Bioinformatics

DISCOVERY NOTES:

Alex V. Kochetov and Akinori Sarai

Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 445-447; doi:10.1093/bioinformatics/btg443 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zoltán Gáspári, Csaba Ortutay, and András Perczel

A simple fold with variations: the pacifastin inhibitor family
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 448-451; doi:10.1093/bioinformatics/btg451 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

E. Manduchi, G. R. Grant, H. He, J. Liu, M. D. Mailman, A. D. Pizarro, P. L. Whetzel, and C. J. Stoeckert, Jr

RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 452-459; doi:10.1093/bioinformatics/btg428 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yue Huang and Ling Zhang

Rapid and sensitive dot-matrix methods for genome analysis
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 460-466; doi:10.1093/bioinformatics/btg429 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, and William Stafford Noble

Mismatch string kernels for discriminative protein classification
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 467-476; doi:10.1093/bioinformatics/btg431 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shandar Ahmad, M. Michael Gromiha, and Akinori Sarai

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 477-486; doi:10.1093/bioinformatics/btg432 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Daehee Hwang, George Stephanopoulos, and Christina Chan

Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 487-499; doi:10.1093/bioinformatics/btg433 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tzu-Ming Chu, B.S. Weir, and Russell D. Wolfinger

Comparison of Li–Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 500-506; doi:10.1093/bioinformatics/btg435 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tatiana V. Karpinets, Brent D. Foy, and John M. Frazier

Tailored gene array databases: applications in mechanistic toxicology
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 507-517; doi:10.1093/bioinformatics/btg436 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Neil D. Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, and Stephan Soullier

Reducing the variability in cDNA microarray image processing by Bayesian inference
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 518-526; doi:10.1093/bioinformatics/btg438 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Eytan Adar

SaRAD: a Simple and Robust Abbreviation Dictionary
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 527-533; doi:10.1093/bioinformatics/btg439 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Olivier Bastien, Jean-Christophe Aude, Sylvaine Roy, and Eric Maréchal

Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 534-537; doi:10.1093/bioinformatics/btg440 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kouichi Takahashi, Kazunari Kaizu, Bin Hu, and Masaru Tomita

A multi-algorithm, multi-timescale method for cell simulation
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 538-546; doi:10.1093/bioinformatics/btg442 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner

Predicting subcellular localization of proteins using machine-learned classifiers
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 547-556; doi:10.1093/bioinformatics/btg447 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Florence Horn, Anthony L. Lau, and Fred E. Cohen

Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 557-568; doi:10.1093/bioinformatics/btg449 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wen Xue, Jin Wang, Zhirong Shen, and Huaiqiu Zhu

Enrichment of transcriptional regulatory sites in non-coding genomic region
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 569-575; doi:10.1093/bioinformatics/btg450 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Sven Ekdahl and Erik L. L. Sonnhammer

ChromoWheel: a new spin on eukaryotic chromosome visualization
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 576-577; doi:10.1093/bioinformatics/btg448 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Fátima Al-Shahrour, Ramón Díaz-Uriarte, and Joaquín Dopazo

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 578-580; doi:10.1093/bioinformatics/btg455 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Soohyun Lee and Changwon Kang

CHOISS for selection of single nucleotide polymorphism markers on interval regularity
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 581-582; doi:10.1093/bioinformatics/btg458 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Giovanni Lavorgna, Luca Sessa, Alessandro Guffanti, Lelio Lassandro, and Giorgio Casari

AntiHunter: searching BLAST output for EST antisense transcripts
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 583-585; doi:10.1093/bioinformatics/btg460 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Paul Pavlidis, Ilan Wapinski, and William Stafford Noble

Support vector machine classification on the web
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 586-587; doi:10.1093/bioinformatics/btg461 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kevin Murphy, Towfique Raj, R. Scott Winters, and Peter S. White

me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 588-590; doi:10.1093/bioinformatics/btg466 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Marijke J. van Baren and Peter Heutink

The PCR Suite
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 591-593; doi:10.1093/bioinformatics/btg473 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kentaro Tomii and Yutaka Akiyama

FORTE: a profile–profile comparison tool for protein fold recognition
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 594-595; doi:10.1093/bioinformatics/btg474 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yukimitsu Yabuki, Yuri Mukai, Mark B. Swindells, and Makiko Suwa

GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 596-598; doi:10.1093/bioinformatics/btg478 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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