Bioinformatics

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Suparna Mitra, Bernhard Klar, and Daniel H. Huson

Visual and statistical comparison of metagenomes
Bioinformatics Advance Access published on June 10, 2009
Bioinformatics 2009 25: 1849-1855; doi:10.1093/bioinformatics/btp341 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Andrew F. Neuwald

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 1869-1875; doi:10.1093/bioinformatics/btp342 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Andrea Zen, Cesira de Chiara, Annalisa Pastore, and Cristian Micheletti

Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains
Bioinformatics Advance Access published on May 31, 2009
Bioinformatics 2009 25: 1876-1883; doi:10.1093/bioinformatics/btp339 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Kristin K. Nicodemus and James D. Malley

Predictor correlation impacts machine learning algorithms: implications for genomic studies
Bioinformatics Advance Access published on May 21, 2009
Bioinformatics 2009 25: 1884-1890; doi:10.1093/bioinformatics/btp331 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Guimei Liu, Limsoon Wong, and Hon Nian Chua

Complex discovery from weighted PPI networks
Bioinformatics Advance Access published on May 12, 2009
Bioinformatics 2009 25: 1891-1897; doi:10.1093/bioinformatics/btp311 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chang H. Seo, Jeong-Rae Kim, Man-Sun Kim, and Kwang-Hyun Cho

Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks
Bioinformatics Advance Access published on May 13, 2009
Bioinformatics 2009 25: 1898-1904; doi:10.1093/bioinformatics/btp316 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Wandaliz Torres-García, Weiwen Zhang, George C. Runger, Roger H. Johnson, and Deirdre R. Meldrum

Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins
Bioinformatics Advance Access published on May 15, 2009
Bioinformatics 2009 25: 1905-1914; doi:10.1093/bioinformatics/btp325 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, and J. Timmer

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 1923-1929; doi:10.1093/bioinformatics/btp358 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Tianwei Yu, Youngja Park, Jennifer M. Johnson, and Dean P. Jones

apLCMS—adaptive processing of high-resolution LC/MS data
Bioinformatics Advance Access published on May 4, 2009
Bioinformatics 2009 25: 1930-1936; doi:10.1093/bioinformatics/btp291 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rene Hussong, Barbara Gregorius, Andreas Tholey, and Andreas Hildebrandt

Highly accelerated feature detection in proteomics data sets using modern graphics processing units
Bioinformatics Advance Access published on May 14, 2009
Bioinformatics 2009 25: 1937-1943; doi:10.1093/bioinformatics/btp294 [Abstract] [Full Text] [Print PDF] [Supplementary Data 1] [Supplementary Data] [Request Permissions]  

Get checked abstract Shanfeng Zhu, Jia Zeng, and Hiroshi Mamitsuka

Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity
Bioinformatics Advance Access published on June 3, 2009
Bioinformatics 2009 25: 1944-1951; doi:10.1093/bioinformatics/btp338 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, and Weiqun Peng

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 1952-1958; doi:10.1093/bioinformatics/btp340 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract M. Bahlo and C. J. Bromhead

Generating linkage mapping files from Affymetrix SNP chip data
Bioinformatics Advance Access published on May 12, 2009
Bioinformatics 2009 25: 1961-1962; doi:10.1093/bioinformatics/btp313 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Rodrigo Gouveia-Oliveira, Francisco S. Roque, Rasmus Wernersson, Thomas Sicheritz-Ponten, Peter W. Sackett, Anne Mølgaard, and Anders G. Pedersen

InterMap3D: predicting and visualizing co-evolving protein residues
Bioinformatics Advance Access published on June 15, 2009
Bioinformatics 2009 25: 1963-1965; doi:10.1093/bioinformatics/btp335 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, and Jun Wang

SOAP2: an improved ultrafast tool for short read alignment
Bioinformatics Advance Access published on June 3, 2009
Bioinformatics 2009 25: 1966-1967; doi:10.1093/bioinformatics/btp336 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS

Get checked abstract Rodrigo Santamaría and Roberto Therón

Treevolution: visual analysis of phylogenetic trees
Bioinformatics Advance Access published on May 26, 2009
Bioinformatics 2009 25: 1970-1971; doi:10.1093/bioinformatics/btp333 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFOMATICS

GENE EXPRESSION

Get checked abstract Véronique Dupierris, Christophe Masselon, Magali Court, Sylvie Kieffer-Jaquinod, and Christophe Bruley

A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa
Bioinformatics Advance Access published on May 6, 2009
Bioinformatics 2009 25: 1980-1981; doi:10.1093/bioinformatics/btp301 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Michael Matschiner and Walter Salzburger

TANDEM: integrating automated allele binning into genetics and genomics workflows
Bioinformatics Advance Access published on May 6, 2009
Bioinformatics 2009 25: 1982-1983; doi:10.1093/bioinformatics/btp303 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Qiong Cheng, Robert Harrison, and Alexander Zelikovsky

MetNetAligner: a web service tool for metabolic network alignments
Bioinformatics Advance Access published on May 4, 2009
Bioinformatics 2009 25: 1989-1990; doi:10.1093/bioinformatics/btp287 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract G. L. Papadopoulos, P. Alexiou, M. Maragkakis, M. Reczko, and A. G. Hatzigeorgiou

DIANA-mirPath: Integrating human and mouse microRNAs in pathways
Bioinformatics Advance Access published on May 12, 2009
Bioinformatics 2009 25: 1991-1993; doi:10.1093/bioinformatics/btp299 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING

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