Dr. Ay joined joined the La Jolla Institute for Allergy and Immunology as Institute Leadership Assistant Professor of Computational Biology in the Division of Vaccine Discovery, in 2016. His research focuses on understanding the relationship between genome architecture and the regulation of gene activity in the malaria parasite Plasmodium falciparum as well as related issues concerning genome architecture in different organisms and in human cells, such as breast cancer and leukemia cells.

Born and raised in Turkey, Dr. 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 at the University of Florida in Gainesville, he developed efficient algorithms to comparatively analyze genome-wide networks that govern metabolic activity and gene regulation in multiple organisms including the fruit fly D. melanogaster. His studies revealed that the fruit fly genome regulates its genes in a transcriptional hierarchy with extensive post-transcriptional feedback.

In recognition of his graduate work, which had revealed novel and unexpected topological patterns and relationships between different metabolic and gene regulatory networks, Dr. Ay was named- Computing Innovation Fellow by the Computing Research Association. This extremely competitive fellowship matched him with Dr. William Noble’s laboratory in the Department of Genome Sciences at the University of Washington, Seattle, where he turned his attention to the influence of the genome’s three-dimensional architecture on gene activity.

His trailblazing work provided the first evidence that the 3D configuration of DNA in the nucleus acts as a major gene regulatory mechanism in the most lethal form of malaria, Plasmodium falciparum. By providing fundamental insight into the regulatory mechanisms controlling the infectious cycle of Plasmodium, he paved the way for the development of novel lines of defense against malaria.

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.