Bioinformatics

ORIGINAL PAPERS:

Lugang Li, Renchao Jin, Poh-Lin Kok, and Honghui Wan

Pseudo-periodic partitions of biological sequences
Bioinformatics 2004 20: 295-306; doi:10.1093/bioinformatics/btg404 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, and Rafael A. Irizarry

affy—analysis of Affymetrix GeneChip data at the probe level
Bioinformatics 2004 20: 307-315; doi:10.1093/bioinformatics/btg405 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Thomas R. Kiehl, Robert M. Mattheyses, and Melvin K. Simmons

Hybrid simulation of cellular behavior
Bioinformatics 2004 20: 316-322; doi:10.1093/bioinformatics/btg409 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Leslie M. Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, and Terence P. Speed

A benchmark for Affymetrix GeneChip expression measures
Bioinformatics 2004 20: 323-331; doi:10.1093/bioinformatics/btg410 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Y. Luan and H. Li

Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data
Bioinformatics 2004 20: 332-339; doi:10.1093/bioinformatics/btg413 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

N. Przulj, D.A. Wigle, and I. Jurisica

Functional topology in a network of protein interactions
Bioinformatics 2004 20: 340-348; doi:10.1093/bioinformatics/btg415 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, and R. Cetin-Atalay

An ontology for collaborative construction and analysis of cellular pathways
Bioinformatics 2004 20: 349-356; doi:10.1093/bioinformatics/btg416 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zoltan Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip Butcher, Jason Hinds, Kwang-Hyun Cho, and Olaf Wolkenhauer

Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis
Bioinformatics 2004 20: 357-363; doi:10.1093/bioinformatics/btg417 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jeanne Kowalski, Charles Drake, Ronald H. Schwartz, and Jonathan Powell

Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes
Bioinformatics 2004 20: 364-373; doi:10.1093/bioinformatics/btg418 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ulisses M. Braga-Neto and Edward R. Dougherty

Is cross-validation valid for small-sample microarray classification?
Bioinformatics 2004 20: 374-380; doi:10.1093/bioinformatics/btg419 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sung Geun Lee, Jung Uk Hur, and Yang Seok Kim

A graph-theoretic modeling on GO space for biological interpretation of gene clusters
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 381-388; doi:10.1093/bioinformatics/btg420 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, and Harold R. Garner

Knowledge discovery by automated identification and ranking of implicit relationships
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 389-398; doi:10.1093/bioinformatics/btg421 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jacques van Helden

Metrics for comparing regulatory sequences on the basis of pattern counts
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 399-406; doi:10.1093/bioinformatics/btg425 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, and Fredrik Ronquist

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 407-415; doi:10.1093/bioinformatics/btg427 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Mikael Thollesson

LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 416-418; doi:10.1093/bioinformatics/btg422 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Matthew J. Wood and Jonathan D. Hirst

Predicting protein secondary structure by cascade-correlation neural networks
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 419-420; doi:10.1093/bioinformatics/btg423 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Manoj Bhasin and G. P. S. Raghava

SVM based method for predicting HLA-DRB1^*0401 binding peptides in an antigen sequence
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 421-423; doi:10.1093/bioinformatics/btg424 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nir Orlev, Ron Shamir, and Yosef Shiloh

PIVOT: Protein Interacions VisualizatiOn Tool
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 424-425; doi:10.1093/bioinformatics/btg426 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michele Clamp, James Cuff, Stephen M. Searle, and Geoffrey J. Barton

The Jalview Java alignment editor
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 426-427; doi:10.1093/bioinformatics/btg430 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Henrik Hornshøj, Henrik Stengaard, Frank Panitz, and Christian Bendixen

SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target T_m algorithm for reducing cross-hybridization in microarray gene expression experiments
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 428-429; doi:10.1093/bioinformatics/btg434 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Natasha Levenkova, Qingjuan Gu, and John J. Rux

Gene specific siRNA selector
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 430-432; doi:10.1093/bioinformatics/btg437 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michael Spitzer, Georg Fuellen, Paul Cullen, and Stefan Lorkowski

VisCoSe: visualization and comparison of consensus sequences
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 433-435; doi:10.1093/bioinformatics/btg444 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Susanna Lamers, Scott Beason, Luke Dunlap, Robert Compton, and Marco Salemi

HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 436-438; doi:10.1093/bioinformatics/btg445 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tu H. Nguyen, Chunyu Liu, Elliot S. Gershon, and Francis J. McMahon

Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 439-443; doi:10.1093/bioinformatics/btg446 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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