PhD conferral M. El-Kebir
Networks, modules and breeding schedules. Applications of Combinatorial Optimization to Computational Biology
Prof. J. Heringa and Prof. G. Klau
Amsterdam Institute for Molecules, Medicines and Systems
On the 27th of October, Mohammed El-Kebir, PhD candidate in the AIMMS Integrative Bioinformatics research group, will defend his PhD thesis entitled ‘Networks, modules and breeding schedules. Applications of Combinatorial Optimization to Computational Biology’.
Getting sense out of a wealth of data
‘Data, data everywhere but not a thought to think.’
Jesse H. Shera (1903-1982)
Nowadays there is a wealth of biological data. The main challenge in the post-genomic era is to interpret and make sense out of these data and ultimately answer important biological questions ranging from determining the function and structure of proteins to elucidating the evolution of species and tumors.
Combinatorial optimization problems
Many of these questions can be formulated as combinatorial optimization problems where the goal is to find, given an objective function, an optimal object from a finite set of feasible objects. By carefully studying the combinatorial structure of the problem and patterns that are common to typical input data, one can often design an algorithm that performs well in practice.
El-Kebir’s thesis concerns several combinatorial optimization problems in computational biology for which he has developed algorithms that are of practical use. Problems that are considered in his thesis include the identification of commonalities between biological networks from different strains or species, the prediction of protein-protein interactions, the extraction of smaller connected subnetworks from a larger network, the partitioning of a molecule into charge groups and the crossing schedule optimization problem.
BioSB Young Investigator Award
Earlier this year, Mohammed El-Kebir was awarded the BioSB Young Investigator Award 2015 for best PhD thesis in the field of bioinformatics and systems biology in the Netherlands. The jury stated that “Mohammed El-Kebir enjoys collaborating in complex projects, especially when they are not clearcut from the beginning and require an interdisciplinary team effort. Using the analytical skills he obtained during his studies, he aims at decomposing complex problems into manageable components without losing their essential characteristics.”
A more elaborate description of El-Kebir's PhD research can be found here.