Bioinformatics

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Get checked abstract Isabelle Callebaut, Jean-Paul Mornon, and Philippe Monget

Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 1871-1874; doi:10.1093/bioinformatics/btm265 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract Xing Xu, Yongmei Ji, and Gary D. Stormo

RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Bioinformatics Advance Access published on May 30, 2007
Bioinformatics 2007 23: 1883-1891; doi:10.1093/bioinformatics/btm272 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract James A. R. Dalton and Richard M. Jackson

An evaluation of automated homology modelling methods at low target–template sequence similarity
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 1901-1908; doi:10.1093/bioinformatics/btm262 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Mainak Guharoy and Pinak Chakrabarti

Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein–protein interactions
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 1909-1918; doi:10.1093/bioinformatics/btm274 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Gennady M. Verkhivker

Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics
Bioinformatics Advance Access published on May 30, 2007
Bioinformatics 2007 23: 1919-1926; doi:10.1093/bioinformatics/btm277 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Attila Gyenesei, Ulrich Wagner, Simon Barkow-Oesterreicher, Etzard Stolte, and Ralph Schlapbach

Mining co-regulated gene profiles for the detection of functional associations in gene expression data
Bioinformatics Advance Access published on May 30, 2007
Bioinformatics 2007 23: 1927-1935; doi:10.1093/bioinformatics/btm276 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract P. Sykacek, R. Clarkson, C. Print, R. Furlong, and G. Micklem

Bayesian modelling of shared gene function
Bioinformatics Advance Access published on May 31, 2007
Bioinformatics 2007 23: 1936-1944; doi:10.1093/bioinformatics/btm280 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract J.G. Liao and Khew-Voon Chin

Logistic regression for disease classification using microarray data: model selection in a large p and small n case
Bioinformatics Advance Access published on May 31, 2007
Bioinformatics 2007 23: 1945-1951; doi:10.1093/bioinformatics/btm287 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Marko Laakso, Sari Tuupanen, Auli Karhu, Rainer Lehtonen, Lauri A. Aaltonen, and Sampsa Hautaniemi

Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays
Bioinformatics Advance Access published on May 17, 2007
Bioinformatics 2007 23: 1952-1961; doi:10.1093/bioinformatics/btm263 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Scotland C. Leman, Marcy K. Uyenoyama, Michael Lavine, and Yuguo Chen

The evolutionary forest algorithm
Bioinformatics Advance Access published on May 22, 2007
Bioinformatics 2007 23: 1962-1968; doi:10.1093/bioinformatics/btm264 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Maciej Dobrzynski, Jordi Vidal Rodríguez, Jaap A. Kaandorp, and Joke G. Blom

Computational methods for diffusion-influenced biochemical reactions
Bioinformatics Advance Access published on May 30, 2007
Bioinformatics 2007 23: 1969-1977; doi:10.1093/bioinformatics/btm278 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Sebastian Wernicke and Florian Rasche

Simple and fast alignment of metabolic pathways by exploiting local diversity
Bioinformatics Advance Access published on May 31, 2007
Bioinformatics 2007 23: 1978-1985; doi:10.1093/bioinformatics/btm279 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jianhua Hu, Xuming He, Keith A. Baggerly, Kevin R. Coombes, Bryan T.J. Hennessy, and Gordon B. Mills

Non-parametric quantification of protein lysate arrays
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 1986-1994; doi:10.1093/bioinformatics/btm283 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Mark F. Burkart, Jonathan D. Wren, Jason I. Herschkowitz, Charles M. Perou, and Harold R. Garner

Clustering microarray-derived gene lists through implicit literature relationships
Bioinformatics Advance Access published on May 30, 2007
Bioinformatics 2007 23: 1995-2003; doi:10.1093/bioinformatics/btm261 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

SEQUENCE ANALYSIS:

STRUCTURAL BIOINFORMATICS:

DATA AND TEXT MINING:

Get checked abstract Matthew E. Monroe, Nikola Tolic, Navdeep Jaitly, Jason L. Shaw, Joshua N. Adkins, and Richard D. Smith

VIPER: an advanced software package to support high-throughput LC-MS peptide identification
Bioinformatics Advance Access published on June 1, 2007
Bioinformatics 2007 23: 2021-2023; doi:10.1093/bioinformatics/btm281 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Jiajing Wang, Huai Li, Yitan Zhu, Malik Yousef, Michael Nebozhyn, Michael Showe, Louise Showe, Jianhua Xuan, Robert Clarke, and Yue Wang

VISDA: an open-source caBIG^TM analytical tool for data clustering and beyond
Bioinformatics Advance Access published on May 31, 2007
Bioinformatics 2007 23: 2024-2027; doi:10.1093/bioinformatics/btm290 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

CORRIGENDUM:

Qifang Xu, Adrian Canutescu, Zoran Obradovic, and Roland L. Dunbrack, Jr

ProtBuD: a database of biological unit structures of protein families and superfamilies
Bioinformatics 2007 23: 2028; doi:10.1093/bioinformatics/btm273 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Xin Zhou and David P. Tuck

MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data
Bioinformatics 2007 23: 2029; doi:10.1093/bioinformatics/btm284 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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