Gurkan Bebek, Ph.D.
Case Western Reserve University
Center for Proteomics and Mass Spectrometry
10900 Euclid Ave. BRB Bldg. 9th Floor
Cleveland-OH 44106-4988
{myfirstname} at case.edu
Phone: (216) 368 2288
Fax: (216) 368 6846
Research
The significant technological progress and the completion of many genome sequencing projects, including that of the human, have provided us with a reasonably detailed view of the cell. From this new point of view, i. e. our new knowledge of cellular networks, we have the means to understand the principles underlying the dynamic behavior of cells. However, this will require integration of theoretical and experimental approaches at a variety of levels.
My research objective is to develop computational tools and approaches for expanding the use of biological and medical data. To accomplish this, methods as well as tools and models are needed to acquire, analyze and integrate this knowledge. By formulating new hypotheses to explain observations not predicted by these models and tools, additional analysis and experiments can be carried out. We can then utilize this knowledgebase for new discoveries.
Following is a list of current research topics studied:
- Developing new measures that can improve understanding of large and complex biological networks
- Analyzing Proteomics data and building models to infer signal transduction pathway segments
Academic History
- Ph.D. Case Western Reserve University, Electrical Engineering and Computer Science. (2006)
- B.Sc. Bilkent University, Computer Engineering (2001)
Funding
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Training in Computational Genomic Epidemiology of Cancer (CoGEC) R25T CA094186 (August 2007- Current)
Publications
- Bebek, G., Berenbrink, P., Cooper, C., Firedetzky, T., Nadeau, J.H., & Sahinalp, S.C. (2005). Improved Duplication Models for Proteome Network Evolution, RECOMB 2005 Ws on Regulatory Genomics, LNBI 4023, pp. 119-137. (doi:10.1007/978-3-540-48540-7_11)
- Bebek, G., Berenbrink, P., Cooper, C., Firedetzky, T., Nadeau, J.H., & Sahinalp, S.C. (2006). The degree distribution of the generalized duplication model. Theoretical Computer Science, 369, pp. 239-249. (doi:10.1016/j.tcs.2006.08.045)
- Bebek, G., Yang, J. (2007). PathFinder: Mining Signal Transduction Pathway Segments from Protein Protein Interaction Networks, BMC Bioinformatics, 8:335.
(doi:10.1186/1471-2105-8-335)
Seminars/Workshops/Posters
- Department of Electrical Engineering and Computer Science Seminar: Proteome Network Evolution by Gene Duplication, Case Western Reserve University, November 23, 2004.
- DIMACS Workshop on Biomolecular Networks: Topological Properties and Evolution - Duplication Based Models for Proteome Network Evolution, DIMACS Center, Rutgers University, May 11-13, 2005.
- Department of Electrical Engineering and Computer Science Seminar: Predicting Signal Transduction Pathways via Variable Length Markov Model Case Western Reserve University, October 20, 2005.
- The First Annual RECOMB Satellite Workshop on Systems Biology and The Second Annual RECOMB Satellite Workshop on Regulatory Genomics, University of California, San Diego, December 2nd-4th, 2005.
- Bebek, G. Takamoto, K., Accurate Elimination of False Protein-Protein Interactions, RECOMB 2007, Oakland, CA, April 21-25, 2007 (accepted poster).
Thesis
- Analyzing and Modeling Large Biological Networks: Inferring Signal Transduction Pathways, Doctor of Philosophy, Case Western Reserve University, Computing and Information Science, 2006.
Gürkan is pronounced as "GyuirkΛn"
What is Bioinformatics? - Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.
What is Computational Biology? - The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. (Working Definition of Bioinformatics and Computational Biology - July 17, 2000).