Bioinformatics

EDITORIALS:

Alex Bateman and Alfonso Valencia

An update from the Bioinformatics Editors
Bioinformatics 2005 21: 4319; doi:10.1093/bioinformatics/bti768 [Extract] [Full Text] [Print PDF] [Request Permissions]  

LETTER TO THE EDITOR:

Steven L. Salzberg and James A. Yorke

Beware of mis-assembled genomes
Bioinformatics 2005 21: 4320-4321; doi:10.1093/bioinformatics/bti769 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Pernille Nielsen and Anders Krogh

Large-scale prokaryotic gene prediction and comparison to genome annotation
Bioinformatics Advance Access published on October 25, 2005
Bioinformatics 2005 21: 4322-4329; doi:10.1093/bioinformatics/bti701 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

PHYLOGENETICS:

GENE EXPRESSION:

Get checked abstract Shuangge Ma and Jian Huang

Regularized ROC method for disease classification and biomarker selection with microarray data
Bioinformatics Advance Access published on October 18, 2005
Bioinformatics 2005 21: 4356-4362; doi:10.1093/bioinformatics/bti724 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fumihito Miura, Chihiro Uematsu, Yoshiyuki Sakaki, and Takashi Ito

A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences
Bioinformatics Advance Access published on October 18, 2005
Bioinformatics 2005 21: 4363-4370; doi:10.1093/bioinformatics/bti716 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Ezgi O. Booth, Nancy Van Driessche, Olga Zhuchenko, Adam Kuspa, and Gad Shaulsky

Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes
Bioinformatics Advance Access published on October 18, 2005
Bioinformatics 2005 21: 4371-4377; doi:10.1093/bioinformatics/bti726 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Shu-Dong Zhang and Timothy W. Gant

Effect of pooling samples on the efficiency of comparative studies using microarrays
Bioinformatics Advance Access published on October 18, 2005
Bioinformatics 2005 21: 4378-4383; doi:10.1093/bioinformatics/bti717 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Jing Li and Tao Jiang

Haplotype-based linkage disequilibrium mapping via direct data mining
Bioinformatics Advance Access published on October 25, 2005
Bioinformatics 2005 21: 4384-4393; doi:10.1093/bioinformatics/bti732 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Xue-Wen Chen and Mei Liu

Prediction of protein–protein interactions using random decision forest framework
Bioinformatics Advance Access published on October 18, 2005
Bioinformatics 2005 21: 4394-4400; doi:10.1093/bioinformatics/bti721 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Lena Strömbäck and Patrick Lambrix

Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
Bioinformatics Advance Access published on October 18, 2005
Bioinformatics 2005 21: 4401-4407; doi:10.1093/bioinformatics/bti718 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Timothy R. O'Connor, Curtis Dyreson, and John J. Wyrick

Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences
Bioinformatics Advance Access published on October 13, 2005
Bioinformatics 2005 21: 4411-4413; doi:10.1093/bioinformatics/bti714 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract James A. Smagala, Erica D. Dawson, Martin Mehlmann, Michael B. Townsend, Robert D. Kuchta, and Kathy L. Rowlen

ConFind: a robust tool for conserved sequence identification
Bioinformatics Advance Access published on October 20, 2005
Bioinformatics 2005 21: 4420-4422; doi:10.1093/bioinformatics/bti719 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Paul J. Planet and Indra Neil Sarkar

mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests
Bioinformatics Advance Access published on November 2, 2005
Bioinformatics 2005 21: 4423-4424; doi:10.1093/bioinformatics/bti744 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Fabian Birzele, Jan E. Gewehr, and Ralf Zimmer

QUASAR—scoring and ranking of sequence–structure alignments
Bioinformatics Advance Access published on October 10, 2005
Bioinformatics 2005 21: 4425-4426; doi:10.1093/bioinformatics/bti712 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Fabio Pardi, Douglas F. Levinson, and Cathryn M. Lewis

GSMA: software implementation of the genome search meta-analysis method
Bioinformatics Advance Access published on October 25, 2005
Bioinformatics 2005 21: 4430-4431; doi:10.1093/bioinformatics/bti725 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Sean D. Hooper and Peer Bork

Medusa: a simple tool for interaction graph analysis
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4432-4433; doi:10.1093/bioinformatics/bti696 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MIXING:

Erratum
Bioinformatics 2005 21: 4434; doi:10.1093/bioinformatics/bti758 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 4435; doi:10.1093/bioinformatics/bti777 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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