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Previous Next 		Contents: Volume 25, Number 17, 1 September 2009   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     SYSTEMS BIOLOGY
Down CORRIGENDUM
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ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Henrik Bengtsson, Pratyaksha Wirapati, and Terence P. Speed
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2149-2156; doi:10.1093/bioinformatics/btp371 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, and Bertil Schmidt
SHREC: a short-read error correction method
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2157-2163; doi:10.1093/bioinformatics/btp379 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Reid F. Thompson, Masako Suzuki, Kevin W. Lau, and John M. Greally
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2164-2170; doi:10.1093/bioinformatics/btp382 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Don Gilbert and Andreas Rechtsteiner
Comments on sequence normalization of tiling array expression
Bioinformatics Advance Access published on July 4, 2009
Bioinformatics 2009 25: 2171-2173; doi:10.1093/bioinformatics/btp389 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS Back

Xiaowen Liu, Yonghua Han, Denis Yuen, and Bin Ma
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2174-2180; doi:10.1093/bioinformatics/btp366 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Liang-Tsung Huang and M. Michael Gromiha
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2181-2187; doi:10.1093/bioinformatics/btp370 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Te-Chin Chu, Tsunglin Liu, D. T. Lee, Greg C. Lee, and Arthur Chun-Chieh Shih
GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2188-2193; doi:10.1093/bioinformatics/btp372 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nava Whiteford, Tom Skelly, Christina Curtis, Matt E. Ritchie, Andrea Löhr, Alexander Wait Zaranek, Irina Abnizova, and Clive Brown
Swift: primary data analysis for the Illumina Solexa sequencing platform
Bioinformatics Advance Access published on June 23, 2009
Bioinformatics 2009 25: 2194-2199; doi:10.1093/bioinformatics/btp383 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Christophe N. Magnan, Arlo Randall, and Pierre Baldi
SOLpro: accurate sequence-based prediction of protein solubility
Bioinformatics Advance Access published on June 23, 2009
Bioinformatics 2009 25: 2200-2207; doi:10.1093/bioinformatics/btp386 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Jun Liu, Nirmalya Bandyopadhyay, Sanjay Ranka, M. Baudis, and Tamer Kahveci
Inferring progression models for CGH data
Bioinformatics Advance Access published on June 15, 2009
Bioinformatics 2009 25: 2208-2215; doi:10.1093/bioinformatics/btp365 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

David L. Gold, Jeffrey C. Miecznikowski, and Song Liu
Error control variability in pathway-based microarray analysis
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2216-2221; doi:10.1093/bioinformatics/btp385 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Ali Torkamani and Nicholas J. Schork
Prestige centrality-based functional outlier detection in gene expression analysis
Bioinformatics Advance Access published on June 23, 2009
Bioinformatics 2009 25: 2222-2228; doi:10.1093/bioinformatics/btp388 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Lars Kaderali, Eva Dazert, Ulf Zeuge, Michael Frese, and Ralf Bartenschlager
Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2229-2235; doi:10.1093/bioinformatics/btp375 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Xuerui Yang, Yang Zhou, Rong Jin, and Christina Chan
Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2236-2243; doi:10.1093/bioinformatics/btp376 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Lun Yang, Langlai Xu, and Lin He
A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction
Bioinformatics Advance Access published on June 15, 2009
Bioinformatics 2009 25: 2244-2250; doi:10.1093/bioinformatics/btp369 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Lianyi Han, Yanli Wang, and Stephen H. Bryant
A survey of across-target bioactivity results of small molecules in PubChem
Bioinformatics Advance Access published on June 23, 2009
Bioinformatics 2009 25: 2251-2255; doi:10.1093/bioinformatics/btp380 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Zheng Rong Yang, Ganjana Lertmemongkolchai, Gladys Tan, Philip L. Felgner, and Richard Titball
A genetic programming approach for Burkholderia Pseudomallei diagnostic pattern discovery
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2256-2262; doi:10.1093/bioinformatics/btp390 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

S. M. Wimalaratne, M. D. B. Halstead, C. M. Lloyd, E. J. Crampin, and P. F. Nielsen
Biophysical annotation and representation of CellML models
Bioinformatics Advance Access published on June 29, 2009
Bioinformatics 2009 25: 2263-2270; doi:10.1093/bioinformatics/btp391 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Victor M. Markowitz, Konstantinos Mavromatis, Natalia N. Ivanova, I-Min A. Chen, Ken Chu, and Nikos C. Kyrpides
IMG ER: a system for microbial genome annotation expert review and curation
Bioinformatics Advance Access published on June 27, 2009
Bioinformatics 2009 25: 2271-2278; doi:10.1093/bioinformatics/btp393 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, and Simon J. Puglisi
A fast hybrid short read fragment assembly algorithm
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2279-2280; doi:10.1093/bioinformatics/btp374 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Davide Rambaldi and Francesca D. Ciccarelli
FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2281-2282; doi:10.1093/bioinformatics/btp381 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Daniel C. Koboldt, Ken Chen, Todd Wylie, David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, and Li Ding
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 2283-2285; doi:10.1093/bioinformatics/btp373 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

PHYLOGENETICS Back

Nicolas Lartillot, Thomas Lepage, and Samuel Blanquart
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2286-2288; doi:10.1093/bioinformatics/btp368 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Mieszko Lis, Maxim N. Artyomov, Srinivas Devadas, and Arup K. Chakraborty
Efficient stochastic simulation of reaction–diffusion processes via direct compilation
Bioinformatics Advance Access published on July 3, 2009
Bioinformatics 2009 25: 2289-2291; doi:10.1093/bioinformatics/btp387 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Neil Swainston and Pedro Mendes
libAnnotationSBML: a library for exploiting SBML annotations
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2292-2293; doi:10.1093/bioinformatics/btp392 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

CORRIGENDUM Back

Macha Nikolski and David J. Sherman
Family relationships: should consensus reign?—consensus clustering for protein families
Bioinformatics 2009 25: 2294; doi:10.1093/bioinformatics/btp440 [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.