Lab Group

Ferhat Ay’s primary research areas are bioinformatics, computational biology, epigenomics and regulatory genomics. He is particularly interested in understanding the relationship between genome architecture and gene regulation in different human cell lines and organisms, such as breast cancer and leukemia cells, and the human malaria parasite Plasmodium falciparum, through data integration, computational modeling and statistical approaches. Ay received a dual B.S. in Computer Engineering and Mathematics from the Middle East Technical University in Ankara, Turkey. As part of his doctoral thesis in the Department of Computer Science at the University of Florida in Gainesville, he developed algorithms that mine metabolic networks for conserved connectivity patterns and that reveal novel topological properties of gene regulatory networks. Before joining the La Jolla Institute as an Assistant Professor of Computational Biology, Ay worked as a Research Assistant Professor in the Department of Preventive Medicine-Health and Biomedical Informatics at Northwestern University in Chicago, IL.

Biosketch: I did my graduation in Microbiology from India with a B.Sc degree in 2007 followed by an M.Sc degree in the ​same the subject in 2009. I then qualified the National Eligibility Test (NET) conducted by Council of Scientific and Industrial Research (CSIR), Govt. of India in 2009​ ​and joined CSIR-Indian Institute of Chemical Biology in 2010 to carry out my Ph.D. research in computational biology. I successfully completed the tenure and obtained the degree in May, 2016. Research Focus: I began working as a postdoctoral fellow in Dr. Ay's lab from May 2016. Here, my research focuses on ​understanding the gene regulation and diseases from high-throughput genomics and epigenomics data. I am interested in developing methods to understand these high-throughput data especially the chromosome conformational capture techniques like the Hi-C data. Further, I am also interested in developing 3D models of genomes using the chromosome conformational capture techniques.
Career Goal: My goal is to pursue a career in scientific research focused on understanding the gene regulation and diseases in human.

Biosketch: I completed my Bachelors in Biotechnology in the year 2014 from Jawaharlala Nehru Technology University, India. I am currently a Master's student at San Diego State University in Bioinformatics. I started working in Ay lab at La Jolla Institute of Allergy and Immunology in March 2016 as a Bioinformatics Intern.
Research Focus: My current research project is focused on modeling and analysis of three-dimensional genome structure of high-throughput chromatin conformation capture data (Hi-C data) and to understand the affects of these 3D structure on gene expression.
Career Goals: My plan is to develop a career in research field as a bioinformatics scientist.

Biosketch: I am an undergraduate at UCSD studying biology with specification in bioinformatics.
Research Focus: My research under Dr. Ay at the La Jolla Institute is focused on next generation sequencing and analysis of Hi-C data. I am interested in the application of bioinformatics methods to develop solutions for medical problems.
Career Goals: I plan to pursue a career in medicine, ideally as a physician, but I am intrigued by non-patient care career prospects as well.