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Previous Next 		Contents: Volume 23, Number 3, 1 February 2007   [Index by Author] 
       DISCOVERY NOTES
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                DATA AND TEXT MINING
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
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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 NOTES:

SEQUENCE ANALYSIS:

Richard Thilakaraj, Krishnan Raghunathan, Sharmila Anishetty, and Gautam Pennathur
In silico identification of putative metal binding motifs
Bioinformatics Advance Access published on December 5, 2006
Bioinformatics 2007 23: 267-271; doi:10.1093/bioinformatics/btl617 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Alexander P. Gultyaev, Hans A. Heus, and René C. L. Olsthoorn
An RNA conformational shift in recent H5N1 influenza A viruses
Bioinformatics Advance Access published on November 7, 2006
Bioinformatics 2007 23: 272-276; doi:10.1093/bioinformatics/btl559 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

Roger Higdon and Eugene Kolker
A predictive model for identifying proteins by a single peptide match
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 277-280; doi:10.1093/bioinformatics/btl595 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Liang Goh, Susan K. Murphy, Sayan Muhkerjee, and Terrence S. Furey
Genomic sweeping for hypermethylated genes
Bioinformatics Advance Access published on December 5, 2006
Bioinformatics 2007 23: 281-288; doi:10.1093/bioinformatics/btl620 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Jaebum Kim and Saurabh Sinha
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Bioinformatics Advance Access published on November 15, 2006
Bioinformatics 2007 23: 289-297; doi:10.1093/bioinformatics/btl578 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENE EXPRESSION:

Ian B. Jeffery, Stephen F. Madden, Paul A. McGettigan, Guy Perrière, Aedín C. Culhane, and Desmond G. Higgins
Integrating transcription factor binding site information with gene expression datasets
Bioinformatics Advance Access published on November 24, 2006
Bioinformatics 2007 23: 298-305; doi:10.1093/bioinformatics/btl597 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zhen Jiang and Robert Gentleman
Extensions to gene set enrichment
Bioinformatics Advance Access published on November 24, 2006
Bioinformatics 2007 23: 306-313; doi:10.1093/bioinformatics/btl599 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D. Dynlacht, Guangliang Chen, and Bud Mishra
Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data
Bioinformatics Advance Access published on December 12, 2006
Bioinformatics 2007 23: 314-320; doi:10.1093/bioinformatics/btl606 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Zhongxue Chen, Monnie McGee, Qingzhong Liu, and Richard H. Scheuermann
A distribution free summarization method for Affymetrix GeneChip® arrays
Bioinformatics Advance Access published on December 5, 2006
Bioinformatics 2007 23: 321-327; doi:10.1093/bioinformatics/btl609 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Kenneth Lo and Raphael Gottardo
Flexible empirical Bayes models for differential gene expression
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 328-335; doi:10.1093/bioinformatics/btl612 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

L. Jason Steggles, Richard Banks, Oliver Shaw, and Anil Wipat
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 336-343; doi:10.1093/bioinformatics/btl596 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Christian Klukas and Falk Schreiber
Dynamic exploration and editing of KEGG pathway diagrams
Bioinformatics Advance Access published on December 1, 2006
Bioinformatics 2007 23: 344-350; doi:10.1093/bioinformatics/btl611 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Andrea L. Knorr, Rishi Jain, and Ranjan Srivastava
Bayesian-based selection of metabolic objective functions
Bioinformatics Advance Access published on December 6, 2006
Bioinformatics 2007 23: 351-357; doi:10.1093/bioinformatics/btl619 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Neda Bagheri, Jörg Stelling, and Francis J. Doyle, III
Quantitative performance metrics for robustness in circadian rhythms
Bioinformatics Advance Access published on December 8, 2006
Bioinformatics 2007 23: 358-364; doi:10.1093/bioinformatics/btl627 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Katrin Fundel, Robert Küffner, and Ralf Zimmer
RelEx—Relation extraction using dependency parse trees
Bioinformatics Advance Access published on December 1, 2006
Bioinformatics 2007 23: 365-371; doi:10.1093/bioinformatics/btl616 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

SEQUENCE ANALYSIS:

Kazutaka Katoh and Hiroyuki Toh
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
Bioinformatics Advance Access published on November 21, 2006
Bioinformatics 2007 23: 372-374; doi:10.1093/bioinformatics/btl592 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Kreshna Gopal, Erik McKee, Tod Romo, Reetal Pai, Jacob Smith, James Sacchettini, and Thomas Ioerger
Crystallographic protein model-building on the web
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 375-377; doi:10.1093/bioinformatics/btl584 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lisa Fukui and Yuan Chen
NvMap: automated analysis of NMR chemical shift perturbation data
Bioinformatics Advance Access published on November 21, 2006
Bioinformatics 2007 23: 378-380; doi:10.1093/bioinformatics/btl585 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Thérèse E. Malliavin, and Michael Nilges
ARIA2: Automated NOE assignment and data integration in NMR structure calculation
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 381-382; doi:10.1093/bioinformatics/btl589 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Stephen Cammer
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol
Bioinformatics Advance Access published on January 3, 2007
Bioinformatics 2007 23: 383-384; doi:10.1093/bioinformatics/btl603 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

E. Capriotti and R. Casadio
K-Fold: a tool for the prediction of the protein folding kinetic order and rate
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 385-386; doi:10.1093/bioinformatics/btl610 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Giorgio Valentini
Mosclust: a software library for discovering significant structures in bio-molecular data
Bioinformatics Advance Access published on November 24, 2006
Bioinformatics 2007 23: 387-389; doi:10.1093/bioinformatics/btl600 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ignacio Medina, David Montaner, Joaquín Tárraga, and Joaquín Dopazo
Prophet, a web-based tool for class prediction using microarray data
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 390-391; doi:10.1093/bioinformatics/btl602 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, and Richard Bonneau
BioNetBuilder: automatic integration of biological networks
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 392-393; doi:10.1093/bioinformatics/btl604 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-Racine, Alain Jacquier, Benno Schwikowski, and Tero Aittokallio
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
Bioinformatics Advance Access published on November 24, 2006
Bioinformatics 2007 23: 394-396; doi:10.1093/bioinformatics/btl605 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Areum Han, Woo-Yeon Kim, and Seong-Min Park
SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 397-399; doi:10.1093/bioinformatics/btl593 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

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.