Bioinformatics

CHIA PAPERS:

Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini

STRING: finding tandem repeats in DNA sequences
Bioinformatics 2003 19: 1733-1738; doi:10.1093/bioinformatics/btg268 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alessandro Marongiu, Paolo Palazzari, and Vittorio Rosato

Designing hardware for protein sequence analysis
Bioinformatics 2003 19: 1739-1740; doi:10.1093/bioinformatics/btg228 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Rebecca Thomson, T. Charles Hodgman, Zheng Rong Yang, and Austin K. Doyle

Characterizing proteolytic cleavage site activity using bio-basis function neural networks
Bioinformatics 2003 19: 1741-1747; doi:10.1093/bioinformatics/btg237 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andrew Harrison, Frances Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet Thornton, and Christine Orengo

Recognizing the fold of a protein structure
Bioinformatics 2003 19: 1748-1759; doi:10.1093/bioinformatics/btg240 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. Vinayagam, J. Shi, G. Pugalenthi, B. Meenakshi, T.L. Blundell, and R. Sowdhamini

DDBASE2.0: updated domain database with improved identification of structural domains
Bioinformatics 2003 19: 1760-1764; doi:10.1093/bioinformatics/btg233 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, and Zhiping Weng

Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules
Bioinformatics 2003 19: 1765-1772; doi:10.1093/bioinformatics/btg247 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lusheng Wang and Ying Xu

Haplotype inference by maximum parsimony
Bioinformatics 2003 19: 1773-1780; doi:10.1093/bioinformatics/btg239 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gábor Firneisz, Idit Zehavi, Csaba Vermes, Anita Hanyecz, Joshua A. Frieman, and Tibor T. Glant

Identification and quantification of disease-related gene clusters
Bioinformatics 2003 19: 1781-1786; doi:10.1093/bioinformatics/btg252 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Roded Sharan, Adi Maron-Katz, and Ron Shamir

CLICK and EXPANDER: a system for clustering and visualizing gene expression data
Bioinformatics 2003 19: 1787-1799; doi:10.1093/bioinformatics/btg232 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. M. Bagirov, B. Ferguson, S. Ivkovic, G. Saunders, and J. Yearwood

New algorithms for multi-class cancer diagnosis using tumor gene expression signatures
Bioinformatics 2003 19: 1800-1807; doi:10.1093/bioinformatics/btg238 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Steve W. Cole, Zoran Galic, and Jerome A. Zack

Controlling false-negative errors in microarray differential expression analysis: a PRIM approach
Bioinformatics 2003 19: 1808-1816; doi:10.1093/bioinformatics/btg242 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Sue C. Geller, Jeff P. Gregg, Paul Hagerman, and David M. Rocke

Transformation and normalization of oligonucleotide microarray data
Bioinformatics 2003 19: 1817-1823; doi:10.1093/bioinformatics/btg245 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Vitaly L. Galinsky

Automatic registration of microarray images. I. Rectangular grid
Bioinformatics 2003 19: 1824-1831; doi:10.1093/bioinformatics/btg259 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Vitaly L. Galinsky

Automatic registration of microarray images. II. Hexagonal grid
Bioinformatics 2003 19: 1832-1836; doi:10.1093/bioinformatics/btg260 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tim Carver and Alan Bleasby

The design of Jemboss: a graphical user interface to EMBOSS
Bioinformatics 2003 19: 1837-1843; doi:10.1093/bioinformatics/btg251 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Donny Tjandra, Stephen Wong, Weimin Shen, Brian Pulliam, Elaine Yu, and Laura Esserman

An XML message broker framework for exchange and integration of microarray data
Bioinformatics 2003 19: 1844-1845; doi:10.1093/bioinformatics/btg246 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

N. H. Shah, D. C. King, P. N. Shah, and N. V. Fedoroff

A tool-kit for cDNA microarray and promoter analysis
Bioinformatics 2003 19: 1846-1848; doi:10.1093/bioinformatics/btg253 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shandar Ahmad, M. Michael Gromiha, and Akinori Sarai

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences
Bioinformatics 2003 19: 1849-1851; doi:10.1093/bioinformatics/btg249 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alan A. Dombkowski

Disulfide by Design^TM: a computational method for the rational design of disulfide bonds in proteins
Bioinformatics 2003 19: 1852-1853; doi:10.1093/bioinformatics/btg231 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Fabien Campagne, Emmanuel Bettler, Gert Vriend, and Harel Weinstein

Batch mode generation of residue-based diagrams of proteins
Bioinformatics 2003 19: 1854-1855; doi:10.1093/bioinformatics/btg236 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dushyanthan Puvanendrampillai and John B. O. Mitchell

Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
Bioinformatics 2003 19: 1856-1857; doi:10.1093/bioinformatics/btg243 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sean D. Mooney and Russ B. Altman

MutDB: annotating human variation with functionally relevant data
Bioinformatics 2003 19: 1858-1860; doi:10.1093/bioinformatics/btg241 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Rasko Leinonen, Francesco Nardone, Olalekan Oyewole, Nicole Redaschi, and Peter Stoehr

The EMBL sequence version archive
Bioinformatics 2003 19: 1861-1862; doi:10.1093/bioinformatics/btg248 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jiren Wang and Qing Mu

Soap-HT-BLAST: high throughput BLAST based on Web services
Bioinformatics 2003 19: 1863-1864; doi:10.1093/bioinformatics/btg244 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David R. Mathog

Parallel BLAST on split databases
Bioinformatics 2003 19: 1865-1866; doi:10.1093/bioinformatics/btg250 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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