yang,Anne Campagna,Javier Delgado Blanco,Peter Vanhee,Luis Serrano,Christina Kiel:
  SAPIN: A framework for the structural analysis of protein interaction networks.2998-2999
• 
  John Eargle,Zaida Luthey-Schulten:
  NetworkView: 3D display and analysis of protein·RNA interaction networks.3000-3001
• 
  Emmanouil Athanasiadis,Zoe Cournia,George M. Spyrou:
  ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery.3002-3003

Systems Biology

• 
  Jason Lloyd-Price,Abhishekh Gupta,Andre S. Ribeiro:
  SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations.3004-3005

Databases and Ontologies

• 
  Pablo Cordero,Julius B. Lucks,Rhiju Das:
  An RNA Mapping DataBase for curating RNA structure mapping experiments.3006-3008

Bioimage Informatics

• 
  Tobias Pietzsch,Stephan Preibisch,Pavel Tomancak,Stephan Saalfeld:
  ImgLib2 - generic image processing in Java.3009-3011

Volume 28, Number 23, December 2012

Original Papers - Genome Analysis

• 
  Philip J. Uren,Emad Bahrami Samani,Suzanne C. Burns,Mei Qiao,Fedor V. Karginov,Emily Hodges,Gregory J. Hannon,Jeremy R. Sanford,Luiz O. F. Penalva,Andrew D. Smith:
  Site identification in high-throughput RNA-protein interaction data.3013-3020
• 
  Clemens Wrzodek,Johannes Eichner,Andreas Zell:
  Pathway-based visualization of cross-platform microarray datasets.3021-3026

Sequence Analysis

• 
  Heide Loehlein Fier,Sungho Won,Dmitry Prokopenko,Taofik AlChawa,Kerstin U. Ludwig,Rolf Fimmers,Edwin K. Silverman,Marcello Pagano,Elisabeth Mangold,Christoph Lange:
  'Location, Location, Location': a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate.3027-3033
• 
  Nuno D. Mendes,Steffen Heyne,Ana T. Freitas,Marie-France Sagot,Rolf Backofen:
  Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.3034-3041
• 
  Dennis K. Gascoigne,Seth W. Cheetham,Pierre B. Cattenoz,Michael B. Clark,Paulo P. Amaral,Ryan J. Taft,Dagmar Wilhelm,Marcel E. Dinger,John S. Mattick:
  Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.3042-3050
• 
  Faraz Hach,Ibrahim Numanagic,Can Alkan,Süleyman Cenk Sahinalp:
  SCALCE: boosting sequence compression algorithms using locally consistent encoding.3051-3057

Structural Bioinformatics

• 
  Jana Sperschneider,Amitava Datta,Michael J. Wise:
  Predicting pseudoknotted structures across two RNA sequences.3058-3065
• 
  Jesse Eickholt,Jianlin Cheng:
  Predicting protein residue-residue contacts using deep networks and boosting.3066-3072

Gene Expression

• 
  Yasir Rahmatallah,Frank Emmert-Streib,Galina V. Glazko:
  Gene set analysis for self-contained tests: complex null and specific alternative hypotheses.3073-3080

Systems Biology

• 
  Daniela Börnigen,Léon-Charles Tranchevent,Francisco Bonachela Capdevila,Koenraad Devriendt,Bart De Moor,Patrick De Causmaecker,Yves Moreau:
  An unbiased evaluation of gene prioritization tools.3081-3088
• 
  Robert J. Flassig,Kai Sundmacher:
  Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks.3089-3096
• 
  Jole Costanza,Giovanni Carapezza,Claudio Angione,Pietro Liò,Giuseppe Nicosia:
  Robust design of microbial strains.3097-3104
• 
  Rob Patro,Carl Kingsford:
  Global network alignment using multiscale spectral signatures.3105-3114
• 
  David P. Nusinow,Adam Kiezun,Daniel J. O'Connell,Joel M. Chick,Yingzi Yue,Richard L. Maas,Steven Gygi,Shamil R. Sunyaev:
  Network-based inference from complex proteomic mixtures using SNIPE.3115-3122

Data and Text Mining

• 
  Kjell Johnson,Cen Guo,Mark Gosink,Vicky Wang,Manfred Hauben:
  Multinomial modeling and an evaluation of common data-mining algorithms for identifying signals of disproportionate reporting in pharmacovigilance databases.3123-3130

Applications Note Genome Analysis

• 
  Ming Hu,Ke Deng,Siddarth Selvaraj,Zhaohui S. Qin,Bing Ren,Jun S. Liu:
  HiCNorm: removing biases in Hi-C data via Poisson regression.3131-3133
• 
  Alan Gray,I. Stewart,Albert Tenesa:
  Advanced Complex Trait Analysis.3134-3136
• 
  Christian Frech,Caleb Choo,Nansheng Chen:
  FeatureStack: Perl module for comparative visualization of gene features.3137-3138
• 
  Ross Lazarus,Antony Kaspi,Mark Ziemann,The Galaxy Team:
  Creating reusable tools from scripts: the Galaxy Tool Factory.3139-3140
• 
  Chuang Ma,Hao Chen,Mingming Xin,Ruolin Yang,Xiangfeng Wang:
  KGBassembler: a karyotype-based genome assembler forBrassicaceae species.3141-3143

Sequence Analysis

• 
  Kazutaka Katoh,Martin C. Frith:
  Adding unaligned sequences into an existing alignment using MAFFT and LAST.3144-3146
• 
  Chong-Jian Chen,Nicolas Servant,Joern Toedling,Alexis Sarazin,Antonin Marchais,Evelyne Duvernois-Berthet,Valérie Cognat,Vincent Colot,Olivier Voinnet,Edith Heard,Constance Ciaudo,Emmanuel Barillot:
  ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.3147-3149
• 
  Limin Fu,Beifang Niu,Zhengwei Zhu,Sitao Wu,Weizhong Li:
  CD-HIT: accelerated for clustering the next-generation sequencing data.3150-3152

Gene Expression

• 
  Matthew N. McCall,Harris A. Jaffee,Rafael A. Irizarry:
  fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.3153-3154

Systems Biology

• 
  David Fange,Anel Mahmutovic,Johan Elf:
  MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.3155-3157

Data and Text Mining

• 
  Halil Kilicoglu,Dongwook Shin,Marcelo Fiszman,Graciela Rosemblat,Thomas C. Rindflesch:
  SemMedDB: a PubMed-scale repository of biomedical semantic predications.3158-3160
• 
  Nicolas Parisot,Jérémie Denonfoux,Eric Dugat-Bony,Pierre Peyret,Eric Peyretaillade:
  KASpOD - a web service for highly specific and explorative oligonucleotide design.3161-3162

Databases and Ontologies

• 
  Richard N. Smith,Jelena Aleksic,Daniela Butano,Adrian Carr,Sergio Contrino,Fengyuan Hu,Mike Lyne,Rachel Lyne,Alex Kalderimis,Kim Rutherford,Radek Stepan,Julie M. Sullivan,Matthew Wakeling,Xavier Watkins,Gos Micklem:
  InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.3163-3165
• 
  Alessandro Laganà,Alessio Paone,Dario Veneziano,Luciano Cascione,Pierluigi Gasparini,Stefania Carasi,Francesco Russo,Giovanni Nigita,Valentina Macca,Rosalba Giugno,Alfredo Pulvirenti,Dennis E. Shasha,Alfredo Ferro,Carlo Maria Croce:
  miR-EdiTar: a database of predicted A-to-I edited miRNA target sites.3166-3168

Volume 28, Number 24, December 2012

Review - Sequence Analysis

• 
  Nuno A. Fonseca,Johan Rung,Alvis Brazma,John C. Marioni:
  Tools for mapping high-throughput sequencing data.3169-3177

Discovery Notes - Genome Analysis

• 
  Cho-Yi Chen,Shui-Tein Chen,Hsueh-Fen Juan,Hsuan-Cheng Huang:
  Lengthening of 3′UTR increases with morphological complexity in animal evolution.3178-3181

Sequence Analysis

• 
  John Spencer Evans:
  Aragonite-associated biomineralization proteins are disordered and contain interactive motifs.3182-3185
• 
  Darius Kazlauskas,Ceslovas Venclovas:
  Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses.3186-3190

Systems Biology

• 
  Jinyu Hu,David Zhiwei Gao:
  Distinction immune genes of hepatitis-induced heptatocellular carcinoma.3191-3194

Original Papers - Genome Analysis

• 
  Jurgen F. Nijkamp,Marcel van den Broek,Jan-Maarten A. Geertman,Marcel J. T. Reinders,Jean-Marc Daran,Dick de Ridder:
  De novo detection of copy number variation by co-assembly.3195-3202

Sequence Analysis

• 
  Shaul Ashkenazi,Rotem Snir,Yanay Ofran:
  Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins.3203-3210
• 
  Evguenia Kopylova,Laurent Noé,Hélène Touzet:
  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.3211-3217
• 
  Kengo Sato,Yuki Kato,Tatsuya Akutsu,Kiyoshi Asai,Yasubumi Sakakibara:
  DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.3218-3224
• 
  Bas E. Dutilh,Robert Schmieder,James Nulton,Ben Felts,Peter Salamon,Robert A. Edwards,John Mokili:
  Reference-independent comparative metagenomics using cross-assembly: crAss.3225-3231
• 
  Matteo Benelli,Chiara Pescucci,Giuseppina Marseglia,Marco Severgnini,Francesca Torricelli,Alberto Magi:
  Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.3232-3239
• 
  Christof Angermüller,Andreas Biegert,Johannes Söding:
  Discriminative modelling of context-specific amino acid substitution probabilities.3240-3247

Phylogenetics

• 
  Philippe Lemey,Vladimir N. Minin,Filip Bielejec,Sergei L. Kosakovsky Pond,Marc A. Suchard:
  A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.3248-3256

Structural Bioinformatics

• 
  Ian Walsh,Francesco Sirocco,Giovanni Minervini,Tomás Di Domenico,Carlo Ferrari,Silvio C. E. Tosatto:
  RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures.3257-3264
• 
  Mitul Saha,Marc C. Morais:
  FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.3265-3273
• 
  David W. Ritchie,Anisah W. Ghoorah,Lazaros Mavridis,Vishwesh Venkatraman:
  Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity.3274-3281
• 
  Dina Schneidman-Duhovny,Andrea Rossi,Agustin Avila-Sakar,Seung Joong Kim,Javier A. Velázquez-Muriel,Pavel Strop,Hong Liang,Kristin A. Krukenberg,Maofu Liao,Ho Min Kim,Solmaz Sobhanifar,Volker Dötsch,Arvind Rajpal,Jaume Pons,David A. Agard,Yifan Cheng,Andrej Sali:
  A method for integrative structure determination of protein-protein complexes.3282-3289

Systems Biology

• 
  Paul D. W. Kirk,Jim E. Griffin,Richard S. Savage,Zoubin Ghahramani,David L. Wild:
  Bayesian correlated clustering to integrate multiple datasets.3290-3297
• 
  Thomas Thorne,Michael P. H. Stumpf:
  Inference of temporally varying Bayesian Networks.3298-3305

Data and Text Mining

• 
  Yongjun Piao,Minghao Piao,Kiejung Park,Keun Ho Ryu:
  An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data.3306-3315

Applications Note - Genome Analysis

• 
  Robert A. Edwards,Robert Olson,Terry Disz,Gordon D. Pusch,Veronika Vonstein,Rick Stevens,Ross A. Overbeek:
  Real Time Metagenomics: Usingk-mers to annotate metagenomes.3316-3317
• 
  András Aszódi:
  MULTOVL: fast multiple overlaps of genomic regions.3318-3319
• 
  James A. Morris,Jeffrey C. Barrett:
  Olorin: combining gene flow with exome sequencing in large family studies of complex disease.3320-3321

Sequence Analysis

• 
  Phillipe Loher,Isidore Rigoutsos:
  Interactive exploration of RNA22 microRNA target predictions.3322-3323

Phylogenetics

• 
  Yu Lin,Vaibhav Rajan,Bernard M. E. Moret:
  TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis.3324-3325

Genetics and Population Analysis

• 
  Xiuwen Zheng,David Levine,Jess Shen,Stephanie M. Gogarten,Cathy C. Laurie,Bruce S. Weir:
  A high-performance computing toolset for relatedness and principal component analysis of SNP data.3326-3328
• 
  Stephanie M. Gogarten,Tushar Bhangale,Matthew P. Conomos,Cecelia A. Laurie,Caitlin P. McHugh,Ian S. Painter,Xiuwen Zheng,David R. Crosslin,David Levine,Thomas Lumley,Sarah C. Nelson,Ken Rice,Jess Shen,Rohit Swarnkar,Bruce S. Weir,Cathy C. Laurie:
  GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies.3329-3331
• 
  Fabio Zanini,Richard A. Neher:
  FFPopSim: an efficient forward simulation package for the evolution of large populations.3332-3333

Data and Text Mining

• 
  Gong-Hua Li,Jing-Fei Huang:
  CDRUG: a web server for predicting anticancer activity of chemical compounds.3334-3335