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Previous Next 		Contents: Volume 22, Number 11, 1 June 2006   [Index by Author] 
       DISCOVERY NOTES
                STRUCTURAL BIOINFORMATICS
                SYSTEMS BIOLOGY
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTE
                STRUCTURAL BIOINFORMATICS
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
       CORRIGENDUM
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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:

STRUCTURAL BIOINFORMATICS:

Emmanuelle Becker, Vincent Meyer, Hocine Madaoui, and Raphaël Guerois
Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response
Bioinformatics Advance Access published on March 7, 2006
Bioinformatics 2006 22: 1289-1292; doi:10.1093/bioinformatics/btl075 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Ute Müller, Günther Ernst, Christian Melle, Reinhard Guthke, and Ferdinand von Eggeling
Convergence of the proteomic pattern in cancer
Bioinformatics Advance Access published on March 7, 2006
Bioinformatics 2006 22: 1293-1296; doi:10.1093/bioinformatics/btl077 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Kira S. Makarova, Eugene V. Koonin, Robert Haselkorn, and Michael Y. Galperin
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1297-1301; doi:10.1093/bioinformatics/btl096 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Florencia G. Leonardi
A generalization of the PST algorithm: modeling the sparse nature of protein sequences
Bioinformatics Advance Access published on March 9, 2006
Bioinformatics 2006 22: 1302-1307; doi:10.1093/bioinformatics/btl088 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Stephen McCauley and Jotun Hein
Using hidden Markov models and observed evolution to annotate viral genomes
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 1308-1316; doi:10.1093/bioinformatics/btl092 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov, and Mikhail A. Roytberg
Analysis of internal loops within the RNA secondary structure in almost quadratic time
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1317-1324; doi:10.1093/bioinformatics/btl083 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, and Michael K. Showe
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1325-1334; doi:10.1093/bioinformatics/btl094 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Nicholas J. Burgoyne and Richard M. Jackson
Predicting protein interaction sites: binding hot-spots in protein–protein and protein–ligand interfaces
Bioinformatics Advance Access published on March 7, 2006
Bioinformatics 2006 22: 1335-1342; doi:10.1093/bioinformatics/btl079 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Gilad Wainreb, Nurit Haspel, Haim J. Wolfson, and Ruth Nussinov
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1343-1352; doi:10.1093/bioinformatics/btl098 [Abstract] [FREE Full Text] [Print PDF] [Supplementary material]   OPEN ACCESS ARTICLE  

Konrad H. Paszkiewicz, Michael J. E. Sternberg, and Michael Lappe
Prediction of viable circular permutants using a graph theoretic approach
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1353-1358; doi:10.1093/bioinformatics/btl095 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Gaëlle Lelandais, Pierre Vincens, Anne Badel-Chagnon, Stéphane Vialette, Claude Jacq, and Serge Hazout
Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
Bioinformatics Advance Access published on March 9, 2006
Bioinformatics 2006 22: 1359-1366; doi:10.1093/bioinformatics/btl087 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Xue-wen Chen, Gopalakrishna Anantha, and Xinkun Wang
An effective structure learning method for constructing gene networks
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1367-1374; doi:10.1093/bioinformatics/btl090 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Chao-Ping Hsu, Pei-Hsuan Lee, Ching-Wei Chang, and Cheng-Tsung Lee
Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors
Bioinformatics Advance Access published on March 7, 2006
Bioinformatics 2006 22: 1375-1382; doi:10.1093/bioinformatics/btl082 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Chris Rawlings, Paul Verrier, and Stephan Philippi
Graph-based analysis and visualization of experimental results with ONDEX
Bioinformatics Advance Access published on March 13, 2006
Bioinformatics 2006 22: 1383-1390; doi:10.1093/bioinformatics/btl081 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

David P. De Souza, Eleanor C. Saunders, Malcolm J. McConville, and Vladimir A. Likic
Progressive peak clustering in GC-MS Metabolomic experiments applied to Leishmania parasites
Bioinformatics Advance Access published on March 9, 2006
Bioinformatics 2006 22: 1391-1396; doi:10.1093/bioinformatics/btl085 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

STRUCTURAL BIOINFORMATICS:

Christian X. Weichenberger and Manfred J. Sippl
NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1397-1398; doi:10.1093/bioinformatics/btl128 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

David L. Aylor, Eric W. Price, and Ignazio Carbone
SNAP: Combine and Map modules for multilocus population genetic analysis
Bioinformatics Advance Access published on April 6, 2006
Bioinformatics 2006 22: 1399-1401; doi:10.1093/bioinformatics/btl136 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Claire Bardel, Vincent Danjean, and Emmanuelle Génin
ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1402-1403; doi:10.1093/bioinformatics/btl131 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Mario Falchi and Cesare Cappio Borlino
PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies
Bioinformatics Advance Access published on April 3, 2006
Bioinformatics 2006 22: 1404-1405; doi:10.1093/bioinformatics/btl124 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, and Christoph Flamm
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
Bioinformatics Advance Access published on March 9, 2006
Bioinformatics 2006 22: 1406-1407; doi:10.1093/bioinformatics/btl086 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Vladimir Makarenkov, Dmytro Kevorkov, Pablo Zentilli, Andrei Gagarin, Nathalie Malo, and Robert Nadon
HTS-Corrector: software for the statistical analysis and correction of experimental high-throughput screening data
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1408-1409; doi:10.1093/bioinformatics/btl126 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

Hyunsoo Kim, Gene H. Golub, and Haesun Park
Missing value estimation for DNA microarray gene expression data: local least squares imputation
Bioinformatics 2006 22: 1410-1411; doi:10.1093/bioinformatics/btk053 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, and John D. Storey
EDGE: extraction and analysis of differential gene expression
Bioinformatics 2006 22: 1412; doi:10.1093/bioinformatics/btl149 [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.