Bioinformatics

EDITORIALS:

Alex Bateman and Alfonso Valencia

New Leadership for Bioinformatics
Bioinformatics 2004 20: 1821; doi:10.1093/bioinformatics/bth403 [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Thijs Beuming and Harel Weinstein

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1822-1835; doi:10.1093/bioinformatics/bth143 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nadia El-Mabrouk and Damian Labuda

Haplotypes histories as pathways of recombinations
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1836-1841; doi:10.1093/bioinformatics/bth148 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Eran Halperin and Eleazar Eskin

Haplotype reconstruction from genotype data using Imperfect Phylogeny
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1842-1849; doi:10.1093/bioinformatics/bth149 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jon D. McAuliffe, Lior Pachter, and Michael I. Jordan

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1850-1860; doi:10.1093/bioinformatics/bth153 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Danny Barash

Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1861-1869; doi:10.1093/bioinformatics/bth157 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hong-Wu Ma, Xue-Ming Zhao, Ying-Jin Yuan, and An-Ping Zeng

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1870-1876; doi:10.1093/bioinformatics/bth167 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Eduardo Sontag, Anatoly Kiyatkin, and Boris N. Kholodenko

Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1877-1886; doi:10.1093/bioinformatics/bth173 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

K. Ljungberg, S. Holmgren, and Ö. Carlborg

Simultaneous search for multiple QTL using the global optimization algorithm DIRECT
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1887-1895; doi:10.1093/bioinformatics/bth175 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kimberly D. Siegmund, Peter W. Laird, and Ite A. Laird-Offringa

A comparison of cluster analysis methods using DNA methylation data
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1896-1904; doi:10.1093/bioinformatics/bth176 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yi Qu and Shizhong Xu

Supervised cluster analysis for microarray data based on multivariate Gaussian mixture
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1905-1913; doi:10.1093/bioinformatics/bth177 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hong-Chu Chen, Hsiao-Ching Lee, Tsai-Yun Lin, Wen-Hsiung Li, and Bor-Sen Chen

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1914-1927; doi:10.1093/bioinformatics/bth178 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dirk Steinhauser, Björn H. Junker, Alexander Luedemann, Joachim Selbig, and Joachim Kopka

Hypothesis-driven approach to predict transcriptional units from gene expression data
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1928-1939; doi:10.1093/bioinformatics/bth182 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D. Pekurovsky, I. N. Shindyalov, and P. E. Bourne

A case study of high-throughput biological data processing on parallel platforms
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1940-1947; doi:10.1093/bioinformatics/bth184 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yan Fu, Qiang Yang, Ruixiang Sun, Dequan Li, Rong Zeng, Charles X. Ling, and Wen Gao

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1948-1954; doi:10.1093/bioinformatics/bth186 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Troy D. Querec, Radka Stoyanova, Eric Ross, and Christos Patriotis

A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1955-1961; doi:10.1093/bioinformatics/bth188 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Urban Liebel, Bjoern Kindler, and Rainer Pepperkok

‘Harvester’: a fast meta search engine of human protein resources
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1962-1963; doi:10.1093/bioinformatics/bth146 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jomuna V. Choudhuri, Chris Schleiermacher, Stefan Kurtz, and Robert Giegerich

GenAlyzer: interactive visualization of sequence similarities between entire genomes
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1964-1965; doi:10.1093/bioinformatics/bth161 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Voigt, Steffen Möller, Saleh M. Ibrahim, and Pablo Serrano-Fernández

Non-linear conversion between genetic and physical chromosomal distances
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1966-1967; doi:10.1093/bioinformatics/bth168 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Mikita Suyama, David Torrents, and Peer Bork

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1968-1970; doi:10.1093/bioinformatics/bth172 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Pieler, F. Sanchez-Cabo, H. Hackl, G. G. Thallinger, and Z. Trajanoski

ArrayNorm: comprehensive normalization and analysis of microarray data
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 1971-1973; doi:10.1093/bioinformatics/bth174 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stein Aerts, Peter Van Loo, Yves Moreau, and Bart De Moor

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1974-1976; doi:10.1093/bioinformatics/bth179 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Carolyn J. Lawrence, Christian M. Zmasek, R. Kelly Dawe, and Russell L. Malmberg

LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1977-1979; doi:10.1093/bioinformatics/bth180 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Maksym Korotkiy, Rutger Middelburg, Henk Dekker, Frank van Harmelen, and Jan Lankelma

A tool for gene expression based PubMed search through combining data sources
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1980-1982; doi:10.1093/bioinformatics/bth183 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. H. Higa, A. J. Montagner, R. C. Togawa, P. R. Kuser, M. E. B. Yamagishi, A. L. Mancini, G. Pappas, Jr., R. T. Miura, L. G. Horita, and G. Neshich

ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1983-1985; doi:10.1093/bioinformatics/bth185 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David H. Ardell

SCANMS: adjusting for multiple comparisons in sliding window neutrality tests
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 1986-1988; doi:10.1093/bioinformatics/bth187 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. H. Higa, A. G. Oliveira, L. G. Horita, R. T. Miura, M. K. Inoue, P. R. Kuser, A. L. Mancini, M. E. B. Yamagishi, R. C. Togawa, and G. Neshich

Defining 3D residue environment in protein structures using SCORPION and FORMIGA
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1989-1991; doi:10.1093/bioinformatics/bth190 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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