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Previous Next 		Contents: Volume 25, Number 9, 1 May 2009   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down CORRIGENDUM
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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 Back

GENOME ANALYSIS Back

Mark A. van de Wiel, Rebecca Brosens, Paul H. C. Eilers, Candy Kumps, Gerrit A. Meijer, Björn Menten, Erik Sistermans, Frank Speleman, Marieke E. Timmerman, and Bauke Ylstra
Smoothing waves in array CGH tumor profiles
Bioinformatics Advance Access published on March 10, 2009
Bioinformatics 2009 25: 1099-1104; doi:10.1093/bioinformatics/btp132 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Cole Trapnell, Lior Pachter, and Steven L. Salzberg
TopHat: discovering splice junctions with RNA-Seq
Bioinformatics Advance Access published on March 16, 2009
Bioinformatics 2009 25: 1105-1111; doi:10.1093/bioinformatics/btp120 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Zhu-Jin Zhang
DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences
Bioinformatics Advance Access published on March 10, 2009
Bioinformatics 2009 25: 1112-1117; doi:10.1093/bioinformatics/btp130 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, and Knut Reinert
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads
Bioinformatics Advance Access published on March 5, 2009
Bioinformatics 2009 25: 1118-1124; doi:10.1093/bioinformatics/btp131 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Cristina Marino Buslje, Javier Santos, Jose Maria Delfino, and Morten Nielsen
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information
Bioinformatics Advance Access published on March 10, 2009
Bioinformatics 2009 25: 1125-1131; doi:10.1093/bioinformatics/btp135 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Anatoly M. Ruvinsky and Ilya A. Vakser
The ruggedness of protein–protein energy landscape and the cutoff for 1/rn potentials
Bioinformatics Advance Access published on February 23, 2009
Bioinformatics 2009 25: 1132-1136; doi:10.1093/bioinformatics/btp108 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jinkyu Kim, Seunghak Yu, Byonghyo Shim, Hanjoo Kim, Hyeyoung Min, Eui-Young Chung, Rhiju Das, and Sungroh Yoon
A robust peak detection method for RNA structure inference by high-throughput contact mapping
Bioinformatics Advance Access published on February 26, 2009
Bioinformatics 2009 25: 1137-1144; doi:10.1093/bioinformatics/btp110 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Michael C. Wu, Lingsong Zhang, Zhaoxi Wang, David C. Christiani, and Xihong Lin
Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection
Bioinformatics Advance Access published on January 25, 2009
Bioinformatics 2009 25: 1145-1151; doi:10.1093/bioinformatics/btp019 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ashok Sharma, Robert Podolsky, Jieping Zhao, and Richard A. McIndoe
A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets
Bioinformatics Advance Access published on March 4, 2009
Bioinformatics 2009 25: 1152-1157; doi:10.1093/bioinformatics/btp123 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Igor Ulitsky and Ron Shamir
Identifying functional modules using expression profiles and confidence-scored protein interactions
Bioinformatics Advance Access published on March 17, 2009
Bioinformatics 2009 25: 1158-1164; doi:10.1093/bioinformatics/btp118 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Bracken M. King and Bruce Tidor
MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets
Bioinformatics Advance Access published on March 4, 2009
Bioinformatics 2009 25: 1165-1172; doi:10.1093/bioinformatics/btp109 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

Mark F. Rogers and Asa Ben-Hur
The use of gene ontology evidence codes in preventing classifier assessment bias
Bioinformatics Advance Access published on March 2, 2009
Bioinformatics 2009 25: 1173-1177; doi:10.1093/bioinformatics/btp122 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Troy Ruths, Derek Ruths, and Luay Nakhleh
GS2: an efficiently computable measure of GO-based similarity of gene sets
Bioinformatics Advance Access published on March 16, 2009
Bioinformatics 2009 25: 1178-1184; doi:10.1093/bioinformatics/btp128 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Igor B. Kuznetsov, Michael McDuffie, and Roxana Moslehi
A web server for inferring the human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype
Bioinformatics Advance Access published on March 4, 2009
Bioinformatics 2009 25: 1185-1186; doi:10.1093/bioinformatics/btp121 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Ilya Plyusnin, Liisa Holm, and Matti Kankainen
LOCP—locating pilus operons in Gram-positive bacteria
Bioinformatics Advance Access published on March 4, 2009
Bioinformatics 2009 25: 1187-1188; doi:10.1093/bioinformatics/btp127 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Andrew M. Waterhouse, James B. Procter, David M. A. Martin, Michèle Clamp, and Geoffrey J. Barton
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Bioinformatics Advance Access published on January 16, 2009
Bioinformatics 2009 25: 1189-1191; doi:10.1093/bioinformatics/btp033 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

David Talavera, Roman A. Laskowski, and Janet M. Thornton
WSsas: a web service for the annotation of functional residues through structural homologues
Bioinformatics Advance Access published on February 27, 2009
Bioinformatics 2009 25: 1192-1194; doi:10.1093/bioinformatics/btp116 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yongjian Guo, Jose M. C. Ribeiro, Jennifer M. Anderson, and Stephan Bour
dCAS: a desktop application for cDNA sequence annotation
Bioinformatics Advance Access published on March 24, 2009
Bioinformatics 2009 25: 1195-1196; doi:10.1093/bioinformatics/btp129 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Robert J. Gifford, Tommy F. Liu, Soo-Yon Rhee, Mark Kiuchi, Stephane Hue, Deenan Pillay, and Robert W. Shafer
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance
Bioinformatics Advance Access published on March 20, 2009
Bioinformatics 2009 25: 1197-1198; doi:10.1093/bioinformatics/btp134 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

PHYLOGENETICS Back

Martin Lott, Andreas Spillner, Katharina T. Huber, and Vincent Moulton
PADRE: a package for analyzing and displaying reticulate evolution
Bioinformatics Advance Access published on March 5, 2009
Bioinformatics 2009 25: 1199-1200; doi:10.1093/bioinformatics/btp133 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Timothy V. Pyrkov, Anton O. Chugunov, Nikolay A. Krylov, Dmitry E. Nolde, and Roman G. Efremov
PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
Bioinformatics Advance Access published on February 25, 2009
Bioinformatics 2009 25: 1201-1202; doi:10.1093/bioinformatics/btp111 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Jeffrey T. Leek
The tspair package for finding top scoring pair classifiers in R
Bioinformatics Advance Access published on March 10, 2009
Bioinformatics 2009 25: 1203-1204; doi:10.1093/bioinformatics/btp126 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Hendrik Hache, Christoph Wierling, Hans Lehrach, and Ralf Herwig
GeNGe: systematic generation of gene regulatory networks
Bioinformatics Advance Access published on February 27, 2009
Bioinformatics 2009 25: 1205-1207; doi:10.1093/bioinformatics/btp115 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Tim McComb, Oliver Cairncross, Andrew B. Noske, David L. A. Wood, Brad J. Marsh, and Mark A. Ragan
IllouraTM: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data
Bioinformatics Advance Access published on March 3, 2009
Bioinformatics 2009 25: 1208-1210; doi:10.1093/bioinformatics/btp125 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Francesco Piva, Matteo Giulietti, Linda Nocchi, and Giovanni Principato
SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans
Bioinformatics Advance Access published on March 4, 2009
Bioinformatics 2009 25: 1211-1213; doi:10.1093/bioinformatics/btp124 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM Back

Kristoffer Forslund and Erik L. L. Sonnhammer
Predicting protein function from domain content
Bioinformatics 2009 25: 1214; doi:10.1093/bioinformatics/btp186 [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.