Mohammed El -Kebir, University of Illinois, Urbana-Champaign
The School of Informatics, Computing, and Engineering Center for Bioinformatics Research Talk
Speaker: Mohammed El-Kebir, University of Illinois-Urbana-Champaign
Where: Indiana Memorial Union (IMU), Oak Room
When: Thursday, April 19, 2018, 3:00 pm
Topic: Combinatorial Algorithms for Tumor Phylogenetics
Abstract: Cancer is a genetic disease, where cell division, mutation and selection produce a heterogeneous tumor composed of multiple subpopulations of cells with different sets of mutations. During later stages of cancer progression, cancerous cells from the primary tumor migrate and seed metastases at distant anatomical sites. The cell division and mutation history of an individual tumor can be represented by a phylogenetic tree, which helps guide patient-specific treatments.
In this talk, I will introduce combinatorial algorithms for reconstructing tumor phylogenies from bulk DNA sequencing data, where the measurements are a mixture of thousands of cells. These algorithms are based on a combinatorial characterization of phylogenetic trees as a restricted class of spanning trees in a graph, a characterization that also demonstrates the computational complexity of the problem. In addition, I will introduce a novel framework for analyzing the history of cellular migrations between anatomical sites in metastatic cancers. Using these methods, I analyze several cancers and identify tumor phylogenies and migration histories that are more biologically plausible than previously reported analyses.
Biography: Dr. Mohammed El-Kebir is an assistant professor at the University of Illinois at Urbana-Champaign in the Department of Computer Science. Previously, Dr. El-Kebir received postdoctoral training at Princeton and Brown University, and his PhD at CWI and VU University Amsterdam in the Netherlands. He was awarded the BioSB Young Investigator Award for his PhD thesis. Dr. El-Kebir's research focuses on tumor phylogenetics, where he develops algorithms for studying the progression of tumors.