Bioinformatics

ORIGINAL PAPERS:

A. Carbone, A. Zinovyev, and F. Képès

Codon adaptation index as a measure of dominating codon bias
Bioinformatics 2003 19: 2005-2015; doi:10.1093/bioinformatics/btg272 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gerhard Kauer and Helmut Blöcker

Applying signal theory to the analysis of biomolecules
Bioinformatics 2003 19: 2016-2021; doi:10.1093/bioinformatics/btg273 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

H. Sanchez-Villeda, S. Schroeder, M. Polacco, M. McMullen, S. Havermann, G. Davis, I. Vroh-Bi, K. Cone, N. Sharopova, Y. Yim, L. Schultz, N. Duru, T. Musket, K. Houchins, Z. Fang, J. Gardiner, and E. Coe

Development of an integrated laboratory information management system for the maize mapping project
Bioinformatics 2003 19: 2022-2030; doi:10.1093/bioinformatics/btg274 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli Kallioniemi, and Outi Monni

A novel strategy for microarray quality control using Bayesian networks
Bioinformatics 2003 19: 2031-2038; doi:10.1093/bioinformatics/btg275 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jason Gertz, Georgiy Elfond, Anna Shustrova, Matt Weisinger, Matteo Pellegrini, Shawn Cokus, and Bruce Rothschild

Inferring protein interactions from phylogenetic distance matrices
Bioinformatics 2003 19: 2039-2045; doi:10.1093/bioinformatics/btg278 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Joshua M. Temkin and Mark R. Gilder

Extraction of protein interaction information from unstructured text using a context-free grammar
Bioinformatics 2003 19: 2046-2053; doi:10.1093/bioinformatics/btg279 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

S.P. Mielke and V.V. Krishnan

Protein structural class identification directly from NMR spectra using averaged chemical shifts
Bioinformatics 2003 19: 2054-2064; doi:10.1093/bioinformatics/btg280 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Marcel Smid, Lambert C.J. Dorssers, and Guido Jenster

Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes
Bioinformatics 2003 19: 2065-2071; doi:10.1093/bioinformatics/btg282 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xiaohong Huang and Wei Pan

Linear regression and two-class classification with gene expression data
Bioinformatics 2003 19: 2072-2078; doi:10.1093/bioinformatics/btg283 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Humberto González Díaz, Ronal Ramos de Armas, and Reinaldo Molina

Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 -RNA packaging region with drugs
Bioinformatics 2003 19: 2079-2087; doi:10.1093/bioinformatics/btg285 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shigeyuki Oba, Masa-aki Sato, Ichiro Takemasa, Morito Monden, Ken-ichi Matsubara, and Shin Ishii

A Bayesian missing value estimation method for gene expression profile data
Bioinformatics 2003 19: 2088-2096; doi:10.1093/bioinformatics/btg287 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jie Qin, Darrin P. Lewis, and William Stafford Noble

Kernel hierarchical gene clustering from microarray expression data
Bioinformatics 2003 19: 2097-2104; doi:10.1093/bioinformatics/btg288 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Z. Fang, K. Cone, H. Sanchez-Villeda, M. Polacco, M. McMullen, S. Schroeder, J. Gardiner, G. Davis, S. Havermann, Y. Yim, I. Vroh Bi, and E. Coe

iMap: a database-driven utility to integrate and access the genetic and physical maps of maize
Bioinformatics 2003 19: 2105-2111; doi:10.1093/bioinformatics/btg289 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kristian Rother, Robert Preissner, Andrean Goede, and Cornelius Frömmel

Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins
Bioinformatics 2003 19: 2112-2121; doi:10.1093/bioinformatics/btg292 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hasan H. Otu and Khalid Sayood

A new sequence distance measure for phylogenetic tree construction
Bioinformatics 2003 19: 2122-2130; doi:10.1093/bioinformatics/btg295 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Arthur L. Hsu, Sen-Lin Tang, and Saman K. Halgamuge

An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data
Bioinformatics 2003 19: 2131-2140; doi:10.1093/bioinformatics/btg296 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Mark Harris, Jeremy M. R. Martin, John F. Peden, and Christopher J. Rawlings

SNP cherry picker: maximizing the chance of finding an association with a disease SNP
Bioinformatics 2003 19: 2141-2143; doi:10.1093/bioinformatics/btg258 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dong-Yup Lee, Hongsoek Yun, Sunwon Park, and Sang Yup Lee

MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis
Bioinformatics 2003 19: 2144-2146; doi:10.1093/bioinformatics/btg271 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Keyue Ding, Kaixin Zhou, Fuchu He, and Yan Shen

LDA—a java-based linkage disequilibrium analyzer
Bioinformatics 2003 19: 2147-2148; doi:10.1093/bioinformatics/btg276 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Aubrey Hill and Helen Kim

The UAB Proteomics Database
Bioinformatics 2003 19: 2149-2151; doi:10.1093/bioinformatics/btg281 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kamyar Farahi, William B. Whitman, and Eileen T. Kraemer

RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events
Bioinformatics 2003 19: 2152-2154; doi:10.1093/bioinformatics/btg284 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Nikitin, Sergei Egorov, Nikolai Daraselia, and Ilya Mazo

Pathway studio—the analysis and navigation of molecular networks
Bioinformatics 2003 19: 2155-2157; doi:10.1093/bioinformatics/btg290 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Luis A. Martínez-Cruz, Angel Rubio, María L. Martínez-Chantar, Alberto Labarga, Isabel Barrio, Adam Podhorski, Victor Segura, José L. Sevilla Campo, Matías A. Avila, and Jose M. Mato

GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data
Bioinformatics 2003 19: 2158-2160; doi:10.1093/bioinformatics/btg291 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Bairong Shen and Mauno Vihinen

RankViaContact: ranking and visualization of amino acid contacts
Bioinformatics 2003 19: 2161-2162; doi:10.1093/bioinformatics/btg293 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gianluigi Cardinali, Francesco Maraziti, and Sabrina Selvi

Electrophoretic data classification for phylogenetics and biostatistics
Bioinformatics 2003 19: 2163-2165; doi:10.1093/bioinformatics/btg294 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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