Session J - BioSB Young Investigator Award winner: Mohammed El-Kebir

Mohammed El-Kebir

Affiliation: Department of Computer Science, Center of Computational Molecular Biology, Brown University, US

During the BioSB 2015 on May 20 (17:30 - 18:00 h in room Europa), we will present the BioSB Young Investigator Award 2015 followed by an honorary lecture of 20 minutes. The winner, Mohammed El-Kebir, will receive a prize of 250 Euros sponsored by the BioSB research school and will present an honorary lecture.

 

Summary statement

Mohammed El-Kebir enjoys collaborating in complex projects, especially when they are not clear cut from the beginning and require an interdisciplinary team e ffort. Using the analytical skills he obtained during his studies, he aims at decomposing complex problems into manageable components without losing their essential characteristics. At Brown University, Mohammed develops algorithms for studying intra-tumor heterogeneity.


Research interests

Combinatorial optimization, integrative network analysis, computational biology, integer linear programming, exact algorithms, graph algorithms.
 


Abstract

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

DNA sequencing of multiple samples from the same tumor provides data to analyze the process of clonal evolution in the population of cells that give rise to a tumor. We formalize the problem of reconstructing the clonal evolution of a tumor using single-nucleotide mutations as the Variant Allele Frequency Factorization Problem (VAFFP). We derive a combinatorial characterization of the solutions to this problem and show that the problem is NP-complete. We derive an integer linear programming solution to the VAFFP in the case of error-free data and extend this solution to real data with a probabilistic model for errors. The resulting AncesTree algorithm is better able to identify ancestral relationships between individual mutations than existing approaches, particularly in ultra-deep sequencing data when high read counts for mutations yield high confidence variant allele frequencies.
 

Award committee

Each year the chair will leave the Award Committee after the conference and invite a new member to the committee. For 2015 the members of the committee are:

Dr. ir. Perry Moerland, AMC Amsterdam/University of Amsterdam (chair)
Dr. Judith Boer, Erasmus Medical Centre, Rotterdam
Prof. dr. Berend Snel, Utrecht University
Dr. ir. Jeroen de Ridder, TU Delft
Prof. dr. R.M.H. Merks, Centrum Wiskunde & Informatica (CWI)