Bioinformatics

EDITORIALS

Alfonso Valencia

PROTEIN REFINEMENT: A NEW CHALLENGE FOR CASP IN ITS 10TH ANNIVERSARY
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 277; doi:10.1093/bioinformatics/bti249 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Graham J. Etherington, Jo Dicks, and Ian N. Roberts

Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination
Bioinformatics Advance Access published on August 27, 2004
Bioinformatics 2005 21: 278-281; doi:10.1093/bioinformatics/bth500 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andrew E. Firth and Chris M. Brown

Detecting overlapping coding sequences with pairwise alignments
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 282-292; doi:10.1093/bioinformatics/bti007 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Daniel H. Haft, Jeremy D. Selengut, Lauren M. Brinkac, Nikhat Zafar, and Owen White

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 293-306; doi:10.1093/bioinformatics/bti015 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Dustin E. Schones, Pavel Sumazin, and Michael Q. Zhang

Similarity of position frequency matrices for transcription factor binding sites
Bioinformatics Advance Access published on August 19, 2004
Bioinformatics 2005 21: 307-313; doi:10.1093/bioinformatics/bth480 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Haiquan Li and Jinyan Li

Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 314-324; doi:10.1093/bioinformatics/bti019 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Anders Andersson, Rolf Bernander, and Peter Nilsson

Dual-genome primer design for construction of DNA microarrays
Bioinformatics Advance Access published on August 27, 2004
Bioinformatics 2005 21: 325-332; doi:10.1093/bioinformatics/bti001 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Juan M. Gonzalez, Johannes Zimmermann, and Cesareo Saiz-Jimenez

Evaluating putative chimeric sequences from PCR-amplified products
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 333-337; doi:10.1093/bioinformatics/bti008 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Luca Ferrarini, Luca Bertelli, Jacob Feala, Andrew D. McCulloch, and Giovanni Paternostro

A more efficient search strategy for aging genes based on connectivity
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 338-348; doi:10.1093/bioinformatics/bti004 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Matthew J. Beal, Francesco Falciani, Zoubin Ghahramani, Claudia Rangel, and David L. Wild

A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
Bioinformatics Advance Access published on September 7, 2004
Bioinformatics 2005 21: 349-356; doi:10.1093/bioinformatics/bti014 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Antti Pettinen, Tommi Aho, Olli-Pekka Smolander, Tiina Manninen, Antti Saarinen, Kaisa-Leena Taattola, Olli Yli-Harja, and Marja-Leena Linne

Simulation tools for biochemical networks: evaluation of performance and usability
Bioinformatics Advance Access published on September 9, 2004
Bioinformatics 2005 21: 357-363; doi:10.1093/bioinformatics/bti018 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Vicente Arnau, Sergio Mars, and Ignacio Marín

Iterative Cluster Analysis of Protein Interaction Data
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 364-378; doi:10.1093/bioinformatics/bti021 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

Get checked abstract Carla Kuiken, Karina Yusim, Laura Boykin, and Russell Richardson

The Los Alamos hepatitis C sequence database
Bioinformatics Advance Access published on September 17, 2004
Bioinformatics 2005 21: 379-384; doi:10.1093/bioinformatics/bth485 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Stefan Weckx, Peter De Rijk, Christine Van Broeckhoven, and Jurgen Del-Favero

SNPbox: a modular software package for large-scale primer design
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 385-387; doi:10.1093/bioinformatics/bti006 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Madelaine Marchin, Paul T. Kelly, and Jianwen Fang

Tracker: continuous HMMER and BLAST searching
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 388-389; doi:10.1093/bioinformatics/bti012 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS

Get checked abstract C. J. Creevey and J. O. McInerney

Clann: investigating phylogenetic information through supertree analyses
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 390-392; doi:10.1093/bioinformatics/bti020 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Paolo Fontana, Eckart Bindewald, Stefano Toppo, Riccardo Velasco, Giorgio Valle, and Silvio C. E. Tosatto

The SSEA server for protein secondary structure alignment
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 393-395; doi:10.1093/bioinformatics/bti013 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Tomaz Curk, Janez Demsar, Qikai Xu, Gregor Leban, Uros Petrovic, Ivan Bratko, Gad Shaulsky, and Blaz Zupan

Microarray data mining with visual programming
Bioinformatics Advance Access published on August 12, 2004
Bioinformatics 2005 21: 396-398; doi:10.1093/bioinformatics/bth474 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xiaoyun Tang, Lishuang Shen, and Julie A. Dickerson

BarleyExpress: a web-based submission tool for enriched microarray database annotations
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 399-401; doi:10.1093/bioinformatics/bti002 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Eric W. Price and Ignazio Carbone

SNAP: workbench management tool for evolutionary population genetic analysis
Bioinformatics Advance Access published on September 7, 2004
Bioinformatics 2005 21: 402-404; doi:10.1093/bioinformatics/bti003 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Tom H. Lindner and K. Hoffmann

easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses
Bioinformatics Advance Access published on September 3, 2004
Bioinformatics 2005 21: 405-407; doi:10.1093/bioinformatics/bti009 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ian Bradford, Robin Winter, Carl Evans, and Jonathan Bard

Human–Mouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databases
Bioinformatics Advance Access published on September 9, 2004
Bioinformatics 2005 21: 408-409; doi:10.1093/bioinformatics/bti017 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Robert D. Finn, Mhairi Marshall, and Alex Bateman

iPfam: visualization of protein–protein interactions in PDB at domain and amino acid resolutions
Bioinformatics Advance Access published on September 7, 2004
Bioinformatics 2005 21: 410-412; doi:10.1093/bioinformatics/bti011 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Gregor Leban, Ivan Bratko, Uros Petrovic, Tomaz Curk, and Blaz Zupan

VizRank: finding informative data projections in functional genomics by machine learning
Bioinformatics Advance Access published on September 9, 2004
Bioinformatics 2005 21: 413-414; doi:10.1093/bioinformatics/bti016 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

Get checked abstract Daniel Shegogue and W. Jim Zheng

Capturing biological information with class–responsibility–collaboration cards
Bioinformatics Advance Access published on September 7, 2004
Bioinformatics 2005 21: 415-417; doi:10.1093/bioinformatics/bti005 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Abdullah Kahraman, Andrey Avramov, Lyubomir G. Nashev, Dimitar Popov, Rainer Ternes, Hans-Dieter Pohlenz, and Bertram Weiss

PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 418-420; doi:10.1093/bioinformatics/bti010 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Yong Wang and Frederick C. C. Leung

Erratum
Bioinformatics 2005 21: 421; doi:10.1093/bioinformatics/bti265 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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