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Previous Next 		Contents: Volume 22, Number 8, 15 April 2006   [Index by Author] 
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       CORRIGENDUM
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To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

A. M. Quirke, F. Jerry Reen, Marcus J. Claesson, and E. Fidelma Boyd
Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen
Bioinformatics Advance Access published on January 27, 2006
Bioinformatics 2006 22: 905-910; doi:10.1093/bioinformatics/btl015 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Philippe Broët and Sylvia Richardson
Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model
Bioinformatics Advance Access published on February 2, 2006
Bioinformatics 2006 22: 911-918; doi:10.1093/bioinformatics/btl035 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Hao Xiong
Non-linear tests for identifying differentially expressed genes or genetic networks
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 919-923; doi:10.1093/bioinformatics/btl034 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Benjamin R. Jefferys, Lawrence A. Kelley, Marek J. Sergot, John Fox, and Michael J. E. Sternberg
Capturing expert knowledge with argumentation: a case study in bioinformatics
Bioinformatics Advance Access published on January 29, 2006
Bioinformatics 2006 22: 924-933; doi:10.1093/bioinformatics/btl018 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Kay C. Wiese and Andrew Hendriks
Comparison of P-RnaPredict and mfold—algorithms for RNA secondary structure prediction
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 934-942; doi:10.1093/bioinformatics/btl043 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Sepp Hochreiter, Djork-Arné Clevert, and Klaus Obermayer
A new summarization method for affymetrix probe level data
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 943-949; doi:10.1093/bioinformatics/btl033 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ja-Yong Koo, Insuk Sohn, Sujong Kim, and Jae Won Lee
Structured polychotomous machine diagnosis of multiple cancer types using gene expression
Bioinformatics Advance Access published on February 1, 2006
Bioinformatics 2006 22: 950-958; doi:10.1093/bioinformatics/btl029 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Peng Qiu, Z. Jane Wang, and K. J. Ray Liu
Polynomial model approach for resynchronization analysis of cell-cycle gene expression data
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 959-966; doi:10.1093/bioinformatics/btl017 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Xiang Guo, Rongxiang Liu, Craig D. Shriver, Hai Hu, and Michael N. Liebman
Assessing semantic similarity measures for the characterization of human regulatory pathways
Bioinformatics Advance Access published on February 21, 2006
Bioinformatics 2006 22: 967-973; doi:10.1093/bioinformatics/btl042 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

N. Przulj, D. G. Corneil, and I. Jurisica
Efficient estimation of graphlet frequency distributions in protein–protein interaction networks
Bioinformatics Advance Access published on February 1, 2006
Bioinformatics 2006 22: 974-980; doi:10.1093/bioinformatics/btl030 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Claudia Plant, Christian Böhm, Bernhard Tilg, and Christian Baumgartner
Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data
Bioinformatics Advance Access published on January 27, 2006
Bioinformatics 2006 22: 981-988; doi:10.1093/bioinformatics/btl027 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Haiquan Li, Jinyan Li, and Limsoon Wong
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
Bioinformatics Advance Access published on January 29, 2006
Bioinformatics 2006 22: 989-996; doi:10.1093/bioinformatics/btl020 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Philipp Pagel, Matthias Oesterheld, Volker Stümpflen, and Dmitrij Frishman
The DIMA web resource—exploring the protein domain network
Bioinformatics Advance Access published on February 15, 2006
Bioinformatics 2006 22: 997-998; doi:10.1093/bioinformatics/btl050 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Voichita D. Marinescu, Isaac S. Kohane, Tae-Kyung Kim, David A. Harmin, Michael E. Greenberg, and Alberto Riva
START: an automated tool for serial analysis of chromatin occupancy data
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 999-1001; doi:10.1093/bioinformatics/btl062 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Martin Eisenacher, Jürgen de Braaf, and Simone König
Mass Analysis Peptide Sequence Prediction (MAPSP)
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 1002-1003; doi:10.1093/bioinformatics/btl052 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Michael J. Sanderson
Paloverde: an OpenGL 3D phylogeny browser
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 1004-1006; doi:10.1093/bioinformatics/btl044 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Surjit B. Dixit and David L. Beveridge
Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
Bioinformatics Advance Access published on February 17, 2006
Bioinformatics 2006 22: 1007-1009; doi:10.1093/bioinformatics/btl059 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Janko Dietzsch, Nils Gehlenborg, and Kay Nieselt
Mayday-a microarray data analysis workbench
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 1010-1012; doi:10.1093/bioinformatics/btl070 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Jing Hua Zhao
Pedigree-drawing with R and graphviz
Bioinformatics Advance Access published on February 17, 2006
Bioinformatics 2006 22: 1013-1014; doi:10.1093/bioinformatics/btl058 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Ramon Aragues, Daniel Jaeggi, and Baldo Oliva
PIANA: protein interactions and network analysis
Bioinformatics Advance Access published on March 1, 2006
Bioinformatics 2006 22: 1015-1017; doi:10.1093/bioinformatics/btl072 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Maria J. Schilstra, Lu Li, Joanne Matthews, Andrew Finney, Michael Hucka, and Nicolas Le Novère
CellML2SBML: conversion of CellML into SBML
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 1018-1020; doi:10.1093/bioinformatics/btl047 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Balázs Adamcsek, Gergely Palla, Illés J. Farkas, Imre Derényi, and Tamás Vicsek
CFinder: locating cliques and overlapping modules in biological networks
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 1021-1023; doi:10.1093/bioinformatics/btl039 [Abstract] [Full Text] [Print PDF] [supplementary data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, and Jan Komorowski
The LCB Data Warehouse
Bioinformatics Advance Access published on February 2, 2006
Bioinformatics 2006 22: 1024-1026; doi:10.1093/bioinformatics/btl036 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yongliang Ren, Wuming Gong, Qiqi Xu, Xin Zheng, Dong Lin, Yejun Wang, and Tongbin Li
siRecords: an extensive database of mammalian siRNAs with efficacy ratings
Bioinformatics Advance Access published on January 28, 2006
Bioinformatics 2006 22: 1027-1028; doi:10.1093/bioinformatics/btl026 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

Baolin Wu
Differential gene expression detection and sample classification using penalized linear regression models
Bioinformatics 2006 22: 1029; doi:10.1093/bioinformatics/btl061 [Extract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.