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Previous Next 		Contents: Volume 23, Number 8, 15 April 2007   [Index by Author] 
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       CORRIGENDA
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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.

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Minmei Hou, Piotr Berman, Chih-Hao Hsu, and Robert S. Harris
HomologMiner: looking for homologous genomic groups in whole genomes
Bioinformatics Advance Access published on February 18, 2007
Bioinformatics 2007 23: 917-925; doi:10.1093/bioinformatics/btm048 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Elfar Torarinsson, Jakob H. Havgaard, and Jan Gorodkin
Multiple structural alignment and clustering of RNA sequences
Bioinformatics Advance Access published on February 25, 2007
Bioinformatics 2007 23: 926-932; doi:10.1093/bioinformatics/btm049 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Andrija Tomovic and Edward J. Oakeley
Position dependencies in transcription factor binding sites
Bioinformatics Advance Access published on February 18, 2007
Bioinformatics 2007 23: 933-941; doi:10.1093/bioinformatics/btm055 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Chun-Wei Tung and Shinn-Ying Ho
POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 942-949; doi:10.1093/bioinformatics/btm061 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Monika Fuxreiter, Peter Tompa, and István Simon
Local structural disorder imparts plasticity on linear motifs
Bioinformatics Advance Access published on March 25, 2007
Bioinformatics 2007 23: 950-956; doi:10.1093/bioinformatics/btm035 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Monica Nicolau, Robert Tibshirani, Anne-Lise Børresen-Dale, and Stefanie S. Jeffrey
Disease-specific genomic analysis: identifying the signature of pathologic biology
Bioinformatics Advance Access published on February 3, 2007
Bioinformatics 2007 23: 957-965; doi:10.1093/bioinformatics/btm033 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, and X. Shirley Liu
Microarray blob-defect removal improves array analysis
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 966-971; doi:10.1093/bioinformatics/btm043 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Sijian Wang and Ji Zhu
Improved centroids estimation for the nearest shrunken centroid classifier
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 972-979; doi:10.1093/bioinformatics/btm046 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jelle J. Goeman and Peter Bühlmann
Analyzing gene expression data in terms of gene sets: methodological issues
Bioinformatics Advance Access published on February 15, 2007
Bioinformatics 2007 23: 980-987; doi:10.1093/bioinformatics/btm051 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Thomas E. Royce, Joel S. Rozowsky, and Mark B. Gerstein
Assessing the need for sequence-based normalization in tiling microarray experiments
Bioinformatics Advance Access published on March 25, 2007
Bioinformatics 2007 23: 988-997; doi:10.1093/bioinformatics/btm052 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dorothy S. V. Wong, Frederick K. Wong, and Graham R. Wood
A multi-stage approach to clustering and imputation of gene expression profiles
Bioinformatics Advance Access published on February 18, 2007
Bioinformatics 2007 23: 998-1005; doi:10.1093/bioinformatics/btm053 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Susann Stjernqvist, Tobias Rydén, Martin Sköld, and Johan Staaf
Continuous-index hidden Markov modelling of array CGH copy number data
Bioinformatics Advance Access published on February 19, 2007
Bioinformatics 2007 23: 1006-1014; doi:10.1093/bioinformatics/btm059 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

DATA AND TEXT MINING:

Hua Xu, Jung-Wei Fan, George Hripcsak, Eneida A. Mendonça, Marianthi Markatou, and Carol Friedman
Gene symbol disambiguation using knowledge-based profiles
Bioinformatics Advance Access published on February 21, 2007
Bioinformatics 2007 23: 1015-1022; doi:10.1093/bioinformatics/btm056 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Robert Davey, George Savva, Jo Dicks, and Ian N. Roberts
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 1023-1025; doi:10.1093/bioinformatics/btm038 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Jan Krumsiek, Roland Arnold, and Thomas Rattei
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
Bioinformatics Advance Access published on February 19, 2007
Bioinformatics 2007 23: 1026-1028; doi:10.1093/bioinformatics/btm039 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, and Robert H. Gross
SPACER: identification of cis-regulatory elements with non-contiguous critical residues
Bioinformatics 2007 23: 1029-1031; doi:10.1093/bioinformatics/btm041 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dmitri Papatsenko
ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
Bioinformatics Advance Access published on February 18, 2007
Bioinformatics 2007 23: 1032-1034; doi:10.1093/bioinformatics/btm047 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Pascal Auffinger and Yaser Hashem
SwS: a solvation web service for nucleic acids
Bioinformatics Advance Access published on February 25, 2007
Bioinformatics 2007 23: 1035-1037; doi:10.1093/bioinformatics/btm067 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

D. A. Tregouet and V. Garelle
A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies
Bioinformatics Advance Access published on February 18, 2007
Bioinformatics 2007 23: 1038-1039; doi:10.1093/bioinformatics/btm058 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Aaron Barsky, Jennifer L. Gardy, Robert E. W. Hancock, and Tamara Munzner
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
Bioinformatics Advance Access published on February 19, 2007
Bioinformatics 2007 23: 1040-1042; doi:10.1093/bioinformatics/btm057 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Andrea Caprera, Barbara Lazzari, Alessandra Stella, Ivan Merelli, Alexandre R. Caetano, and Paola Mariani
GoSh: a web-based database for goat and sheep EST sequences
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 1043-1045; doi:10.1093/bioinformatics/btm063 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

CORRIGENDA:

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller
Maximum likelihood of phylogenetic networks
Bioinformatics 2007 23: 1046-1047; doi:10.1093/bioinformatics/btm075 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz, and Mark Gerstein
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
Bioinformatics 2007 23: 1048; doi:10.1093/bioinformatics/btm099 [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.