Bioinformatics

ORIGINAL PAPERS:

Shuyu Li, Gene Cutler, Jane Jijun Liu, Timothy Hoey, Liangbiao Chen, Peter G. Schultz, Jiayu Liao, and Xuefeng Bruce Ling

A comparative analysis of HGSC and Celera human genome assemblies and gene sets
Bioinformatics 2003 19: 1597-1605; doi:10.1093/bioinformatics/btg219 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Diego di Bernardo, Thomas Down, and Tim Hubbard

ddbRNA: detection of conserved secondary structures in multiple alignments
Bioinformatics 2003 19: 1606-1611; doi:10.1093/bioinformatics/btg229 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Inderjit S. Dhillon, Edward M. Marcotte, and Usman Roshan

Diametrical clustering for identifying anti-correlated gene clusters
Bioinformatics 2003 19: 1612-1619; doi:10.1093/bioinformatics/btg209 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Paul Pavlidis, Qinghong Li, and William Stafford Noble

The effect of replication on gene expression microarray experiments
Bioinformatics 2003 19: 1620-1627; doi:10.1093/bioinformatics/btg227 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xu Guo, Huilin Qi, Catherine M. Verfaillie, and Wei Pan

Statistical significance analysis of longitudinal gene expression data
Bioinformatics 2003 19: 1628-1635; doi:10.1093/bioinformatics/btg206 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, and Hongyu Zhao

Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
Bioinformatics 2003 19: 1636-1643; doi:10.1093/bioinformatics/btg210 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan A. Barker and Janet M. Thornton

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
Bioinformatics 2003 19: 1644-1649; doi:10.1093/bioinformatics/btg226 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

J. J. Ward, L. J. McGuffin, B. F. Buxton, and D. T. Jones

Secondary structure prediction with support vector machines
Bioinformatics 2003 19: 1650-1655; doi:10.1093/bioinformatics/btg223 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Keun-Joon Park and Minoru Kanehisa

Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs
Bioinformatics 2003 19: 1656-1663; doi:10.1093/bioinformatics/btg222 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A.L. Mitchell, J.R. Reich, and T.K. Attwood

PRECIS: Protein reports engineered from concise information in SWISS-PROT
Bioinformatics 2003 19: 1664-1671; doi:10.1093/bioinformatics/btg204 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David P. Kreil and Christos A. Ouzounis

Comparison of sequence masking algorithms and the detection of biased protein sequence regions
Bioinformatics 2003 19: 1672-1681; doi:10.1093/bioinformatics/btg212 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

J.C. Prasad, S.R. Comeau, S. Vajda, and C.J. Camacho

Consensus alignment for reliable framework prediction in homology modeling
Bioinformatics 2003 19: 1682-1691; doi:10.1093/bioinformatics/btg211 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D.C. McShan, S. Rao, and I. Shah

PathMiner: predicting metabolic pathways by heuristic search
Bioinformatics 2003 19: 1692-1698; doi:10.1093/bioinformatics/btg217 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Svetlana Novichkova, Sergei Egorov, and Nikolai Daraselia

MedScan, a natural language processing engine for MEDLINE abstracts
Bioinformatics 2003 19: 1699-1706; doi:10.1093/bioinformatics/btg207 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Christophe Pichon and Brice Felden

Intergenic sequence inspector: searching and identifying bacterial RNAs
Bioinformatics 2003 19: 1707-1709; doi:10.1093/bioinformatics/btg235 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D. P. Wall, H. B. Fraser, and A. E. Hirsh

Detecting putative orthologs
Bioinformatics 2003 19: 1710-1711; doi:10.1093/bioinformatics/btg213 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jian Wang and Eileen Kraemer

GFPE: gene-finding program evaluation
Bioinformatics 2003 19: 1712-1713; doi:10.1093/bioinformatics/btg216 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, and Anne Kallioniemi

CGH-Plotter: MATLAB toolbox for CGH-data analysis
Bioinformatics 2003 19: 1714-1715; doi:10.1093/bioinformatics/btg230 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R.J. Laws, T.L. Bergemann, F. Quiaoit, and L.P. Zhao

SignalViewer: analyzing microarray images
Bioinformatics 2003 19: 1716-1717; doi:10.1093/bioinformatics/btg208 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert J. Blick, Andrew T. Revel, and Eric J. Hansen

FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis
Bioinformatics 2003 19: 1718-1719; doi:10.1093/bioinformatics/btg218 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chunhong Mao, John C. Cushman, Gregory D. May, and Jennifer W. Weller

ESTAP—an automated system for the analysis of EST data
Bioinformatics 2003 19: 1720-1722; doi:10.1093/bioinformatics/btg205 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Razif R. Gabdoulline, René Hoffmann, Florian Leitner, and Rebecca C. Wade

ProSAT: functional annotation of protein 3D structures
Bioinformatics 2003 19: 1723-1725; doi:10.1093/bioinformatics/btg220 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

C.J. Creevey and J.O. McInerney

CRANN: detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics 2003 19: 1726; doi:10.1093/bioinformatics/btg225 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

K. Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, F. Miyoshi, Y. Naito, Y. Nakayama, and M. Tomita

E-Cell 2: Multi-platform E-Cell simulation system
Bioinformatics 2003 19: 1727-1729; doi:10.1093/bioinformatics/btg221 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sinan Güler, Andreas Eberhart, and Isabel Rojas

Web-based exchange of biochemical information
Bioinformatics 2003 19: 1730-1731; doi:10.1093/bioinformatics/btg234 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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