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Previous Next 		Contents: Volume 23, Number 22, 15 November 2007   [Index by Author] 
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATABASES AND ONTOLOGIES
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ORIGINAL PAPERS:

GENOME ANALYSIS:

Alexis A. Rodriguez, Tanuja Bompada, Mustafa Syed, Parantu K. Shah, and Natalia Maltsev
Evolutionary analysis of enzymes using Chisel
Bioinformatics Advance Access published on September 13, 2007
Bioinformatics 2007 23: 2961-2968; doi:10.1093/bioinformatics/btm421 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Lucian Ilie and Silvana Ilie
Multiple spaced seeds for homology search
Bioinformatics Advance Access published on September 5, 2007
Bioinformatics 2007 23: 2969-2977; doi:10.1093/bioinformatics/btm422 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Stephen McCauley, Saskia de Groot, Thomas Mailund, and Jotun Hein
Annotation of selection strengths in viral genomes
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 2978-2986; doi:10.1093/bioinformatics/btm472 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe, and Michael K. Showe
Naïve Bayes for microRNA target predictions—machine learning for microRNA targets
Bioinformatics Advance Access published on October 8, 2007
Bioinformatics 2007 23: 2987-2992; doi:10.1093/bioinformatics/btm484 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

PHYLOGENETICS:

Patricia Buendia and Giri Narasimhan
Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach
Bioinformatics Advance Access published on August 23, 2007
Bioinformatics 2007 23: 2993-3000; doi:10.1093/bioinformatics/btm413 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

J.R. Davies, R.M. Jackson, K.V. Mardia, and C.C. Taylor
The Poisson Index: a new probabilistic model for protein–ligand binding site similarity
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 3001-3008; doi:10.1093/bioinformatics/btm470 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Chris Deutsch and Bala Krishnamoorthy
Four-Body Scoring Function for Mutagenesis
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 3009-3015; doi:10.1093/bioinformatics/btm481 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Franz F. Roos, Riko Jacob, Jonas Grossmann, Bernd Fischer, Joachim M. Buhmann, Wilhelm Gruissem, Sacha Baginsky, and Peter Widmayer
PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra
Bioinformatics Advance Access published on September 3, 2007
Bioinformatics 2007 23: 3016-3023; doi:10.1093/bioinformatics/btm417 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, and Martin Vingron
Improved detection of overrepresentation of Gene-Ontology annotations with parent–child analysis
Bioinformatics Advance Access published on September 11, 2007
Bioinformatics 2007 23: 3024-3031; doi:10.1093/bioinformatics/btm440 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Nandini Raghavan, An M. I. M. De Bondt, Willem Talloen, Dieder Moechars, Hinrich W. H. Göhlmann, and Dhammika Amaratunga
The high-level similarity of some disparate gene expression measures
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 3032-3038; doi:10.1093/bioinformatics/btm448 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Shinsheng Yuan and Ker-Chau Li
Context-dependent clustering for dynamic cellular state modeling of microarray gene expression
Bioinformatics Advance Access published on September 10, 2007
Bioinformatics 2007 23: 3039-3047; doi:10.1093/bioinformatics/btm457 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Bonnie Kirkpatrick, Carlos Santos Armendariz, Richard M. Karp, and Eran Halperin
HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 3048-3055; doi:10.1093/bioinformatics/btm435 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, and Luonan Chen
Inferring transcriptional regulatory networks from high-throughput data
Bioinformatics Advance Access published on September 22, 2007
Bioinformatics 2007 23: 3056-3064; doi:10.1093/bioinformatics/btm465 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Richard Pelikan, William L. Bigbee, David Malehorn, James Lyons-Weiler, and Milos Hauskrecht
Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models
Bioinformatics Advance Access published on August 30, 2007
Bioinformatics 2007 23: 3065-3072; doi:10.1093/bioinformatics/btm415 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Andrew Smith, Kei Cheung, Michael Krauthammer, Martin Schultz, and Mark Gerstein
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics
Bioinformatics Advance Access published on October 7, 2007
Bioinformatics 2007 23: 3073-3079; doi:10.1093/bioinformatics/btm452 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Lennart J. G. Post, Marco Roos, M. Scott Marshall, Roel van Driel, and Timo M. Breit
A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data
Bioinformatics Advance Access published on September 19, 2007
Bioinformatics 2007 23: 3080-3087; doi:10.1093/bioinformatics/btm461 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Sungsoo Kang, Sung-Jin Yang, Sangsoo Kim, and Jong Bhak
CONSORF: a consensus prediction system for prokaryotic coding sequences
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3088-3090; doi:10.1093/bioinformatics/btm512 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

John E. Major
Genomic mutation consequence calculator
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 3091-3092; doi:10.1093/bioinformatics/btm339 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Matthew R. Huska, Henrik Buschmann, and Miguel A. Andrade-Navarro
BiasViz: visualization of amino acid biased regions in protein alignments
Bioinformatics Advance Access published on October 6, 2007
Bioinformatics 2007 23: 3093-3094; doi:10.1093/bioinformatics/btm489 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Emmanuelle Becker, Aurélie Cotillard, Vincent Meyer, Hocine Madaoui, and Raphaël Guérois
HMM-Kalign: a tool for generating sub-optimal HMM alignments
Bioinformatics Advance Access published on October 6, 2007
Bioinformatics 2007 23: 3095-3097; doi:10.1093/bioinformatics/btm492 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Pablo Minguez, Fátima Al-Shahrour, David Montaner, and Joaquín Dopazo
Functional profiling of microarray experiments using text-mining derived bioentities
Bioinformatics Advance Access published on September 13, 2007
Bioinformatics 2007 23: 3098-3099; doi:10.1093/bioinformatics/btm445 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Shouguo Gao and Xujing Wang
TAPPA: topological analysis of pathway phenotype association
Bioinformatics Advance Access published on September 21, 2007
Bioinformatics 2007 23: 3100-3102; doi:10.1093/bioinformatics/btm460 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, and Paul Horton
CellMontage: similar expression profile search server
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 3103-3104; doi:10.1093/bioinformatics/btm462 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

M.-X. Li, L. Jiang, S.-L. Ho, Y.-Q. Song, and P.-C. Sham
IGG: A tool to integrate GeneChips for genetic studies
Bioinformatics Advance Access published on September 14, 2007
Bioinformatics 2007 23: 3105-3107; doi:10.1093/bioinformatics/btm458 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Adnane Nemri, Michael M. Neff, Michael Burrell, Jonathan D.G. Jones, and David J. Studholme
Marker development for the genetic study of natural variation in Arabidopsis thaliana
Bioinformatics 2007 23: 3108-3109; doi:10.1093/bioinformatics/btm501 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Nitin Bhardwaj, Robert V. Stahelin, Guijun Zhao, Wonhwa Cho, and Hui Lu
MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins
Bioinformatics Advance Access published on August 25, 2007
Bioinformatics 2007 23: 3110-3112; doi:10.1093/bioinformatics/btm395 [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.