Volume 27, Issue 8, April 2011

ORIGINAL PAPERS

GENOME ANALYSIS

eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study

Zhengkui Wang and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1045–1051, https://doi.org/10.1093/bioinformatics/btr091

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Performance assessment of copy number microarray platforms using a spike-in experiment

Eitan Halper-Stromberg and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1052–1060, https://doi.org/10.1093/bioinformatics/btr106

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SEQUENCE ANALYSIS

Topological entropy of DNA sequences

David Koslicki

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1061–1067, https://doi.org/10.1093/bioinformatics/btr077

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Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

Marcus Kinsella and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1068–1075, https://doi.org/10.1093/bioinformatics/btr085

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STRUCTURAL BIOINFORMATICS

Topology and prediction of RNA pseudoknots

Christian M. Reidys and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1076–1085, https://doi.org/10.1093/bioinformatics/btr090

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All-atom knowledge-based potential for RNA structure prediction and assessment

Emidio Capriotti and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1086–1093, https://doi.org/10.1093/bioinformatics/btr093

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GENE EXPRESSION

Defining an informativeness metric for clustering gene expression data

Jessica C. Mar and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1094–1100, https://doi.org/10.1093/bioinformatics/btr074

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Automatically identifying and annotating mouse embryo gene expression patterns

Liangxiu Han and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1101–1107, https://doi.org/10.1093/bioinformatics/btr105

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SYSTEMS BIOLOGY

Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets

Marie Brown and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1108–1112, https://doi.org/10.1093/bioinformatics/btr079

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The effects of feedback loops on disease comorbidity in human signaling networks

Duc-Hau Le and Yung-Keun Kwon

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1113–1120, https://doi.org/10.1093/bioinformatics/btr082

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Interactive, multiscale navigation of large and complicated biological networks

Thanet Praneenararat and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1121–1127, https://doi.org/10.1093/bioinformatics/btr083

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Assigning spectrum-specific P-values to protein identifications by mass spectrometry

Victor Spirin and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1128–1134, https://doi.org/10.1093/bioinformatics/btr089

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Connectedness of PPI network neighborhoods identifies regulatory hub proteins

Andrew D. Fox and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1135–1142, https://doi.org/10.1093/bioinformatics/btr099

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DATA AND TEXT MINING

Condensing biomedical journal texts through paragraph ranking

Jung-Hsien Chiang and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1143–1149, https://doi.org/10.1093/bioinformatics/btr080

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APPLICATIONS NOTE

GENOME ANALYSIS

eGOB: eukaryotic Gene Order Browser

Marcela Dávila López and Tore Samuelsson

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1150–1151, https://doi.org/10.1093/bioinformatics/btr075

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ACT: aggregation and correlation toolbox for analyses of genome tracks

Justin Jee and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1152–1154, https://doi.org/10.1093/bioinformatics/btr092

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Human variation database: an open-source database template for genomic discovery

Anthony P. Fejes and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1155–1156, https://doi.org/10.1093/bioinformatics/btr100

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SEQUENCE ANALYSIS

Improving SNP discovery by base alignment quality

Heng Li

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1157–1158, https://doi.org/10.1093/bioinformatics/btr076

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PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

William A. Walters and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1159–1161, https://doi.org/10.1093/bioinformatics/btr087

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R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data

Hans-Ulrich Klein and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1162–1163, https://doi.org/10.1093/bioinformatics/btr102

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PHYLOGENETICS

ProtTest 3: fast selection of best-fit models of protein evolution

Diego Darriba and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1164–1165, https://doi.org/10.1093/bioinformatics/btr088

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GENE EXPRESSION

libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data

Marc Kirchner and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1166–1167, https://doi.org/10.1093/bioinformatics/btr084

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SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data

Haleh Yasrebi

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1168–1169, https://doi.org/10.1093/bioinformatics/btr103

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SYSTEMS BIOLOGY

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Guido Klingbeil and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1170–1171, https://doi.org/10.1093/bioinformatics/btr068

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SiGN-SSM: open source parallel software for estimating gene networks with state space models

Yoshinori Tamada and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1172–1173, https://doi.org/10.1093/bioinformatics/btr078

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BiC: a web server for calculating bimodality of coexpression between gene and protein networks

George C. Linderman and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1174–1175, https://doi.org/10.1093/bioinformatics/btr086

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A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data

Isthiaq Ahmad and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1176–1178, https://doi.org/10.1093/bioinformatics/btr094

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Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

Lee Kamentsky and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1179–1180, https://doi.org/10.1093/bioinformatics/btr095

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FNV: light-weight flash-based network and pathway viewer

Ruth Dannenfelser and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1181–1182, https://doi.org/10.1093/bioinformatics/btr098

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DATA AND TEXT MINING

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows

Michael Specht and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1183–1184, https://doi.org/10.1093/bioinformatics/btr081

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AGRA: analysis of gene ranking algorithms

Simon Kocbek and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1185–1186, https://doi.org/10.1093/bioinformatics/btr097

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DATABASES AND ONTOLOGIES

Gene List significance at-a-glance with GeneValorization

Bryan Brancotte and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1187–1189, https://doi.org/10.1093/bioinformatics/btr073

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A comprehensive protein-centric ID mapping service for molecular data integration

Hongzhan Huang and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1190–1191, https://doi.org/10.1093/bioinformatics/btr101

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MPID-T2: a database for sequence–structure–function analyses of pMHC and TR/pMHC structures

Javed Mohammed Khan and others

Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1192–1193, https://doi.org/10.1093/bioinformatics/btr104

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LETTER TO THE EDITOR

GENE EXPRESSION

Comments on ‘Bayesian variable selection for disease classification using gene expression data’

Meïli C. Baragatti and Denys Pommeret

Bioinformatics, Volume 27, Issue 8, April 2011, Page 1194, https://doi.org/10.1093/bioinformatics/btr071

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