J. Nicholas Fisk


Dr. Fisk received their Ph.D. from Yale University (2023) in the lab of Jeffrey Townsend as a part of the interdepartmental program in Computational Biology and Bioinformatics. At Yale, they were the first person from the Computational Biology and Bioinformatics program to complete NIH-funded cross-training program (Cancer Biology Training Program) at the Smilow Cancer Center, was awarded an NCI F31-Diversity Fellowship, and served as the president of graduate and professional students. Dr. Fisk’s research focused on the applied use of evolutionary techniques—especially phylogenetics—to solve a wide range of medically-relevant questions. In particular, they studied therapeutic resistance in cancer, preferential site-migration in cancer and B cells, and immunogenetic interactions with tumor evolution. They also worked to advance phylogenetic experimental design, including implementation of signal and information-based methods for optimal site-gene-taxa sampling. Additionally, Dr. Fisk worked for four years at the Poorvu Center for Teaching and Learning at Yale, developing and running workshops for graduate students and post-docs to improve their pedagogy skills, including the first evidence-based teaching workshop and a number of workshops focused on DEI and technology in the classroom.

Dr. Fisk joined the College of the Environment and Life Sciences at URI in the department of Cell and Molecular Biology in the Fall of 2023. Here, Dr. Fisk continues work on translating “basic science” methods in genomic, evolution, and bioinformatics to address “real-world” problems, as well as operates a laboratory focused on Discipline-Based Education Research in Computational Biology.


The Fisk lab has two main arms: Computational and translational biology and Discipline-Based Education Research (DBER).

The computational arm of the lab focuses on using computational approaches in evolution, genomics, and bioinformatics to address many problems across a relatively broad range of biological and biomedical problems. Most prominently, we are concerned with using evolution and population genetics to better understand cancer progression and therapeutic resistance, as well as characterizing dynamic disease etiologies. But we also work and collaborate on several other, non-cancer systems—including more theory-leaden phylogenetic experimental design. In short, the computational arm of the lab is more focused on the methods and effective collaboration than any singular system.

The DBER arm of the lab is presently investigating the effects of differing modes of failure and the intersection of marginalization and adaptation to interdisciplinary fields, with aims of improving the ways in which increasingly inter- and cross-disciplinary fields are taught and removing barriers to entry for all. We are also working to establish collaborations on using Natural Language Processing and Large Language Models as educational tools across a wide variety of fields, including, of course, computational biology.


  • Ph.D.in Computational Biology and Bioinformatics, Yale University 2023
  • M.S. in Computational Biology and Bioinformatics, Yale University 2019
  • B.S./M.S. in Bioinformatics, Rochester Institute of Technology 2016
  • B.S. in Biotechnology and Molecular Bioscience, Rochester Institute of Technology 2016

Selected Publications

Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2
Jeffrey P. Townsend, Stephen Gaughran, Hayley B. Hassler, J. Nicholas Fisk, Mofeed Nagib, Yinfei Wu, Yaning Wang, Zheng Wang, Alison P. Galvani, Alex Dornburg
bioRxiv 2023.08.07.552269; doi: https://doi.org/10.1101/2023.08.07.552269

Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapy. Cancer Res 1 April 2023; 83 (7_Supplement): 126. https://doi.org/10.1158/1538-7445.AM2023-126
J Nicholas Fisk, Stephen Gaffney, Katerina Politi, Scott Gettinger, Fernando de Miguel, Jeffrey Townsend

Not only mutations but also tumorigenesis can be substantially attributed to DNA damage from reactive oxygen species in RUNX1::RUNX1T1-fusion-positive acute myeloid leukemia. Leukemia. 2022 Dec;36(12):2931-2933. doi: 10.1038/s41375-022-01752-5. Epub 2022 Nov 11. PMID: 36369483; PMCID: PMC9712081.
Mandell JD, Fisk JN, Cyrenne E, Xu ML, Cannataro VL, Townsend JP.

“Navigating Evidence and Knowledge Equity” (2022). Exploring How We Teach. Paper 14.
Fisk, J. Nick

Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma,
Cancer Letters, Volume 526, 2022, ISSN 0304-3835, https://doi.org/10.1016/j.canlet.2021.11.011.
J. Nicholas Fisk, Amandeep R. Mahal, Alex Dornburg, Stephen G. Gaffney, Sanjay Aneja, Joseph N. Contessa, David Rimm, James B. Yu, Jeffrey P. Townsend

Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders. Hum Genomics 16, 1 (2022). https://doi.org/10.1186/s40246-021-00374-9
Ho, M., Thompson, B., Fisk, J.N. et al.