MATH Seminar

Title: A shape-based method for determining protein binding sites in a genome
Colloquium: Topology
Speaker: Valerie Hower of University of California, Berkeley
Contact: Susan Guppy, sguppy@emory.edu
Date: 2011-01-31 at 4:30PM
Venue: MSC W201
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Abstract: We present a new algorithm for the identification of bound regions from ChIP-Seq experiments. ChIP-Seq is a relatively new assay for measuring the interactions of proteins with DNA. The binding sites for a given protein in a genome are "peaks" in the data, which is given by an integer-valued height function defined on the genome. Our method for identifying statistically significant peaks is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.html and provides a fast and accurate solution for ChIP-Seq peak finding.