
Overview
The focus of Dr. Ay’s work is to understand gene regulation in complex organisms and diseases by developing novel methods that leverage high-throughput genomics and epigenomics data. He develops computational methods that are based in statistics, machine learning, optimization and graph theory. He is particularly interested in the analysis and modeling of the 3D genome architecture from high-throughput chromatin conformation capture data to understand how do changes in this 3D architecture affect cellular outcome such as development, differentiation, gene expression and disease phenotypes. He is also interested in uncovering epigenetic mechanisms behind precise regulation of gene expression in the deadly malaria parasite Plasmodium falciparum during its sexual and asexual life cycles. He also has ongoing interests in systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of chromatin conformation data sets with one-dimensional measurements such as histone modifications, nucleosome occupancy and DNA accessibility.
Featured publications
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
Identification of significant chromatin contacts from HiChIP data by FitHiChIP
Comparative 3D genome organization in apicomplexan parasites
Lab Members

Ferhat Ay, Ph.D.
Associate Professor Institute Leadership Asst. Prof. of Computational Biology, Center for Autoimmunity and Inflammation, Center for Cancer ImmunotherapyResearch Projects
Epigenomics Session at PSB 2013
Epigenomics Session. Pacific Symposium on Biocomputing 2013 Project Link
Fit-Hi-C: Statistical Confidence Estimation for Hi-C Data
Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such
P. Falciparum 3 D Genome Organization
Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene
P. Falciparum Epigenetic Gene Regulation
The third dimension of epigenetic gene regulation in the malaria parasite Plasmodium falciparum. Project Link
Tutorial at ACM-BCB 2015
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), 2015 The field of regulatory genomics has recently witnessed
From the lab

Genome structure of malaria parasites linked to virulence
LA JOLLA, Calif. – An international research team led by scientists at the University of California, Riverside, and the La

LJI researcher Ferhat Ay has been awarded prestigious MIRA Grant
LA JOLLA, CA—The National Institute of General Medical Sciences (NIGMS) has awarded La Jolla Institute’s Ferhat Ay, Ph.D., $ 2.24

Q&A with Ferhat Ay, Ph.D.
Before Ferhat Ay, Ph.D., entered first grade, he had already announced to the world that he wanted to become a