CS Forum: Ferhat Ay, University of California "Modeling the 3D chromatin structure of the human genome"
Modeling the 3D chromatin structure of the human genome
University of California
The field of regulatory genomics has recently witnessed significantly increased interest in the three-dimensional structure of DNA in the nucleus, catalyzed by the development of chromosome conformation capture techniques (e.g., Hi-C, HiChIP) that profile genomic proximities on a genome-wide scale. Systematic analysis of these proximities is particularly important to identify targets of disease-associated genetic variants, more than 90% of which reside in noncoding regions with unknown gene targets. Our lab works on developing computational methods to understand the role of human genetic variation in gene regulation through various epigenetic mechanisms, and in particular, through chromatin structure. I will talk about our work in assigning statistical confidence estimates to Hi-C and HiChIP data in order to determine functional loops between regulatory elements in our DNA. I will then present the results of our ongoing work, in which we profile such loops in primary human immune cell types and revisit the functional roles of GWAS SNPs in immune-mediated diseases. Our results highlight the problems with "the nearest gene" approach for mapping GWAS hits or enhancers to target genes and the importance of combining high resolution, high throughput experiments with novel computational techniques to achieve an accurate mapping of target genes.
Ferhat Ay received his B.S. degrees in Computer Engineering and Mathematics both from Middle East Technical University (METU), Turkey in 2007 and his Ph.D. in Computer Science at the University of Florida in 2011. He subsequently joined the Department of Genome Sciences at the University of Washington as a Computing Innovation Fellow awarded by Computing Research Association and National Science Foundation (NSF). He was a Research Assistant Professor in the Department of Preventive Medicine-Health and Biomedical Informatics at Northwestern University in 2015 before establishing his lab at the La Jolla Institute for Immunology (LJI) as the Institute Leadership Assistant Professor of Computational Biology 2016. Ferhat is an adjunct faculty at the UC San Diego School of Medicine and is affiliated with UCSD’s Bioinformatics Ph.D. Program. His primary research areas are bioinformatics, computational biology, epigenomics, and regulatory genomics. Ferhat works on understanding the relationship between three-dimensional genome architecture and gene regulation in the context of different diseases including cancer, malaria and immune-mediated diseases. He is a recipient of an R35 MIRA grant (5 years) from National Institutes of Health (NIH) and serves as an Associate Editor of PLoS Computational Biology.
Associate Professor at the department of Computer Science
CS forum is a seminar series arranged at the CS department. The talks are intended for presentations of postdoctoral level researchers and professors, both for visiting and CS-department-based researchers.