Bioinformatics

ORIGINAL PAPERS:

Jan Ihmels, Sven Bergmann, and Naama Barkai

Defining transcription modules using large-scale gene expression data
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 1993-2003; doi:10.1093/bioinformatics/bth166 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sandhya Xirasagar, Scott Gustafson, B. Alex Merrick, Kenneth B. Tomer, Stanley Stasiewicz, Denny D. Chan, Kenneth J. Yost, III, John R. Yates, III, Susan Sumner, Nianqing Xiao, and Michael D. Waters

CEBS object model for systems biology data, SysBio-OM
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2004-2015; doi:10.1093/bioinformatics/bth189 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

HyungJun Cho and Jae K. Lee

Bayesian hierarchical error model for analysis of gene expression data
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2016-2025; doi:10.1093/bioinformatics/bth192 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David P. Kreil, Natasha A. Karp, and Kathryn S. Lilley

DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2026-2034; doi:10.1093/bioinformatics/bth193 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hiroshi Wako, Masaki Kato, and Shigeru Endo

ProMode: a database of normal mode analyses on protein molecules with a full-atom model
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2035-2043; doi:10.1093/bioinformatics/bth197 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Daniel H. Huson and Mike Steel

Phylogenetic trees based on gene content
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2044-2049; doi:10.1093/bioinformatics/bth198 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. B. Horne, T. C. Hodgman, H. D. Spence, and A. R. Dalby

Constructing an enzyme-centric view of metabolism
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2050-2055; doi:10.1093/bioinformatics/bth199 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Momiao Xiong, Jinying Zhao, and Hao Xiong

Network-based regulatory pathways analysis
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2056-2066; doi:10.1093/bioinformatics/bth201 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Mark Chaisson, Pavel Pevzner, and Haixu Tang

Fragment assembly with short reads
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2067-2074; doi:10.1093/bioinformatics/bth205 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Morris A. Swertz, E. O. de Brock, Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Richard J. S. Baerends, Jan Kok, Oscar P. Kuipers, and Ritsert C. Jansen

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2075-2083; doi:10.1093/bioinformatics/bth206 [Abstract] [Print PDF][Screen PDF] Supplementary dataSupplementary dataSupplementary dataSupplementary dataSupplementary data [Request Permissions]  

Antonio J. Pérez, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, and Miguel A. Andrade

Gene annotation from scientific literature using mappings between keyword systems
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2084-2091; doi:10.1093/bioinformatics/bth207 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Chagoyen, M. E. Kurul, P. A. De-Alarcón, J. M. Carazo, and A. Gupta

Designing and executing scientific workflows with a programmable integrator
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2092-2100; doi:10.1093/bioinformatics/bth209 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jie Zheng, Timothy J. Close, Tao Jiang, and Stefano Lonardi

Efficient selection of unique and popular oligos for large EST databases
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2101-2112; doi:10.1093/bioinformatics/bth210 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Vladimir Makarenkov and François-Joseph Lapointe

A weighted least-squares approach for inferring phylogenies from incomplete distance matrices
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2113-2121; doi:10.1093/bioinformatics/bth211 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tamer Kahveci, Vebjorn Ljosa, and Ambuj K. Singh

Speeding up whole-genome alignment by indexing frequency vectors
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2122-2134; doi:10.1093/bioinformatics/bth212 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Liting Wen and Jin-An Feng

Repair-FunMap: a functional database of proteins of the DNA repair systems
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2135-2137; doi:10.1093/bioinformatics/bth194 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, and David T. Jones

The DISOPRED server for the prediction of protein disorder
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2138-2139; doi:10.1093/bioinformatics/bth195 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nikola Stojanovic and Ken Dewar

Identifying multiple alignment regions satisfying simple formulas and patterns
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2140-2142; doi:10.1093/bioinformatics/bth196 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Brett G. Olivier and Jacky L. Snoep

Web-based kinetic modelling using JWS Online
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2143-2144; doi:10.1093/bioinformatics/bth200 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. L. Mancini, R. H. Higa, A. Oliveira, F. Dominiquini, P. R. Kuser, M. E. B. Yamagishi, R. C. Togawa, and G. Neshich

STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2145-2147; doi:10.1093/bioinformatics/bth203 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andrés Moreira and Alejandro Maass

TIP: protein backtranslation aided by genetic algorithms
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2148-2149; doi:10.1093/bioinformatics/bth204 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gad Getz, Alina Starovolsky, and Eytan Domany

F2CS: FSSP to CATH and SCOP prediction server
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2150-2152; doi:10.1093/bioinformatics/bth208 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, and John Westbrook

Ligand Depot: a data warehouse for ligands bound to macromolecules
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2153-2155; doi:10.1093/bioinformatics/bth214 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ritu Pandey, Raghavendra K. Guru, and David W. Mount

Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2156-2158; doi:10.1093/bioinformatics/bth215 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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