Cigdem Sevim Bayrak


Computational scientist specialized in human genetics

Who I am:

I'm a postdoctoral researcher at Icahn School of Medicine at Mount Sinai. My research bridges the areas of data science, bioinformatics, genetics, and structural biology. My interest in computational sciences began when I started college to study mathematics and computer science. My passion always has been problem solving and using technology for this purpose. Knowing that the outcomes of my studies have the ability to provide valuable information for understanding nature and science motivates me to continue conducting my research. Specifically, I find the most satisfaction in conducting computational biology research work to better understand human diseases, as the information I collect has the ability to inform and improve health care practices.

What I do:

My ongoing research focuses on exploring the consequences of human disease-causing mutations in terms of their effects on protein structure and function. My work combines various computational approaches, including natural language processing (NLP), protein sequence analysis, structure prediction, and machine learning techniques. My goal is to develop a classifier for gain-of-function (GOF) and loss-of-function (LOF) mutations which will allow us to generate a computational method to predict the functional consequence of a given mutation. 

During my postdoc, I had opportunities to participate in several collaboration projects focusing on different diseases to explore disease-causing mutations and genes in next generation sequencing data of patients. These studies include congenital heart disease (CHD), obesity, Parkinson's and inflammatory bowel disease (IBD). 

My prior studies focused on RNA structure analysis and design by employing graph theory methods, and protein structure and dynamics in the denatured state. 

Publications


A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity


Peng Zhang, Aurelie Cobat, Yoon-Seung Lee, Yiming Wu, Cigdem Sevim Bayrak, Clementine Boccon-Gibod, Daniela Matuozzo, Lazaro Lorenzo, Aayushee Jain, Soraya Boucherit, others


American journal of human genetics, pp. S0002--9297


Identification of Discriminative Gene-level and Protein-level Features Associated with Gain-of-Function and Loss-of-Function Mutations


Cigdem Sevim Bayrak, Aayushee Jain, David Stein, Kumardeep Chaudhary, Girish Nadkarni, Tielman T Van Vleck, Stephanie Boisson-Dupuis, Peter Stenson, David N Cooper, Avner N Schlessinger, others


bioRxiv, Cold Spring Harbor Laboratory, 2021


Genome-wide discovery of genetic loci that uncouple excess adiposity from its comorbidities


Lam O. Huang, Alexander Rauch, Eugenia Mazzaferro, Michael Preuss, Stefania Carobbio, Cigdem S. Bayrak, Nathalie Chami, Zhe Wang, Ursula M. Schick, Nancy Yang, Yuval Itan, Antonio Vidal-Puig, Marcel den Hoed, Susanne Mandrup, Tuomas O. Kilpeläinen, Ruth J. F. Loos


Nature Metabolism, 2021, pp. 228–243


Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients


Yiming Wu, Kyle Gettler, Mamta Giri, Dalin Li, Cigdem Sevim Bayrak, Aayushee Jain, Patrick Maffucci, Ksenija Sabic, Tielman Van Vleck, Girish Nadkarni, Lee A Denson, Harry Ostrer, Subra Kugathasan, Peter D Stenson, David N Cooper, L Philip Schumm, Scott Snapper, Mark J Daly, Talin Haritunians, Richard H Duerr, Mark S Silverberg, John D Rioux, Steven R Brant, Dermot McGovern, Judy H Cho, Yuval Itan


medRxiv, 2020 Jun 1


Identifying disease-causing mutations in genomes of single patients by computational approaches.


Cigdem Sevim Bayrak, Yuval Itan


Human Genetics, 2020 Apr 12, pp. 769-776


View all

Contact


Cigdem Sevim Bayrak


Postdoctoral researcher


Institute for Personalized Medicine


Icahn School of Medicine at Mount Sinai