UNIVERSITY PARK, Pa. — Shaun Mahony, professor of biochemistry and molecular biology in the Penn State Eberly College of Science, has been named the Dorothy Foehr Huck and J. Lloyd Huck Chair in Genomics and AI.
The appointment recognizes Mahony's work developing computational tools that decode how proteins control which genes are active in a given cell, research that sits at the intersection of molecular biology, genomics and artificial intelligence.
"Every cell in your body carries the same DNA, yet a neuron and a liver cell behave nothing alike," Mahony said. "The difference comes down to which genes are switched on, and that switching is regulated by proteins called transcription factors that bind to specific stretches of DNA and control cascades of gene activity. My research group develops machine learning methods to work out where these proteins bind and what they do there. We build neural networks that learn the subtle genomic patterns a transcription factor recognizes, and pair them with experimental data — generated by our collaborators and in our own laboratory — that pinpoints binding locations on the genome."
"We also develop tools to read the repetitive half of the genome, much of it made of sequences that copied themselves across the genome, which most analyses skip because the same sequence recurs many times and the copies are hard to tell apart. Applying these approaches, we study how transcription factors drive cells to become neurons and other specialized cell types. Understanding this control system matters because most of the DNA variation linked to human disease sits not in genes themselves, but in the switches that regulate them."
Santhosh Girirajan, T. Ming Chu Professor of Genomics and head of the Department of Biochemistry and Molecular Biology, said Mahony's interdisciplinary approach has strengthened both the department and the wider University research community.
"Shaun has been an integral part of my department and our institution's success," Girirajan said. "Whether it is molecular biology, genomics or computer science, Shaun's research embodies the interdisciplinary spirit that is central to the Huck Institutes' mission. I am very excited about this well-deserved recognition for Shaun."
Christina Grozinger, Publius Vergilius Maro Professor of Entomology and director of the Huck Institutes of the Life Sciences, said Mahony's work fills a critical need created by the rapid growth of genomic data.
"With new sequencing technologies and instruments — including our incredible resources at the Huck Genomics Core Facility — we can rapidly sequence genomes from individuals, populations and species," Grozinger said. "But understanding what those genomes mean and how they create biological complexity requires sophisticated computational techniques. Shaun is a pioneer in creating these innovative approaches, and just as importantly, he has made them accessible to the broader community, at Penn State and across the world."
Mahony joined Penn State in 2012 as an assistant professor, earning tenure and rising to associate professor in 2021 before being promoted to professor this year. He holds affiliations with the Center for Eukaryotic Gene Regulation, the Center for Computational Biology and Bioinformatics, and the College of Information Sciences and Technology, and in 2024 was named an Eberly Distinguished Senior Scholar in Genomics. He also serves as associate department head for research and strategic initiatives in the Department of Biochemistry and Molecular Biology.
Before arriving at Penn State, Mahony held research positions at the Massachusetts Institute of Technology, including a postdoctoral fellowship and staff scientist role in the Computer Science and Artificial Intelligence Laboratory, and was a visiting scientist in Harvard University's Department of Stem Cell and Regenerative Biology. He earned a doctoral degree in information technology, with a focus on computational biology, and a bachelor's degree in electronic and computer engineering, both from the University of Galway in Ireland.