Bioinformatics

ORIGINAL PAPERS:

L. da F. Costa, M. S. Barbosa, E. T. M. Manoel, J. Streicher, and G. B. Müller

Mathematical characterization of three-dimensional gene expression patterns
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1653-1662; doi:10.1093/bioinformatics/bth135 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Debashis Ghosh

Mixture models for assessing differential expression in complex tissues using microarray data
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1663-1669; doi:10.1093/bioinformatics/bth139 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Eberhard O. Voit and Jonas Almeida

Decoupling dynamical systems for pathway identification from metabolic profiles
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1670-1681; doi:10.1093/bioinformatics/bth140 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, and Tatsuya Akutsu

Protein homology detection using string alignment kernels
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1682-1689; doi:10.1093/bioinformatics/bth141 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nabil Belacel, Miroslava Cuperlovic-Culf, Mark Laflamme, and Rodney Ouellette

Fuzzy J-Means and VNS methods for clustering genes from microarray data
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1690-1701; doi:10.1093/bioinformatics/bth142 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Thorsteinn Rögnvaldsson and Liwen You

Why neural networks should not be used for HIV-1 protease cleavage site prediction
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1702-1709; doi:10.1093/bioinformatics/bth144 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jain-Shing Wu, Chungnan Lee, Chien-Chang Wu, and Yow-Ling Shiue

Primer design using genetic algorithm
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1710-1717; doi:10.1093/bioinformatics/bth147 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Audrius Meskauskas, Frank Lehmann-Horn, and Karin Jurkat-Rott

Sight: automating genomic data-mining without programming skills
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1718-1720; doi:10.1093/bioinformatics/bth151 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. S. Anderssen, Y. Wu, R. Dolferus, and I. Saunders

An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1721-1727; doi:10.1093/bioinformatics/bth152 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Mia Hubert and Sanne Engelen

Robust PCA and classification in biosciences
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1728-1736; doi:10.1093/bioinformatics/bth158 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stan Pounds and Cheng Cheng

Improving false discovery rate estimation
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1737-1745; doi:10.1093/bioinformatics/bth160 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

N. Kashtan, S. Itzkovitz, R. Milo, and U. Alon

Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs
Bioinformatics Advance Access published on March 4, 2004
Bioinformatics 2004 20: 1746-1758; doi:10.1093/bioinformatics/bth163 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tetsuro Toyoda and Akiyoshi Wada

Omic space: coordinate-based integration and analysis of genomic phenomic interactions
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1759-1765; doi:10.1093/bioinformatics/bth165 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Fenghai Duan and Heping Zhang

Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 1766-1771; doi:10.1093/bioinformatics/bth169 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Radka Stoyanova, Troy D. Querec, Truman R. Brown, and Christos Patriotis

Normalization of single-channel DNA array data by principal component analysis
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1772-1784; doi:10.1093/bioinformatics/bth170 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chittibabu Guda, Eoin Fahy, and Shankar Subramaniam

MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins
Bioinformatics Advance Access published on March 22, 2004
Bioinformatics 2004 20: 1785-1794; doi:10.1093/bioinformatics/bth171 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Reich, K. Ohm, M. Angelo, P. Tamayo, and J. P. Mesirov

GeneCluster 2.0: an advanced toolset for bioarray analysis
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1797-1798; doi:10.1093/bioinformatics/bth138 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Katsuyuki Yugi and Masaru Tomita

A general computational model of mitochondrial metabolism in a whole organelle scale
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1795-1796; doi:10.1093/bioinformatics/bth125 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xinglai Ji, Yuan Yuan, Jesse Li-Ling, Yanda Li, and Zhirong Sun

HMMGEP: clustering gene expression data using hidden Markov models
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1799-1800; doi:10.1093/bioinformatics/bth145 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chesley M. Leslin, Alex Abyzov, and Valentin A. Ilyin

Structural exon database, SEDB, mapping exon boundaries on multiple protein structures
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1801-1803; doi:10.1093/bioinformatics/bth150 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wei Wu and William S. Noble

Genomic data visualization on the Web
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1804-1805; doi:10.1093/bioinformatics/bth154 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Iain Milne, Frank Wright, Glenn Rowe, David F. Marshall, Dirk Husmeier, and Gràinne McGuire

TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1806-1807; doi:10.1093/bioinformatics/bth155 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Chang-Xing Ma, Rongling Wu, and George Casella

FunMap: functional mapping of complex traits
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1808-1811; doi:10.1093/bioinformatics/bth156 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert Kerkhoven, Frank H. J. van Enckevort, Jos Boekhorst, Douwe Molenaar, and Roland J. Siezen

Visualization for genomics: the Microbial Genome Viewer
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1812-1814; doi:10.1093/bioinformatics/bth159 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Peter M. Haverty and Zhiping Weng

CisML: an XML-based format for sequence motif detection software
Bioinformatics Advance Access published on March 4, 2004
Bioinformatics 2004 20: 1815-1817; doi:10.1093/bioinformatics/bth162 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Luquan Wang and Forest Y. Mu

A Web-based design center for vector-based siRNA and siRNA cassette
Bioinformatics Advance Access published on March 4, 2004
Bioinformatics 2004 20: 1818-1820; doi:10.1093/bioinformatics/bth164 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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