Bioinformatics

REVIEW:

DATA AND TEXT MINING:

Get checked abstract Julia Handl, Joshua Knowles, and Douglas B. Kell

Computational cluster validation in post-genomic data analysis
Bioinformatics Advance Access published on May 24, 2005
Bioinformatics 2005 21: 3201-3212; doi:10.1093/bioinformatics/bti517 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE:

GENOME ANALYSIS:

Get checked abstract Mingyi Liu, Shaoping Wu, Heiko Walch, and Andrei Grigoriev

Exon–domain correlation and its corollaries
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3213-3216; doi:10.1093/bioinformatics/bti509 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Jason McDermott, Roger Bumgarner, and Ram Samudrala

Functional annotation from predicted protein interaction networks
Bioinformatics Advance Access published on May 26, 2005
Bioinformatics 2005 21: 3217-3226; doi:10.1093/bioinformatics/bti514 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Hsin-Nan Lin, Jia-Ming Chang, Kuen-Pin Wu, Ting-Yi Sung, and Wen-Lian Hsu

HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence
Bioinformatics Advance Access published on June 2, 2005
Bioinformatics 2005 21: 3227-3233; doi:10.1093/bioinformatics/bti524 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Daeui Park, Semin Lee, Dan Bolser, Michael Schroeder, Michael Lappe, Donghoon Oh, and Jong Bhak

Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)
Bioinformatics Advance Access published on May 24, 2005
Bioinformatics 2005 21: 3234-3240; doi:10.1093/bioinformatics/bti512 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jason Weston, Christina Leslie, Eugene Ie, Dengyong Zhou, Andre Elisseeff, and William Stafford Noble

Semi-supervised protein classification using cluster kernels
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3241-3247; doi:10.1093/bioinformatics/bti497 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract D. R. Goucher, S. M. Wincovitch, S. H. Garfield, K. M. Carbone, and T. H. Malik

A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3248-3254; doi:10.1093/bioinformatics/bti531 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dmitry Lupyan, Alejandra Leo-Macias, and Angel R. Ortiz

A new progressive-iterative algorithm for multiple structure alignment
Bioinformatics Advance Access published on June 7, 2005
Bioinformatics 2005 21: 3255-3263; doi:10.1093/bioinformatics/bti527 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Jianhua Hu, Fei Zou, and Fred A. Wright

Practical FDR-based sample size calculations in microarray experiments
Bioinformatics Advance Access published on June 2, 2005
Bioinformatics 2005 21: 3264-3272; doi:10.1093/bioinformatics/bti519 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Andrei S. Rodin and Eric Boerwinkle

Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels)
Bioinformatics Advance Access published on May 24, 2005
Bioinformatics 2005 21: 3273-3278; doi:10.1093/bioinformatics/bti505 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Editorial Note] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Yin Liu, Nianjun Liu, and Hongyu Zhao

Inferring protein–protein interactions through high-throughput interaction data from diverse organisms
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3279-3285; doi:10.1093/bioinformatics/bti492 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, and Adam P. Arkin

A latent variable model for chemogenomic profiling
Bioinformatics Advance Access published on May 26, 2005
Bioinformatics 2005 21: 3286-3293; doi:10.1093/bioinformatics/bti515 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yu Hao, Xiaoyan Zhu, Minlie Huang, and Ming Li

Discovering patterns to extract protein–protein interactions from the literature: Part II
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 3294-3300; doi:10.1093/bioinformatics/bti493 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Annette M. Molinaro, Richard Simon, and Ruth M. Pfeiffer

Prediction error estimation: a comparison of resampling methods
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3301-3307; doi:10.1093/bioinformatics/bti499 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Adam A. Margolin, Joel Greshock, Tara L. Naylor, Yael Mosse, John M. Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, and Barbara L. Weber

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3308-3311; doi:10.1093/bioinformatics/bti500 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Anke Busch, Sebastian Will, and Rolf Backofen

SECISDesign: a server to design SECIS-elements within the coding sequence
Bioinformatics Advance Access published on May 26, 2005
Bioinformatics 2005 21: 3312-3313; doi:10.1093/bioinformatics/bti507 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andrew E. Firth and Wayne M. Patrick

Statistics of protein library construction
Bioinformatics Advance Access published on June 2, 2005
Bioinformatics 2005 21: 3314-3315; doi:10.1093/bioinformatics/bti516 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Swanand P. Gore, David F. Burke, and Tom L. Blundell

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes
Bioinformatics Advance Access published on June 2, 2005
Bioinformatics 2005 21: 3316-3317; doi:10.1093/bioinformatics/bti523 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jason Vertrees, Phillip Barritt, Steve Whitten, and Vincent J. Hilser

COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures
Bioinformatics Advance Access published on May 27, 2005
Bioinformatics 2005 21: 3318-3319; doi:10.1093/bioinformatics/bti520 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fabrice Jossinet and Eric Westhof

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3320-3321; doi:10.1093/bioinformatics/bti504 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Zoltán Gáspári, Kristian Vlahovicek, and Sándor Pongor

Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm
Bioinformatics Advance Access published on May 24, 2005
Bioinformatics 2005 21: 3322-3323; doi:10.1093/bioinformatics/bti513 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, and John Quackenbush

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms
Bioinformatics Advance Access published on May 26, 2005
Bioinformatics 2005 21: 3324-3326; doi:10.1093/bioinformatics/bti503 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Liskin Swint-Kruse and Curties S. Brown

Resmap: automated representation of macromolecular interfaces as two-dimensional networks
Bioinformatics Advance Access published on May 24, 2005
Bioinformatics 2005 21: 3327-3328; doi:10.1093/bioinformatics/bti511 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Hongseok Yun, Dong-Yup Lee, Joonwoo Jeong, Seunghyun Lee, and Sang Yup Lee

MFAML: a standard data structure for representing and exchanging metabolic flux models
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3329-3330; doi:10.1093/bioinformatics/bti502 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 3331; doi:10.1093/bioinformatics/bti552 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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