Bioinformatics

DISCOVERY NOTES:

Alexander E. Vinogradov

Silent DNA: speaking RNA language?
Bioinformatics 2003 19: 2167-2170; doi:10.1093/bioinformatics/btg320 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Mario Albrecht, Thomas Lengauer, and Stefan Schreiber

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
Bioinformatics 2003 19: 2171-2175; doi:10.1093/bioinformatics/btg370 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

REVIEWS:

Christos A. Ouzounis and Alfonso Valencia

Early bioinformatics: the birth of a discipline—a personal view
Bioinformatics 2003 19: 2176-2190; doi:10.1093/bioinformatics/btg309 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Vincent Thareau, Patrice Déhais, Carine Serizet, Pierre Hilson, Pierre Rouzé, and Sébastien Aubourg

Automatic design of gene-specific sequence tags for genome-wide functional studies
Bioinformatics 2003 19: 2191-2198; doi:10.1093/bioinformatics/btg286 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

V.G. Krishnan and D.R. Westhead

A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
Bioinformatics 2003 19: 2199-2209; doi:10.1093/bioinformatics/btg297 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Junbai Wang, Ola Myklebost, and Eivind Hovig

MGraph: graphical models for microarray data analysis
Bioinformatics 2003 19: 2210-2211; doi:10.1093/bioinformatics/btg298 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Anders Wallqvist, Alfred A. Rabow, Robert H. Shoemaker, Edward A. Sausville, and David G. Covell

Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data
Bioinformatics 2003 19: 2212-2224; doi:10.1093/bioinformatics/btg302 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ivan Erill, Marcos Escribano, Susana Campoy, and Jordi Barbé

In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon
Bioinformatics 2003 19: 2225-2236; doi:10.1093/bioinformatics/btg303 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lusheng Wang and Jianyun Zhao

Parametric alignment of ordered trees
Bioinformatics 2003 19: 2237-2245; doi:10.1093/bioinformatics/btg305 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

S. K. Shevade and S. S. Keerthi

A simple and efficient algorithm for gene selection using sparse logistic regression
Bioinformatics 2003 19: 2246-2253; doi:10.1093/bioinformatics/btg308 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Peter J. Giles and David Kipling

Normality of oligonucleotide microarray data and implications for parametric statistical analyses
Bioinformatics 2003 19: 2254-2262; doi:10.1093/bioinformatics/btg311 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

I.A. Doytchinova and D.R. Flower

Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction
Bioinformatics 2003 19: 2263-2270; doi:10.1093/bioinformatics/btg312 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dirk Husmeier

Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
Bioinformatics 2003 19: 2271-2282; doi:10.1093/bioinformatics/btg313 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Anthony L. Duran, Jian Yang, Liangjiang Wang, and Lloyd W. Sumner

Metabolomics spectral formatting, alignment and conversion tools (MSFACTs)
Bioinformatics 2003 19: 2283-2293; doi:10.1093/bioinformatics/btg315 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yuna Hou, Wynne Hsu, Mong Li Lee, and Christopher Bystroff

Efficient remote homology detection using local structure
Bioinformatics 2003 19: 2294-2301; doi:10.1093/bioinformatics/btg317 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xiaobo Zhou, Xiaodong Wang, and Edward R. Dougherty

Missing-value estimation using linear and non-linear regression with Bayesian gene selection
Bioinformatics 2003 19: 2302-2307; doi:10.1093/bioinformatics/btg323 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Thomas Hamelryck and Bernard Manderick

PDB file parser and structure class implemented in Python
Bioinformatics 2003 19: 2308-2310; doi:10.1093/bioinformatics/btg299 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yanming Yang and Li M. Fu

TSGDB: a database system for tumor suppressor genes
Bioinformatics 2003 19: 2311-2312; doi:10.1093/bioinformatics/btg300 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kim Carter and Matthew Bellgard

MASV—Multiple (BLAST) Annotation System Viewer
Bioinformatics 2003 19: 2313-2315; doi:10.1093/bioinformatics/btg301 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jason S. Iacovoni

GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome
Bioinformatics 2003 19: 2316-2318; doi:10.1093/bioinformatics/btg304 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. W. Matthiessen

BioWareDB: the biomedical software and database search engine
Bioinformatics 2003 19: 2319-2320; doi:10.1093/bioinformatics/btg306 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gabriel S. Eichler, Sui Huang, and Donald E. Ingber

Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles
Bioinformatics 2003 19: 2321-2322; doi:10.1093/bioinformatics/btg307 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hao Wang, Beng Chin Ooi, Kian-Lee Tan, Twee-Hee Ong, and Lei Zhou

BLAST++: BLASTing queries in batches
Bioinformatics 2003 19: 2323-2324; doi:10.1093/bioinformatics/btg310 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kevin Thornton

libsequence: a C++ class library for evolutionary genetic analysis
Bioinformatics 2003 19: 2325-2327; doi:10.1093/bioinformatics/btg316 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jorge García de la Nava, Sacha van Hijum, and Oswaldo Trelles

PreP: gene expression data pre-processing
Bioinformatics 2003 19: 2328-2329; doi:10.1093/bioinformatics/btg318 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Paul O. Lewis

NCL: a C++ class library for interpreting data files in NEXUS format
Bioinformatics 2003 19: 2330-2331; doi:10.1093/bioinformatics/btg319 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Carsten O. Daub, Sebastian Kloska, and Joachim Selbig

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data
Bioinformatics 2003 19: 2332-2333; doi:10.1093/bioinformatics/btg321 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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