Bioinformatics

ORIGINAL PAPERS

SEQUENCE ANALYSIS

Get checked abstract Krishna R. Kalari, Thomas L. Casavant, and Todd E. Scheetz

A knowledge-based approach to predict intragenic deletions or duplications
Bioinformatics Advance Access published on July 21, 2008
Bioinformatics 2008 24: 1975-1979; doi:10.1093/bioinformatics/btn370 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Matthew N. Davies, Andrew Secker, Alex A. Freitas, Edward Clark, Jon Timmis, and Darren R. Flower

Optimizing amino acid groupings for GPCR classification
Bioinformatics Advance Access published on August 1, 2008
Bioinformatics 2008 24: 1980-1986; doi:10.1093/bioinformatics/btn382 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Xiang Chen, Si-Min He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, and Wen Gao

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
Bioinformatics Advance Access published on June 27, 2008
Bioinformatics 2008 24: 1994-2001; doi:10.1093/bioinformatics/btn327 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Majid Masso and Iosif I. Vaisman

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 2002-2009; doi:10.1093/bioinformatics/btn353 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Dhammika Amaratunga, Javier Cabrera, and Yung-Seop Lee

Enriched random forests
Bioinformatics Advance Access published on July 22, 2008
Bioinformatics 2008 24: 2010-2014; doi:10.1093/bioinformatics/btn356 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Liang Chen, Tiejun Tong, and Hongyu Zhao

Considering dependence among genes and markers for false discovery control in eQTL mapping
Bioinformatics Advance Access published on July 17, 2008
Bioinformatics 2008 24: 2015-2022; doi:10.1093/bioinformatics/btn373 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Jean-Pierre Kocher, Dennis A. Wigle, Vipin Kumar, and Rui Kuang

Robust and efficient identification of biomarkers by classifying features on graphs
Bioinformatics Advance Access published on July 24, 2008
Bioinformatics 2008 24: 2023-2029; doi:10.1093/bioinformatics/btn383 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

SYSTEMS BIOLOGY

Get checked abstract Markus W. Covert, Nan Xiao, Tiffany J. Chen, and Jonathan R. Karr

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Bioinformatics Advance Access published on July 10, 2008
Bioinformatics 2008 24: 2044-2050; doi:10.1093/bioinformatics/btn352 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Viviane Galvão, José Garcia Vivas Miranda, and Ricardo Ribeiro-dos-Santos

Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation
Bioinformatics Advance Access published on July 17, 2008
Bioinformatics 2008 24: 2051-2056; doi:10.1093/bioinformatics/btn362 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Min Zhang, Chen Yao, Zheng Guo, Jinfeng Zou, Lin Zhang, Hui Xiao, Dong Wang, Da Yang, Xue Gong, Jing Zhu, Yanhui Li, and Xia Li

Apparently low reproducibility of true differential expression discoveries in microarray studies
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 2057-2063; doi:10.1093/bioinformatics/btn365 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Mudassar Iqbal, Alex A. Freitas, Colin G. Johnson, and Massimo Vergassola

Message-passing algorithms for the prediction of protein domain interactions from protein–protein interaction data
Bioinformatics Advance Access published on July 17, 2008
Bioinformatics 2008 24: 2064-2070; doi:10.1093/bioinformatics/btn366 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Marco Grzegorczyk, Dirk Husmeier, Kieron D. Edwards, Peter Ghazal, and Andrew J. Millar

Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler
Bioinformatics Advance Access published on July 28, 2008
Bioinformatics 2008 24: 2071-2078; doi:10.1093/bioinformatics/btn367 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Kathrin Fenner, Junfeng Gao, Stefan Kramer, Lynda Ellis, and Larry Wackett

Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction
Bioinformatics Advance Access published on July 19, 2008
Bioinformatics 2008 24: 2079-2085; doi:10.1093/bioinformatics/btn378 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE

SEQUENCE ANALYSIS

Get checked abstract Marco Lippi, Andrea Passerini, Marco Punta, Burkhard Rost, and Paolo Frasconi

MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 2094-2095; doi:10.1093/bioinformatics/btn371 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS

Get checked abstract Campbell O. Webb, David D. Ackerly, and Steven W. Kembel

Phylocom: software for the analysis of phylogenetic community structure and trait evolution
Bioinformatics Advance Access published on August 4, 2008
Bioinformatics 2008 24: 2098-2100; doi:10.1093/bioinformatics/btn358 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Romain Gautier, Dominique Douguet, Bruno Antonny, and Guillaume Drin

HELIQUEST: a web server to screen sequences with specific -helical properties
Bioinformatics Advance Access published on July 28, 2008
Bioinformatics 2008 24: 2101-2102; doi:10.1093/bioinformatics/btn392 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract William D. Nelson, Kert Viele, and Bert C. Lynn

An integrated approach for automating validation of extracted ion chromatographic peaks
Bioinformatics Advance Access published on July 24, 2008
Bioinformatics 2008 24: 2103-2104; doi:10.1093/bioinformatics/btn385 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

SYSTEMS BIOLOGY

Get checked abstract H. Ramos, P. Shannon, and R. Aebersold

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 2110-2111; doi:10.1093/bioinformatics/btn363 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jan Krumsiek, Caroline C. Friedel, and Ralf Zimmer

ProCope—protein complex prediction and evaluation
Bioinformatics Advance Access published on July 17, 2008
Bioinformatics 2008 24: 2115-2116; doi:10.1093/bioinformatics/btn376 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Bing Xiong, Ke Liu, Jie Wu, David L. Burk, Hualiang Jiang, and Jingkang Shen

DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
Bioinformatics Advance Access published on July 25, 2008
Bioinformatics 2008 24: 2117-2118; doi:10.1093/bioinformatics/btn389 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

Get checked abstract Rafael C. Jimenez, Antony F. Quinn, Alexander Garcia, Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A. Salazar, and Henning Hermjakob

Dasty2, an Ajax protein DAS client
Bioinformatics Advance Access published on August 11, 2008
Bioinformatics 2008 24: 2119-2121; doi:10.1093/bioinformatics/btn387 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Catherine M. Lloyd, James R. Lawson, Peter J. Hunter, and Poul F. Nielsen

The CellML Model Repository
Bioinformatics Advance Access published on July 25, 2008
Bioinformatics 2008 24: 2122-2123; doi:10.1093/bioinformatics/btn390 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTER TO THE EDITOR

GENOME ANALYSIS

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