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Previous Next 		Contents: Volume 23, Number 9, 1 May 2007   [Index by Author] 
       DISCOVERY NOTE
                SYSTEMS BIOLOGY
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
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DISCOVERY NOTE:

SYSTEMS BIOLOGY:

Qingzhao Wang, Yudi Yang, Hongwu Ma, and Xueming Zhao
Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions
Bioinformatics Advance Access published on March 6, 2007
Bioinformatics 2007 23: 1049-1052; doi:10.1093/bioinformatics/btm074 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Gangman Yi, Sing-Hoi Sze, and Michael R. Thon
Identifying clusters of functionally related genes in genomes
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 1053-1060; doi:10.1093/bioinformatics/btl673 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Genis Parra, Keith Bradnam, and Ian Korf
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 1061-1067; doi:10.1093/bioinformatics/btm071 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Mitsuhiro Kanazawa, Hisae Anyoji, Atsushi Ogiwara, and Umpei Nagashima
De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio
Bioinformatics Advance Access published on March 6, 2007
Bioinformatics 2007 23: 1068-1072; doi:10.1093/bioinformatics/btm062 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jason S. Papadopoulos and Richa Agarwala
COBALT: constraint-based alignment tool for multiple protein sequences
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 1073-1079; doi:10.1093/bioinformatics/btm076 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Saskia de Groot, Thomas Mailund, and Jotun Hein
Comparative annotation of viral genomes with non-conserved gene structure
Bioinformatics Advance Access published on March 6, 2007
Bioinformatics 2007 23: 1080-1089; doi:10.1093/bioinformatics/btm078 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert, and William Stafford Noble
A structural alignment kernel for protein structures
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 1090-1098; doi:10.1093/bioinformatics/btl642 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Richard E. Smith, Simon C. Lovell, David F. Burke, Rinaldo W. Montalvao, and Tom L. Blundell
Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities
Bioinformatics Advance Access published on March 6, 2007
Bioinformatics 2007 23: 1099-1105; doi:10.1093/bioinformatics/btm073 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Xin Zhou and David P. Tuck
MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data
Bioinformatics 2007 23: 1106-1114; doi:10.1093/bioinformatics/btm036 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Supplementary data] [Request Permissions]  

SYSTEMS BIOLOGY:

Jiusheng Chen, Haoran Zheng, Haiyan Liu, Junqing Niu, Jianping Liu, Tie Shen, Bin Rui, and Yunyu Shi
Improving metabolic flux estimation via evolutionary optimization for convex solution space
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 1115-1123; doi:10.1093/bioinformatics/btm050 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, and Michael Schroeder
Clustering by common friends finds locally significant proteins mediating modules
Bioinformatics Advance Access published on February 21, 2007
Bioinformatics 2007 23: 1124-1131; doi:10.1093/bioinformatics/btm064 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

Kyle J. Gaulton, Karen L. Mohlke, and Todd J. Vision
A computational system to select candidate genes for complex human traits
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 1132-1140; doi:10.1093/bioinformatics/btm001 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Je-Gun Joung, Kyu-Baek Hwang, Jin-Wu Nam, Soo-Jin Kim, and Byoung-Tak Zhang
Discovery of microRNA–mRNA modules via population-based probabilistic learning
Bioinformatics Advance Access published on March 9, 2007
Bioinformatics 2007 23: 1141-1147; doi:10.1093/bioinformatics/btm045 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Christopher D. Fjell, Robert E.W. Hancock, and Artem Cherkasov
AMPer: a database and an automated discovery tool for antimicrobial peptides
Bioinformatics Advance Access published on March 6, 2007
Bioinformatics 2007 23: 1148-1155; doi:10.1093/bioinformatics/btm068 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Alejandro A. Schäffer, Edward Stallknecht Rice, William Cook, and Richa Agarwala
rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 1156-1158; doi:10.1093/bioinformatics/btm077 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Romain Fremez, Thomas Faraut, Gwennaele Fichant, Jérôme Gouzy, and Yves Quentin
Phylogenetic exploration of bacterial genomic rearrangements
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 1172-1174; doi:10.1093/bioinformatics/btm070 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Markus Brameier, Andrea Krings, and Robert M. MacCallum
NucPred—Predicting nuclear localization of proteins
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 1159-1160; doi:10.1093/bioinformatics/btm066 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B. T. M. Roerdink, and Oscar P. Kuipers
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 1161-1163; doi:10.1093/bioinformatics/btl658 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther, and Joachim Selbig
pcaMethods—a bioconductor package providing PCA methods for incomplete data
Bioinformatics Advance Access published on March 7, 2007
Bioinformatics 2007 23: 1164-1167; doi:10.1093/bioinformatics/btm069 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Diego Diez, Rebeca Alvarez, and Ana Dopazo
Codelink: an R package for analysis of GE healthcare gene expression bioarrays
Bioinformatics Advance Access published on March 7, 2007
Bioinformatics 2007 23: 1168-1169; doi:10.1093/bioinformatics/btm072 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tancred Frickey and Georg Weiller
Analyzing microarray data using CLANS
Bioinformatics Advance Access published on March 7, 2007
Bioinformatics 2007 23: 1170-1171; doi:10.1093/bioinformatics/btm079 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Ying Sun, Shuqi Zhao, Huashan Yu, Ge Gao, and Jingchu Luo
ABCGrid: Application for Bioinformatics Computing Grid
Bioinformatics Advance Access published on March 7, 2007
Bioinformatics 2007 23: 1175-1177; doi:10.1093/bioinformatics/btm086 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Paul M.K. Gordon, Quang Trinh, and Christoph W. Sensen
Semantic Web Service provision: a realistic framework for Bioinformatics programmers
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 1178-1180; doi:10.1093/bioinformatics/btm060 [Abstract] [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.