Bioinformatics

EDITORIAL

Get checked abstract Jonathan D. Wren and Alex Bateman

Databases, data tombs and dust in the wind
Bioinformatics 2008 24: 2127-2128; doi:10.1093/bioinformatics/btn464 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Alejandro Cruz-Marcelo, Rudy Guerra, Marina Vannucci, Yiting Li, Ching C. Lau, and Tsz-Kwong Man

Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data
Bioinformatics Advance Access published on August 11, 2008
Bioinformatics 2008 24: 2129-2136; doi:10.1093/bioinformatics/btn398 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Chandra Erdman and John W. Emerson

A fast Bayesian change point analysis for the segmentation of microarray data
Bioinformatics Advance Access published on July 29, 2008
Bioinformatics 2008 24: 2143-2148; doi:10.1093/bioinformatics/btn404 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract M. Peifer, J. E. Karro, and H. H. von Grünberg

Is there an acceleration of the CpG transition rate during the mammalian radiation?
Bioinformatics Advance Access published on July 28, 2008
Bioinformatics 2008 24: 2157-2164; doi:10.1093/bioinformatics/btn391 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Virpi Ahola, Tero Aittokallio, Mauno Vihinen, and Esa Uusipaikka

Model-based prediction of sequence alignment quality
Bioinformatics Advance Access published on August 4, 2008
Bioinformatics 2008 24: 2165-2171; doi:10.1093/bioinformatics/btn414 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Karl Frank and Manfred J. Sippl

High-performance signal peptide prediction based on sequence alignment techniques
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2172-2176; doi:10.1093/bioinformatics/btn422 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS

Get checked abstract Andrew D. Fernandes and William R. Atchley

Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative
Bioinformatics Advance Access published on July 28, 2008
Bioinformatics 2008 24: 2177-2183; doi:10.1093/bioinformatics/btn395 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Michael Hirsch and Michael Habeck

Mixture models for protein structure ensembles
Bioinformatics Advance Access published on July 28, 2008
Bioinformatics 2008 24: 2184-2192; doi:10.1093/bioinformatics/btn396 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Jianhua Hu

Cancer outlier detection based on likelihood ratio test
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2193-2199; doi:10.1093/bioinformatics/btn372 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Eleni Giannoulatou, Christopher Yau, Stefano Colella, Jiannis Ragoussis, and Christopher C. Holmes

GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population
Bioinformatics Advance Access published on July 24, 2008
Bioinformatics 2008 24: 2209-2214; doi:10.1093/bioinformatics/btn386 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Zhihong Ding, Thomas Mailund, and Yun S. Song

Efficient whole-genome association mapping using local phylogenies for unphased genotype data
Bioinformatics Advance Access published on July 30, 2008
Bioinformatics 2008 24: 2215-2221; doi:10.1093/bioinformatics/btn406 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Gilles Guillot

Inference of structure in subdivided populations at low levels of genetic differentiation—the correlated allele frequencies model revisited
Bioinformatics Advance Access published on August 18, 2008
Bioinformatics 2008 24: 2222-2228; doi:10.1093/bioinformatics/btn419 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Marco Terzer and Jörg Stelling

Large-scale computation of elementary flux modes with bit pattern trees
Bioinformatics Advance Access published on August 1, 2008
Bioinformatics 2008 24: 2229-2235; doi:10.1093/bioinformatics/btn401 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Diogo A. R. S. Latino, Qing-You Zhang, and João Aires-de-Sousa

Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps
Bioinformatics Advance Access published on August 1, 2008
Bioinformatics 2008 24: 2236-2244; doi:10.1093/bioinformatics/btn405 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Albert Gevorgyan, Mark G. Poolman, and David A. Fell

Detection of stoichiometric inconsistencies in biomolecular models
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2245-2251; doi:10.1093/bioinformatics/btn425 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Simon Moxon, Frank Schwach, Tamas Dalmay, Dan MacLean, David J. Studholme, and Vincent Moulton

A toolkit for analysing large-scale plant small RNA datasets
Bioinformatics Advance Access published on August 19, 2008
Bioinformatics 2008 24: 2252-2253; doi:10.1093/bioinformatics/btn428 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Wencheng Li, Bo Yang, Shaoguang Liang, Yonghua Wang, Chris Whiteley, Yicheng Cao, and Xiaoning Wang

BLogo: a tool for visualization of bias in biological sequences
Bioinformatics Advance Access published on August 4, 2008
Bioinformatics 2008 24: 2254-2255; doi:10.1093/bioinformatics/btn407 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Patrick Ng and Uri Keich

GIMSAN: a Gibbs motif finder with significance analysis
Bioinformatics Advance Access published on August 14, 2008
Bioinformatics 2008 24: 2256-2257; doi:10.1093/bioinformatics/btn408 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Doroteya K. Staykova, Jonas Fredriksson, and Martin Billeter

PRODECOMPv3: decompositions of NMR projections for protein backbone and side-chain assignments and structural studies
Bioinformatics Advance Access published on August 13, 2008
Bioinformatics 2008 24: 2258-2259; doi:10.1093/bioinformatics/btn423 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Lin S. Chen and John D. Storey

Eigen-R² for dissecting variation in high-dimensional studies
Bioinformatics Advance Access published on August 20, 2008
Bioinformatics 2008 24: 2260-2262; doi:10.1093/bioinformatics/btn411 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Ananyo Choudhury and Ansuman Lahiri

Arabidopsis thaliana regulatory element analyzer
Bioinformatics Advance Access published on August 11, 2008
Bioinformatics 2008 24: 2263-2264; doi:10.1093/bioinformatics/btn417 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesús Izaguirre

Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference
Bioinformatics Advance Access published on July 24, 2008
Bioinformatics 2008 24: 2265-2266; doi:10.1093/bioinformatics/btn380 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Anastasia Alexandridou, George Th. Tsangaris, Konstantinos Vougas, Konstantina Nikita, and George Spyrou

Peptide Finder: mapping measured molecular masses to peptides and proteins
Bioinformatics Advance Access published on August 6, 2008
Bioinformatics 2008 24: 2267-2269; doi:10.1093/bioinformatics/btn413 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

Get checked abstract Tiago L. Moda, Leonardo G. Torres, Alexandre E. Carrara, and Adriano D. Andricopulo

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models
Bioinformatics Advance Access published on August 6, 2008
Bioinformatics 2008 24: 2270-2271; doi:10.1093/bioinformatics/btn415 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDA

Sofia Wichert, Konstantinos Fokianos, and Korbinian Strimmer

Identifying periodically expressed transcripts in microarray time series data
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2274; doi:10.1093/bioinformatics/btn430 [Extract] [Full Text] [Print PDF] [Request Permissions]  

Kristoffer Forslund and Erik L. L. Sonnhammer

Predicting protein function from domain content
Bioinformatics 2008 24: 2275; doi:10.1093/bioinformatics/btn447 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ERRATUM

Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, and Yidong Chen

A probe-density-based analysis method for array CGH data: simulation, normalization and centralization
Bioinformatics 2008 24: 2276; doi:10.1093/bioinformatics/btn448 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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