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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2024

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 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 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 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

Mutation of NOTCH1 is selected within normal esophageal tissues, yet leads to selective epistasis suppressive of further evolution into cancer
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
Cold Spring Harbor Laboratory   ·   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
Cold Spring Harbor Laboratory   ·   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

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
Cold Spring Harbor Laboratory   ·   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

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.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