Overview
Computational biology, machine learning, Bayesian statistics, transcriptional regulation, genomics and epigenomics, graphical models, Bayesian networks, hidden Markov models, systems biology, computational neurobiology, classification, feature selection
Current Appointments & Affiliations
Professor of Computer Science
·
2013 - Present
Computer Science,
Trinity College of Arts & Sciences
Professor of Biology
·
2013 - Present
Biology,
Trinity College of Arts & Sciences
Bass Fellow
·
2014 - Present
Computer Science,
Trinity College of Arts & Sciences
Recent Publications
Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.
Journal Article Genome Res · January 5, 2026 Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the genome. Despite numerous studies focusing on changes in gene expression, the intricate ... Full text Link to item CiteInferring differential protein binding from time-series chromatin accessibility data.
Journal Article Bioinformatics advances · January 2025 MotivationDue to internal and external factors, the epigenomic landscape is constantly changing in ways that are linked to changes in gene expression. Chromatin accessibility data, such as MNase-seq, provide valuable insights into this landscape a ... Full text CiteAuthor Correction: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis.
Journal Article Nature genetics · June 2024 Full text CiteRecent Grants
Methods to Elucidate the Dynamic Interplay of Transcriptional Regulation and Chromatin Occupancy
ResearchPrincipal Investigator · Awarded by National Institute of General Medical Sciences · 2021 - 2026Elucidating the Molecular Basis of Cellular Metal Stress by using Mass Spectrometry-Based Proteomic Methods
ResearchCollaborator · Awarded by National Institute of General Medical Sciences · 2022 - 2026IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome
ResearchMentor · Awarded by National Science Foundation · 2019 - 2023View All Grants
Education, Training & Certifications
Massachusetts Institute of Technology ·
2001
Ph.D.
University of Oxford (United Kingdom) ·
1996
M.Phil.
Duke University ·
1994
B.S.