Genome Bioinformatics and Genomic Disorders
Schulich School of Medicine, The University of
Transcription Factor Binding Site
Definition of cis-recognition elements
Development and refinement of pregnane X receptor DNA binding site model using information theory: Insights into PXR mediated gene regulation
Carrie A. Vyhlidal, Peter K. Rogan, and J. Steven Leeder, J. Biol. Chem., Vol. 279, Issue 45, 46779-46786, November 5, 2004.
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- Genome wide analysis
- Delila-Genome - A software tool for
complete genome scanning for and display of protein binding sites
Genome-wide prediction, display and refinement of binding sites with information theory-based models
Gadiraju S, Vyhlidal CA, Leeder JS, Rogan PK. BMC Bioinformatics, 4:38, 2003.
Tandem machine learning for the identification of genes regulated by transcription factors
Deendayal Dinakarpandian, Venetia Raheja, Saumil Mehta, Erin G. Schuetz, Peter K Rogan. BMC Bioinformatics, 6: 204, 2005.
BIPAD: A Web Server for Modeling Bipartite Sequence Elements
C Bi and Peter K. Rogan, BMC Bioinformatics 7:76 (2006).
Bipartite Pattern Discovery by Entropy Minimization-Based Multiple Local Alignment
C Bi and Peter K. Rogan, Nucleic Acids Research, 32:4979-4991(2004).
Determining Thresholds of Binding Site Sequence Models Using Information Theory
C Bi and Peter K. Rogan, Proceedings of the JCIS/6th International Symposium on Computational Biology and Genome Informatics, July 21-26, 2005, Salt Lake City UT.
Defining sequence elements that regulate CYP450 gene expression
Peter K. Rogan, Proceedings of the 14th Intl. Conf. on Cytochromes P450, Dallas TX, 5/31-6/5/2005 (in press).
US Ser. No. 5,867,402:
Computational analysis of nucleic acid information defines binding sites. Thomas D. Schneider and Peter K. Rogan, 1998.