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Ferhat Ay, Ph.D.
Associate Professor
Institute Leadership Asst. Prof. of Computational Biology, Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy
“We look beyond the linear sequence of DNA to understand how the three-dimensional architecture of the genomes influences a wide range of biological processes from the malignant transformation of cancer cells to the life cycle of the deadly malaria parasite.”

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

Feb 19, 2019 Proc Natl Acad Sci U S A
Comparative 3D genome organization in apicomplexan parasites
Bunnik EM, Venkat A, Shao J, McGovern KE, Batugedara G, Worth D, Prudhomme J, Lapp SA, Andolina C, Ross LS, Lawres L, Brady D, Sinnis P, Nosten F, Fidock DA, Wilson EH, Tewari R, Galinski MR, Ben Mamoun C, Ay F, Le Roch KG
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Lab Members

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Jun 23, 2020
Ferhat Ay, Ph.D.
Associate Professor Institute Leadership Asst. Prof. of Computational Biology, Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy

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Research Projects

Ay
Epigenomics Session at PSB 2013

Epigenomics Session. Pacific Symposium on Biocomputing 2013 Project Link

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Ay
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

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Ay
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

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Ay
P. Falciparum Epigenetic Gene Regulation

The third dimension of epigenetic gene regulation in the malaria parasite Plasmodium falciparum. Project Link

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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

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From the lab

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