Shaun Mahony receives 2021 National Science Foundation CAREER Award
Shaun Mahony, assistant professor of biochemistry and molecular biology, has been honored with a Faculty Early Career Development (CAREER) award from the National Science Foundation (NSF). The CAREER award is NSF’s most prestigious award in support of early-career faculty members who have the potential to serve as academic role models in research and education and to lead advances in the mission of their department or organization.
The CAREER award will provide five years of funding to support Mahony’s research to develop machine learning methods to predict where transcription factors—proteins that control gene expression—bind to the genome. Experimental approaches to determine where these proteins bind can be expensive and laborious. Mahony will use existing experimental data to train neural networks to recognize features of gene regulatory sites. Then, the software will be used to predict gene regulatory sites in repetitive DNA areas, in other cell types, in diseased cells, and in the genomes of other species.
“Neural networks can be trained to accurately recognize gene regulatory sites in a genome,” Mahony said. “But they don’t always do well in predicting regulatory sites in new contexts – for example in a previously unseen genome. This NSF CAREER award will allow us to develop neural networks that can adapt across different genomic contexts.”
The software resulting from this project will be made freely available to the research community and will provide important insight into gene regulation in situations that were previously hard to study.
The award will also provide funding for an integrated educational initiative. Mahony will work with Penn State’s Center for Science and the Schools and Pennsylvanian high school teachers to develop educational modules that will introduce high school students to bioinformatics research.
Mahony has published nearly 50 papers in peer reviewed journals, including Nature, Nature Neuroscience, Cell Stem Cell, and Molecular Cell, and has mentored nearly 30 undergraduate and graduate students. He currently serves on the editorial board for the journal Biochimica et Biophysica Acta.
Prior to joining the faculty at Penn State in 2012, Mahony was a visiting scientist at Harvard University from 2011 to 2012. He was a research scientist from 2010 to 2012 and a postdoctoral research associate from 2007 to 2010 at the Massachusetts Institute of Technology and a postdoctoral research associate at the University of Pittsburgh from 2005 to 2007. Mahony earned a doctoral degree in information technology and a bachelor's degree in electronic and computer engineering at the National University of Ireland in Galway in 2006 and 2002, respectively.