Bioinformatics -- Table of Contents (25 [1])

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Contents: Volume 25, Number 1, 1 January 2009   [Index by Author]

DISCOVERY NOTE

     SEQUENCE ANALYSIS

ORIGINAL PAPERS

     SEQUENCE ANALYSIS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

     SYSTEMS BIOLOGY

     DATA AND TEXT MINING

APPLICATIONS NOTE

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     PHYLOGENETICS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

     SYSTEMS BIOLOGY

     DATA AND TEXT MINING

ISCB NEWS

LETTERS TO THE EDITOR

     PHYLOGENETICS

ERRATUM

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DISCOVERY NOTE

SEQUENCE ANALYSIS

Get checked abstract Francesca Diella, Sophie Chabanis, Katja Luck, Claudia Chica, Chenna Ramu, Claus Nerlov, and Toby J. Gibson: KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
Bioinformatics Advance Access published on November 24, 2008
Bioinformatics 2009 25: 1-5; doi:10.1093/bioinformatics/btn594 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

ORIGINAL PAPERS

SEQUENCE ANALYSIS

Get checked abstract Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, and Steven J. M. Jones: Slider—maximum use of probability information for alignment of short sequence reads and SNP detection
Bioinformatics Advance Access published on October 30, 2008
Bioinformatics 2009 25: 6-13; doi:10.1093/bioinformatics/btn565 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Anna Ritz, Gregory Shakhnarovich, Arthur R. Salomon, and Benjamin J. Raphael: Discovery of phosphorylation motif mixtures in phosphoproteomics data
Bioinformatics Advance Access published on November 7, 2008
Bioinformatics 2009 25: 14-21; doi:10.1093/bioinformatics/btn569 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Anton V. Persikov, Robert Osada, and Mona Singh: Predicting DNA recognition by Cys₂His₂ zinc finger proteins
Bioinformatics Advance Access published on November 13, 2008
Bioinformatics 2009 25: 22-29; doi:10.1093/bioinformatics/btn580 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Jiansheng Wu, Hongde Liu, Xueye Duan, Yan Ding, Hongtao Wu, Yunfei Bai, and Xiao Sun: Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
Bioinformatics Advance Access published on November 12, 2008
Bioinformatics 2009 25: 30-35; doi:10.1093/bioinformatics/btn583 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

GENE EXPRESSION

Get checked abstract Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, and Tetsuya Yomo: Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays
Bioinformatics Advance Access published on October 31, 2008
Bioinformatics 2009 25: 36-41; doi:10.1093/bioinformatics/btn570 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract A. Marie Fitch and M. Beatrix Jones: Shortest path analysis using partial correlations for classifying gene functions from gene expression data
Bioinformatics Advance Access published on November 3, 2008
Bioinformatics 2009 25: 42-47; doi:10.1093/bioinformatics/btn574 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Adam L. Asare, Zhong Gao, Vincent J. Carey, Richard Wang, and Vicki Seyfert-Margolis: Power enhancement via multivariate outlier testing with gene expression arrays
Bioinformatics Advance Access published on November 16, 2008
Bioinformatics 2009 25: 48-53; doi:10.1093/bioinformatics/btn591 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

GENETICS AND POPULATION ANALYSIS

Get checked abstract James A. Koziol, Anne C. Feng, Zhenyu Jia, Yipeng Wang, Seven Goodison, Michael McClelland, and Dan Mercola: The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis
Bioinformatics Advance Access published on July 15, 2008
Bioinformatics 2009 25: 54-60; doi:10.1093/bioinformatics/btn354 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, and Stephen T. C. Wong: Conditional random pattern algorithm for LOH inference and segmentation
Bioinformatics Advance Access published on October 29, 2008
Bioinformatics 2009 25: 61-67; doi:10.1093/bioinformatics/btn561 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Sharlee Climer, Gerold Jäger, Alan R. Templeton, and Weixiong Zhang: How frugal is mother nature with haplotypes?
Bioinformatics Advance Access published on November 4, 2008
Bioinformatics 2009 25: 68-74; doi:10.1093/bioinformatics/btn572 [Abstract] [Full Text] [Print PDF] [Request Permissions]

SYSTEMS BIOLOGY

Get checked abstract Adi Laurentiu Tarca, Sorin Draghici, Purvesh Khatri, Sonia S. Hassan, Pooja Mittal, Jung-sun Kim, Chong Jai Kim, Juan Pedro Kusanovic, and Roberto Romero: A novel signaling pathway impact analysis
Bioinformatics Advance Access published on November 5, 2008
Bioinformatics 2009 25: 75-82; doi:10.1093/bioinformatics/btn577 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Hao Zhang, Claus Lundegaard, and Morten Nielsen: Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods
Bioinformatics Advance Access published on November 7, 2008
Bioinformatics 2009 25: 83-89; doi:10.1093/bioinformatics/btn579 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Ross P. Carlson: Decomposition of complex microbial behaviors into resource-based stress responses
Bioinformatics Advance Access published on November 13, 2008
Bioinformatics 2009 25: 90-97; doi:10.1093/bioinformatics/btn589 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Xuebing Wu, Qifang Liu, and Rui Jiang: Align human interactome with phenome to identify causative genes and networks underlying disease families
Bioinformatics Advance Access published on November 13, 2008
Bioinformatics 2009 25: 98-104; doi:10.1093/bioinformatics/btn593 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Jingkai Yu and Russell L. Finley, Jr: Combining multiple positive training sets to generate confidence scores for protein–protein interactions
Bioinformatics Advance Access published on November 14, 2008
Bioinformatics 2009 25: 105-111; doi:10.1093/bioinformatics/btn597 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

DATA AND TEXT MINING

Get checked abstract Rachel Cavill, Hector C. Keun, Elaine Holmes, John C. Lindon, Jeremy K. Nicholson, and Timothy M. D. Ebbels: Genetic algorithms for simultaneous variable and sample selection in metabonomics
Bioinformatics Advance Access published on November 14, 2008
Bioinformatics 2009 25: 112-118; doi:10.1093/bioinformatics/btn586 [Abstract] [Full Text] [Print PDF] [Request Permissions]

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Tim Carver, Nick Thomson, Alan Bleasby, Matthew Berriman, and Julian Parkhill: DNAPlotter: circular and linear interactive genome visualization
Bioinformatics Advance Access published on November 5, 2008
Bioinformatics 2009 25: 119-120; doi:10.1093/bioinformatics/btn578 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

SEQUENCE ANALYSIS

Get checked abstract Iain Melvin, Jason Weston, Christina Leslie, and William Stafford Noble: RANKPROP: a web server for protein remote homology detection
Bioinformatics Advance Access published on November 6, 2008
Bioinformatics 2009 25: 121-122; doi:10.1093/bioinformatics/btn567 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Gang-Qing Hu, Xiaobin Zheng, Huai-Qiu Zhu, and Zhen-Su She: Prediction of translation initiation site for microbial genomes with TriTISA
Bioinformatics Advance Access published on November 10, 2008
Bioinformatics 2009 25: 123-125; doi:10.1093/bioinformatics/btn576 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

PHYLOGENETICS

Get checked abstract Iain Milne, Dominik Lindner, Micha Bayer, Dirk Husmeier, Gráinne McGuire, David F. Marshall, and Frank Wright: TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
Bioinformatics Advance Access published on November 4, 2008
Bioinformatics 2009 25: 126-127; doi:10.1093/bioinformatics/btn575 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

GENE EXPRESSION

Get checked abstract G. Golfier, S. Lemoine, A. van Miltenberg, A. Bendjoudi, J. Rossier, S. Le Crom, and M.-C. Potier: Selection of oligonucleotides for whole-genome microarrays with semi-automatic update
Bioinformatics Advance Access published on November 10, 2008
Bioinformatics 2009 25: 128-129; doi:10.1093/bioinformatics/btn573 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract Charles Addo-Quaye, Webb Miller, and Michael J. Axtell: CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
Bioinformatics Advance Access published on November 18, 2008
Bioinformatics 2009 25: 130-131; doi:10.1093/bioinformatics/btn604 [Abstract] [Full Text] [Print PDF] [Request Permissions]

GENETICS AND POPULATION ANALYSIS

Get checked abstract Manuel A. R. Ferreira and Shaun M. Purcell: A multivariate test of association
Bioinformatics Advance Access published on November 19, 2008
Bioinformatics 2009 25: 132-133; doi:10.1093/bioinformatics/btn563 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Christine Herold and Tim Becker: Genetic association analysis with FAMHAP: a major program update
Bioinformatics Advance Access published on November 9, 2008
Bioinformatics 2009 25: 134-136; doi:10.1093/bioinformatics/btn581 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

SYSTEMS BIOLOGY

Get checked abstract Jing Gao, Alex S. Ade, V. Glenn Tarcea, Terry E. Weymouth, Barbara R. Mirel, H.V. Jagadish, and David J. States: Integrating and annotating the interactome using the MiMI plugin for cytoscape
Bioinformatics Advance Access published on September 23, 2008
Bioinformatics 2009 25: 137-138; doi:10.1093/bioinformatics/btn501 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Rutger W. W. Brouwer, Sacha A. F. T. van Hijum, and Oscar P. Kuipers: MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
Bioinformatics Advance Access published on November 12, 2008
Bioinformatics 2009 25: 139-140; doi:10.1093/bioinformatics/btn588 [Abstract] [Full Text] [Print PDF] [Request Permissions]

DATA AND TEXT MINING

Get checked abstract Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, H.-Werner Mewes, and Andreas Ruepp: CRONOS: the cross-reference navigation server
Bioinformatics Advance Access published on November 13, 2008
Bioinformatics 2009 25: 141-143; doi:10.1093/bioinformatics/btn590 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

ISCB NEWS

Clare Sansom: ISMB 2008 conference report
Bioinformatics Advance Access published on December 12, 2008
Bioinformatics 2009 25: 144-146; doi:10.1093/bioinformatics/btn619 [Extract] [Full Text] [Print PDF] [Request Permissions]

LETTERS TO THE EDITOR

PHYLOGENETICS

Get checked abstract Anne Kupczok and Arndt von Haeseler: Comment on ‘A congruence index for testing topological similarity between trees’
Bioinformatics Advance Access published on October 14, 2008
Bioinformatics 2009 25: 147-149; doi:10.1093/bioinformatics/btn539 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Damien M. de Vienne, Tatiana Giraud, and Olivier C. Martin: In response to comment on ‘A congruence index for testing topological similarity between trees’
Bioinformatics Advance Access published on October 17, 2008
Bioinformatics 2009 25: 150-151; doi:10.1093/bioinformatics/btn535 [Abstract] [Full Text] [Print PDF] [Request Permissions]

ERRATUM

Get checked abstract Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, and David A. Fell: Can sugars be produced from fatty acids? A test case for pathway analysis tools
Bioinformatics 2009 25: 152-158; doi:10.1093/bioinformatics/btn621 [Abstract] [Full Text] [Print PDF] [Request Permissions]