Bioinformatics

C. Sander

The Journal Bioinformatics, key medium for computational biology
Bioinformatics 2002 18: 1-2; doi:10.1093/bioinformatics/18.1.1 [Print PDF][Screen PDF] [Request Permissions]  

James K. Bonfield and Rodger Staden

ZTR: a new format for DNA sequence trace data
Bioinformatics 2002 18: 3-10; doi:10.1093/bioinformatics/18.1.3 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Trond H. Bø, Inge Jonassen, Ingvar Eidhammer, and Carsten Helgesen

A fast top–down method for constructing reliable radiation hybrid frameworks
Bioinformatics 2002 18: 11-18; doi:10.1093/bioinformatics/18.1.11 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Vladimir Pavlovic, Ashutosh Garg, and Simon Kasif

A Bayesian framework for combining gene predictions
Bioinformatics 2002 18: 19-27; doi:10.1093/bioinformatics/18.1.19 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jirí Macas, Tibor Mészáros, and Marcela Nouzová

PlantSat: a specialized database for plant satellite repeats
Bioinformatics 2002 18: 28-35; doi:10.1093/bioinformatics/18.1.28 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Bernhard Haubold and Thomas Wiehe

Calculating the SNP-effective sample size from an alignment
Bioinformatics 2002 18: 36-38; doi:10.1093/bioinformatics/18.1.36 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Danh V. Nguyen and David M. Rocke

Tumor classification by partial least squares using microarray gene expression data
Bioinformatics 2002 18: 39-50; doi:10.1093/bioinformatics/18.1.39 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wolfram Liebermeister

Linear modes of gene expression determined by independent component analysis
Bioinformatics 2002 18: 51-60; doi:10.1093/bioinformatics/18.1.51 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Sásik, N. Iranfar, T. Hwa, and W. F. Loomis

Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development
Bioinformatics 2002 18: 61-66; doi:10.1093/bioinformatics/18.1.61 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Christian Siehs, Rainer Oberbauer, Gert Mayer, Arno Lukas, and Bernd Mayer

Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase
Bioinformatics 2002 18: 67-76; doi:10.1093/bioinformatics/18.1.67 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Weizhong Li, Lukasz Jaroszewski, and Adam Godzik

Tolerating some redundancy significantly speeds up clustering of large protein databases
Bioinformatics 2002 18: 77-82; doi:10.1093/bioinformatics/18.1.77 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Philip J. Cotter, Daniel R. Caffrey, and Denis C. Shields

Improved database searches for orthologous sequences by conditioning on outgroup sequences
Bioinformatics 2002 18: 83-91; doi:10.1093/bioinformatics/18.1.83 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Christian E. V. Storm and Erik L. L. Sonnhammer

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
Bioinformatics 2002 18: 92-99; doi:10.1093/bioinformatics/18.1.92 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gary W. Stuart, Karen Moffett, and Steve Baker

Integrated gene and species phylogenies from unaligned whole genome protein sequences
Bioinformatics 2002 18: 100-108; doi:10.1093/bioinformatics/18.1.100 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ursula Rost and Erich Bornberg-Bauer

TreeWiz: interactive exploration of huge trees
Bioinformatics 2002 18: 109-114; doi:10.1093/bioinformatics/18.1.109 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tae-Kun Seo, Jeffrey L. Thorne, Masami Hasegawa, and Hirohisa Kishino

A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
Bioinformatics 2002 18: 115-123; doi:10.1093/bioinformatics/18.1.115 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Goesmann, Martin Haubrock, Folker Meyer, Jörn Kalinowski, and Robert Giegerich

PathFinder: reconstruction and dynamic visualization of metabolic pathways
Bioinformatics 2002 18: 124-129; doi:10.1093/bioinformatics/18.1.124 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xi Chen, Yuhmei Lin, Ming Liu, and Michael K. Gilson

The Binding Database: data management and interface design
Bioinformatics 2002 18: 130-139; doi:10.1093/bioinformatics/18.1.130 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hiroshi Nagata, Hiroshi Mizushima, and Hiroshi Tanaka

Concept and prototype of protein–ligand docking simulator with force feedback technology
Bioinformatics 2002 18: 140-146; doi:10.1093/bioinformatics/18.1.140 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Rachel Karchin, Kevin Karplus, and David Haussler

Classifying G-protein coupled receptors with support vector machines
Bioinformatics 2002 18: 147-159; doi:10.1093/bioinformatics/18.1.147 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Amanda Clare and Ross D. King

Machine learning of functional class from phenotype data
Bioinformatics 2002 18: 160-166; doi:10.1093/bioinformatics/18.1.160 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

S. Dietmann and C. Frömmel

Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks
Bioinformatics 2002 18: 167-174; doi:10.1093/bioinformatics/18.1.167 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lee C. Allcorn and Andrew C. R. Martin

SACS—Self-maintaining database of antibody crystal structure information
Bioinformatics 2002 18: 175-181; doi:10.1093/bioinformatics/18.1.175 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Darrell Conklin, Inge Jonassen, Rein Aasland, and William R. Taylor

Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences
Bioinformatics 2002 18: 182-189; doi:10.1093/bioinformatics/18.1.182 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Edouard Yeramian, Serge Bonnefoy, and Gordon Langsley

Physics-based gene identification: proof of concept for Plasmodium falciparum
Bioinformatics 2002 18: 190-193; doi:10.1093/bioinformatics/18.1.190 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

James K. Bonfield, Kathryn F. Beal, Matthew J. Betts, and Rodger Staden

Trev: a DNA trace editor and viewer
Bioinformatics 2002 18: 194-195; doi:10.1093/bioinformatics/18.1.194 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Biju Issac, Harpreet Singh, Harpreet Kaur, and G. P. S. Raghava

Locating probable genes using Fourier transform approach
Bioinformatics 2002 18: 196-197; doi:10.1093/bioinformatics/18.1.196 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Vladimir B. Bajic, Seng Hong Seah, Allen Chong, Guanglan Zhang, Judice L. Y. Koh, and Vladimir Brusic

Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters
Bioinformatics 2002 18: 198-199; doi:10.1093/bioinformatics/18.1.198 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ashley C. Stuart, Valentin A. Ilyin, and Andrej Sali

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures
Bioinformatics 2002 18: 200-201; doi:10.1093/bioinformatics/18.1.200 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Scott Chapman, Peer Schenk, Kemal Kazan, and John Manners

Using biplots to interpret gene expression patterns in plants
Bioinformatics 2002 18: 202-204; doi:10.1093/bioinformatics/18.1.202 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Daniel R. Rhodes, Jeremy C. Miller, Brian B. Haab, and Kyle A. Furge

CIT: identification of differentially expressed clusters of genes from microarray data
Bioinformatics 2002 18: 205-206; doi:10.1093/bioinformatics/18.1.205 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Sturn, John Quackenbush, and Zlatko Trajanoski

Genesis: cluster analysis of microarray data
Bioinformatics 2002 18: 207-208; doi:10.1093/bioinformatics/18.1.207 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. Hofmann and A. Wlodawer

PCSB—a program collection for structural biology and biophysical chemistry
Bioinformatics 2002 18: 209-210; doi:10.1093/bioinformatics/18.1.209 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

A. Lobley, L. Whitmore, and B. A. Wallace

DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra
Bioinformatics 2002 18: 211-212; doi:10.1093/bioinformatics/18.1.211 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Christophe Combet, Martin Jambon, Gilbert Deléage, and Christophe Geourjon

Geno3D: automatic comparative molecular modelling of protein
Bioinformatics 2002 18: 213-214; doi:10.1093/bioinformatics/18.1.213 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D. R. Forsdyke

Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia
Bioinformatics 2002 18: 215-217; doi:10.1093/bioinformatics/18.1.215 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Steffen Möller, Michael D. R. Croning, and Rolf Apweiler

Evaluation of methods for the prediction of membrane spanning regions
Bioinformatics 2002 18: 218; doi:10.1093/bioinformatics/18.1.218 [Print PDF][Screen PDF] [Request Permissions]  

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