
Overview
Our research uses computational and statistical modeling to understand the genetic and epigenetic bases of gene regulation in the context of several important systemic, infectious, and immune-related diseases. We work on bringing systematic and unbiased approaches to help develop and test specific hypotheses in human genetics, molecular biology, and immunology. We are particularly interested in the analysis and modeling of the 3D genome organization from high-throughput chromatin conformation capture data to understand how changes in this 3D structure affect outcomes such as development, differentiation, and disease progression. Our lab develops broadly used computational methods based in statistics, graph theory, data mining, and machine learning for the analysis of high-throughput data sets. We also have ongoing interests in systems-level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression, analysis of single-cell data, as well as integrative, comparative, and high-resolution analysis of chromosomes conformation data such as Hi-C and HiChIP.
Featured publications
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
Identification of copy number variations and translocations in cancer cells from Hi-C data
Lab Members

Ferhat Ay, Ph.D.
Associate Professor Institute Leadership Asst. Prof. of Computational Biology, Center for Autoimmunity and Inflammation, Center for Cancer ImmunotherapyFrom the lab

A new window into autoimmune diseases
LJI scientists uncover coordinated immune cell activity as a driver of systemic lupus erythematosus

The Conrad Prebys Foundation grants more than $450,000 for studies into childhood cancer, cardiovascular disease
New funding will support high-risk, high-reward projects led by two early-career scientists

LJI asthma researcher Jermaine Khumalo receives AAI Intersect Fellowship
New fellowship will support data science and immunology cross-training in two pioneering LJI labs