Bioinformatics

DISCOVERY NOTE:

Shao-Wu Meng, Zhuo Zhang, and Jinyan Li

Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshifts
Bioinformatics 2004 20: 1-4; doi:10.1093/bioinformatics/btg381 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Sofia Wichert, Konstantinos Fokianos, and Korbinian Strimmer

Identifying periodically expressed transcripts in microarray time series data
Bioinformatics 2004 20: 5-20; doi:10.1093/bioinformatics/btg364 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ying Huang and Yanda Li

Prediction of protein subcellular locations using fuzzy k-NN method
Bioinformatics 2004 20: 21-28; doi:10.1093/bioinformatics/btg366 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tetsuo Shibuya, Hisashi Kashima, and Akihiko Konagaya

Efficient filtering methods for clustering cDNAs with spliced sequence alignment
Bioinformatics 2004 20: 29-39; doi:10.1093/bioinformatics/btg367 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Saejoon Kim

Protein ß-turn prediction using nearest-neighbor method
Bioinformatics 2004 20: 40-44; doi:10.1093/bioinformatics/btg368 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stephen R. Comeau, David W. Gatchell, Sandor Vajda, and Carlos J. Camacho

ClusPro: an automated docking and discrimination method for the prediction of protein complexes
Bioinformatics 2004 20: 45-50; doi:10.1093/bioinformatics/btg371 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stephan Philippi

Light-weight integration of molecular biological databases
Bioinformatics 2004 20: 51-57; doi:10.1093/bioinformatics/btg372 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jianhua Ruan, Gary D. Stormo, and Weixiong Zhang

An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
Bioinformatics 2004 20: 58-66; doi:10.1093/bioinformatics/btg373 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

O. Michael Melko and Arcady R. Mushegian

Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes
Bioinformatics 2004 20: 67-74; doi:10.1093/bioinformatics/btg374 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Qiang Tu, Haixu Tang, and Dafu Ding

MedBlast: searching articles related to a biological sequence
Bioinformatics 2004 20: 75-77; doi:10.1093/bioinformatics/btg375 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Karan Vasudeva and Upinder S. Bhalla

Adaptive stochastic-deterministic chemical kinetic simulations
Bioinformatics 2004 20: 78-84; doi:10.1093/bioinformatics/btg376 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Li Zhang, Aidong Zhang, and Murali Ramanathan

VizStruct: exploratory visualization for gene expression profiling
Bioinformatics 2004 20: 85-92; doi:10.1093/bioinformatics/btg377 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jelle J. Goeman, Sara A. van de Geer, Floor de Kort, and Hans C. van Houwelingen

A global test for groups of genes: testing association with a clinical outcome
Bioinformatics 2004 20: 93-99; doi:10.1093/bioinformatics/btg382 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Song Wang and Stewart Ethier

A generalized likelihood ratio test to identify differentially expressed genes from microarray data
Bioinformatics 2004 20: 100-104; doi:10.1093/bioinformatics/btg384 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Monica Benito, Joel Parker, Quan Du, Junyuan Wu, Dong Xiang, Charles M. Perou, and J. S. Marron

Adjustment of systematic microarray data biases
Bioinformatics 2004 20: 105-114; doi:10.1093/bioinformatics/btg385 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, Adriana N. dos Reis, and José C. M. Mombach

Essentiality and damage in metabolic networks
Bioinformatics 2004 20: 115-119; doi:10.1093/bioinformatics/btg386 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Jung-Hsien Chiang, Hsu-Chun Yu, and Huai-Jen Hsu

GIS: a biomedical text-mining system for gene information discovery
Bioinformatics 2004 20: 120-121; doi:10.1093/bioinformatics/btg369 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Aaron E. Darling, Bob Mau, Frederick R. Blattner, and Nicole T. Perna

GRIL: genome rearrangement and inversion locator
Bioinformatics 2004 20: 122-124; doi:10.1093/bioinformatics/btg378 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Nils Blüthgen, Szymon M. Kielbasa, Branka Cajavec, and Hanspeter Herzel

HOMGL—comparing genelists across species and with different accession numbers
Bioinformatics 2004 20: 125-126; doi:10.1093/bioinformatics/btg379 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andreas Prlic, Francisco S. Domingues, Peter Lackner, and Manfred J. Sippl

WILMA—automated annotation of protein sequences
Bioinformatics 2004 20: 127-128; doi:10.1093/bioinformatics/btg380 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David P. Leader

BugView: a browser for comparing genomes
Bioinformatics 2004 20: 129-130; doi:10.1093/bioinformatics/btg383 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Liam J. McGuffin, Stefano Street, Søren-Aksel Sørensen, and David T. Jones

The Genomic Threading Database
Bioinformatics 2004 20: 131-132; doi:10.1093/bioinformatics/btg387 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, and Alain Trubuil

PARIS: a proteomic analysis and resources indexation system
Bioinformatics 2004 20: 133-135; doi:10.1093/bioinformatics/btg389 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Miklos Cserzo, Frank Eisenhaber, Birgit Eisenhaber, and Istvan Simon

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter
Bioinformatics 2004 20: 136-137; doi:10.1093/bioinformatics/btg394 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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