Bioinformatics

ORIGINAL PAPERS:

Brian Marsden and Ruben Abagyan

SAD—a normalized structural alignment database: improving sequence–structure alignments
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2333-2344; doi:10.1093/bioinformatics/bth244 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ruxandra I. Dima and D. Thirumalai

Proteins associated with diseases show enhanced sequence correlation between charged residues
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2345-2354; doi:10.1093/bioinformatics/bth245 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Charles Semple, Philip Daniel, Wim Hordijk, Roderic D.M. Page, and Mike Steel

Supertree algorithms for ancestral divergence dates and nested taxa
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2355-2360; doi:10.1093/bioinformatics/bth246 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Neil F. W. Saunders, Paul M. G. Curmi, and Ricardo Cavicchioli

An online database for the detection of novel archaeal sequences in human ESTs
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2361-2362; doi:10.1093/bioinformatics/bth249 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jukka Corander, Patrik Waldmann, Pekka Marttinen, and Mikko J. Sillanpää

BAPS 2: enhanced possibilities for the analysis of genetic population structure
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2363-2369; doi:10.1093/bioinformatics/bth250 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

N. Simonis, S. J. Wodak, G. N. Cohen, and J. van Helden

Combining pattern discovery and discriminant analysis to predict gene co-regulation
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2370-2379; doi:10.1093/bioinformatics/bth252 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ricardo Núñez Miguel

Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2380-2389; doi:10.1093/bioinformatics/bth255 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yan Zhang, David A. Eberhard, Gretchen D. Frantz, Patrick Dowd, Thomas D. Wu, Yan Zhou, Colin Watanabe, Shiuh-Ming Luoh, Paul Polakis, Kenneth J. Hillan, William I. Wood, and Zemin Zhang

GEPIS—quantitative gene expression profiling in normal and cancer tissues
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2390-2398; doi:10.1093/bioinformatics/bth256 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Paul C. Boutros and Allan B. Okey

PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2399-2400; doi:10.1093/bioinformatics/bth257 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan M. Keith, Peter Adams, Darryn Bryant, Duncan A. E. Cochran, Gita H. Lala, and Keith R. Mitchelson

Algorithms for sequence analysis via mutagenesis
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2401-2410; doi:10.1093/bioinformatics/bth258 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jyrki P. Kukkonen

Explicit formulation of different receptor–G-protein interactions and effector regulation
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2411-2420; doi:10.1093/bioinformatics/bth263 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yuriy Fofanov, Yi Luo, Charles Katili, Jim Wang, Yuri Belosludtsev, Thomas Powdrill, Chetan Belapurkar, Viacheslav Fofanov, Tong-Bin Li, Sergey Chumakov, and B. Montgomery Pettitt

How independent are the appearances of n-mers in different genomes?
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2421-2428; doi:10.1093/bioinformatics/bth266 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tao Li, Chengliang Zhang, and Mitsunori Ogihara

A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2429-2437; doi:10.1093/bioinformatics/bth267 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jeroen J. Jansen, Huub C. J. Hoefsloot, Hans F. M. Boelens, Jan van der Greef, and Age K. Smilde

Analysis of longitudinal metabolomics data
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2438-2446; doi:10.1093/bioinformatics/bth268 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Scholz, S. Gatzek, A. Sterling, O. Fiehn, and J. Selbig

Metabolite fingerprinting: detecting biological features by independent component analysis
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2447-2454; doi:10.1093/bioinformatics/bth270 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

José M. Fernández and Alfonso Valencia

YAdumper: extracting and translating large information volumes from relational databases to structured flat files
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2455-2457; doi:10.1093/bioinformatics/bth243 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jan K. Rainey and M. Cynthia Goh

An interactive triple-helical collagen builder
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2458-2459; doi:10.1093/bioinformatics/bth247 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Aleksey A. Porollo, Rafal Adamczak, and Jaroslaw Meller

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2460-2462; doi:10.1093/bioinformatics/bth248 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kevin L. Garwood, Chris F. Taylor, Kai J. Runte, Andy Brass, Stephen G. Oliver, and Norman W. Paton

Pedro: a configurable data entry tool for XML
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2463-2465; doi:10.1093/bioinformatics/bth251 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong, and Jong Park

HPID: The Human Protein Interaction Database
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2466-2470; doi:10.1093/bioinformatics/bth253 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Owen J. Marshall

PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2471-2472; doi:10.1093/bioinformatics/bth254 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jiren Wang, Kuo-Bin Li, and Wing-Kin Sung

G-PRIMER: greedy algorithm for selecting minimal primer set
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2473-2475; doi:10.1093/bioinformatics/bth259 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Seán I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, and Karsten Fries

The SRS 3D module: integrating structures, sequences and features
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2476-2478; doi:10.1093/bioinformatics/bth260 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Eibe Frank, Mark Hall, Len Trigg, Geoffrey Holmes, and Ian H. Witten

Data mining in bioinformatics using Weka
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2479-2481; doi:10.1093/bioinformatics/bth261 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Daniel Fischer, Jakub Pas, and Leszek Rychlewski

The PDB-Preview database: a repository of in-silico models of ‘on-hold’ PDB entries
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2482-2484; doi:10.1093/bioinformatics/bth262 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Guillaume Laval and Laurent Excoffier

SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2485-2487; doi:10.1093/bioinformatics/bth264 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alistair M. Chalk, Martin Wennerberg, and Erik L. L. Sonnhammer

Sfixem—graphical sequence feature display in Java
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2488-2490; doi:10.1093/bioinformatics/bth265 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alexander G. Williams and Robert W. Williams

GenomeMixer: a complex genetic cross simulator
Bioinformatics 2004 20: 2491-2492; doi:10.1093/bioinformatics/bth269 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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