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Previous Next 		Contents: Volume 21, Number 23, December 1, 2005   [Index by Author] 
       LETTER TO THE EDITOR
                DATA AND TEXT MINING
       DISCOVERY NOTE
                STRUCTURAL BIOINFORMATICS
                SYSTEMS BIOLOGY
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                GENETICS AND POPULATION ANALYSIS
                DATABASES AND ONTOLOGIES
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LETTER TO THE EDITOR:

DATA AND TEXT MINING:

Christian Blaschke, Alexander Yeh, Evelyn Camon, Marc Colosimo, Rolf Apweiler, Lynette Hirschman, and Alfonso Valencia
Do you do text?
Bioinformatics Advance Access published on September 29, 2005
Bioinformatics 2005 21: 4199-4200; doi:10.1093/bioinformatics/bti695 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE:

STRUCTURAL BIOINFORMATICS:

Ruta Furmonaviciene, Brian J. Sutton, Fabian Glaser, Charlie A. Laughton, Nick Jones, Herb F. Sewell, and Farouk Shakib
An attempt to define allergen-specific molecular surface features: a bioinformatic approach
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4201-4204; doi:10.1093/bioinformatics/bti700 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Shinichiro Wachi, Ken Yoneda, and Reen Wu
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4205-4208; doi:10.1093/bioinformatics/bti688 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Frédéric Boyer, Anne Morgat, Laurent Labarre, Joël Pothier, and Alain Viari
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data
Bioinformatics Advance Access published on October 10, 2005
Bioinformatics 2005 21: 4209-4215; doi:10.1093/bioinformatics/bti711 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Eddo Kim and Yossef Kliger
Discovering hidden viral piracy
Bioinformatics Advance Access published on October 6, 2005
Bioinformatics 2005 21: 4216-4222; doi:10.1093/bioinformatics/bti706 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Keun-Joon Park, M. Michael Gromiha, Paul Horton, and Makiko Suwa
Discrimination of outer membrane proteins using support vector machines
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4223-4229; doi:10.1093/bioinformatics/bti697 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Robert W. Janes
Bioinformatics analyses of circular dichroism protein reference databases
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4230-4238; doi:10.1093/bioinformatics/bti690 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Huzefa Rangwala and George Karypis
Profile-based direct kernels for remote homology detection and fold recognition
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4239-4247; doi:10.1093/bioinformatics/bti687 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Björn Wallner and Arne Elofsson
Pcons5: combining consensus, structural evaluation and fold recognition scores
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4248-4254; doi:10.1093/bioinformatics/bti702 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Hassan M. Fathallah-Shaykh
Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays
Bioinformatics Advance Access published on September 22, 2005
Bioinformatics 2005 21: 4255-4262; doi:10.1093/bioinformatics/bti684 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Stan Pounds and Cheng Cheng
Sample size determination for the false discovery rate
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4263-4271; doi:10.1093/bioinformatics/bti699 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ida Scheel, Magne Aldrin, Ingrid K. Glad, Ragnhild Sørum, Heidi Lyng, and Arnoldo Frigessi
The influence of missing value imputation on detection of differentially expressed genes from microarray data
Bioinformatics Advance Access published on October 10, 2005
Bioinformatics 2005 21: 4272-4279; doi:10.1093/bioinformatics/bti708 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yang Xie, Wei Pan, and Arkady B. Khodursky
A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4280-4288; doi:10.1093/bioinformatics/bti685 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Maris Lapinsh, Peteris Prusis, Staffan Uhlén, and Jarl E. S. Wikberg
Improved approach for proteochemometrics modeling: application to organic compound—amine G protein-coupled receptor interactions
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4289-4296; doi:10.1093/bioinformatics/bti703 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Andrew C. R. Martin
Mapping PDB chains to UniProtKB entries
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4297-4301; doi:10.1093/bioinformatics/bti694 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Alberto M. R. Dávila, Daniel M. Lorenzini, Pablo N. Mendes, Thiago S. Satake, Gabriel R. Sousa, Linair M. Campos, Camila J. Mazzoni, Glauber Wagner, Paulo F. Pires, Edmundo C. Grisard, Maria C. R. Cavalcanti, and Maria Luiza M. Campos
GARSA: genomic analysis resources for sequence annotation
Bioinformatics Advance Access published on October 6, 2005
Bioinformatics 2005 21: 4302-4303; doi:10.1093/bioinformatics/bti705 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Tobias Hindemitt and Klaus F. X. Mayer
CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4304-4306; doi:10.1093/bioinformatics/bti691 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Hongyu Yang and Alan R. Gingle
OxfordGrid: a web interface for pairwise comparative map views
Bioinformatics Advance Access published on October 4, 2005
Bioinformatics 2005 21: 4307-4308; doi:10.1093/bioinformatics/bti698 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Giovanni Montana
HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4309-4311; doi:10.1093/bioinformatics/bti689 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Jun Cai, Jing Zhang, Ying Huang, and Yanda Li
ATID: a web-oriented database for collection of publicly available alternative translational initiation events
Bioinformatics Advance Access published on October 10, 2005
Bioinformatics 2005 21: 4312-4314; doi:10.1093/bioinformatics/bti704 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Noel M. O'Boyle, Peter Murray-Rust, Janet M. Thornton, and John B. O. Mitchell
MACiE: a database of enzyme reaction mechanisms
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4315-4316; doi:10.1093/bioinformatics/bti693 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Erratum
Bioinformatics 2005 21: 4317; doi:10.1093/bioinformatics/bti734 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 4318; doi:10.1093/bioinformatics/bti735 [Extract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.