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Previous Next 		Contents: Volume 23, Number 7, 1 April 2007   [Index by Author] 
       DISCOVERY NOTES
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       CORRIGENDUM
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DISCOVERY NOTES:

PHYLOGENETICS:

Farhat Habib, Andrew D. Johnson, Ralf Bundschuh, and Daniel Janies
Large scale genotype–phenotype correlation analysis based on phylogenetic trees
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 785-788; doi:10.1093/bioinformatics/btm003 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

George Nicola and Ilya A. Vakser
A simple shape characteristic of protein–protein recognition
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 789-792; doi:10.1093/bioinformatics/btm018 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Kristian Hanekamp, Uta Bohnebeck, Bánk Beszteri, and Klaus Valentin
PhyloGena—a user-friendly system for automated phylogenetic annotation of unknown sequences
Bioinformatics Advance Access published on March 1, 2007
Bioinformatics 2007 23: 793-801; doi:10.1093/bioinformatics/btm016 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Jimin Pei and Nick V. Grishin
PROMALS: towards accurate multiple sequence alignments of distantly related proteins
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 802-808; doi:10.1093/bioinformatics/btm017 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Alex Bateman and Robert D. Finn
SCOOP: a simple method for identification of novel protein superfamily relationships
Bioinformatics Advance Access published on February 3, 2007
Bioinformatics 2007 23: 809-814; doi:10.1093/bioinformatics/btm034 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

PHYLOGENETICS:

B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, and M. A. Huynen
Assessment of phylogenomic and orthology approaches for phylogenetic inference
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 815-824; doi:10.1093/bioinformatics/btm015 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

Robert G. Beiko and Robert L. Charlebois
A simulation test bed for hypotheses of genome evolution
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 825-831; doi:10.1093/bioinformatics/btm024 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Juris Viksna and David Gilbert
Assessment of the probabilities for evolutionary structural changes in protein folds
Bioinformatics Advance Access published on February 4, 2007
Bioinformatics 2007 23: 832-841; doi:10.1093/bioinformatics/btm022 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Takashi Yoneya and Hiroshi Mamitsuka
A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 842-849; doi:10.1093/bioinformatics/btl667 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Serban Nacu, Rebecca Critchley-Thorne, Peter Lee, and Susan Holmes
Gene expression network analysis and applications to immunology
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 850-858; doi:10.1093/bioinformatics/btm019 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Andreas Schlicker, Carola Huthmacher, Fidel Ramírez, Thomas Lengauer, and Mario Albrecht
Functional evaluation of domain–domain interactions and human protein interaction networks
Bioinformatics 2007 23: 859-865; doi:10.1093/bioinformatics/btm012 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Shawn Martin, Zhaoduo Zhang, Anthony Martino, and Jean-Loup Faulon
Boolean dynamics of genetic regulatory networks inferred from microarray time series data
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 866-874; doi:10.1093/bioinformatics/btm021 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Pratap R. Patnaik
Robustness analysis of the E.coli chemosensory system to perturbations in chemoattractant concentrations
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 875-881; doi:10.1093/bioinformatics/btm028 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

A. Antofie, M. Lateur, R. Oger, A. Patocchi, C. E. Durel, and W. E. Van de Weg
A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 882-891; doi:10.1093/bioinformatics/btm013 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Mark A. van de Wiel, Kyung In Kim, Sjoerd J. Vosse, Wessel N. van Wieringen, Saskia M. Wilting, and Bauke Ylstra
CGHcall: calling aberrations for array CGH tumor profiles
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 892-894; doi:10.1093/bioinformatics/btm030 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

SEQUENCE ANALYSIS:

Christian R. Ingrell, Martin L. Miller, Ole N. Jensen, and Nikolaj Blom
NetPhosYeast: prediction of protein phosphorylation sites in yeast
Bioinformatics Advance Access published on February 5, 2007
Bioinformatics 2007 23: 895-897; doi:10.1093/bioinformatics/btm020 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, and Markus Göker
COPYCAT : cophylogenetic analysis tool
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 898-900; doi:10.1093/bioinformatics/btm027 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

José Ignacio Garzón, Julio Kovacs, Ruben Abagyan, and Pablo Chacón
DFprot: a webtool for predicting local chain deformability
Bioinformatics Advance Access published on February 3, 2007
Bioinformatics 2007 23: 901-902; doi:10.1093/bioinformatics/btm014 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Pedro A. F. Galante, Jeff Trimarchi, Constance L. Cepko, Sandro J. de Souza, Lucila Ohno-Machado, and Winston P. Kuo
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
Bioinformatics Advance Access published on February 3, 2007
Bioinformatics 2007 23: 903-905; doi:10.1093/bioinformatics/btm023 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Anuj R. Shah, Mudita Singhal, Kyle R. Klicker, Eric G. Stephan, H. Steven Wiley, and Katrina M. Waters
Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager
Bioinformatics Advance Access published on February 25, 2007
Bioinformatics 2007 23: 906-909; doi:10.1093/bioinformatics/btm031 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

A. Ferro, R. Giugno, G. Pigola, A. Pulvirenti, D. Skripin, G. D. Bader, and D. Shasha
NetMatch: a Cytoscape plugin for searching biological networks
Bioinformatics Advance Access published on February 3, 2007
Bioinformatics 2007 23: 910-912; doi:10.1093/bioinformatics/btm032 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Alexander D. Diehl, Jamie A. Lee, Richard H. Scheuermann, and Judith A. Blake
Ontology development for biological systems: immunology
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 913-915; doi:10.1093/bioinformatics/btm029 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

CORRIGENDUM:

Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou, and Richard H. Scheuermann
Modular organization of protein interaction networks
Bioinformatics 2007 23: 916; doi:10.1093/bioinformatics/btm037 [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.