Volume 27, Issue 9, May 2011

ORIGINAL PAPERS

GENOME ANALYSIS

aCGH.Spline—an R package for aCGH dye bias normalization

Tomas W. Fitzgerald and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1195–1200, https://doi.org/10.1093/bioinformatics/btr107

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PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies

Jie Huang and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1201–1206, https://doi.org/10.1093/bioinformatics/btr116

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Histogram-based DNA analysis for the visualization of chromosome, genome and species information

António M. Costa and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1207–1214, https://doi.org/10.1093/bioinformatics/btr131

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SplamiR—prediction of spliced miRNAs in plants

Christoph J. Thieme and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1215–1223, https://doi.org/10.1093/bioinformatics/btr132

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SEQUENCE ANALYSIS

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes

Andrea Pierleoni and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1224–1230, https://doi.org/10.1093/bioinformatics/btr108

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Identifying discriminative classification-based motifs in biological sequences

Celine Vens and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1231–1238, https://doi.org/10.1093/bioinformatics/btr110

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A probabilistic model of nuclear import of proteins

Ahmed M. Mehdi and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1239–1246, https://doi.org/10.1093/bioinformatics/btr121

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Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map

Liisa Heikkinen and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1247–1254, https://doi.org/10.1093/bioinformatics/btr144

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PHYLOGENETICS

MrBayes on a Graphics Processing Unit

Jianfu Zhou and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1255–1261, https://doi.org/10.1093/bioinformatics/btr140

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STRUCTURAL BIOINFORMATICS

Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

Wei Zhao and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1262–1268, https://doi.org/10.1093/bioinformatics/btr133

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GENE EXPRESSION

Mixtures of common t-factor analyzers for clustering high-dimensional microarray data

Jangsun Baek and Geoffrey J. McLachlan

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1269–1276, https://doi.org/10.1093/bioinformatics/btr112

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Large-scale learning of combinatorial transcriptional dynamics from gene expression

H. M. Shahzad Asif and Guido Sanguinetti

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1277–1283, https://doi.org/10.1093/bioinformatics/btr113

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A wholly defined Agilent microarray spike-in dataset

Qianqian Zhu and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1284–1289, https://doi.org/10.1093/bioinformatics/btr135

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COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

Haisu Ma and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1290–1298, https://doi.org/10.1093/bioinformatics/btr136

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SYSTEMS BIOLOGY

Customizable views on semantically integrated networks for systems biology

Jochen Weile and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1299–1306, https://doi.org/10.1093/bioinformatics/btr134

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APPLICATIONS NOTE

GENOME ANALYSIS

Comparative visualization of genetic and physical maps with Strudel

Micha Bayer and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1307–1308, https://doi.org/10.1093/bioinformatics/btr111

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GBOOST: a GPU-based tool for detecting gene–gene interactions in genome–wide case control studies

Ling Sing Yung and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1309–1310, https://doi.org/10.1093/bioinformatics/btr114

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ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments

Ernesto Picardi and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1311–1312, https://doi.org/10.1093/bioinformatics/btr117

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GeCo++: a C++ library for genomic features computation and annotation in the presence of variants

Matteo Cereda and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1313–1315, https://doi.org/10.1093/bioinformatics/btr123

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SEQUENCE ANALYSIS

TEQC: an R package for quality control in target capture experiments

Manuela Hummel and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1316–1317, https://doi.org/10.1093/bioinformatics/btr122

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Agos—a universal web tool for GW Argonaute-binding domain prediction

Andrzej Zielezinski and Wojciech M. Karlowski

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1318–1319, https://doi.org/10.1093/bioinformatics/btr128

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STRUCTURAL BIOINFORMATICS

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics

Teong Han Chew and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1320–1321, https://doi.org/10.1093/bioinformatics/btr109

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Rapid membrane protein topology prediction

Aron Hennerdal and Arne Elofsson

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1322–1323, https://doi.org/10.1093/bioinformatics/btr119

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sc-PDB: a database for identifying variations and multiplicity of ‘druggable’ binding sites in proteins

Jamel Meslamani and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1324–1326, https://doi.org/10.1093/bioinformatics/btr120

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Rigid substructure search

David Shirvanyants and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1327–1329, https://doi.org/10.1093/bioinformatics/btr129

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GENE EXPRESSION

SC²ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data

Amy L. Olex and Jacquelyn S. Fetrow

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1330–1331, https://doi.org/10.1093/bioinformatics/btr115

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GENETICS AND POPULATION ANALYSIS

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

Laurent Excoffier and Matthieu Foll

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1332–1334, https://doi.org/10.1093/bioinformatics/btr124

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ogaraK: a population genetics simulator for malaria

Tiago Antao and Ian M. Hastings

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1335–1336, https://doi.org/10.1093/bioinformatics/btr139

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SYSTEMS BIOLOGY

High-throughput feature counting and measurement of roots

Asad Naeem and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1337–1338, https://doi.org/10.1093/bioinformatics/btr126

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AStream: an R package for annotating LC/MS metabolomic data

Arnald Alonso and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1339–1340, https://doi.org/10.1093/bioinformatics/btr138

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DATA AND TEXT MINING

Compounds In Literature (CIL): screening for compounds and relatives in PubMed

Björn A. Grüning and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1341–1342, https://doi.org/10.1093/bioinformatics/btr130

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DATABASES AND ONTOLOGIES

UniCarb-DB: a database resource for glycomic discovery

Catherine A. Hayes and others

Bioinformatics, Volume 27, Issue 9, May 2011, Pages 1343–1344, https://doi.org/10.1093/bioinformatics/btr137

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