Volume 27, Issue 10, May 2011

EDITORIAL

On the organization of bioinformatics core services in biology-based research institutes

Olli Kallioniemi and others

Bioinformatics, Volume 27, Issue 10, May 2011, Page 1345, https://doi.org/10.1093/bioinformatics/btr125

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DISCOVERY NOTE

SEQUENCE ANALYSIS

The sufficient minimal set of miRNA seed types

Daniel C. Ellwanger and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1346–1350, https://doi.org/10.1093/bioinformatics/btr149

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ORIGINAL PAPERS

SEQUENCE ANALYSIS

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1351–1358, https://doi.org/10.1093/bioinformatics/btr151

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PHYLOGENETICS

Faster exact maximum parsimony search with XMP

W. Timothy J. White and Barbara R. Holland

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1359–1367, https://doi.org/10.1093/bioinformatics/btr147

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STRUCTURAL BIOINFORMATICS

PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs

Ping Xuan and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1368–1376, https://doi.org/10.1093/bioinformatics/btr153

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GENE EXPRESSION

Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes

Klaus Jung and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1377–1383, https://doi.org/10.1093/bioinformatics/btr152

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GENETICS AND POPULATION ANALYSIS

High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans

Erdal Cosgun and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1384–1389, https://doi.org/10.1093/bioinformatics/btr159

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SYSTEMS BIOLOGY

Integrative network alignment reveals large regions of global network similarity in yeast and human

Oleksii Kuchaiev and Nataša Pržulj

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1390–1396, https://doi.org/10.1093/bioinformatics/btr127

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Mass-balanced randomization of metabolic networks

Georg Basler and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1397–1403, https://doi.org/10.1093/bioinformatics/btr145

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A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk

Martial Sankar and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1404–1412, https://doi.org/10.1093/bioinformatics/btr158

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DATA AND TEXT MINING

Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition

Christophe Bécavin and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1413–1421, https://doi.org/10.1093/bioinformatics/btr143

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Inference of transcriptional regulatory network by bootstrapping patterns

Hei-Chia Wang and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1422–1428, https://doi.org/10.1093/bioinformatics/btr155

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DATABASES AND ONTOLOGIES

The caBIG® Life Science Business Architecture Model

Lauren Becnel Boyd and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1429–1435, https://doi.org/10.1093/bioinformatics/btr141

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APPLICATIONS NOTE

SEQUENCE ANALYSIS

Prediction of novel pre-microRNAs with high accuracy through boosting and SVM

Yuanwei Zhang and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1436–1437, https://doi.org/10.1093/bioinformatics/btr148

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STRUCTURAL BIOINFORMATICS

The MEMPACK alpha-helical transmembrane protein structure prediction server

Timothy Nugent and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1438–1439, https://doi.org/10.1093/bioinformatics/btr096

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GENE EXPRESSION

anota: analysis of differential translation in genome-wide studies

Ola Larsson and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1440–1441, https://doi.org/10.1093/bioinformatics/btr146

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pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery

Marc Johannes and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1442–1443, https://doi.org/10.1093/bioinformatics/btr157

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DATABASES AND ONTOLOGIES

GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns

Xinan Yang and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1444–1446, https://doi.org/10.1093/bioinformatics/btr142

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hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

Li Chen and others

Bioinformatics, Volume 27, Issue 10, May 2011, Pages 1447–1448, https://doi.org/10.1093/bioinformatics/btr156

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