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Contents: Volume 25, Number 23, 1 December 2009   [Index by Author] 
Down REVIEW
     GENE EXPRESSION
Down DISCOVERY NOTE
     GENE EXPRESSION
     DATA AND TEXT MINING
Down ORIGINAL PAPERS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATIONS NOTE
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down LETTER TO THE EDITOR
     SYSTEMS BIOLOGY
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To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

REVIEW Back

GENE EXPRESSION Back

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 Back

GENE EXPRESSION Back

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 Back

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 Back

SEQUENCE ANALYSIS Back

Vera Afreixo, Carlos A. C. Bastos, Armando J. Pinho, Sara P. Garcia, and Paulo J. S. G. Ferreira
Genome analysis with inter-nucleotide distances
Bioinformatics Advance Access published on September 16, 2009
Bioinformatics 2009 25: 3064-3070; doi:10.1093/bioinformatics/btp546 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

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]  

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]  

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 Back

Christian Blouin, Scott Perry, Allan Lavell, Edward Susko, and Andrew J. Roger
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier
Bioinformatics Advance Access published on September 21, 2009
Bioinformatics 2009 25: 3093-3098; doi:10.1093/bioinformatics/btp552 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

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]  

Kei Yura and Steven Hayward
The interwinding nature of protein–protein interfaces and its implication for protein complex formation
Bioinformatics Advance Access published on September 29, 2009
Bioinformatics 2009 25: 3108-3113; doi:10.1093/bioinformatics/btp563 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENE EXPRESSION Back

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]  

Peter J. Park, Sek Won Kong, Toma Tebaldi, Weil R. Lai, Simon Kasif, and Isaac S. Kohane
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
Bioinformatics Advance Access published on September 28, 2009
Bioinformatics 2009 25: 3121-3127; doi:10.1093/bioinformatics/btp559 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

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 Back

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]  

Jimin Song and Mona Singh
How and when should interactome-derived clusters be used to predict functional modules and protein function?
Bioinformatics Advance Access published on September 21, 2009
Bioinformatics 2009 25: 3143-3150; doi:10.1093/bioinformatics/btp551 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

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]  

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]  

Waqar Ali and Charlotte M. Deane
Functionally guided alignment of protein interaction networks for module detection
Bioinformatics Advance Access published on October 1, 2009
Bioinformatics 2009 25: 3166-3173; doi:10.1093/bioinformatics/btp569 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATA AND TEXT MINING Back

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 Back

SEQUENCE ANALYSIS Back

Janne Korhonen, Petri Martinmäki, Cinzia Pizzi, Pasi Rastas, and Esko Ukkonen
MOODS: fast search for position weight matrix matches in DNA sequences
Bioinformatics Advance Access published on September 22, 2009
Bioinformatics 2009 25: 3181-3182; doi:10.1093/bioinformatics/btp554 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

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]  

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]  

Thomas C. Bishop
VDNA: The virtual DNA plug-in for VMD
Bioinformatics Advance Access published on September 29, 2009
Bioinformatics 2009 25: 3187-3188; doi:10.1093/bioinformatics/btp566 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

Dmitry A. Filatov
Processing and population genetic analysis of multigenic datasets with ProSeq3 software
Bioinformatics Advance Access published on October 1, 2009
Bioinformatics 2009 25: 3189-3190; doi:10.1093/bioinformatics/btp572 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Victor X. Jin, Jeff Apostolos, Naga Satya Venkateswara Ra Nagisetty, and Peggy J. Farnham
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data
Bioinformatics Advance Access published on October 1, 2009
Bioinformatics 2009 25: 3191-3193; doi:10.1093/bioinformatics/btp570 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

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]  

Carl Herrmann, Sèverine Bérard, and Laurent Tichit
SimCT: a generic tool to visualize ontology-based relationships for biological objects
Bioinformatics Advance Access published on September 23, 2009
Bioinformatics 2009 25: 3197-3198; doi:10.1093/bioinformatics/btp553 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

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 Back

SYSTEMS BIOLOGY Back

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]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.