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Previous Next 		Contents: Volume 24, Number 6, 15 March 2008   [Index by Author] 
       DISCOVERY NOTE
                SYSTEMS BIOLOGY
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASE AND ONTOLOGIES
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DISCOVERY NOTE:

SYSTEMS BIOLOGY:

Scott Grandison and Richard J. Morris
Biological pathway kinetic rate constants are scale-invariant
Bioinformatics Advance Access published on January 30, 2008
Bioinformatics 2008 24: 741-743; doi:10.1093/bioinformatics/btn041 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, and John K. Colbourne
A machine-learning approach to combined evidence validation of genome assemblies
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 744-750; doi:10.1093/bioinformatics/btm608 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Robin Andersson, Carl E. G. Bruder, Arkadiusz Piotrowski, Uwe Menzel, Helena Nord, Johanna Sandgren, Torgeir R. Hvidsten, Teresita Diaz de Ståhl, Jan P. Dumanski, and Jan Komorowski
A segmental maximum a posteriori approach to genome-wide copy number profiling
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 751-758; doi:10.1093/bioinformatics/btn003 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

H. Bengtsson, R. Irizarry, B. Carvalho, and T. P. Speed
Estimation and assessment of raw copy numbers at the single locus level
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 759-767; doi:10.1093/bioinformatics/btn016 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Guillem Rigaill, Philippe Hupé, Anna Almeida, Philippe La Rosa, Jean-Philippe Meyniel, Charles Decraene, and Emmanuel Barillot
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays
Bioinformatics Advance Access published on February 5, 2008
Bioinformatics 2008 24: 768-774; doi:10.1093/bioinformatics/btn048 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Nanjiang Shu, Tuping Zhou, and Sven Hovmöller
Prediction of zinc-binding sites in proteins from sequence
Bioinformatics Advance Access published on February 1, 2008
Bioinformatics 2008 24: 775-782; doi:10.1093/bioinformatics/btm618 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Anuj R. Shah, Christopher S. Oehmen, and Bobbie-Jo Webb-Robertson
SVM-HUSTLE—an iterative semi-supervised machine learning approach for pairwise protein remote homology detection
Bioinformatics Advance Access published on February 1, 2008
Bioinformatics 2008 24: 783-790; doi:10.1093/bioinformatics/btn028 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

T. W. Lam, W. K. Sung, S. L. Tam, C. K. Wong, and S. M. Yiu
Compressed indexing and local alignment of DNA
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 791-797; doi:10.1093/bioinformatics/btn032 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Mark N. Wass and Michael J. E. Sternberg
ConFunc—functional annotation in the twilight zone
Bioinformatics Advance Access published on February 8, 2008
Bioinformatics 2008 24: 798-806; doi:10.1093/bioinformatics/btn037 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

A. Biegert and J. Söding
De novo identification of highly diverged protein repeats by probabilistic consistency
Bioinformatics Advance Access published on February 1, 2008
Bioinformatics 2008 24: 807-814; doi:10.1093/bioinformatics/btn039 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Bruce R. Southey, Jonathan V. Sweedler, and Sandra L. Rodriguez-Zas
Prediction of neuropeptide cleavage sites in insects
Bioinformatics Advance Access published on February 5, 2008
Bioinformatics 2008 24: 815-825; doi:10.1093/bioinformatics/btn044 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

PHYLOGENETICS:

Hadas Birin, Zohar Gal-Or, Isaac Elias, and Tamir Tuller
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 826-832; doi:10.1093/bioinformatics/btn024 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Vladislav Vyshemirsky and Mark A. Girolami
Bayesian ranking of biochemical system models
Bioinformatics Advance Access published on December 5, 2007
Bioinformatics 2008 24: 833-839; doi:10.1093/bioinformatics/btm607 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Julio Saez-Rodriguez, Arthur Goldsipe, Jeremy Muhlich, Leonidas G. Alexopoulos, Bjorn Millard, Douglas A. Lauffenburger, and Peter K. Sorger
Flexible informatics for linking experimental data to mathematical models via DataRail
Bioinformatics Advance Access published on January 24, 2008
Bioinformatics 2008 24: 840-847; doi:10.1093/bioinformatics/btn018 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Henning Schmidt, Mads F. Madsen, Sune Danø, and Gunnar Cedersund
Complexity reduction of biochemical rate expressions
Bioinformatics Advance Access published on February 10, 2008
Bioinformatics 2008 24: 848-854; doi:10.1093/bioinformatics/btn035 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Frank M. Graziano, Samira Y. Kettoola, Judy M. Munshower, Jack T. Stapleton, and George J. Towfic
Effect of spatial distribution of T-Cells and HIV load on HIV progression
Bioinformatics Advance Access published on January 10, 2008
Bioinformatics 2008 24: 855-860; doi:10.1093/bioinformatics/btn008 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Gavin C. Conant and Kenneth H. Wolfe
GenomeVx: simple web-based creation of editable circular chromosome maps
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 861-862; doi:10.1093/bioinformatics/btm598 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Gipsi Lima-Mendez, Jacques Van Helden, Ariane Toussaint, and Raphaël Leplae
Prophinder: a computational tool for prophage prediction in prokaryotic genomes
Bioinformatics Advance Access published on January 30, 2008
Bioinformatics 2008 24: 863-865; doi:10.1093/bioinformatics/btn043 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

B. Slabbinck, P. Dawyndt, M. Martens, P. De Vos, and B. De Baets
TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 866-867; doi:10.1093/bioinformatics/btn031 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Mark Derthick
Interactive visualization software for exploring phylogenetic trees and clades
Bioinformatics Advance Access published on February 8, 2008
Bioinformatics 2008 24: 868-869; doi:10.1093/bioinformatics/btn038 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Manfred J. Sippl, Stefan J. Suhrer, Markus Gruber, and Markus Wiederstein
A discrete view on fold space
Bioinformatics Advance Access published on January 24, 2008
Bioinformatics 2008 24: 870-871; doi:10.1093/bioinformatics/btn020 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Manfred J. Sippl
On distance and similarity in fold space
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 872-873; doi:10.1093/bioinformatics/btn040 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Yongsung Joo, James G. Booth, Younghwan Namkoong, and George Casella
Model-based Bayesian clustering (MBBC)
Bioinformatics Advance Access published on February 1, 2008
Bioinformatics 2008 24: 874-875; doi:10.1093/bioinformatics/btn030 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Andrei Zinovyev, Eric Viara, Laurence Calzone, and Emmanuel Barillot
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
Bioinformatics Advance Access published on November 16, 2007
Bioinformatics 2008 24: 876-877; doi:10.1093/bioinformatics/btm553 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

D. Sarkar, N. Le Meur, and R. Gentleman
Using flowViz to visualize flow cytometry data
Bioinformatics Advance Access published on February 1, 2008
Bioinformatics 2008 24: 878-879; doi:10.1093/bioinformatics/btn021 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Benjamin J. Bornstein, Sarah M. Keating, Akiya Jouraku, and Michael Hucka
LibSBML: an API Library for SBML
Bioinformatics Advance Access published on February 5, 2008
Bioinformatics 2008 24: 880-881; doi:10.1093/bioinformatics/btn051 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

HyungJun Cho, Yang-jin Kim, Hee Jung Jung, Sang-Won Lee, and Jae Won Lee
OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data
Bioinformatics Advance Access published on January 10, 2008
Bioinformatics 2008 24: 882-884; doi:10.1093/bioinformatics/btn012 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

DATABASE AND ONTOLOGIES:

Erick Antezana, Mikel Egaña, Bernard De Baets, Martin Kuiper, and Vladimir Mironov
ONTO-PERL: An API for supporting the development and analysis of bio-ontologies
Bioinformatics Advance Access published on February 1, 2008
Bioinformatics 2008 24: 885-887; doi:10.1093/bioinformatics/btn042 [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.