Bioinformatics -- Table of Contents (25 [11])

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Contents: Volume 25, Number 11, 1 June 2009   [Index by Author]

DISCOVERY NOTE

     SEQUENCE ANALYSIS

ORIGINAL PAPERS

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     PHYLOGENETICS

     GENETICS AND POPULATION ANALYSIS

     SYSTEMS BIOLOGY

     DATA AND TEXT MINING

APPLICATIONS NOTE

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     STRUCTURAL BIOINFORMATICS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

     SYSTEMS BIOLOGY

     DATA AND TEXT MINING

ERRATUM

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DISCOVERY NOTE

SEQUENCE ANALYSIS

Get checked abstract Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Olof Olsson, and Björn Olsson: In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
Bioinformatics Advance Access published on March 25, 2009
Bioinformatics 2009 25: 1345-1348; doi:10.1093/bioinformatics/btp172 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Triinu Koressaar, Kai Jõers, and Maido Remm: Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms
Bioinformatics Advance Access published on April 8, 2009
Bioinformatics 2009 25: 1349-1355; doi:10.1093/bioinformatics/btp241 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

SEQUENCE ANALYSIS

Get checked abstract Eric L. Peterson, Jané Kondev, Julie A. Theriot, and Rob Phillips: Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Bioinformatics Advance Access published on April 7, 2009
Bioinformatics 2009 25: 1356-1362; doi:10.1093/bioinformatics/btp164 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Michael C. Schatz: CloudBurst: highly sensitive read mapping with MapReduce
Bioinformatics Advance Access published on April 8, 2009
Bioinformatics 2009 25: 1363-1369; doi:10.1093/bioinformatics/btp236 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

PHYLOGENETICS

Get checked abstract Marc A. Suchard and Andrew Rambaut: Many-core algorithms for statistical phylogenetics
Bioinformatics Advance Access published on April 15, 2009
Bioinformatics 2009 25: 1370-1376; doi:10.1093/bioinformatics/btp244 [Abstract] [Full Text] [Print PDF] [Request Permissions]

GENETICS AND POPULATION ANALYSIS

Get checked abstract Jules Hernández-Sánchez, Jean-Alain Grunchec, and Sara Knott: A web application to perform linkage disequilibrium and linkage analyses on a computational grid
Bioinformatics Advance Access published on March 24, 2009
Bioinformatics 2009 25: 1377-1383; doi:10.1093/bioinformatics/btp171 [Abstract] [Full Text] [Print PDF] [Request Permissions]

SYSTEMS BIOLOGY

Get checked abstract E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes, and Keith A. Baggerly: Variable slope normalization of reverse phase protein arrays
Bioinformatics Advance Access published on March 31, 2009
Bioinformatics 2009 25: 1384-1389; doi:10.1093/bioinformatics/btp174 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Wei Pan: Network-based multiple locus linkage analysis of expression traits
Bioinformatics Advance Access published on March 31, 2009
Bioinformatics 2009 25: 1390-1396; doi:10.1093/bioinformatics/btp177 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

DATA AND TEXT MINING

Get checked abstract Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Rong Wang, Zhihua Li, Luiz O. Penalva, Margaret Myers, Edward M. Marcotte, and Daniel P. Miranker: Integrating shotgun proteomics and mRNA expression data to improve protein identification
Bioinformatics Advance Access published on March 24, 2009
Bioinformatics 2009 25: 1397-1403; doi:10.1093/bioinformatics/btp168 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract Irena Spasic, Evangelos Simeonidis, Hanan L. Messiha, Norman W. Paton, and Douglas B. Kell: KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways
Bioinformatics Advance Access published on March 31, 2009
Bioinformatics 2009 25: 1404-1411; doi:10.1093/bioinformatics/btp175 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, and Dietrich Rebholz-Schuhmann: MeSH Up: effective MeSH text classification for improved document retrieval
Bioinformatics Advance Access published on April 17, 2009
Bioinformatics 2009 25: 1412-1418; doi:10.1093/bioinformatics/btp249 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Feng-Chi Chen, Yen-Zho Chen, and Trees-Juen Chuang: CNVVdb: a database of copy number variations across vertebrate genomes
Bioinformatics Advance Access published on March 25, 2009
Bioinformatics 2009 25: 1419-1421; doi:10.1093/bioinformatics/btp166 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

SEQUENCE ANALYSIS

Get checked abstract Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics
Bioinformatics Advance Access published on March 20, 2009
Bioinformatics 2009 25: 1422-1423; doi:10.1093/bioinformatics/btp163 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract You Jung Kim, Nikhil Teletia, Victor Ruotti, Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, and Jignesh M. Patel: ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches
Bioinformatics Advance Access published on April 7, 2009
Bioinformatics 2009 25: 1424-1425; doi:10.1093/bioinformatics/btp178 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

STRUCTURAL BIOINFORMATICS

Get checked abstract R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, and Olivier Lichtarge: Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
Bioinformatics Advance Access published on March 23, 2009
Bioinformatics 2009 25: 1426-1427; doi:10.1093/bioinformatics/btp160 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Massimo Sandal, Fabrizio Benedetti, Marco Brucale, Alberto Gomez-Casado, and Bruno Samorì: Hooke: an open software platform for force spectroscopy
Bioinformatics Advance Access published on March 31, 2009
Bioinformatics 2009 25: 1428-1430; doi:10.1093/bioinformatics/btp180 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Michael Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, and Rachel Karchin: LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures
Bioinformatics Advance Access published on April 15, 2009
Bioinformatics 2009 25: 1431-1432; doi:10.1093/bioinformatics/btp242 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Xuefeng Xia, Song Zhang, Yu Su, and Zhirong Sun: MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields
Bioinformatics Advance Access published on April 9, 2009
Bioinformatics 2009 25: 1433-1434; doi:10.1093/bioinformatics/btp251 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Yanga Byun and Kyungsook Han: PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
Bioinformatics Advance Access published on April 15, 2009
Bioinformatics 2009 25: 1435-1437; doi:10.1093/bioinformatics/btp252 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

GENE EXPRESSION

Get checked abstract Paul Geeleher, Dermot Morris, John P. Hinde, and Aaron Golden: BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server
Bioinformatics Advance Access published on March 23, 2009
Bioinformatics 2009 25: 1438-1439; doi:10.1093/bioinformatics/btp165 [Abstract] [Full Text] [Print PDF] [Request Permissions]

GENETICS AND POPULATION ANALYSIS

Get checked abstract Ambra Giovannini, Gaetano Zanghirati, Mark A. Beaumont, Lounès Chikhi, and Guido Barbujani: A novel parallel approach to the likelihood-based estimation of admixture in population genetics
Bioinformatics Advance Access published on March 13, 2009
Bioinformatics 2009 25: 1440-1441; doi:10.1093/bioinformatics/btp136 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Xavier Didelot, Daniel Lawson, and Daniel Falush: SimMLST: simulation of multi-locus sequence typing data under a neutral model
Bioinformatics Advance Access published on March 13, 2009
Bioinformatics 2009 25: 1442-1444; doi:10.1093/bioinformatics/btp145 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract John Watkinson and Dimitris Anastassiou: Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype
Bioinformatics Advance Access published on March 17, 2009
Bioinformatics 2009 25: 1445-1446; doi:10.1093/bioinformatics/btp159 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract Vincent J. Carey, Adam R. Davis, Michael F. Lawrence, Robert Gentleman, and Benjamin A. Raby: Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x
Bioinformatics Advance Access published on April 5, 2009
Bioinformatics 2009 25: 1447-1448; doi:10.1093/bioinformatics/btp169 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Miao-Xin Li, Lin Jiang, Patrick Yu-Ping Kao, Pak-C. Sham, and You-Qiang Song: IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis
Bioinformatics Advance Access published on April 3, 2009
Bioinformatics 2009 25: 1449-1450; doi:10.1093/bioinformatics/btp183 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract P. Librado and J. Rozas: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
Bioinformatics Advance Access published on April 3, 2009
Bioinformatics 2009 25: 1451-1452; doi:10.1093/bioinformatics/btp187 [Abstract] [Full Text] [Print PDF] [Request Permissions]

SYSTEMS BIOLOGY

Get checked abstract Frédéric Y. Bois: GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models
Bioinformatics Advance Access published on March 20, 2009
Bioinformatics 2009 25: 1453-1454; doi:10.1093/bioinformatics/btp162 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, and Andreas Zell: SBML2L^AT_EX: Conversion of SBML files into human-readable reports
Bioinformatics Advance Access published on March 23, 2009
Bioinformatics 2009 25: 1455-1456; doi:10.1093/bioinformatics/btp170 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, and William S. Hlavacek: GetBonNie for building, analyzing and sharing rule-based models
Bioinformatics Advance Access published on March 25, 2009
Bioinformatics 2009 25: 1457-1460; doi:10.1093/bioinformatics/btp173 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Xuefeng Bruce Ling, Harvey Cohen, Joseph Jin, Irwin Lau, and James Schilling: FDR made easy in differential feature discovery and correlation analyses
Bioinformatics Advance Access published on April 17, 2009
Bioinformatics 2009 25: 1461-1462; doi:10.1093/bioinformatics/btp176 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Stephan Preibisch, Stephan Saalfeld, and Pavel Tomancak: Globally optimal stitching of tiled 3D microscopic image acquisitions
Bioinformatics Advance Access published on April 3, 2009
Bioinformatics 2009 25: 1463-1465; doi:10.1093/bioinformatics/btp184 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Giorgio F. Gilestro and Chiara Cirelli: pySolo: a complete suite for sleep analysis in Drosophila
Bioinformatics Advance Access published on April 15, 2009
Bioinformatics 2009 25: 1466-1467; doi:10.1093/bioinformatics/btp237 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Mauro A. A. Castro, José L. Rybarczyk Filho, Rodrigo J. S. Dalmolin, Marialva Sinigaglia, José C. F. Moreira, José C. M. Mombach, and Rita M. C. de Almeida: ViaComplex: software for landscape analysis of gene expression networks in genomic context
Bioinformatics Advance Access published on April 15, 2009
Bioinformatics 2009 25: 1468-1469; doi:10.1093/bioinformatics/btp246 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

DATA AND TEXT MINING

Get checked abstract Jitao David Zhang and Stefan Wiemann: KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
Bioinformatics Advance Access published on March 23, 2009
Bioinformatics 2009 25: 1470-1471; doi:10.1093/bioinformatics/btp167 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract Bas van Breukelen, Henk W. P. van den Toorn, Madalina M. Drugan, and Albert J. R. Heck: StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry
Bioinformatics Advance Access published on March 31, 2009
Bioinformatics 2009 25: 1472-1473; doi:10.1093/bioinformatics/btp181 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

ERRATUM

Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, and Yasubumi Sakakibara: Accurate identification of orthologous segments among multiple genomes
Bioinformatics 2009 25: 1474; doi:10.1093/bioinformatics/btp263 [Extract] [Full Text] [Print PDF] [Request Permissions]