Speaker:Hector Corrada Bravo, University of Maryland
Title: Cell-specific methylation pattern reconstruction using minimum cost network flow algorithms.
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
4400 University Drive, MS 3F2
Fairfax, VA 22030-4444
Tel. 703-993-1460, Fax. 703-993-1491