Bioinformatics

ORIGINAL PAPERS:

Niranjan Nagarajan and Golan Yona

Automatic prediction of protein domains from sequence information using a hybrid learning system
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1335-1360; doi:10.1093/bioinformatics/bth086 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Rangel, John Angus, Zoubin Ghahramani, Maria Lioumi, Elizabeth Sotheran, Alessia Gaiba, David L. Wild, and Francesco Falciani

Modeling T-cell activation using gene expression profiling and state-space models
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1361-1372; doi:10.1093/bioinformatics/bth093 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Andreini, Ivano Bertini, and Antonio Rosato

A hint to search for metalloproteins in gene banks
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1373-1380; doi:10.1093/bioinformatics/bth095 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Gerhard Kauer and Helmut Blöcker

Analysis of disturbed images
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1381-1387; doi:10.1093/bioinformatics/bth099 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, and Ole Lund

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1388-1397; doi:10.1093/bioinformatics/bth100 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley, and Mark Blaxter

PartiGene—constructing partial genomes
Bioinformatics Advance Access published on February 26, 2004
Bioinformatics 2004 20: 1398-1404; doi:10.1093/bioinformatics/bth101 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Deepak Sharma, Biju Issac, G. P. S. Raghava, and R. Ramaswamy

Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1405-1412; doi:10.1093/bioinformatics/bth103 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Phuong-Van Luc and Paul Tempst

PINdb: a database of nuclear protein complexes from human and yeast
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 1413-1415; doi:10.1093/bioinformatics/bth114 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jeffrey Yuan, Bruce Bush, Alex Elbrecht, Yuan Liu, Theresa Zhang, Wenqing Zhao, and Richard Blevins

Enhanced homology searching through genome reading frame predetermination
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1416-1427; doi:10.1093/bioinformatics/bth115 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ivo Van Walle, Ignace Lasters, and Lode Wyns

Align-m—a new algorithm for multiple alignment of highly divergent sequences
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1428-1435; doi:10.1093/bioinformatics/bth116 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

James J. Chen, Robert R. Delongchamp, Chen-An Tsai, Huey-miin Hsueh, Frank Sistare, Karol L. Thompson, Varsha G. Desai, and James C. Fuscoe

Analysis of variance components in gene expression data
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1436-1446; doi:10.1093/bioinformatics/bth118 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Henrik Nilsson, Karl-Henrik Larsson, and Björn M. Ursing

galaxie—CGI scripts for sequence identification through automated phylogenetic analysis
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1447-1452; doi:10.1093/bioinformatics/bth119 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

M.J.L. de Hoon, S. Imoto, J. Nolan, and S. Miyano

Open source clustering software
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1453-1454; doi:10.1093/bioinformatics/bth078 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nizar N. Batada

CNplot: visualizing pre-clustered networks
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1455-1456; doi:10.1093/bioinformatics/bth080 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Vered Chalifa-Caspi, Itai Yanai, Ron Ophir, Naomi Rosen, Michael Shmoish, Hila Benjamin-Rodrig, Maxim Shklar, Tsippi Iny Stein, Orit Shmueli, Marilyn Safran, and Doron Lancet

GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1457-1458; doi:10.1093/bioinformatics/bth081 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Schmollinger, I. Fischer, C. Nerz, S. Pinkenburg, F. Götz, M. Kaufmann, K.-J. Lange, R. Reuter, W. Rosenstiel, and A. Zell

ParSeq: searching motifs with structural and biochemical properties
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1459-1461; doi:10.1093/bioinformatics/bth083 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jill Cheng, Shaw Sun, Adam Tracy, Earl Hubbell, Joseph Morris, Venu Valmeekam, Andrew Kimbrough, Melissa S. Cline, Guoying Liu, Ron Shigeta, David Kulp, and Michael A. Siani-Rose

NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1462-1463; doi:10.1093/bioinformatics/bth087 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tim Beißbarth and Terence P. Speed

GOstat: find statistically overrepresented Gene Ontologies within a group of genes
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1464-1465; doi:10.1093/bioinformatics/bth088 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robertson Craig and Ronald C. Beavis

TANDEM: matching proteins with tandem mass spectra
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1466-1467; doi:10.1093/bioinformatics/bth092 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Martin C. Frith, Anason S. Halees, Ulla Hansen, and Zhiping Weng

Site2genome: locating short DNA sequences in whole genomes
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1468-1469; doi:10.1093/bioinformatics/bth094 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Daniel Hanisch, Florian Sohler, and Ralf Zimmer

ToPNet—an application for interactive analysis of expression data and biological networks
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1470-1471; doi:10.1093/bioinformatics/bth096 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

G. Pavesi, G. Mauri, F. Iannelli, C. Gissi, and G. Pesole

GeneSyn: a tool for detecting conserved gene order across genomes
Bioinformatics Advance Access published on February 19, 2004
Bioinformatics 2004 20: 1472-1474; doi:10.1093/bioinformatics/bth102 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andrew J. Robinson, Christopher G. Love, Jacqueline Batley, Gary Barker, and David Edwards

Simple sequence repeat marker loci discovery using SSR primer
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1475-1476; doi:10.1093/bioinformatics/bth104 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chengpeng Bi and Craig J. Benham

WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 1477-1479; doi:10.1093/bioinformatics/bth304 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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