Fisk Lab at URI Cancer Evolution and Education

Research

The Fisk lab has broad interests, but has worked on projects in comparative genomics, cancer evolution, phylogenetic experimental design, community microbiology, and more! On the education side, we have two main focuses at the moment. The first is in trying to understand what makes interdisciplinary fields like computational biology so difficult to teach and learn, how that affects marginalized students, and what we can do to remedy it. The second is trying to improve STEM education in underserved communities while respecting thier modes of knowledge production.

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2026

Abstract 2729: The selective landscape of somatic mutations encodes histopathological information in breast cancer.
Abstract 2729: The selective landscape of somatic mutations encodes histopathological information in breast cancer.
Gift Asefon, Nic Fisk
Cancer Research   ·   03 Apr 2026   ·   doi:10.1158/1538-7445.AM2026-2729
Abstract 707: Phylogenetic and machine learning analyses of simulated ancestral sequences reveals heterogeneous ccRCC evolution.
Abstract 707: Phylogenetic and machine learning analyses of simulated ancestral sequences reveals heterogeneous ccRCC evolution.
Nic Fisk, Christopher Cross, Brian M. Shuch, Jeffrey Peter Townsend
Cancer Research   ·   03 Apr 2026   ·   doi:10.1158/1538-7445.AM2026-707
Abstract 5566: Molecular evolution reveals low-prevalence driver mutations, mutational synergies, and associated immune dynamics in ovarian cancer
Abstract 5566: Molecular evolution reveals low-prevalence driver mutations, mutational synergies, and associated immune dynamics in ovarian cancer
Julia McAdams, Nic Fisk
Cancer Research   ·   03 Apr 2026   ·   doi:10.1158/1538-7445.AM2026-5566
Signal, noise, and bias in phylogenetic inference: potential and limits to the resolution of phylogenetic trees in the phylogenomic era
Signal, noise, and bias in phylogenetic inference: potential and limits to the resolution of phylogenetic trees in the phylogenomic era
Alex Dornburg, Zhuo Tony Su, Yide Jin, J. Nic Fisk, Jeffrey P. Townsend
openRxiv   ·   01 Apr 2026   ·   doi:10.64898/2026.03.30.714540

2025

Abstract IA007: Evolutionary cancer epidemiology
Abstract IA007: Evolutionary cancer epidemiology
Carlo Maley, Katherine Lawson-Michod, Hannah Carter, Kathleen Curtius, Kathleen Houlahan, ..., Charles Swanton, Zachary T. Compton, Athena Aktipis, Robert Hiatt, Arcadi Navarro
Cancer Research   ·   04 Dec 2025   ·   doi:10.1158/1538-7445.CANEVOL25-IA007
Abstract A007: Characterization of the recurrent and parallel evolution of non-small cell lung cancer metastases to the brain
Abstract A007: Characterization of the recurrent and parallel evolution of non-small cell lung cancer metastases to the brain
Nic Fisk, Sarah Goldberg, Jeffrey P. Townsend
Cancer Research   ·   04 Dec 2025   ·   doi:10.1158/1538-7445.CANEVOL25-A007
TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations
TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations
Jessie J. Fielding, Sherry Wu, Hunter J. Melton, Crystal Z. Wang, Nic Fisk, Louis du Plessis, Kenneth B. Hoehn
openRxiv   ·   22 Oct 2025   ·   doi:10.1101/2025.10.21.683591
Somatic evolution of prostate cancer: mutation, selection, and epistasis across disease stages
Somatic evolution of prostate cancer: mutation, selection, and epistasis across disease stages
Moein Rajaei, Alexander Yang, Kira A. Glasmacher, Christopher N. Cross, Nic Fisk, ..., Jose Costa, Peter Humphrey, Vincent L. Cannataro, Paul C. Boutros, Jeffrey P. Townsend
openRxiv   ·   28 Sep 2025   ·   doi:10.1101/2025.09.25.678387
Abstract 1016: Reduction of social disparities in clinical cancer feature prediction via somatic evolutionary embedding of mutational data
Abstract 1016: Reduction of social disparities in clinical cancer feature prediction via somatic evolutionary embedding of mutational data
Nic Fisk, Jeffrey P. Townsend
Cancer Research   ·   21 Apr 2025   ·   doi:10.1158/1538-7445.AM2025-1016
Abstract 7496: Evolutionary trajectories inferred by selective epistasis and phylogenetic analysis reveal the malignant progression of intraductal papillary mucinous neoplasms to pancreatic ductal adenocarcinoma
Abstract 7496: Evolutionary trajectories inferred by selective epistasis and phylogenetic analysis reveal the malignant progression of intraductal papillary mucinous neoplasms to pancreatic ductal adenocarcinoma
Derek C. Song, Nic Fisk, Margaret Moore, Vincent L. Cannataro, Jeffrey D. Mandell, Luisa Escobar-Hoyos, Leanne Brown, Lu Qiao, John W. Kunstman, Jeffrey P. Townsend
Cancer Research   ·   21 Apr 2025   ·   doi:10.1158/1538-7445.AM2025-7496
Abstract 2671: Divergent evolutionary trajectories of the molecular subtypes of breast cancer are driven by differential selection and selective epistasis
Abstract 2671: Divergent evolutionary trajectories of the molecular subtypes of breast cancer are driven by differential selection and selective epistasis
Jessica Liu, Krishna Dasari, Nicholas Fisk, Carolyn Kravitz, Lajos Pusztai, Jeffrey Townsend
Cancer Research   ·   21 Apr 2025   ·   doi:10.1158/1538-7445.am2025-2671
Overcoming Barriers to Cross-Disciplinary Education: A Productive Failure Framework
Overcoming Barriers to Cross-Disciplinary Education: A Productive Failure Framework
Nic Fisk
2025 Women in Bioinformatics Workshop (WIBI)   ·   06 Feb 2025   ·   doi:10.1109/WIBI64774.2025.11115477

2024

Abstract C030: Evolutionary and epistatic analyses reveal genic interactions with KRAS during malignant progression of pancreatic ductal adenocarcinoma
Abstract C030: Evolutionary and epistatic analyses reveal genic interactions with KRAS during malignant progression of pancreatic ductal adenocarcinoma
Nic Fisk, Derek Song, Margaret Moore, Cole G Jensen, Vincent L. Cannataro, Mofeed Nagib, Jeffrey D Mandell, Luisa Escobar-Hoyos, John W Kunstman, Jeffrey P Townsend
Cancer Research   ·   15 Sep 2024   ·   doi:10.1158/1538-7445.PANCREATIC24-C030
Abstract 548: Exploiting pronounced selection pressure from therapeutic bottlenecks to identify orthogonal immunotherapy targets
Abstract 548: Exploiting pronounced selection pressure from therapeutic bottlenecks to identify orthogonal immunotherapy targets
J. Nic Fisk, Jeffrey P. Townsend
Cancer Research   ·   22 Mar 2024   ·   doi:10.1158/1538-7445.AM2024-548
Abstract 1627: Persistence and dynamics of mutation, selection, and epistasis during the somatic evolution of low-risk, high-risk, and metastatic prostate cancer
Abstract 1627: Persistence and dynamics of mutation, selection, and epistasis during the somatic evolution of low-risk, high-risk, and metastatic prostate cancer
Moein Rajaei, Alexander Yang, Christopher N. Cross, J Nick Fisk, Elizabeth B. Perry, ..., Vincent L. Cannataro, Peter Humphrey, Jose Costa, Paul C. Boutros, Jeffrey P. Townsend
Cancer Research   ·   22 Mar 2024   ·   doi:10.1158/1538-7445.am2024-1627
Abstract IA006: Leveraging the extreme selection induced by therapeutic bottlenecks to subvert resistance via identifying evolutionarily-informed targets for orthogonal immunotherapy
Abstract IA006: Leveraging the extreme selection induced by therapeutic bottlenecks to subvert resistance via identifying evolutionarily-informed targets for orthogonal immunotherapy
J. Nic Fisk, Katerina Politi, Scott Gettinger, Jeffrey P Townsend
Cancer Research   ·   01 Feb 2024   ·   doi:10.1158/1538-7445.CANEVOL23-IA006
Abstract IA010: Unraveling mutation and selection to better understand early cancer evolution
Abstract IA010: Unraveling mutation and selection to better understand early cancer evolution
Vincent L. Cannataro, Kira A. Glasmacher, Mary Summers, Jeffrey D. Mandell, J. Nic Fisk, Mia Jackson, Sem Asmelash, Jeffrey P. Townsend
Cancer Research   ·   01 Feb 2024   ·   doi:10.1158/1538-7445.canevol23-ia010
Abstract A035: Mutation of <i>NOTCH</i>1 is selected within normal esophageal tissues, yet leads to selective epistasis suppressive of further evolution into cancer
Abstract A035: Mutation of NOTCH1 is selected within normal esophageal tissues, yet leads to selective epistasis suppressive of further evolution into cancer
Kira A. Glasmacher, Vincent L. Cannataro, Jeffrey D. Mandell, Mia Jackson, J. Nic Fisk, Jeffrey P. Townsend
Cancer Research   ·   01 Feb 2024   ·   doi:10.1158/1538-7445.canevol23-a035

2023

Early <i>NOTCH1</i> mutation is positively selected but epistatically suppresses evolution of later esophageal squamous-cell carcinoma drivers
Early NOTCH1 mutation is positively selected but epistatically suppresses evolution of later esophageal squamous-cell carcinoma drivers
Kira A. Glasmacher, Jeffrey D. Mandell, Mia Jackson, Nic Fisk, Vincent L. Cannataro, Jeffrey P. Townsend
openRxiv   ·   05 Nov 2023   ·   doi:10.1101/2023.11.03.565535
Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2
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
openRxiv   ·   07 Aug 2023   ·   doi:10.1101/2023.08.07.552269
Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapy
Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapy
J Nicholas Fisk, Stephen Gaffney, Katerina Politi, Scott Gettinger, Fernando de Miguel, Jeffrey Townsend
Cancer Research   ·   04 Apr 2023   ·   doi:10.1158/1538-7445.am2023-126
Abstract P5-14-07: Somatic mutations of ER and HER2 subtypes exhibit divergent evolutionary trajectories determined by selective epistasis revealed in phylogenetic reconstruction and stage-specific analyses
Abstract P5-14-07: Somatic mutations of ER and HER2 subtypes exhibit divergent evolutionary trajectories determined by selective epistasis revealed in phylogenetic reconstruction and stage-specific analyses
Krishna Dasari, J. Nick Fisk, Jeffrey Townsend
Cancer Research   ·   01 Mar 2023   ·   doi:10.1158/1538-7445.sabcs22-p5-14-07

2022

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
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
Jeffrey D. Mandell, J. Nick Fisk, Ethan Cyrenne, Mina L. Xu, Vincent L. Cannataro, Jeffrey P. Townsend
Leukemia   ·   11 Nov 2022   ·   doi:10.1038/S41375-022-01752-5
Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma
Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma
J. Nicholas Fisk, Amandeep R. Mahal, Alex Dornburg, Stephen G. Gaffney, Sanjay Aneja, Joseph N. Contessa, David Rimm, James B. Yu, Jeffrey P. Townsend
Cancer Letters   ·   01 Feb 2022   ·   doi:10.1016/J.CANLET.2021.11.011
Why are keratins important?
Why are keratins important?
Jeffrey Nicholas Fisk, Daniel W. Nebert
Human Genomics   ·   30 Jan 2022   ·   doi:10.1186/s40246-022-00379-y
Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders
Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders
Minh Ho, Brian Thompson, Jeffrey Nicholas Fisk, Daniel W. Nebert, Elspeth A. Bruford, Vasilis Vasiliou, Christopher G. Bunick
Human Genomics   ·   06 Jan 2022   ·   doi:10.1186/s40246-021-00374-9
Exploring How We Teach: Lived Experiences, Lessons, and Research about Graduate Instructors by Graduate Instructors
Exploring How We Teach: Lived Experiences, Lessons, and Research about Graduate Instructors by Graduate Instructors
Audrey Tocco, Avaneesh Narla, Elizabeth Giardina, Erin Hughes, Faqryza Ab Latif, ..., Olivia Wilkins, Nathalie Marinho, Matthew Langley, Hima Rawal, Harrison Parker
Utah State University   ·   01 Jan 2022   ·   doi:10.26079/da16-f285

2021

RNA-Seq analysis of genes involved in pistillate flower initiation in<i>Carya illinoinensis</i>
RNA-Seq analysis of genes involved in pistillate flower initiation inCarya illinoinensis
H. Rhein, S. Barnes, B. Van Scyoc, J.N. Fisk, Mingzhou Song, M. Thompson, R. Heerema, J. Randall
Acta Horticulturae   ·   01 Aug 2021   ·   doi:10.17660/actahortic.2021.1318.24
Insights into the impact of geography and genetics on the microbiome of <i>Carya illinoinensis</i>
Insights into the impact of geography and genetics on the microbiome of Carya illinoinensis
J. Randall, K. Cervantes, D.K. Ray, A. Sanchez, K. Mason, J.N. Fisk, J.R. Soneji, L. Sanchez, L.J. Grauke, X. Wang
Acta Horticulturae   ·   01 Aug 2021   ·   doi:10.17660/actahortic.2021.1318.34
Clinically relevant shifts in endogenous and exogenous mutational processes proximate to metastasis support local consolidative treatment in EGFR-driven non-small cell lung cancer
Clinically relevant shifts in endogenous and exogenous mutational processes proximate to metastasis support local consolidative treatment in EGFR-driven non-small cell lung cancer
J. Nicholas Fisk, Amandeep R. Mahal, Alex Dornburg, Stephen G. Gaffney, Sanjay Aneja, Joseph N. Contessa, David Rimm, James B. Yu, Jeffrey P. Townsend
openRxiv   ·   04 May 2021   ·   doi:10.1101/2021.05.04.21256425

2019

Overexpression of T-bet in HIV infection is associated with accumulation of B cells outside germinal centers and poor affinity maturation
Overexpression of T-bet in HIV infection is associated with accumulation of B cells outside germinal centers and poor affinity maturation
James W. Austin, Clarisa M. Buckner, Lela Kardava, Wei Wang, Xiaozhen Zhang, ..., Tae-Wook Chun, Steven H. Kleinstein, John S. Tsang, Constantinos Petrovas, Susan Moir
Science Translational Medicine   ·   27 Nov 2019   ·   doi:10.1126/scitranslmed.aax0904
Molecular Biology and Evolution of Cancer: From Discovery to Action
Molecular Biology and Evolution of Cancer: From Discovery to Action
Jason A Somarelli, Heather Gardner, Vincent L Cannataro, Ella F Gunady, Amy M Boddy, ..., Kate Megquier, Sudhir Kumar, Alex Dornburg, James DeGregori, Jeffrey P Townsend
Molecular Biology and Evolution   ·   23 Oct 2019   ·   doi:10.1093/MOLBEV/MSZ242
Ivivin
Ivivin
[no author info]
Owl You Need is Books   ·   15 Aug 2019   ·   isbn:0692927557
Killing Two Birds with One Stone: The Concurrent Development of the Novel Alignment Free Tree Building Method, Scrawkov-Phy, and the Extensible Phyloinformatics Utility, EMU-Phy.
Killing Two Birds with One Stone: The Concurrent Development of the Novel Alignment Free Tree Building Method, Scrawkov-Phy, and the Extensible Phyloinformatics Utility, EMU-Phy.
[no author info]
Exploring how we teach: Lived experiences, lessons, and research about graduate instructors by graduate instructors   ·   15 Aug 2019   ·   :

2017

p53 binding sites in normal and cancer cells are characterized by distinct chromatin context
p53 binding sites in normal and cancer cells are characterized by distinct chromatin context
Feifei Bao, Peter R. LoVerso, Jeffrey N. Fisk, Victor B. Zhurkin, Feng Cui
Cell Cycle   ·   28 Sep 2017   ·   doi:10.1080/15384101.2017.1361064
p53 binding sites in normal and cancer cells are characterized by distinct chromatin context
p53 binding sites in normal and cancer cells are characterized by distinct chromatin context
Feifei Bao, Peter R. LoVerso, Jeffrey N. Fisk, Victor B. Zhurkin, Feng Cui
openRxiv   ·   02 Feb 2017   ·   doi:10.1101/105221

2016

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
Alex Dornburg, J. Nick Fisk, Jules Tamagnan, Jeffrey P. Townsend
BMC Evolutionary Biology   ·   01 Dec 2016   ·   doi:10.1186/S12862-016-0837-3
Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool
Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool
Dina L. Newman, Christopher W. Snyder, J. Nick Fisk, L. Kate Wright
CBE—Life Sciences Education   ·   01 Jun 2016   ·   doi:10.1187/CBE.15-06-0124

2015

DEVELOPMENT OF CDCI-SHINE, AN R-BASED WEB APPLICATION FOR THE ANALYSIS OF RESULTS FROM THE CENTRAL DOGMA CONCEPT INVENTORY (CDCI)
DEVELOPMENT OF CDCI-SHINE, AN R-BASED WEB APPLICATION FOR THE ANALYSIS OF RESULTS FROM THE CENTRAL DOGMA CONCEPT INVENTORY (CDCI)
Nic Fisk, Christopher Snyder, Dina Newman, L. Kate Wright
Zenodo   ·   07 Nov 2015   ·   doi:10.5281/zenodo.10059292
DEVELOPMENT OF CDCI-SHINE, AN R-BASED WEB APPLICATION FOR THE ANALYSIS OF RESULTS FROM THE CENTRAL DOGMA CONCEPT INVENTORY (CDCI)
DEVELOPMENT OF CDCI-SHINE, AN R-BASED WEB APPLICATION FOR THE ANALYSIS OF RESULTS FROM THE CENTRAL DOGMA CONCEPT INVENTORY (CDCI)
Nic Fisk, Christopher Snyder, Dina Newman, L. Kate Wright
Zenodo   ·   07 Nov 2015   ·   doi:10.5281/ZENODO.10059291

2014

DNA → RNA: What Do Students Think the Arrow Means?
DNA → RNA: What Do Students Think the Arrow Means?
L. Kate Wright, J. Nick Fisk, Dina L. Newman
CBE—Life Sciences Education   ·   01 Jun 2014   ·   doi:10.1187/CBE.CBE-13-09-0188