I am currently a postdoctoral scholar at Yale University, Computational Biology and Bioinformatics program. I work with Prof. Mark Gerstein on various problems related to genome privacy, personal genomics and 3D genome. In particular, I am interested in understanding the privacy leakages in omics datasets and developing privacy and utility preserving solutions. You can check this website and this tool for some of the softwares I developed. Recently, I’ve been working on blockchain applications for genomics. Our team won the first prize in iDASH’18 Secure Genome Analysis challenge and the third prize in iDASH’19 Secure Genome Analysis challenge blockchain tracks. You can also check out this, this and this tool for some of the blockchain applications we developed. I am currently working on developing algorithms for commonly used genomics tools with homomorphic encryption.
Before joining Yale, I was a Ph.D student at the Bioinformatics program of University of Illinois at Chicago. I worked on the computational construction of 3D genome organization in eukaryotes. I developed three softwares that are Constrained Self-Avoiding Chromatin (CSAC), n-Constrained Self-Avoiding Chromatin (nCSAC) and multichain Constrained Self-Avoiding Chromatins (mCSAC). Please see publications page for more details. I was also involved in modeling stochasticity in biochemical reaction networks.
I received my undergraduate degree from the Chemical Engineering department of Bogazici University in Istanbul, Turkey in 2008. My undergraduate thesis was on application of stochastic differential equations to biochemical processes. I was a visiting research scientist at NASA Center for Advanced Microgravity Materials Processing in Northeastern University, Boston in 2007. I assisted with the project of the chemical kinetics of synthesis of microporous vanadosilicate AM-6. I also worked as a chemical engineer at the Turkey branch of Exxon Mobil before I joined the graduate school.
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