Volume 27, Issue 12, June 2011

ORIGINAL PAPERS

GENOME ANALYSIS

PathScan: a tool for discerning mutational significance in groups of putative cancer genes

Michael C. Wendl and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1595–1602, https://doi.org/10.1093/bioinformatics/btr193

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Improved similarity scores for comparing motifs

Emi Tanaka and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1603–1609, https://doi.org/10.1093/bioinformatics/btr257

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Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data

Justin Bedo and Adam Kowalczyk

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1610–1617, https://doi.org/10.1093/bioinformatics/btr263

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SEQUENCE ANALYSIS

Mixture models for analysis of the taxonomic composition of metagenomes

Peter Meinicke and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1618–1624, https://doi.org/10.1093/bioinformatics/btr266

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STRUCTURAL BIOINFORMATICS

MAISTAS: a tool for automatic structural evaluation of alternative splicing products

Matteo Floris and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1625–1629, https://doi.org/10.1093/bioinformatics/btr198

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A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy

Ali Abdul-Gader and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1630–1636, https://doi.org/10.1093/bioinformatics/btr234

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GENE EXPRESSION

Identification and quantification of metabolites in ¹H NMR spectra by Bayesian model selection

Cheng Zheng and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1637–1644, https://doi.org/10.1093/bioinformatics/btr118

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Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models

Michael Seifert and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1645–1652, https://doi.org/10.1093/bioinformatics/btr199

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DREME: motif discovery in transcription factor ChIP-seq data

Timothy L. Bailey

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1653–1659, https://doi.org/10.1093/bioinformatics/btr261

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SYSTEMS BIOLOGY

An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure

Seongho Kim and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1660–1666, https://doi.org/10.1093/bioinformatics/btr188

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Pathway analysis of high-throughput biological data within a Bayesian network framework

Senol Isci and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1667–1674, https://doi.org/10.1093/bioinformatics/btr269

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DATA AND TEXT MINING

Multiple-rule bias in the comparison of classification rules

Mohammadmahdi R. Yousefi and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1675–1683, https://doi.org/10.1093/bioinformatics/btr262

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DATABASES AND ONTOLOGIES

PLIO: an ontology for formal description of protein–ligand interactions

Olga Ivchenko and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1684–1690, https://doi.org/10.1093/bioinformatics/btr256

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APPLICATIONS NOTE

GENOME ANALYSIS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

Derek W. Barnett and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1691–1692, https://doi.org/10.1093/bioinformatics/btr174

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SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip

Camille Sabbah and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1693–1695, https://doi.org/10.1093/bioinformatics/btr187

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MEME-ChIP: motif analysis of large DNA datasets

Philip Machanick and Timothy L. Bailey

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1696–1697, https://doi.org/10.1093/bioinformatics/btr189

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Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles

Irina Ostrovnaya and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1698–1699, https://doi.org/10.1093/bioinformatics/btr267

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SEQUENCE ANALYSIS

OTUbase: an R infrastructure package for operational taxonomic unit data

Daniel Beck and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1700–1701, https://doi.org/10.1093/bioinformatics/btr196

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KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2

Nanjiang Shu and Arne Elofsson

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1702–1703, https://doi.org/10.1093/bioinformatics/btr235

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FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

Beifang Niu and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1704–1705, https://doi.org/10.1093/bioinformatics/btr252

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Boulder ALignment Editor (ALE): a web-based RNA alignment tool

Jesse Stombaugh and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1706–1707, https://doi.org/10.1093/bioinformatics/btr258

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FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq

Yang Li and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1708–1710, https://doi.org/10.1093/bioinformatics/btr265

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STRUCTURAL BIOINFORMATICS

A graphical interface for the FoldX forcefield

Joost Van Durme and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1711–1712, https://doi.org/10.1093/bioinformatics/btr254

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Grid computing for improving conformational sampling in NMR structure calculation

Fabien Mareuil and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1713–1714, https://doi.org/10.1093/bioinformatics/btr255

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APOLLO: a quality assessment service for single and multiple protein models

Zheng Wang and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1715–1716, https://doi.org/10.1093/bioinformatics/btr268

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GENETICS AND POPULATION ANALYSIS

Mcheza: a workbench to detect selection using dominant markers

Tiago Antao and Mark A. Beaumont

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1717–1718, https://doi.org/10.1093/bioinformatics/btr253

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SYSTEMS BIOLOGY

Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre

Ola Spjuth and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1719–1720, https://doi.org/10.1093/bioinformatics/btr192

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RuleBender: a visual interface for rule-based modeling

Wen Xu and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1721–1722, https://doi.org/10.1093/bioinformatics/btr197

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DATA AND TEXT MINING

Figure summarizer browser extensions for PubMed Central

Shashank Agarwal and Hong Yu

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1723–1724, https://doi.org/10.1093/bioinformatics/btr194

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Cobweb: a Java applet for network exploration and visualisation

Joachim von Eichborn and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1725–1726, https://doi.org/10.1093/bioinformatics/btr195

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PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

Woonghee Lee and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1727–1728, https://doi.org/10.1093/bioinformatics/btr200

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Rgtsp: a generalized top scoring pairs package for class prediction

Vlad Popovici and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1729–1730, https://doi.org/10.1093/bioinformatics/btr233

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ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms

Kangseok Kim and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1731–1733, https://doi.org/10.1093/bioinformatics/btr259

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DATABASES AND ONTOLOGIES

‘Sciencenet’—towards a global search and share engine for all scientific knowledge

Dominic S. Lütjohann and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1734–1735, https://doi.org/10.1093/bioinformatics/btr181

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Signaling gateway molecule pages—a data model perspective

Ashok Reddy Dinasarapu and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1736–1738, https://doi.org/10.1093/bioinformatics/btr190

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Molecular signatures database (MSigDB) 3.0

Arthur Liberzon and others

Bioinformatics, Volume 27, Issue 12, June 2011, Pages 1739–1740, https://doi.org/10.1093/bioinformatics/btr260

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