Bioinformatics

ORIGINAL PAPERS:

Johannes Hüsing, Michael Zeschnigk, Tanja Boes, and Karl-Heinz Jöckel

Combining DNA expression with positional information to detect functional silencing of chromosomal regions
Bioinformatics 2003 19: 2335-2342; doi:10.1093/bioinformatics/btg314 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

I. Landais, M. Ogliastro, K. Mita, J. Nohata, M. López-Ferber, M. Duonor-Cérutti, T. Shimada, P. Fournier, and G. Devauchelle

Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias
Bioinformatics 2003 19: 2343-2350; doi:10.1093/bioinformatics/btg324 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yihua Huang, Tianyun Ni, Lei Zhou, and Stanley Su

JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration
Bioinformatics 2003 19: 2351-2358; doi:10.1093/bioinformatics/btg327 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, and Mauno Vihinen

Efficient estimation of emission probabilities in profile hidden Markov models
Bioinformatics 2003 19: 2359-2368; doi:10.1093/bioinformatics/btg328 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ting Wang and Gary D. Stormo

Combining phylogenetic data with co-regulated genes to identify regulatory motifs
Bioinformatics 2003 19: 2369-2380; doi:10.1093/bioinformatics/btg329 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

I. Gat-Viks, R. Sharan, and R. Shamir

Scoring clustering solutions by their biological relevance
Bioinformatics 2003 19: 2381-2389; doi:10.1093/bioinformatics/btg330 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shao-Wu Zhang, Quan Pan, Hong-Cai Zhang, Yun-Long Zhang, and Hai-Yu Wang

Classification of protein quaternary structure with support vector machine
Bioinformatics 2003 19: 2390-2396; doi:10.1093/bioinformatics/btg331 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wei-min Liu, Xiaojun Di, Geoffrey Yang, Hajime Matsuzaki, Jing Huang, Rui Mei, Thomas B. Ryder, Teresa A. Webster, Shoulian Dong, Guoying Liu, Keith W. Jones, Giulia C. Kennedy, and David Kulp

Algorithms for large-scale genotyping microarrays
Bioinformatics 2003 19: 2397-2403; doi:10.1093/bioinformatics/btg332 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Peter A. Covitz, Frank Hartel, Carl Schaefer, Sherri De Coronado, Gilberto Fragoso, Himanso Sahni, Scott Gustafson, and Kenneth H. Buetow

caCORE: A common infrastructure for cancer informatics
Bioinformatics 2003 19: 2404-2412; doi:10.1093/bioinformatics/btg335 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chen-Shan Chin and Manoj Pratim Samanta

Global snapshot of a protein interaction network—a percolation based approach
Bioinformatics 2003 19: 2413-2419; doi:10.1093/bioinformatics/btg339 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jacob Köhler, Stephan Philippi, and Matthias Lange

SEMEDA: ontology based semantic integration of biological databases
Bioinformatics 2003 19: 2420-2427; doi:10.1093/bioinformatics/btg340 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Antonio S. Torralba

Susceptibility of non-linear systems as an approach to metabolic responses
Bioinformatics 2003 19: 2428-2435; doi:10.1093/bioinformatics/btg341 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Igor Rojdestvenski

Metabolic pathways in three dimensions
Bioinformatics 2003 19: 2436-2441; doi:10.1093/bioinformatics/btg342 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Cornelius Frömmel, Christoph Gille, Andrean Goede, Clemens Gröpl, Stefan Hougardy, Till Nierhoff, Robert Preißner, and Martin Thimm

Accelerating screening of 3D protein data with a graph theoretical approach
Bioinformatics 2003 19: 2442-2447; doi:10.1093/bioinformatics/btg343 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

George W. Wright and Richard M. Simon

A random variance model for detection of differential gene expression in small microarray experiments
Bioinformatics 2003 19: 2448-2455; doi:10.1093/bioinformatics/btg345 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zhuoran Chen

Assessing sequence comparison methods with the average precision criterion
Bioinformatics 2003 19: 2456-2460; doi:10.1093/bioinformatics/btg349 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ricardo Z.N. Vêncio, Helena Brentani, and Carlos A.B. Pereira

Using credibility intervals instead of hypothesis tests in SAGE analysis
Bioinformatics 2003 19: 2461-2464; doi:10.1093/bioinformatics/btg357 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Anne-Laure Boulesteix, Gerhard Tutz, and Korbinian Strimmer

A CART-based approach to discover emerging patterns in microarray data
Bioinformatics 2003 19: 2465-2472; doi:10.1093/bioinformatics/btg361 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Gary L. Argraves, Jeremy L. Barth, and W. Scott Argraves

The MUSC DNA Microarray Database
Bioinformatics 2003 19: 2473-2474; doi:10.1093/bioinformatics/btg325 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Roman Roset, Juan A. Subirana, and Xavier Messeguer

MREPATT: detection and analysis of exact consecutive repeats in genomic sequences
Bioinformatics 2003 19: 2475-2476; doi:10.1093/bioinformatics/btg326 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Josep F. Abril, Roderic Guigó, and Thomas Wiehe

gff2aplot: Plotting sequence comparisons
Bioinformatics 2003 19: 2477-2479; doi:10.1093/bioinformatics/btg334 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kim Brügger, Peter Redder, and Marie Skovgaard

MUTAGEN: Multi-User Tool for Annotating GENomes
Bioinformatics 2003 19: 2480-2481; doi:10.1093/bioinformatics/btg336 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

T. Lütteke, P. Krieg, G. Fürstenberger, and C.-W. von der Lieth

LOX-DB—a database on lipoxygenases
Bioinformatics 2003 19: 2482-2483; doi:10.1093/bioinformatics/btg337 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Salim Khan, Gang Situ, Keith Decker, and Carl J. Schmidt

GoFigure: Automated Gene Ontology^TM annotation
Bioinformatics 2003 19: 2484-2485; doi:10.1093/bioinformatics/btg338 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Matej Lexa and Giorgio Valle

PRIMEX: rapid identification of oligonucleotide matches in whole genomes
Bioinformatics 2003 19: 2486-2488; doi:10.1093/bioinformatics/btg350 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Christoph Gille, Stephan Lorenzen, Elke Michalsky, and Cornelius Frömmel

KISS for STRAP: user extensions for a protein alignment editor
Bioinformatics 2003 19: 2489-2491; doi:10.1093/bioinformatics/btg354 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Daniel Aguilar, Baldomero Oliva, Francesc X. Aviles, and Enrique Querol

SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names
Bioinformatics 2003 19: 2492-2493; doi:10.1093/bioinformatics/btg355 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nadia Bolshakova and Francisco Azuaje

Machaon CVE: cluster validation for gene expression data
Bioinformatics 2003 19: 2494-2495; doi:10.1093/bioinformatics/btg356 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Julio Rozas, Juan C. Sánchez-DelBarrio, Xavier Messeguer, and Ricardo Rozas

DnaSP, DNA polymorphism analyses by the coalescent and other methods
Bioinformatics 2003 19: 2496-2497; doi:10.1093/bioinformatics/btg359 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Piero Fariselli, Giacomo Finocchiaro, and Rita Casadio

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites
Bioinformatics 2003 19: 2498-2499; doi:10.1093/bioinformatics/btg360 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

András Fiser and Andrej Sali

ModLoop: automated modeling of loops in protein structures
Bioinformatics 2003 19: 2500-2501; doi:10.1093/bioinformatics/btg362 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gabriel F. Berriz, Oliver D. King, Barbara Bryant, Chris Sander, and Frederick P. Roth

Characterizing gene sets with FuncAssociate
Bioinformatics 2003 19: 2502-2504; doi:10.1093/bioinformatics/btg363 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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