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Previous Next 		Contents: Volume 25, Number 22, 15 November 2009   [Index by Author] 
Down ORIGINAL PAPERS
     SYSTEMS BIOLOGY
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down CORRIGENDUM
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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.

ORIGINAL PAPERS Back

SYSTEMS BIOLOGY Back

Ruslan I. Sadreyev, Jamison D. Feramisco, Hensin Tsao, and Nick V. Grishin
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways
Bioinformatics Advance Access published on September 10, 2009
Bioinformatics 2009 25: 2891-2896; doi:10.1093/bioinformatics/btp538 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GENOME ANALYSIS Back

Thao T. Tran, Fengfeng Zhou, Sarah Marshburn, Mark Stead, Sidney R. Kushner, and Ying Xu
De novo computational prediction of non-coding RNA genes in prokaryotic genomes
Bioinformatics Advance Access published on September 10, 2009
Bioinformatics 2009 25: 2897-2905; doi:10.1093/bioinformatics/btp537 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Ronglai Shen, Adam B. Olshen, and Marc Ladanyi
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
Bioinformatics Advance Access published on September 16, 2009
Bioinformatics 2009 25: 2906-2912; doi:10.1093/bioinformatics/btp543 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Babak Bostan, Russell Greiner, Duane Szafron, and Paul Lu
Predicting homologous signaling pathways using machine learning
Bioinformatics Advance Access published on September 7, 2009
Bioinformatics 2009 25: 2913-2920; doi:10.1093/bioinformatics/btp532 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Ofer Rahat, Uri Alon, Yaakov Levy, and Gideon Schreiber
Understanding hydrogen-bond patterns in proteins using network motifs
Bioinformatics Advance Access published on September 18, 2009
Bioinformatics 2009 25: 2921-2928; doi:10.1093/bioinformatics/btp541 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Shahzia Anjum, Arnaud Doucet, and Chris C. Holmes
A boosting approach to structure learning of graphs with and without prior knowledge
Bioinformatics Advance Access published on August 20, 2009
Bioinformatics 2009 25: 2929-2936; doi:10.1093/bioinformatics/btp485 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Tarmo Äijö and Harri Lähdesmäki
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics
Bioinformatics Advance Access published on August 25, 2009
Bioinformatics 2009 25: 2937-2944; doi:10.1093/bioinformatics/btp511 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Alexander Senf and Xue-wen Chen
Identification of genes involved in the same pathways using a Hidden Markov Model-based approach
Bioinformatics Advance Access published on August 31, 2009
Bioinformatics 2009 25: 2945-2954; doi:10.1093/bioinformatics/btp521 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. Penalva, Edward M. Marcotte, and Daniel P. Miranker
Mining gene functional networks to improve mass-spectrometry-based protein identification
Bioinformatics Advance Access published on July 24, 2009
Bioinformatics 2009 25: 2955-2961; doi:10.1093/bioinformatics/btp461 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Hisashi Kashima, Yoshihiro Yamanishi, Tsuyoshi Kato, Masashi Sugiyama, and Koji Tsuda
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach
Bioinformatics Advance Access published on August 17, 2009
Bioinformatics 2009 25: 2962-2968; doi:10.1093/bioinformatics/btp494 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zengyou He and Weichuan Yu
Improving peptide identification with single-stage mass spectrum peaks
Bioinformatics Advance Access published on August 18, 2009
Bioinformatics 2009 25: 2969-2974; doi:10.1093/bioinformatics/btp501 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

M. J. L. de Groot, R. J. P. van Berlo, W. A. van Winden, P. J. T. Verheijen, M. J. T. Reinders, and D. de Ridder
Metabolite and reaction inference based on enzyme specificities
Bioinformatics Advance Access published on August 20, 2009
Bioinformatics 2009 25: 2975-2982; doi:10.1093/bioinformatics/btp507 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Kristina M. Hettne, Rob H. Stierum, Martijn J. Schuemie, Peter J. M. Hendriksen, Bob J. A. Schijvenaars, Erik M. van Mulligen, Jos Kleinjans, and Jan A. Kors
A dictionary to identify small molecules and drugs in free text
Bioinformatics Advance Access published on September 16, 2009
Bioinformatics 2009 25: 2983-2991; doi:10.1093/bioinformatics/btp535 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Paul E. Anderson, Michael L. Raymer, Benjamin J. Kelly, Nicholas V. Reo, Nicholas J. DelRaso, and T. E. Doom
Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets
Bioinformatics Advance Access published on September 16, 2009
Bioinformatics 2009 25: 2992-3000; doi:10.1093/bioinformatics/btp540 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Feng Tian, Parantu K. Shah, Xiangjun Liu, Nicolas Negre, Jia Chen, Oleksiy Karpenko, Kevin P. White, and Robert L. Grossman
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
Bioinformatics Advance Access published on August 5, 2009
Bioinformatics 2009 25: 3001-3004; doi:10.1093/bioinformatics/btp469 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Bertrand Néron, Hervé Ménager, Corinne Maufrais, Nicolas Joly, Julien Maupetit, Sébastien Letort, Sébastien Carrere, Pierre Tuffery, and Catherine Letondal
Mobyle: a new full web bioinformatics framework
Bioinformatics Advance Access published on August 17, 2009
Bioinformatics 2009 25: 3005-3011; doi:10.1093/bioinformatics/btp493 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

S. M. Wimalaratne, M. D. B. Halstead, C. M. Lloyd, M. T. Cooling, E. J. Crampin, and P. F. Nielsen
A method for visualizing CellML models
Bioinformatics Advance Access published on August 24, 2009
Bioinformatics 2009 25: 3012-3019; doi:10.1093/bioinformatics/btp495 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Patrik Björkholm and Erik L. L. Sonnhammer
Comparative analysis and unification of domain–domain interaction networks
Bioinformatics Advance Access published on August 31, 2009
Bioinformatics 2009 25: 3020-3025; doi:10.1093/bioinformatics/btp522 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

SYSTEMS BIOLOGY Back

Allyson L. Lister, Matthew Pocock, Morgan Taschuk, and Anil Wipat
Saint: a lightweight integration environment for model annotation
Bioinformatics Advance Access published on September 4, 2009
Bioinformatics 2009 25: 3026-3027; doi:10.1093/bioinformatics/btp523 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Pauli Rämö, Raphael Sacher, Berend Snijder, Boris Begemann, and Lucas Pelkmans
CellClassifier: supervised learning of cellular phenotypes
Bioinformatics Advance Access published on September 2, 2009
Bioinformatics 2009 25: 3028-3030; doi:10.1093/bioinformatics/btp524 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Richard Tzong-Han Tsai, Hong-Jie Dai, Po-Ting Lai, and Chi-Hsin Huang
PubMed-EX: a web browser extension to enhance PubMed search with text mining features
Bioinformatics Advance Access published on August 4, 2009
Bioinformatics 2009 25: 3031-3032; doi:10.1093/bioinformatics/btp475 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Yue Fan, T. Brendan Murphy, and R. William G. Watson
digeR: a graphical user interface R package for analyzing 2D-DIGE data
Bioinformatics Advance Access published on August 25, 2009
Bioinformatics 2009 25: 3033-3034; doi:10.1093/bioinformatics/btp514 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Anastasia Alexandridou, George Th. Tsangaris, Konstantinos Vougas, Konstantina Nikita, and George Spyrou
UniMaP: finding unique mass and peptide signatures in the human proteome
Bioinformatics Advance Access published on August 27, 2009
Bioinformatics 2009 25: 3035-3037; doi:10.1093/bioinformatics/btp516 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Zhiyong Lu, Natalie Xie, and W. John Wilbur
Identifying related journals through log analysis
Bioinformatics Advance Access published on September 3, 2009
Bioinformatics 2009 25: 3038-3039; doi:10.1093/bioinformatics/btp529 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein, and Doreen Ware
CMap 1.01: a comparative mapping application for the Internet
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 3040-3042; doi:10.1093/bioinformatics/btp458 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Gabriel F. Berriz, John E. Beaver, Can Cenik, Murat Tasan, and Frederick P. Roth
Next generation software for functional trend analysis
Bioinformatics Advance Access published on August 28, 2009
Bioinformatics 2009 25: 3043-3044; doi:10.1093/bioinformatics/btp498 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

David Binns, Emily Dimmer, Rachael Huntley, Daniel Barrell, Claire O'Donovan, and Rolf Apweiler
QuickGO: a web-based tool for Gene Ontology searching
Bioinformatics Advance Access published on September 10, 2009
Bioinformatics 2009 25: 3045-3046; doi:10.1093/bioinformatics/btp536 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

CORRIGENDUM Back

Andrew F. Neuwald
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
Bioinformatics 2009 25: 3047; doi:10.1093/bioinformatics/btp573 [Extract] [Full Text] [Print PDF] [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.