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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.

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.

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).

Patent

US Ser. No. 5,867,402: Computational analysis of nucleic acid information defines binding sites. Thomas D. Schneider and Peter K. Rogan, 1998.

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