Bilkent University
Department of Computer Engineering


Theoretical Foundations and Software Infrastructure of Biological Network Databases


Mehmet Koyutrk
Case Western Reserve University

In biomedical applications, network models are commonly used to represent interactions and higher-level associations among biological entities. Integrated analyses of these interaction and association data has proven useful in extracting knowledge, and generating novel hypotheses for biomedical research. However, existing computational infrastructure for storing and querying, network data target networks at smaller scales. In this talk, we will describe algorithms that use results from classical linear algebra for fast processing of network proximity queries on very large networks. We will then demonstrate sample applications of these algorithms in the context of drug repositioning, where we model prediction of drug response as a link prediction problem on a heterogeneous network, and use network proximity computed on a series of networks as an indicator of a given sample's sensitivity to a given drug.

Bio: Mehmet Koyutrk received his Ph.D. degree in Computer Science from Purdue University, and his B.S. and M.S. degrees from Bilkent University, respectively in Electrical Engineering and Computer Engineering. He is currently T. & A. Schroeder Associate Professor at the Department of Electrical Engineering and Computer Science at Case Western Reserve University (CWRU). His research focuses on the analysis of biological networks, systems biology of complex diseases, and computational genomics. Mehmet also serves in the steering committee of CWRU's graduate programs in Systems Biology and Bioinformatics. He is an associate editor for IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) and EURASIP Journal on Bioinformatics and Systems Biology, and has been serving regularly as a program committee member for prominent computational biology conferences, including RECOMB, ISMB, ACM-BCB, and APBC. Mehmet received an NSF CAREER Award in 2010.


DATE: 08 August 2016, Monday @ 13:40