CAREER: New Technologies for Querying Pathway Databases

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Unlike most bioinformatics data, such as DNA sequences and proteinstructures, pathways show the interactions of different bio-chemicalentities. Thus, each entity or subpathway can have a function in itspathway that the pathway can not realize without it. Formulating thesefunctions presents exciting computational challenges. This proposal develops algorithms for efficient and accuratecomputational analysis of pathways. The first step in achieving thisgoal is to build a mathematical model for functions of pathways andsubpathways. This proposal defines the function of a subpathway as itscontribution to the steady state of the entire pathway. Computing thiscontribution is a difficult problem especially for gene regulatorypathways. Existing methods can compute this for metabolic pathways,but they do not scale to even medium sized gene regulatorypathways. This proposal develops efficient methods for computingfunction.Finding the subpathway that has a desired function is a challengingproblem. There is no clear way of searching for subpathways withdesired functions using existing tools. This proposal developsefficient algorithms for searching subpathways with desired function.This proposal takes this one step further, and develops mathematicallysound algorithms for comparing two pathways so that the entities thatmap are functionally, homologically and topologically similar. Thisproposal also explores feature and reference-based index structuresfor biological pathway databases.Further information on the project can be found at the project webpage: http://bioinformatics.cise.ufl.edu/