Bioinformatics

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Bo Yan, Chongle Pan, Victor N. Olman, Robert L. Hettich, and Ying Xu

A graph-theoretic approach for the separation of b and y ions in tandem mass spectra
Bioinformatics Advance Access published on September 28, 2004
Bioinformatics 2005 21: 563-574; doi:10.1093/bioinformatics/bti044 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yu Chen and Dong Xu

Understanding protein dispensability through machine-learning analysis of high-throughput data
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 575-581; doi:10.1093/bioinformatics/bti058 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Davide Campagna, Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Matej Lexa, Nicola Cannata, and Giorgio Valle

RAP: a new computer program for de novo identification of repeated sequences in whole genomes
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 582-588; doi:10.1093/bioinformatics/bti039 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jinko Graham, Brad McNeney, and Françoise Seillier-Moiseiwitsch

Stepwise detection of recombination breakpoints in sequence alignments
Bioinformatics Advance Access published on September 23, 2004
Bioinformatics 2005 21: 589-595; doi:10.1093/bioinformatics/bti040 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Y. Barash, G. Elidan, T. Kaplan, and N. Friedman

CIS: compound importance sampling method for protein–DNA binding site p-value estimation
Bioinformatics Advance Access published on September 28, 2004
Bioinformatics 2005 21: 596-600; doi:10.1093/bioinformatics/bti041 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract S. Burden, Y.-X. Lin, and R. Zhang

Improving promoter prediction Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences
Bioinformatics Advance Access published on September 28, 2004
Bioinformatics 2005 21: 601-607; doi:10.1093/bioinformatics/bti047 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Luciano da Fontoura Costa

Biological sequence analysis through the one-dimensional percolation transform and its enhanced version
Bioinformatics Advance Access published on September 30, 2004
Bioinformatics 2005 21: 608-616; doi:10.1093/bioinformatics/bti050 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract J. L. Gardy, M. R. Laird, F. Chen, S. Rey, C. J. Walsh, M. Ester, and F. S. L. Brinkman

PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
Bioinformatics Advance Access published on October 22, 2004
Bioinformatics 2005 21: 617-623; doi:10.1093/bioinformatics/bti057 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Ming Zhang, R. Allen White, Liqun Wang, Ronald Goldman, Lydia Kavraki, and Brendan Hassett

Improving conformational searches by geometric screening
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 624-630; doi:10.1093/bioinformatics/bti055 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Alexander Statnikov, Constantin F. Aliferis, Ioannis Tsamardinos, Douglas Hardin, and Shawn Levy

A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 631-643; doi:10.1093/bioinformatics/bti033 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Musa H. Asyali and Musa Alci

Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 644-649; doi:10.1093/bioinformatics/bti036 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Itai Yanai, Hila Benjamin, Michael Shmoish, Vered Chalifa-Caspi, Maxim Shklar, Ron Ophir, Arren Bar-Even, Shirley Horn-Saban, Marilyn Safran, Eytan Domany, Doron Lancet, and Orit Shmueli

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
Bioinformatics Advance Access published on September 23, 2004
Bioinformatics 2005 21: 650-659; doi:10.1093/bioinformatics/bti042 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Cyril Dalmasso, Philippe Broët, and Thierry Moreau

A simple procedure for estimating the false discovery rate
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 660-668; doi:10.1093/bioinformatics/bti063 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Yecheng Huang, Janie Pumphrey, and Alan R. Gingle

ESTminer: a Web interface for mining EST contig and cluster databases
Bioinformatics Advance Access published on September 16, 2004
Bioinformatics 2005 21: 669-670; doi:10.1093/bioinformatics/bti030 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Huiqing Liu, Hao Han, Jinyan Li, and Limsoon Wong

DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences
Bioinformatics Advance Access published on July 29, 2004
Bioinformatics 2005 21: 671-673; doi:10.1093/bioinformatics/bth437 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Robert J. Beynon

A simple tool for drawing proteolytic peptide maps
Bioinformatics Advance Access published on November 11, 2004
Bioinformatics 2005 21: 674-675; doi:10.1093/bioinformatics/bti077 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Sergei L. Kosakovsky Pond, Simon D. W. Frost, and Spencer V. Muse

HyPhy: hypothesis testing using phylogenies
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 676-679; doi:10.1093/bioinformatics/bti079 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Norma H. Pawley, Jason D. Gans, and Ryszard Michalczyk

APART: Automated Preprocessing for NMR Assignments with Reduced Tedium
Bioinformatics Advance Access published on September 23, 2004
Bioinformatics 2005 21: 680-682; doi:10.1093/bioinformatics/bti043 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Frank Zöllner, Steffen Neumann, Franz Kummert, and Gerhard Sagerer

Database driven test case generation for protein–protein docking
Bioinformatics Advance Access published on October 12, 2004
Bioinformatics 2005 21: 683-684; doi:10.1093/bioinformatics/bti061 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Doreen Pahlke, Dietmar Leitner, Urs Wiedemann, and Dirk Labudde

COPS—Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 685-686; doi:10.1093/bioinformatics/bti089 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Henrik Bjørn Nielsen, Laurent Gautier, and Steen Knudsen

Implementation of a gene expression index calculation method based on the PDNN model
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 687-688; doi:10.1093/bioinformatics/bti078 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Johnson Kian-Kok Ng and Wen-Tso Liu

LabArray: real-time imaging and analytical tool for microarrays
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 689-690; doi:10.1093/bioinformatics/bti088 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Rex T. Nelson, David Grant, and Randy C. Shoemaker

ESTminer: a suite of programs for gene and allele identification
Bioinformatics Advance Access published on November 5, 2004
Bioinformatics 2005 21: 691-693; doi:10.1093/bioinformatics/bti075 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Jing Ding and Daniel Berleant

MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations
Bioinformatics Advance Access published on October 27, 2004
Bioinformatics 2005 21: 694-695; doi:10.1093/bioinformatics/bti087 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Marius Felder, Karol Szafranski, Rüdiger Lehmann, Ludwig Eichinger, Angelika A. Noegel, Matthias Platzer, and Gernot Glöckner

DictyMOLD-a Dictyostelium discoideum genome browser database
Bioinformatics Advance Access published on January 28, 2005
Bioinformatics 2005 21: 696-697; doi:10.1093/bioinformatics/bti250 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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