Shaun Mahony
Associate Professor
State College, Pennsylvania, United States
Summary
👤
Senior🎓
Top SchoolShaun Mahony is an Associate Professor and computational biologist with 18 years of experience developing machine learning methods to decode gene regulation and transcription factor binding across cell types and species. Based at Penn State after research positions at MIT and Pittsburgh, he specializes in interpretable neural networks and integrative analysis of regulatory genomics data such as ChIP-seq, ChIP-exo, ATAC-seq, and Hi-C. His PhD work on self-organizing neural networks informs a long-standing focus on melding principled machine learning with biological sequence analysis. Shaun’s lab emphasizes methods that are both accurate and interpretable, enabling cross-species and cell-type comparisons rather than black-box predictions. He combines deep academic rigor with practical tool development that advances how researchers interrogate regulatory landscapes.
18 years of coding experience
7 years of employment as a software developer
Ph.D., Computational Biology, Ph.D., Computational Biology at University of Galway
Github Skills (39)
ssa10
java10
throughput10
sequencing10
java-api10
reproducible-research9
condition9
seq9
motif9
genomics8
stamp8
bioinformatics8
prediction7
science6
pipeline6
Programming languages (8)
Github contributions (5)
shaunmahony/stamp
Mar 2015 - Sep 2016
Contributions:7 commits, 6 pushes, 1 branch in 1 year 6 months
shaunmahony/multigps-archive
Jan 2014 - Nov 2016
Contributions:7 commits, 1 push in 2 years 10 months
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