Bilkent University
Department of Computer Engineering


Network Biology Approaches Identify Dysregulated Disease Pathways and Predict Prognosis


Grkan Bebek
Case Western Reserve University

Personalized medicine aims to tailor treatment options for patients based on the makeup of their diseases. In the case of cancer, the genetic makeup of tumors are characterized to identify unique tendencies and exploit vulnerabilities of these tumors. However, identifying genomic alterations and molecular signatures that better describe or classify cancer to accomplish this goal has been challenging. In this talk I will present two separate approaches to address this problem. First, we hypothesize that frequent graph mining of pathways to gather pathways functionally relevant to tumors can characterize tumor types and provide opportunities for personalized therapies. Second, we utilize an unsupervised bottom-up approach to facilitate the identification of significantly dysregulated functional subnetworks to identify disease phenotypes. We identify n-node subnetworks exhaustively and score each of these subnetworks to carry out feature selection. We have utilized breast cancer and glioma (brain tumor) datasets from microarray and RNA-Seq platforms and identified disease mechanisms differentiating samples. These results could serve to improve prognosis of future LGG patients, and to provide opportunities for improved treatment options and personalized interventions.

Bio: Gurkan Bebek received his Ph.D. degree in Computer Science from Case Western Reserve University, and his B.S. degree from Bilkent University Computer Engineering Department. He is currently Assistant Professor at the Center for Proteomics and Bioinformatics at Case Western Reserve University (CWRU) and Department of Nutrition. He has secondary appointments at the Electrical Engineering and Computer Science Department and the Cleveland Clinic. His research focuses on translational medicine problems to discover new diagnostic tools and treatments for a variety of complex diseases including cancer, hearth disease and cystic fibrosis. He focuses on cancers Gurkan Bebek also serves in the Systems Biology and Bioinformatics Graduate program at Case Western Reserve University.


DATE: 03 August 2016, Wednesday @ 13:40