Bioinformatics

LETTER TO THE EDITOR:

M.-L. Martin-Magniette, J. Aubert, E. Cabannes, and J.-J. Daudin

Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper ‘Evaluation of the gene-specific dye-bias in cDNA microarray experiments’
Bioinformatics Advance Access published on June 7, 2005
Bioinformatics 2005 21: 3065; doi:10.1093/bioinformatics/bti479 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Neal Jeffries

Algorithms for alignment of mass spectrometry proteomic data
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3066-3073; doi:10.1093/bioinformatics/bti482 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Weixiong Zhang, Jianhua Ruan, Tuan-hua David Ho, Youngsook You, Taotao Yu, and Ralph S. Quatrano

Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 3074-3081; doi:10.1093/bioinformatics/bti490 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Rainer Pudimat, Ernst-Günter Schukat-Talamazzini, and Rolf Backofen

A multiple-feature framework for modelling and predicting transcription factor binding sites
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3082-3088; doi:10.1093/bioinformatics/bti477 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Carol L. Ecale Zhou, Adam T. Zemla, Diana Roe, Malin Young, Marisa Lam, Joseph S. Schoeniger, and Rod Balhorn

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3089-3096; doi:10.1093/bioinformatics/bti498 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Sin-Ho Jung

Sample size for FDR-control in microarray data analysis
Bioinformatics Advance Access published on April 21, 2005
Bioinformatics 2005 21: 3097-3104; doi:10.1093/bioinformatics/bti456 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Yan Lu, Peng-Yuan Liu, Peng Xiao, and Hong-Wen Deng

Hotelling's T² multivariate profiling for detecting differential expression in microarrays
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3105-3113; doi:10.1093/bioinformatics/bti496 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Peng Qiu, Z. Jane Wang, and K. J. Ray Liu

Ensemble dependence model for classification and prediction of cancer and normal gene expression data
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3114-3121; doi:10.1093/bioinformatics/bti483 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Katechan Jampachaisri, Lea Valinsky, James Borneman, and S. James Press

Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses
Bioinformatics Advance Access published on April 21, 2005
Bioinformatics 2005 21: 3122-3130; doi:10.1093/bioinformatics/bti452 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Simon Rogers and Mark Girolami

A Bayesian regression approach to the inference of regulatory networks from gene expression data
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3131-3137; doi:10.1093/bioinformatics/bti487 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Pierre Geurts, Marianne Fillet, Dominique de Seny, Marie-Alice Meuwis, Michel Malaise, Marie-Paule Merville, and Louis Wehenkel

Proteomic mass spectra classification using decision tree based ensemble methods
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 3138-3145; doi:10.1093/bioinformatics/bti494 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Tsutomu Matsunaga and Masa-aki Muramatsu

Knowledge-based computational search for genes associated with the metabolic syndrome
Bioinformatics Advance Access published on May 10, 2005
Bioinformatics 2005 21: 3146-3154; doi:10.1093/bioinformatics/bti484 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Konstantinos A. Karasavvas, Richard Baldock, and Albert Burger

A criticality-based framework for task composition in multi-agent bioinformatics integration systems
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 3155-3163; doi:10.1093/bioinformatics/bti491 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

SEQUENCE ANALYSIS:

Get checked abstract D. Benjamin Gordon, Lena Nekludova, Scott McCallum, and Ernest Fraenkel

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3164-3165; doi:10.1093/bioinformatics/bti481 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Olivier Pible, Gilles Imbert, and Jean-Luc Pellequer

INTERALIGN: interactive alignment editor for distantly related protein sequences
Bioinformatics Advance Access published on May 3, 2005
Bioinformatics 2005 21: 3166-3167; doi:10.1093/bioinformatics/bti474 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sebastian Zöllner, Xiaoquan Wen, and Jonathan K. Pritchard

Association mapping and fine mapping with TreeLD
Bioinformatics Advance Access published on April 26, 2005
Bioinformatics 2005 21: 3168-3170; doi:10.1093/bioinformatics/bti453 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Yoon-Seong Jeon, Hwanwon Chung, Sunyoung Park, Inae Hur, Jae-Hak Lee, and Jongsik Chun

jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences
Bioinformatics Advance Access published on April 26, 2005
Bioinformatics 2005 21: 3171-3173; doi:10.1093/bioinformatics/bti463 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract C. Paul Barrett and Martin E. M. Noble

Dynamite extended: two new services to simplify protein dynamic analysis
Bioinformatics Advance Access published on April 26, 2005
Bioinformatics 2005 21: 3174-3175; doi:10.1093/bioinformatics/bti464 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Carles Ferrer-Costa, Josep Lluis Gelpí, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, and Modesto Orozco

PMUT: a web-based tool for the annotation of pathological mutations on proteins
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3176-3178; doi:10.1093/bioinformatics/bti486 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dominik Gront and Andrzej Kolinski

HCPM—program for hierarchical clustering of protein models
Bioinformatics Advance Access published on April 19, 2005
Bioinformatics 2005 21: 3179-3180; doi:10.1093/bioinformatics/bti450 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sergi Vives, Bradford Loucas, Mariel Vazquez, David J. Brenner, Rainer K. Sachs, Lynn Hlatky, Michael Cornforth, and Javier Arsuaga

SCHIP: statistics for chromosome interphase positioning based on interchange data
Bioinformatics Advance Access published on May 10, 2005
Bioinformatics 2005 21: 3181-3182; doi:10.1093/bioinformatics/bti470 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract M. Obreiter, C. Fischer, J. Chang-Claude, and L. Beckmann

SDMinP: a program to control the family wise error rate using step-down minP adjusted P-values
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3183-3184; doi:10.1093/bioinformatics/bti480 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nathalie L. M. M. Pochet, Frizo A. L. Janssens, Frank De Smet, Kathleen Marchal, Johan A. K. Suykens, and Bart L. R. De Moor

M@CBETH: a microarray classification benchmarking tool
Bioinformatics Advance Access published on May 12, 2005
Bioinformatics 2005 21: 3185-3186; doi:10.1093/bioinformatics/bti495 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Alun Thomas

GMCheck: Bayesian error checking for pedigreegenotypes and phenotypes
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3187-3188; doi:10.1093/bioinformatics/bti485 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Mingyi Liu and Andrei Grigoriev

Fast parsers for Entrez Gene
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3189-3190; doi:10.1093/bioinformatics/bti488 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Burr Settles

ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text
Bioinformatics Advance Access published on April 28, 2005
Bioinformatics 2005 21: 3191-3192; doi:10.1093/bioinformatics/bti475 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Mark A. van de Wiel, Serge J. Smeets, Ruud H. Brakenhoff, and Bauke Ylstra

CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3193-3194; doi:10.1093/bioinformatics/bti489 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Thorsten Henrich, Mirana Ramialison, Beate Wittbrodt, Beatrice Assouline, Franck Bourrat, Anja Berger, Heinz Himmelbauer, Takashi Sasaki, Nobuyoshi Shimizu, Monte Westerfield, Hisato Kondoh, and Joachim Wittbrodt

MEPD: a resource for medaka gene expression patterns
Bioinformatics Advance Access published on May 6, 2005
Bioinformatics 2005 21: 3195-3197; doi:10.1093/bioinformatics/bti478 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Philip Jones, Nisha Vinod, Thomas Down, Andre Hackmann, Andreas Kahari, Ernst Kretschmann, Antony Quinn, Daniela Wieser, Henning Hermjakob, and Rolf Apweiler

Dasty and UniProt DAS: a perfect pair for protein feature visualization
Bioinformatics Advance Access published on May 19, 2005
Bioinformatics 2005 21: 3198-3199; doi:10.1093/bioinformatics/bti506 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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