Bioinformatics

REVIEW

GENE EXPRESSION

Get checked abstract Panagiotis Alexiou, Manolis Maragkakis, Giorgos L. Papadopoulos, Martin Reczko, and Artemis G. Hatzigeorgiou

Lost in translation: an assessment and perspective for computational microRNA target identification
Bioinformatics Advance Access published on September 29, 2009
Bioinformatics 2009 25: 3049-3055; doi:10.1093/bioinformatics/btp565 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DISCOVERY NOTE

GENE EXPRESSION

Get checked abstract David Hiller, Hui Jiang, Weihong Xu, and Wing Hung Wong

Identifiability of isoform deconvolution from junction arrays and RNA-Seq
Bioinformatics Advance Access published on September 16, 2009
Bioinformatics 2009 25: 3056-3059; doi:10.1093/bioinformatics/btp544 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Lior Shamir, Catherine A. Wolkow, and Ilya G. Goldberg

Quantitative measurement of aging using image texture entropy
Bioinformatics Advance Access published on October 6, 2009
Bioinformatics 2009 25: 3060-3063; doi:10.1093/bioinformatics/btp571 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS

SEQUENCE ANALYSIS

Get checked abstract Mensur Dlakic

HHsvm: fast and accurate classification of profile–profile matches identified by HHsearch
Bioinformatics Advance Access published on September 22, 2009
Bioinformatics 2009 25: 3071-3076; doi:10.1093/bioinformatics/btp555 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Nicolas Terrapon, Olivier Gascuel, Éric Maréchal, and Laurent Bréehélin

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum
Bioinformatics Advance Access published on September 28, 2009
Bioinformatics 2009 25: 3077-3083; doi:10.1093/bioinformatics/btp560 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Jia Zeng, Reda Alhajj, and Douglas Demetrick

Adaptive multi-agent architecture for functional sequence motifs recognition
Bioinformatics Advance Access published on October 6, 2009
Bioinformatics 2009 25: 3084-3092; doi:10.1093/bioinformatics/btp567 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS

STRUCTURAL BIOINFORMATICS

Get checked abstract Chris Kauffman and George Karypis

LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction
Bioinformatics Advance Access published on September 28, 2009
Bioinformatics 2009 25: 3099-3107; doi:10.1093/bioinformatics/btp561 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Darya Chudova, Alexander Ihler, Kevin K. Lin, Bogi Andersen, and Padhraic Smyth

Bayesian detection of non-sinusoidal periodic patterns in circadian expression data
Bioinformatics Advance Access published on September 22, 2009
Bioinformatics 2009 25: 3114-3120; doi:10.1093/bioinformatics/btp547 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Stefan P. Albaum, Heiko Neuweger, Benjamin Fränzel, Sita Lange, Dominik Mertens, Christian Trötschel, Dirk Wolters, Jörn Kalinowski, Tim W. Nattkemper, and Alexander Goesmann

Qupe—a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
Bioinformatics Advance Access published on October 6, 2009
Bioinformatics 2009 25: 3128-3134; doi:10.1093/bioinformatics/btp568 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Markus Leber, Volker Egelhofer, Ida Schomburg, and Dietmar Schomburg

Automatic assignment of reaction operators to enzymatic reactions
Bioinformatics Advance Access published on September 25, 2009
Bioinformatics 2009 25: 3135-3142; doi:10.1093/bioinformatics/btp549 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hojung Nam, Bong Chul Chung, Younghoon Kim, KiYoung Lee, and Doheon Lee

Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification
Bioinformatics Advance Access published on September 25, 2009
Bioinformatics 2009 25: 3151-3157; doi:10.1093/bioinformatics/btp558 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Luis F. de Figueiredo, Adam Podhorski, Angel Rubio, Christoph Kaleta, John E. Beasley, Stefan Schuster, and Francisco J. Planes

Computing the shortest elementary flux modes in genome-scale metabolic networks
Bioinformatics Advance Access published on September 30, 2009
Bioinformatics 2009 25: 3158-3165; doi:10.1093/bioinformatics/btp564 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Shashank Agarwal and Hong Yu

Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
Bioinformatics Advance Access published on September 25, 2009
Bioinformatics 2009 25: 3174-3180; doi:10.1093/bioinformatics/btp548 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE

SEQUENCE ANALYSIS

STRUCTURAL BIOINFORMATICS

Get checked abstract Romina Oliva, Janet M. Thornton, and Marialuisa Pellegrini-Calace

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins
Bioinformatics Advance Access published on September 17, 2009
Bioinformatics 2009 25: 3183-3184; doi:10.1093/bioinformatics/btp545 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dario Ghersi and Roberto Sanchez

EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures
Bioinformatics Advance Access published on September 29, 2009
Bioinformatics 2009 25: 3185-3186; doi:10.1093/bioinformatics/btp562 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

SYSTEMS BIOLOGY

DATABASES AND ONTOLOGIES

Get checked abstract Richard Easty and Nikolay Nikolov

Client-side integration of life science literature resources
Bioinformatics Advance Access published on September 18, 2009
Bioinformatics 2009 25: 3194-3196; doi:10.1093/bioinformatics/btp550 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ka-Lok Ng, Hsueh-Chuan Liu, and Shan-Chih Lee

ncRNAppi—a tool for identifying disease-related miRNA and siRNA targeting pathways
Bioinformatics Advance Access published on October 6, 2009
Bioinformatics 2009 25: 3199-3201; doi:10.1093/bioinformatics/btp574 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTER TO THE EDITOR

SYSTEMS BIOLOGY

Get checked abstract Karoline Faust, Didier Croes, and Jacques van Helden

In response to ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’
Bioinformatics Advance Access published on September 23, 2009
Bioinformatics 2009 25: 3202-3205; doi:10.1093/bioinformatics/btp557 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

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