Speaker:Hector Corrada Bravo, University of Maryland
Title: Cell-specific methylation pattern reconstruction using minimum cost network flow algorithms.

Abstract: DNA methylation aberrations are now known to, almost universally, accompany the initiation and progression of cancers. In particular, the colon cancer epigenome contains specific genomic regions that, along with differences in methylation levels with respect to normal colon tissue, also show increased epigenetic and gene expression heterogeneity at the population level, i.e., across tumor samples, in comparison to other regions in the genome. Tumors are highly heterogeneous at the clonal level as well, and the relationship between clonal and population heterogeneity is poorly understood. We present an approach that uses sequencing reads from high-throughput sequencing of bisulfite converted DNA to reconstruct heterogeneous cell populations by assembling cell type-specific methylation patterns. Our methodology is based on a regularized method of moments formulation yielding a specific class of minimum cost network flow problems. We present an efficient algorithm for the solution of this general class of linear optimization problems.

Time: Friday, February 21, 2014, 1:30-2:30 p.m.

Place: Exploratory Hall (formerly S & T II), Room 4106

Department of Mathematical Sciences
George Mason University
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Fairfax, VA 22030-4444
http://math.gmu.edu/
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