EECS500 Fall 2013 Department Seminar

Gurkan Bebek
Integrative Network Similarity Pipeline Reveals Functional Characteristics of Cancer Driver Protein Networks
White Bldg., Room 411
11:30am - 12:30pm
December 5, 2013

Recent genomic and proteomic techniques have led to the discovery of cancer
driver genes whose mutations have been associated with increased
carcinogenic activity. However, these mutations are mostly observed in low
frequencies compared to the total number of tumors analyzed, suggesting that
mutations in distinct subsets of driver genes are sufficient for
tumorigenesis. In order to elucidate the relationships between driver genes,
it is important to be able to quantify the functional similarities between
them.   In this work we explore functional similarities of these driver
genes by comparing the networks by which they contribute to tumorigenesis,
as opposed to merely the driver genes themselves.  For this purpose, an
algorithm that is specifically designed for within-species network
similarity quantification is developed. We utilize colorectal cancer driver
gene networks to demonstrate the utility of this network-based approach.


Dr. Gürkan Bebek received a BS in Computer Engineering from Bilkent
University, Turkey. He came to Case Western Reserve University (CWRU)
to pursue graduate studies at the Electrical Engineering and Computer
Science Department in the field of computational biology and
bioinformatics. His doctoral work was centered on identifying
signaling pathways by integrating multiple –omic datasets and novel
data mining approaches from protein-protein interaction networks.
After completing his PhD, he was awarded the NCI funded Training in
Computational Genomic Epidemiology of Cancer (CoGEC) postdoctoral
fellowship, where he received transdisciplinary training at the
intersection of cancer research, epidemiology, biostatistics,
genetics, and computer science. Following his postdoctoral training at
the Case Comprehensive Cancer Center, Dr. Bebek joined the Center for
Proteomics and Bioinformatics at CWRU as a faculty member in 2011. In
2013, he received a Clinical Translational Science Collaborative
(CTSC) Clinical Research Scholar (KL2) Award. As a KL2 Clinical
Research Scholar, Dr. Bebek is investigating colorectal cancer driver
genes and studying their synergistic activity in tumor development
utilizing novel algorithms that is developed by his lab. Dr. Bebek is
an Instructor at the Center for Proteomics and Bioinformatics at CWRU
and a Visiting Scientist at the Genomic Medicine Institute at the
Cleveland Clinic.