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Previous Next 		Contents: Volume 24, Number 9, 1 May 2008   [Index by Author] 
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       CORRIGENDUM
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ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Xin Chen, Lingqiong Guo, Zhaocheng Fan, and Tao Jiang
W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data
Bioinformatics Advance Access published on March 5, 2008
Bioinformatics 2008 24: 1121-1128; doi:10.1093/bioinformatics/btn088 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Haiquan Li, Xinbin Dai, and Xuechun Zhao
A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
Bioinformatics Advance Access published on March 12, 2008
Bioinformatics 2008 24: 1129-1136; doi:10.1093/bioinformatics/btn099 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Victor I. Lesk and Michael J. E. Sternberg
3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
Bioinformatics Advance Access published on March 7, 2008
Bioinformatics 2008 24: 1137-1144; doi:10.1093/bioinformatics/btn093 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Aleksandar Poleksic and Mark Fienup
Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile–profile algorithms
Bioinformatics Advance Access published on March 12, 2008
Bioinformatics 2008 24: 1145-1153; doi:10.1093/bioinformatics/btn097 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Andrey A. Shabalin, Håkon Tjelmeland, Cheng Fan, Charles M. Perou, and Andrew B. Nobel
Merging two gene-expression studies via cross-platform normalization
Bioinformatics Advance Access published on March 5, 2008
Bioinformatics 2008 24: 1154-1160; doi:10.1093/bioinformatics/btn083 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Reid F. Thompson, Mark Reimers, Batbayar Khulan, Mathieu Gissot, Todd A. Richmond, Quan Chen, Xin Zheng, Kami Kim, and John M. Greally
An analytical pipeline for genomic representations used for cytosine methylation studies
Bioinformatics Advance Access published on March 18, 2008
Bioinformatics 2008 24: 1161-1167; doi:10.1093/bioinformatics/btn096 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Meaza Demissie, Barbara Mascialino, Stefano Calza, and Yudi Pawitan
Unequal group variances in microarray data analyses
Bioinformatics Advance Access published on March 14, 2008
Bioinformatics 2008 24: 1168-1174; doi:10.1093/bioinformatics/btn100 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Caiyan Li and Hongzhe Li
Network-constrained regularization and variable selection for analysis of genomic data
Bioinformatics Advance Access published on March 1, 2008
Bioinformatics 2008 24: 1175-1182; doi:10.1093/bioinformatics/btn081 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Cheng-Long Chuang, Chih-Hung Jen, Chung-Ming Chen, and Grace S. Shieh
A pattern recognition approach to infer time-lagged genetic interactions
Bioinformatics Advance Access published on March 12, 2008
Bioinformatics 2008 24: 1183-1190; doi:10.1093/bioinformatics/btn098 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Bayu Jayawardhana, Douglas B. Kell, and Magnus Rattray
Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo
Bioinformatics Advance Access published on March 20, 2008
Bioinformatics 2008 24: 1191-1197; doi:10.1093/bioinformatics/btn103 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Yuanyuan Xiao and Mark R. Segal
Biological sequence classification utilizing positive and unlabeled data
Bioinformatics Advance Access published on March 14, 2008
Bioinformatics 2008 24: 1198-1205; doi:10.1093/bioinformatics/btn089 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTES:

STRUCTURAL BIOINFORMATICS:

Christian X. Weichenberger, Piotr Byzia, and Manfred J. Sippl
Visualization of unfavorable interactions in protein folds
Bioinformatics Advance Access published on March 29, 2008
Bioinformatics 2008 24: 1206-1207; doi:10.1093/bioinformatics/btn108 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Federico Abascal, Pedro Carmona-Saez, Jose-Maria Carazo, and Alberto Pascual-Montano
ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data
Bioinformatics Advance Access published on March 12, 2008
Bioinformatics 2008 24: 1208-1209; doi:10.1093/bioinformatics/btn094 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Angeline M. Loh, Steven Wiltshire, Jon Emery, Kim W. Carter, and Lyle J. Palmer
Celestial3D: a novel method for 3D visualization of familial data
Bioinformatics Advance Access published on March 17, 2008
Bioinformatics 2008 24: 1210-1211; doi:10.1093/bioinformatics/btn091 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

Rodrigo Santamaría, Roberto Therón, and Luis Quintales
BicOverlapper: A tool for bicluster visualization
Bioinformatics Advance Access published on March 5, 2008
Bioinformatics 2008 24: 1212-1213; doi:10.1093/bioinformatics/btn076 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Matthew P. Campbell, Louise Royle, Catherine M. Radcliffe, Raymond A. Dwek, and Pauline M. Rudd
GlycoBase and autoGU: tools for HPLC-based glycan analysis
Bioinformatics Advance Access published on March 14, 2008
Bioinformatics 2008 24: 1214-1216; doi:10.1093/bioinformatics/btn090 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Xiang Xu, Jinyu Wu, Jian Xiao, Yi Tan, Qiyu Bao, Fangqing Zhao, and Xiaokun Li
PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families
Bioinformatics Advance Access published on March 12, 2008
Bioinformatics 2008 24: 1217-1220; doi:10.1093/bioinformatics/btn092 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Hajo N. Krabbenhöft, Steffen Möller, and Daniel Bayer
Integrating ARC grid middleware with Taverna workflows
Bioinformatics Advance Access published on March 19, 2008
Bioinformatics 2008 24: 1221-1222; doi:10.1093/bioinformatics/btn095 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, and Paul Horton
CellMontage: Similar Expression Profile Search Server
Bioinformatics 2008 24: 1223; doi:10.1093/bioinformatics/btn101 [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.