Bioinformatics

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Hyunju Lee, Sek Won Kong, and Peter J. Park

Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
Bioinformatics Advance Access published on February 8, 2008
Bioinformatics 2008 24: 889-896; doi:10.1093/bioinformatics/btn034 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Ian M. Overton, Gianandrea Padovani, Mark A. Girolami, and Geoffrey J. Barton

ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction
Bioinformatics Advance Access published on February 19, 2008
Bioinformatics 2008 24: 901-907; doi:10.1093/bioinformatics/btn055 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Kai Ye, Gert Vriend, and Adriaan P. IJzerman

Tracing evolutionary pressure
Bioinformatics Advance Access published on February 26, 2008
Bioinformatics 2008 24: 908-915; doi:10.1093/bioinformatics/btn057 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Michael Stout, Jaume Bacardit, Jonathan D. Hirst, and Natalio Krasnogor

Prediction of recursive convex hull class assignments for protein residues
Bioinformatics Advance Access published on February 5, 2008
Bioinformatics 2008 24: 916-923; doi:10.1093/bioinformatics/btn050 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Sitao Wu and Yang Zhang

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
Bioinformatics Advance Access published on February 22, 2008
Bioinformatics 2008 24: 924-931; doi:10.1093/bioinformatics/btn069 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, D. Stephen Charnock-Jones, Cristin Print, and Satoru Miyano

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models
Bioinformatics Advance Access published on February 21, 2008
Bioinformatics 2008 24: 932-942; doi:10.1093/bioinformatics/btm639 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Joshua N. Sampson and Steven G. Self

Identifying trait clusters by linkage profiles: application in genetical genomics
Bioinformatics Advance Access published on February 29, 2008
Bioinformatics 2008 24: 958-964; doi:10.1093/bioinformatics/btn064 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Yu Zhang

Tree-guided Bayesian inference of population structures
Bioinformatics Advance Access published on February 22, 2008
Bioinformatics 2008 24: 965-971; doi:10.1093/bioinformatics/btn070 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Shu-Yi Su, David J. Balding, and Lachlan J.M. Coin

Disease association tests by inferring ancestral haplotypes using a hidden markov model
Bioinformatics Advance Access published on February 23, 2008
Bioinformatics 2008 24: 972-978; doi:10.1093/bioinformatics/btn071 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Yung-Keun Kwon and Kwang-Hyun Cho

Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics
Bioinformatics Advance Access published on February 19, 2008
Bioinformatics 2008 24: 987-994; doi:10.1093/bioinformatics/btn060 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Juby Jacob, Marcel Jentsch, Dennis Kostka, Stefan Bentink, and Rainer Spang

Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs
Bioinformatics Advance Access published on February 19, 2008
Bioinformatics 2008 24: 995-1001; doi:10.1093/bioinformatics/btn056 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

APPLICATIONS NOTES:

GENOME ANALYSIS:

Get checked abstract Weil Lai, Vidhu Choudhary, and Peter J. Park

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms
Bioinformatics Advance Access published on February 22, 2008
Bioinformatics 2008 24: 1014-1015; doi:10.1093/bioinformatics/btn067 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract David He and John Parkinson

SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences
Bioinformatics Advance Access published on February 26, 2008
Bioinformatics 2008 24: 1016-1017; doi:10.1093/bioinformatics/btn073 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Liam J. Revell and Alexis S. Harrison

PCCA: a program for phylogenetic canonical correlation analysis
Bioinformatics Advance Access published on February 21, 2008
Bioinformatics 2008 24: 1018-1020; doi:10.1093/bioinformatics/btn065 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, and Richard D. Smith

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Bioinformatics Advance Access published on February 26, 2008
Bioinformatics 2008 24: 1021-1023; doi:10.1093/bioinformatics/btn063 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Bongshin Lee, Kristy Brown, Yetrib Hathout, and Jinwook Seo

GOTreePlus: an interactive gene ontology browser
Bioinformatics Advance Access published on February 21, 2008
Bioinformatics 2008 24: 1026-1028; doi:10.1093/bioinformatics/btn068 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

LETTERS TO THE EDITOR:

GENE EXPRESSION:

Get checked abstract Radhakrishnan Nagarajan and Meenakshi Upreti

Comment on causality and pathway search in microarray time series experiment
Bioinformatics Advance Access published on February 26, 2008
Bioinformatics 2008 24: 1029-1032; doi:10.1093/bioinformatics/btm586 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nitai D. Mukhopadhyay and Snigdhansu Chatterjee

Reply to ‘Comment on causality and pathway search in microarray time series experiment’
Bioinformatics Advance Access published on February 22, 2008
Bioinformatics 2008 24: 1033; doi:10.1093/bioinformatics/btn019 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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