Bioinformatics

DISCOVERY NOTE

GENOME ANALYSIS

Get checked abstract Xiangfeng Wang, Zhihui Yu, Xiaozeng Yang, Xing-Wang Deng, and Lei Li

Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome
Bioinformatics Advance Access published on March 16, 2009
Bioinformatics 2009 25: 1215-1218; doi:10.1093/bioinformatics/btp147 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Agathe Burgess, Jean-Paul Mornon, Geneviève de Saint-Basile, and Isabelle Callebaut

A concanavalin A-like lectin domain in the CHS1/LYST protein, shared by members of the BEACH family
Bioinformatics Advance Access published on March 16, 2009
Bioinformatics 2009 25: 1219-1222; doi:10.1093/bioinformatics/btp151 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Roger Pique-Regi, Antonio Ortega, and Shahab Asgharzadeh

Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA
Bioinformatics Advance Access published on March 10, 2009
Bioinformatics 2009 25: 1223-1230; doi:10.1093/bioinformatics/btp119 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Tianjiao Chu, Kimberly Bunce, W. Allen Hogge, and David G. Peters

Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease
Bioinformatics Advance Access published on March 23, 2009
Bioinformatics 2009 25: 1244-1250; doi:10.1093/bioinformatics/btp156 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Mingyue Zheng, Xiaomin Luo, Qiancheng Shen, Yong Wang, Yun Du, Weiliang Zhu, and Hualiang Jiang

Site of metabolism prediction for six biotransformations mediated by cytochromes P450
Bioinformatics Advance Access published on March 13, 2009
Bioinformatics 2009 25: 1251-1258; doi:10.1093/bioinformatics/btp140 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Patrik Björkholm, Pawel Daniluk, Andriy Kryshtafovych, Krzysztof Fidelis, Robin Andersson, and Torgeir R. Hvidsten

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue–residue contacts
Bioinformatics Advance Access published on March 16, 2009
Bioinformatics 2009 25: 1264-1270; doi:10.1093/bioinformatics/btp149 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Guido Sanguinetti, Andreas Ruttor, Manfred Opper, and Cedric Archambeau

Switching regulatory models of cellular stress response
Bioinformatics Advance Access published on March 11, 2009
Bioinformatics 2009 25: 1280-1286; doi:10.1093/bioinformatics/btp138 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Alun Thomas

A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation
Bioinformatics Advance Access published on March 16, 2009
Bioinformatics 2009 25: 1287-1292; doi:10.1093/bioinformatics/btp146 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Hao Zhang, Ole Lund, and Morten Nielsen

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
Bioinformatics Advance Access published on March 17, 2009
Bioinformatics 2009 25: 1293-1299; doi:10.1093/bioinformatics/btp137 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Lam C. Tsoi, Michael Boehnke, Richard L. Klein, and W. Jim Zheng

Evaluation of genome-wide association study results through development of ontology fingerprints
Bioinformatics Advance Access published on April 5, 2009
Bioinformatics 2009 25: 1314-1320; doi:10.1093/bioinformatics/btp158 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES

APPLICATIONS NOTE

SEQUENCE ANALYSIS

Get checked abstract György Abrusán, Norbert Grundmann, Luc DeMester, and Wojciech Makalowski

TEclass—a tool for automated classification of unknown eukaryotic transposable elements
Bioinformatics Advance Access published on April 5, 2009
Bioinformatics 2009 25: 1329-1330; doi:10.1093/bioinformatics/btp084 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Micah Hamady, Stephanie A. Wilson, Jesse Zaneveld, Noboru Sueoka, and Rob Knight

CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes
Bioinformatics Advance Access published on March 11, 2009
Bioinformatics 2009 25: 1331-1332; doi:10.1093/bioinformatics/btp141 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract David N. Messina and Erik L. L. Sonnhammer

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System
Bioinformatics Advance Access published on March 17, 2009
Bioinformatics 2009 25: 1333-1334; doi:10.1093/bioinformatics/btp153 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Hua Xu and Michael A. Freitas

Automated diagnosis of LC-MS/MS performance
Bioinformatics Advance Access published on March 20, 2009
Bioinformatics 2009 25: 1341-1343; doi:10.1093/bioinformatics/btp155 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

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