Bioinformatics

ORIGINAL PAPERS:

Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S. Bader, Kevin P. White, and Andrey Rzhetsky

Probabilistic inference of molecular networks from noisy data sources
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1205-1213; doi:10.1093/bioinformatics/bth061 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Weijia Xu and Daniel P. Miranker

A metric model of amino acid substitution
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1214-1221; doi:10.1093/bioinformatics/bth065 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Medvedovic, K.Y. Yeung, and R.E. Bumgarner

Bayesian mixture model based clustering of replicated microarray data
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1222-1232; doi:10.1093/bioinformatics/bth068 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, and Cheng Li

dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1233-1240; doi:10.1093/bioinformatics/bth069 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ronaldo F. Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, and Edward R. Dougherty

Growing genetic regulatory networks from seed genes
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1241-1247; doi:10.1093/bioinformatics/bth074 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

H. Shmuely, E. Dinitz, I. Dahan, J. Eichler, D. Fischer, and B. Shaanan

Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1248-1253; doi:10.1093/bioinformatics/bth075 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Viatcheslav R. Akmaev and Clarence J. Wang

Correction of sequence-based artifacts in serial analysis of gene expression
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1254-1263; doi:10.1093/bioinformatics/bth077 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E. Schein, Heesun Shin, and Marco A. Marra

Automated ordering of fingerprinted clones
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1264-1271; doi:10.1093/bioinformatics/bth079 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Keira Curtis and Martin D. Brand

Analysing microarray data using modular regulation analysis
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1272-1284; doi:10.1093/bioinformatics/bth082 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, and Tamar Schlick

RAG: RNA-As-Graphs database—concepts, analysis, and features
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1285-1291; doi:10.1093/bioinformatics/bth084 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yu-Dong Cai and Andrew J. Doig

Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1292-1300; doi:10.1093/bioinformatics/bth085 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert C. Edgar and Kimmen Sjölander

A comparison of scoring functions for protein sequence profile alignment
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1301-1308; doi:10.1093/bioinformatics/bth090 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert C. Edgar and Kimmen Sjölander

COACH: profile–profile alignment of protein families using hidden Markov models
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1309-1318; doi:10.1093/bioinformatics/bth091 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Mandar Chitre, Zhu Hao, and Kishore Sakharkar

Cellware—a multi-algorithmic software for computational systems biology
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1319-1321; doi:10.1093/bioinformatics/bth067 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, and Nir Ben-Tal

ConSeq: the identification of functionally and structurally important residues in protein sequences
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1322-1324; doi:10.1093/bioinformatics/bth070 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jing Hua Zhao

2LD, GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1325-1326; doi:10.1093/bioinformatics/bth071 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Line Olsen, Morten Hansen, Claus T. Ekstrøm, Jesper T. Troelsen, and Jørgen Olsen

CVD: the intestinal crypt/villus in situ hybridization database
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1327-1328; doi:10.1093/bioinformatics/bth072 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kengo Kinoshita and Haruki Nakamura

eF-site and PDBjViewer: database and viewer for protein functional sites
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1329-1330; doi:10.1093/bioinformatics/bth073 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Flavio Mignone, David S. Horner, and Graziano Pesole

WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1331-1333; doi:10.1093/bioinformatics/bth076 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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