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
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
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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
Research 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
Ferhat Ay
@ferhatay Apr 06
RT @ljiresearch: New @genomeresearch study gives us a window into #lupus and other autoimmune diseases: genome.cshlp.org/content/31/4/6… #SLE #immun…
Ferhat Ay
@ferhatay Apr 01
RT @bharatpanwar: Glad to see our SLE research work at @ljiresearch on the cover of @genomeresearch (April 2021). Thank you @ferhatay and V…
Ferhat Ay
@ferhatay Mar 23
So proud of @abhijitchak23 for getting his first major grant to work on a specific subtype of pediatric leukemia from #TheConradPrebysFoundation. This was SPARKed by the funds from LJI’s Tullie and Rickey Families SPARK Awards. Looking forward to working on this project. twitter.com/ljiresearch/st…
Ferhat Ay
@ferhatay Mar 23
After one exact year (March 8th 2020-2021), I returned back to my office two weeks ago the same way I left plus lysol wipes. Not sure if my productivity went up but my morale and motivation certainly did. Work-from-home is great when you choose to do so, not when you have to :)
Ferhat Ay
@ferhatay Mar 23
RT @c_ottensmeier: Read this #preprint on @researchsquare: Immunomodulatory effects of PI3Kδ inhibition in solid tumors – evaluation in a r…
Ferhat Ay
@ferhatay Mar 16
What has kept our institute working safely for many months is now also recognized with this prestigious award! We seem to be the only academic institution among the winners! Congratulations @ljiresearch, Suzie Alarcon and her team, Steve Wilson and the LJI leadership 👏👏 twitter.com/jhuber/status/…
Ferhat Ay
@ferhatay Mar 16
Congratulations @EOSaphire! Looking forward to working with you to take LJI to the next level twitter.com/EOSaphire/stat…
Ferhat Ay
@ferhatay Mar 11
Great to have you on the team @yusufdawodnazar. Happy birthday
Ferhat Ay
@ferhatay Mar 11
Thanks @rassobar!
Ferhat Ay
@ferhatay Mar 11
RT @Society4Science: #RegeneronSTS finalist Jeffrey Wang created an application to evaluate the folded 3D architecture of DNA across cell l…
Ferhat Ay
@ferhatay Mar 06
Thanks a lot for the invitation @mikhaildozmorov
Ferhat Ay
@ferhatay Mar 03
RT @TsangLab: meetings.cshl.edu/meetings.aspx?…: Apr 20-23, 2021 - second @CSHL systems immunology meeting; hope to see you! Apparently you can still…
From the lab
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
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
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