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Previous Next 		Contents: Volume 25, Number 5, 1 March 2009   [Index by Author] 
Down DISCOVERY NOTE
     SEQUENCE ANALYSIS
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     STRUCTURAL BIOINFORMATICS AND DATA MINING
     GENE EXPRESSION
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down LETTER TO THE EDITOR
     GENE EXPRESSION
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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.

DISCOVERY NOTE Back

SEQUENCE ANALYSIS Back

Shahar Alon, Eli Eisenberg, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine, Reiko Toyama, Steven L. Coon, David C. Klein, and Yoav Gothilf
A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 559-562; doi:10.1093/bioinformatics/btp031 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Shamim Ahmed, Ayumu Saito, Miho Suzuki, Naoto Nemoto, and Koichi Nishigaki
Host–parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 563-570; doi:10.1093/bioinformatics/btp003 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xu Ling, Xin He, and Dong Xin
Detecting gene clusters under evolutionary constraint in a large number of genomes
Bioinformatics Advance Access published on January 21, 2009
Bioinformatics 2009 25: 571-577; doi:10.1093/bioinformatics/btp027 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Leila Taher and Ivan Ovcharenko
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
Bioinformatics Advance Access published on January 25, 2009
Bioinformatics 2009 25: 578-584; doi:10.1093/bioinformatics/btp043 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Xue-wen Chen and Jong Cheol Jeong
Sequence-based prediction of protein interaction sites with an integrative method
Bioinformatics Advance Access published on January 19, 2009
Bioinformatics 2009 25: 585-591; doi:10.1093/bioinformatics/btp039 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

PHYLOGENETICS Back

Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, and Todd J. Vision
A hierarchical model for incomplete alignments in phylogenetic inference
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 592-598; doi:10.1093/bioinformatics/btp015 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Naoki Sato
Gclust: trans-kingdom classification of proteins using automatic individual threshold setting
Bioinformatics Advance Access published on January 21, 2009
Bioinformatics 2009 25: 599-605; doi:10.1093/bioinformatics/btp047 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Lee-Wei Yang, Eran Eyal, Ivet Bahar, and Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 606-614; doi:10.1093/bioinformatics/btp023 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Izhar Wallach and Ryan Lilien
The protein–small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding
Bioinformatics Advance Access published on January 19, 2009
Bioinformatics 2009 25: 615-620; doi:10.1093/bioinformatics/btp035 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David Hall, Melissa R. Landon, Carla Mattos, and Sandor Vajda
Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 621-627; doi:10.1093/bioinformatics/btp036 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS AND DATA MINING Back

Wataru Nishima, Guoying Qi, Steven Hayward, and Akio Kitao
DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 628-635; doi:10.1093/bioinformatics/btp032 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Satwik Rajaram
A novel meta-analysis method exploiting consistency of high-throughput experiments
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 636-642; doi:10.1093/bioinformatics/btp007 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Theodore Alexandrov, Jens Decker, Bart Mertens, Andre M. Deelder, Rob A. E. M. Tollenaar, Peter Maass, and Herbert Thiele
Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation
Bioinformatics 2009 25: 643-649; doi:10.1093/bioinformatics/btn662 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Li Zhang, Qingyi Wei, Li Mao, Wenbin Liu, Gordon B. Mills, and Kevin Coombes
Serial dilution curve: a new method for analysis of reverse phase protein array data
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 650-654; doi:10.1093/bioinformatics/btn663 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Claude Chelala, Arshad Khan, and Nicholas R Lemoine
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms
Bioinformatics Advance Access published on December 19, 2008
Bioinformatics 2009 25: 655-661; doi:10.1093/bioinformatics/btn653 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Olivier Martin, Armand Valsesia, Amalio Telenti, Ioannis Xenarios, and Brian J. Stevenson
AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context
Bioinformatics Advance Access published on January 25, 2009
Bioinformatics 2009 25: 662-663; doi:10.1093/bioinformatics/btp017 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Morgan G. I. Langille and Fiona S. L. Brinkman
IslandViewer: an integrated interface for computational identification and visualization of genomic islands
Bioinformatics Advance Access published on January 16, 2009
Bioinformatics 2009 25: 664-665; doi:10.1093/bioinformatics/btp030 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

J. Stenberg, M. Zhang, and H. Ji
Disperse—a software system for design of selector probes for exon resequencing applications
Bioinformatics Advance Access published on January 21, 2009
Bioinformatics 2009 25: 666-667; doi:10.1093/bioinformatics/btp001 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Parvez Anandam, Elfar Torarinsson, and Walter L. Ruzzo
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies
Bioinformatics Advance Access published on January 9, 2009
Bioinformatics 2009 25: 668-669; doi:10.1093/bioinformatics/btp006 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jérôme Gouzy, Sébastien Carrere, and Thomas Schiex
FrameDP: sensitive peptide detection on noisy matured sequences
Bioinformatics Advance Access published on January 19, 2009
Bioinformatics 2009 25: 670-671; doi:10.1093/bioinformatics/btp024 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

PHYLOGENETICS Back

Jacqueline Whalley, Stephen Brooks, and Robert G. Beiko
Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree
Bioinformatics Advance Access published on February 4, 2009
Bioinformatics 2009 25: 672-673; doi:10.1093/bioinformatics/btp044 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Charles E. Chapple, Roderic Guigó, and Alain Krol
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements
Bioinformatics Advance Access published on January 29, 2009
Bioinformatics 2009 25: 674-675; doi:10.1093/bioinformatics/btp020 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen
CPSP-web-tools: a server for 3D lattice protein studies
Bioinformatics Advance Access published on January 16, 2009
Bioinformatics 2009 25: 676-677; doi:10.1093/bioinformatics/btp034 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENE EXPRESSION Back

Nora Rieber, Bettina Knapp, Roland Eils, and Lars Kaderali
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens
Bioinformatics Advance Access published on January 25, 2009
Bioinformatics 2009 25: 678-679; doi:10.1093/bioinformatics/btp014 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Mehdi Sargolzaei and Flavio S Schenkel
QMSim: a large-scale genome simulator for livestock
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 680-681; doi:10.1093/bioinformatics/btp045 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Nils Gehlenborg, Wei Yan, Inyoul Y. Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, and Leroy Hood
Prequips—an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 682-683; doi:10.1093/bioinformatics/btp005 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Alexander Lachmann and Avi Ma'ayan
KEA: kinase enrichment analysis
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 684-686; doi:10.1093/bioinformatics/btp026 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Sebastian Mirschel, Katrin Steinmetz, Michael Rempel, Martin Ginkel, and Ernst Dieter Gilles
PROMOT: modular modeling for systems biology
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 687-689; doi:10.1093/bioinformatics/btp029 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Emilie Chautard, Lionel Ballut, Nicolas Thierry-Mieg, and Sylvie Ricard-Blum
MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 690-691; doi:10.1093/bioinformatics/btp025 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

ClarLynda R. Williams-DeVane, Maritja A. Wolf, and Ann M. Richard
DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages
Bioinformatics Advance Access published on January 21, 2009
Bioinformatics 2009 25: 692-694; doi:10.1093/bioinformatics/btp042 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Hanchuan Peng, Fuhui Long, and Eugene W. Myers
VANO: a volume-object image annotation system
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 695-697; doi:10.1093/bioinformatics/btp046 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

LETTER TO THE EDITOR Back

GENE EXPRESSION Back

Stan Pounds and Cheng Cheng
Erratum: sample size determination for the false discovery rate
Bioinformatics Advance Access published on January 6, 2009
Bioinformatics 2009 25: 698-699; doi:10.1093/bioinformatics/btn661 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [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.