Shaun Mahony

Shaun Mahony is an Associate Professor in the Department of Biochemistry & Molecular Biology and a member of the Center for Eukaryotic Gene Regulation at Penn State University. His research focuses on computational approaches to understand gene regulation, particularly how transcription factors (TFs) interact with genomic elements and chromatin environments. He leads the Mahony Lab, which integrates machine learning with high-throughput genomic data (e.g., ChIP-seq, ATAC-seq, Hi-C) to study TF binding dynamics, chromatin architecture, and cell fate decisions.

Education & Background:

• PhD in Computational Biology (2006), National University of Ireland, Galway
• Postdoctoral Research (2007–2010): MIT, Computational Biology
• Visiting Scientist (2011–2012): Harvard University, Stem Cell Biology

Research Interests: The lab develops algorithms to analyze protein-DNA interactions, chromatin 3D structure, and regulatory networks. Key themes include:

• Machine learning for genomic data integration
• Context-specific TF binding mechanisms
• Cellular reprogramming and differentiation pathways

Grants & Funding:

• NSF CAREER Award (2020) for predicting TF binding dynamics
• NIH NIGMS MIRA (2018–2023) for studying TF regulatory activity

Labs & Affiliations: Mahony collaborates with centers including the Center for Comparative Genomics and Bioinformatics, and is affiliated with graduate programs in Bioinformatics & Genomics (BMMB) and Molecular, Cellular and Integrative Biosciences (MCIBS).