Bioinformatics -- Table of Contents (25 [19])

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Contents: Volume 25, Number 19, 1 October 2009   [Index by Author]

REVIEWS

     SEQUENCE ANALYSIS

     SYSTEMS BIOLOGY

DISCOVERY NOTE

     GENE EXPRESSION

ORIGINAL PAPERS

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     PHYLOGENETICS

     STRUCTURAL BIOINFORMATICS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

APPLICATIONS NOTE

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     PHYLOGENETICS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

ERRATUM

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REVIEWS

SEQUENCE ANALYSIS

Get checked abstract Carsten Kemena and Cedric Notredame: Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2455-2465; doi:10.1093/bioinformatics/btp452 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

SYSTEMS BIOLOGY

Get checked abstract Seth I. Berger and Ravi Iyengar: Network analyses in systems pharmacology
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2466-2472; doi:10.1093/bioinformatics/btp465 [Abstract] [Full Text] [Print PDF] [Request Permissions]

DISCOVERY NOTE

GENE EXPRESSION

Get checked abstract Antonio Marco, Charlotte Konikoff, Timothy L. Karr, and Sudhir Kumar: Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
Bioinformatics Advance Access published on July 24, 2009
Bioinformatics 2009 25: 2473-2477; doi:10.1093/bioinformatics/btp462 [Abstract] [Full Text] [Print PDF] [Request Permissions]

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract David J. Miller, Yanxin Zhang, Guoqiang Yu, Yongmei Liu, Li Chen, Carl D. Langefeld, David Herrington, and Yue Wang: An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions
Bioinformatics Advance Access published on July 16, 2009
Bioinformatics 2009 25: 2478-2485; doi:10.1093/bioinformatics/btp435 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Youngchul Kim, Stefan Bekiranov, Jae K. Lee, and Taesung Park: Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication
Bioinformatics Advance Access published on August 10, 2009
Bioinformatics 2009 25: 2486-2491; doi:10.1093/bioinformatics/btp471 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Mei Liu, Xue-wen Chen, and Raja Jothi: Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks
Bioinformatics Advance Access published on August 10, 2009
Bioinformatics 2009 25: 2492-2499; doi:10.1093/bioinformatics/btp480 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

SEQUENCE ANALYSIS

Get checked abstract Kristoffer Forslund and Erik LL Sonnhammer: Benchmarking homology detection procedures with low complexity filters
Bioinformatics Advance Access published on July 20, 2009
Bioinformatics 2009 25: 2500-2505; doi:10.1093/bioinformatics/btp446 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Byung-Chul Lee and Dongsup Kim: A new method for revealing correlated mutations under the structural and functional constraints in proteins
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2506-2513; doi:10.1093/bioinformatics/btp455 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Yangho Chen, Tade Souaiaia, and Ting Chen: PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics Advance Access published on August 12, 2009
Bioinformatics 2009 25: 2514-2521; doi:10.1093/bioinformatics/btp486 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

PHYLOGENETICS

Get checked abstract Patricia Buendia, Brice Cadwallader, and Victor DeGruttola: A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance
Bioinformatics Advance Access published on August 3, 2009
Bioinformatics 2009 25: 2522-2529; doi:10.1093/bioinformatics/btp466 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Li-Jung Liang, Robert E. Weiss, Benjamin Redelings, and Marc A. Suchard: Improving phylogenetic analyses by incorporating additional information from genetic sequence databases
Bioinformatics Advance Access published on August 6, 2009
Bioinformatics 2009 25: 2530-2536; doi:10.1093/bioinformatics/btp473 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

STRUCTURAL BIOINFORMATICS

Get checked abstract Yves Dehouck, Aline Grosfils, Benjamin Folch, Dimitri Gilis, Philippe Bogaerts, and Marianne Rooman: Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0
Bioinformatics Advance Access published on August 3, 2009
Bioinformatics 2009 25: 2537-2543; doi:10.1093/bioinformatics/btp445 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract José Ignacio Garzon, José Ramón Lopéz-Blanco, Carles Pons, Julio Kovacs, Ruben Abagyan, Juan Fernandez-Recio, and Pablo Chacon: FRODOCK: a new approach for fast rotational protein–protein docking
Bioinformatics Advance Access published on July 20, 2009
Bioinformatics 2009 25: 2544-2551; doi:10.1093/bioinformatics/btp447 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Pablo Carbonell and Antonio del Sol: Methyl side-chain dynamics prediction based on protein structure
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2552-2558; doi:10.1093/bioinformatics/btp463 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Pin-Hao Chi, Bin Pang, Dmitry Korkin, and Chi-Ren Shyu: Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments
Bioinformatics Advance Access published on August 10, 2009
Bioinformatics 2009 25: 2559-2565; doi:10.1093/bioinformatics/btp474 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

GENE EXPRESSION

Get checked abstract Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, and José María Carazo: aGEM: an integrative system for analyzing spatial-temporal gene-expression information
Bioinformatics Advance Access published on July 9, 2009
Bioinformatics 2009 25: 2566-2572; doi:10.1093/bioinformatics/btp422 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract Yuliya V. Karpievitch, Thomas Taverner, Joshua N. Adkins, Stephen J. Callister, Gordon A. Anderson, Richard D. Smith, and Alan R. Dabney: Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition
Bioinformatics Advance Access published on July 14, 2009
Bioinformatics 2009 25: 2573-2580; doi:10.1093/bioinformatics/btp426 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Dustin A. Cartwright, Siobhan M. Brady, David A. Orlando, Bernd Sturmfels, and Philip N. Benfey: Reconstructing spatiotemporal gene expression data from partial observations
Bioinformatics Advance Access published on July 16, 2009
Bioinformatics 2009 25: 2581-2587; doi:10.1093/bioinformatics/btp437 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract K. Van Deun, H. Hoijtink, L. Thorrez, L. Van Lommel, F. Schuit, and I. Van Mechelen: Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach
Bioinformatics Advance Access published on August 11, 2009
Bioinformatics 2009 25: 2588-2594; doi:10.1093/bioinformatics/btp439 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

GENETICS AND POPULATION ANALYSIS

Get checked abstract Jingchun Sun, Peilin Jia, Ayman H. Fanous, Bradley T. Webb, Edwin J.C.G. van den Oord, Xiangning Chen, Jozsef Bukszar, Kenneth S. Kendler, and Zhongming Zhao: A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases–schizophrenia as a case
Bioinformatics Advance Access published on July 14, 2009
Bioinformatics 2009 25: 2595-6602; doi:10.1093/bioinformatics/btp428 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Maik Friedel, Swetlana Nikolajewa, Jürgen Sühnel, and Thomas Wilhelm: DiProGB: the dinucleotide properties genome browser
Bioinformatics Advance Access published on July 15, 2009
Bioinformatics 2009 25: 2603-2604; doi:10.1093/bioinformatics/btp436 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Hyunjin Shin, Tao Liu, Arjun K. Manrai, and X. Shirley Liu: CEAS: cis-regulatory element annotation system
Bioinformatics Advance Access published on August 18, 2009
Bioinformatics 2009 25: 2605-2606; doi:10.1093/bioinformatics/btp479 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

SEQUENCE ANALYSIS

Get checked abstract Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Hervé Pagès, and Robert Gentleman: ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
Bioinformatics Advance Access published on August 3, 2009
Bioinformatics 2009 25: 2607-2608; doi:10.1093/bioinformatics/btp450 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Jill L. Wegrzyn, Jennifer M. Lee, John Liechty, and David B. Neale: PineSAP—sequence alignment and SNP identification pipeline
Bioinformatics Advance Access published on August 10, 2009
Bioinformatics 2009 25: 2609-2610; doi:10.1093/bioinformatics/btp477 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

PHYLOGENETICS

Get checked abstract Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, and David Heckerman: PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees
Bioinformatics Advance Access published on July 24, 2009
Bioinformatics 2009 25: 2611-2612; doi:10.1093/bioinformatics/btp454 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

GENE EXPRESSION

Get checked abstract Takehiro Hashimoto, Michiel J.L. de Hoon, Sean M. Grimmond, Carsten O. Daub, Yoshihide Hayashizaki, and Geoffrey J. Faulkner: Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite
Bioinformatics Advance Access published on July 15, 2009
Bioinformatics 2009 25: 2613-2614; doi:10.1093/bioinformatics/btp438 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Nicole Cloonan, Qinying Xu, Geoffrey J. Faulkner, Darrin F. Taylor, Dave T. P. Tang, Gabriel Kolle, and Sean M. Grimmond: RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2615-2616; doi:10.1093/bioinformatics/btp459 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract Mathieu Clément-Ziza, Christophe Malabat, Christian Weber, Ivan Moszer, Tero Aittokallio, Catherine Letondal, and Sandrine Rousseau: Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
Bioinformatics Advance Access published on August 3, 2009
Bioinformatics 2009 25: 2617-2618; doi:10.1093/bioinformatics/btp464 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract John R. Stevens and Gabriel Nicholas: metahdep: meta-analysis of hierarchically dependent gene expression studies
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2619-2620; doi:10.1093/bioinformatics/btp468 [Abstract] [Full Text] [Print PDF] [Request Permissions]

GENETICS AND POPULATION ANALYSIS

Get checked abstract Matthew E. Ritchie, Benilton S. Carvalho, Kurt N. Hetrick, Simon Tavaré, and Rafael A. Irizarry: R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
Bioinformatics Advance Access published on August 6, 2009
Bioinformatics 2009 25: 2621-2623; doi:10.1093/bioinformatics/btp470 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

ERRATUM

Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan Fokkink, Thilo Kielmann, Henri Bal, and Jaap Heringa: Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development
Bioinformatics 2009 25: 2624; doi:10.1093/bioinformatics/btp509 [Extract] [Full Text] [Print PDF] [Request Permissions]