Bioinformatics

LETTER TO THE EDITOR:

GENE EXPRESSION:

Kevin K. Dobbin, Joanna H. Shih, and Richard M. Simon

Comment on ‘Evaluation of the gene-specific dye bias in cDNA microarray experiments’
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2803-2804; doi:10.1093/bioinformatics/bti428 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Get checked abstract Vivek Anantharaman and L. Aravind

MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2805-2811; doi:10.1093/bioinformatics/bti418 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Alan M. Durham, André Y. Kashiwabara, Fernando T. G. Matsunaga, Paulo H. Ahagon, Flávia Rainone, Leonardo Varuzza, and Arthur Gruber

EGene: a configurable pipeline generation system for automated sequence analysis
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2812-2813; doi:10.1093/bioinformatics/bti424 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, and Andrej Sali

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
Bioinformatics Advance Access published on April 12, 2005
Bioinformatics 2005 21: 2814-2820; doi:10.1093/bioinformatics/bti442 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract B. Anand, V.S. Gowri, and N. Srinivasan

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2821-2826; doi:10.1093/bioinformatics/bti432 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Aleksandar Poleksic, Joseph F. Danzer, Kevin Hambly, and Derek A. Debe

Convergent Island Statistics: a fast method for determining local alignment score significance
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2827-2831; doi:10.1093/bioinformatics/bti433 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Guoying Qi, Richard Lee, and Steven Hayward

A comprehensive and non-redundant database of protein domain movements
Bioinformatics Advance Access published on March 31, 2005
Bioinformatics 2005 21: 2832-2838; doi:10.1093/bioinformatics/bti420 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Geraint L. Thomas, Richard B. Sessions, and Martin J. Parker

Density guided importance sampling: application to a reduced model of protein folding
Bioinformatics Advance Access published on March 31, 2005
Bioinformatics 2005 21: 2839-2843; doi:10.1093/bioinformatics/bti421 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jaehyun Sim, Seung-Yeon Kim, and Julian Lee

Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2844-2849; doi:10.1093/bioinformatics/bti423 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract A. Selim Aytuna, Attila Gursoy, and Ozlem Keskin

Prediction of protein–protein interactions by combining structure and sequence conservation in protein interfaces
Bioinformatics Advance Access published on April 26, 2005
Bioinformatics 2005 21: 2850-2855; doi:10.1093/bioinformatics/bti443 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Daniele Varrazzo, Andrea Bernini, Ottavia Spiga, Arianna Ciutti, Stefano Chiellini, Vincenzo Venditti, Luisa Bracci, and Neri Niccolai

Three-dimensional computation of atom depth in complex molecular structures
Bioinformatics Advance Access published on April 12, 2005
Bioinformatics 2005 21: 2856-2860; doi:10.1093/bioinformatics/bti444 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Dung-Tsa Chen, James J. Chen, and Seng-jaw Soong

Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2861-2866; doi:10.1093/bioinformatics/bti413 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Albert M. Levin, Debashis Ghosh, Kathleen R. Cho, and Sharon L. R. Kardia

A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2867-2874; doi:10.1093/bioinformatics/bti417 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Qunhua Li, Chris Fraley, Roger E. Bumgarner, Ka Yee Yeung, and Adrian E. Raftery

Donuts, scratches and blanks: robust model-based segmentation of microarray images
Bioinformatics Advance Access published on April 21, 2005
Bioinformatics 2005 21: 2875-2882; doi:10.1093/bioinformatics/bti447 [Abstract] [Full Text] [Print PDF] [HTML Page - index.htslp] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Kuang-Chi Chen, Tse-Yi Wang, Huei-Hun Tseng, Chi-Ying F. Huang, and Cheng-Yan Kao

A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
Bioinformatics Advance Access published on March 31, 2005
Bioinformatics 2005 21: 2883-2890; doi:10.1093/bioinformatics/bti415 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract F. Pappalardo, P.-L. Lollini, F. Castiglione, and S. Motta

Modeling and simulation of cancer immunoprevention vaccine
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2891-2897; doi:10.1093/bioinformatics/bti426 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Lawrence Cabusora, Electra Sutton, Andy Fulmer, and Christian V. Forst

Differential network expression during drug and stress response
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 2898-2905; doi:10.1093/bioinformatics/bti440 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Florence Armand, Philipp Bucher, C. Victor Jongeneel, and Edward E. Farmer

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2906-2908; doi:10.1093/bioinformatics/bti435 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Dongsheng Che, Shane Jensen, Liming Cai, and Jun S. Liu

BEST: Binding-site Estimation Suite of Tools
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2909-2911; doi:10.1093/bioinformatics/bti425 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Benjamin Schuster-Böckler and Alex Bateman

Visualizing profile–profile alignment: pairwise HMM logos
Bioinformatics Advance Access published on April 12, 2005
Bioinformatics 2005 21: 2912-2913; doi:10.1093/bioinformatics/bti434 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Adrian A. Canutescu and Roland L. Dunbrack, Jr.

MollDE: a homology modeling framework you can click with
Bioinformatics Advance Access published on April 21, 2005
Bioinformatics 2005 21: 2914-2916; doi:10.1093/bioinformatics/bti438 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Harpreet Kaur Saini and Daniel Fischer

Meta-DP: domain prediction meta-server
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 2917-2920; doi:10.1093/bioinformatics/bti445 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Stefanie Scheid and Rainer Spang

twilight; a Bioconductor package for estimating the local false discovery rate
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2921-2922; doi:10.1093/bioinformatics/bti436 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Johan Hattne, David Fange, and Johan Elf

Stochastic reaction-diffusion simulation with MesoRD
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2923-2924; doi:10.1093/bioinformatics/bti431 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Yu Zheng and Daiwen Yang

STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures
Bioinformatics Advance Access published on April 12, 2005
Bioinformatics 2005 21: 2925-2926; doi:10.1093/bioinformatics/bti437 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Chunhong Mao, Jing Qiu, Chunxia Wang, Trevor C. Charles, and Bruno W. S. Sobral

NodMutDB: a database for genes and mutants involved in symbiosis
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2927-2929; doi:10.1093/bioinformatics/bti427 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Eain C. J. Green, Georgios V. Gkoutos, Heena V. Lad, Andrew Blake, Joseph Weekes, and John M. Hancock

EMPReSS: European Mouse Phenotyping Resource for Standardized Screens
Bioinformatics Advance Access published on April 12, 2005
Bioinformatics 2005 21: 2930-2931; doi:10.1093/bioinformatics/bti441 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 2932; doi:10.1093/bioinformatics/bti501 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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