Bioinformatics

EDITORIALS:

Alex Bateman and Alfonso Valencia

Structural genomics meets computational biology
Bioinformatics 2006 22: 2319; doi:10.1093/bioinformatics/btl426 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL ARTICLES:

GENOME ANALYSIS:

Get checked abstract Yiming Cheng, Robert M. Miura, and Bin Tian

Prediction of mRNA polyadenylation sites by support vector machine
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2320-2325; doi:10.1093/bioinformatics/btl394 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Bin Song, Jeong-Hyeon Choi, Guangyu Chen, Jacek Szymanski, Guo-Qiang Zhang, Anthony K. H. Tung, Jaewoo Kang, Sun Kim, and Jiong Yang

ARCS: an aggregated related column scoring scheme for aligned sequences
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2326-2332; doi:10.1093/bioinformatics/btl398 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract E. Ferraro, A. Via, G. Ausiello, and M. Helmer-Citterich

A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2333-2339; doi:10.1093/bioinformatics/btl403 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Aalt D. J. van Dijk and Alexandre M. J. J. Bonvin

Solvated docking: introducing water into the modelling of biomolecular complexes
Bioinformatics Advance Access published on August 9, 2006
Bioinformatics 2006 22: 2340-2347; doi:10.1093/bioinformatics/btl395 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Gavin C. Cawley and Nicola L. C. Talbot

Gene selection in cancer classification using sparse logistic regression with Bayesian regularization
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2348-2355; doi:10.1093/bioinformatics/btl386 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, and Ralf Zimmer

Reliable gene signatures for microarray classification: assessment of stability and performance
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2356-2363; doi:10.1093/bioinformatics/btl400 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Darlene R. Goldstein

Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2364-2372; doi:10.1093/bioinformatics/btl402 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sek Won Kong, William T. Pu, and Peter J. Park

A multivariate approach for integrating genome-wide expression data and biological knowledge
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2373-2380; doi:10.1093/bioinformatics/btl401 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ann L. Oberg, Douglas W. Mahoney, Karla V. Ballman, and Terry M. Therneau

Joint estimation of calibration and expression for high-density oligonucleotide arrays
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2381-2387; doi:10.1093/bioinformatics/btl399 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Wei Pan, Xiaotong Shen, Aixiang Jiang, and Robert P. Hebbel

Semi-supervised learning via penalized mixture model with application to microarray sample classification
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2388-2395; doi:10.1093/bioinformatics/btl393 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Antonio Reverter, Aaron Ingham, Sigrid A. Lehnert, Siok-Hwee Tan, Yonghong Wang, Abhirami Ratnakumar, and Brian P. Dalrymple

Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
Bioinformatics Advance Access published on July 24, 2006
Bioinformatics 2006 22: 2396-2404; doi:10.1093/bioinformatics/btl392 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Anbupalam Thalamuthu, Indranil Mukhopadhyay, Xiaojing Zheng, and George C. Tseng

Evaluation and comparison of gene clustering methods in microarray analysis
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2405-2412; doi:10.1093/bioinformatics/btl406 [Abstract] [Full Text] [Print PDF] [Supplementary material] [Request Permissions]  

Get checked abstract Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen

Inferring gene regulatory networks from multiple microarray datasets
Bioinformatics Advance Access published on July 24, 2006
Bioinformatics 2006 22: 2413-2420; doi:10.1093/bioinformatics/btl396 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Chao Sima and Edward R. Dougherty

What should be expected from feature selection in small-sample settings
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2430-2436; doi:10.1093/bioinformatics/btl407 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

SEQUENCE ANALYSIS:

Get checked abstract Fabrice Armougom, Olivier Poirot, Sébastien Moretti, Desmond G. Higgins, Phillip Bucher, Vladimir Keduas, and Cedric Notredame

APDB: a web server to evaluate the accuracy of sequence alignments using structural information
Bioinformatics 2006 22: 2439-2440; doi:10.1093/bioinformatics/btl404 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Karsten Hiller, Andreas Grote, Matthias Maneck, Richard Münch, and Dieter Jahn

JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2441-2443; doi:10.1093/bioinformatics/btl409 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, and Ulf Leser

ALIBABA: PubMed as a graph
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2444-2445; doi:10.1093/bioinformatics/btl408 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTER TO EDITOR:

GENE EXPRESSION:

Xiao-Lin Wu, Larry J. Forney, and Paul Joyce

Comments on ‘Bayesian hierarchical error model for analysis of gene expression data’
Bioinformatics Advance Access published on May 26, 2006
Bioinformatics 2006 22: 2446-2451; doi:10.1093/bioinformatics/btl173 [Extract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

Corrigendum
Bioinformatics 2006 22: 2453; doi:10.1093/bioinformatics/btl435 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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