Cait Harrigan, MSc, PhD
charrigan@cs.toronto.edu caitharrigan.ca harrig12
I am a postdoctoral researcher in the Park lab at Harvard Medical School. I use machine learning to study cancer evolution and the selective forces shaping tumor development. I earned my PhD in Computer Science from the University of Toronto in 2026, supervised by Quaid Morris and Kieran Campbell. I was a Doctoral Fellow at the UofT Data Sciences Institute and a graduate researcher at the Vector Institute and Ontario Institute for Cancer Research. In my thesis, I developed probabilistic models and Bayesian optimization approaches to study DNA repair deficiencies using genomic sequencing and spatial proteomic data. I’m passionate about open science, and promoting great mentorship in the sciences.
Research interests
My research focuses on developing machine learning methods to understand cancer evolution through patterns in somatic mutations. I combine computational biology, statistical modeling, and large-scale genomic data analysis to identify the evolutionary constraints that underlie mutation, and identify therapeutically targetable DNA repair deficiencies. With expertise in: cancer genomics, spatial proteomics, deep learning, probabilistic modelling, and programming in python & R in HPC environments.
Education
PhD in Computer Science, University of Toronto
Supervised by Quaid Morris and Kieran Campbell
MSc in Computer Science, University of Toronto
Supervised by Quaid Morris
Honours BSc. in Computational Biology, University of Toronto
Awarded with distinction
Research experience
Visiting graduate researcher
The Francis Crick Institute, London, England
Hosted by Nicholas McGranahan
Visiting graduate researcher
Memorial Sloan Kettering Cancer Center, New York, USA
Hosted by Quaid Morris
Publications
* Indicates joint first authorship, † co-corresponding authorship
1. Damage and misrepair signatures: compact representations of pan-cancer mutational processes, Caitlin F. Harrigan, Kieran R. Campbell, Quaid Morris†, Tyler Funnell†, biorxiv
2. Automated registration of spatial expression data scales multimodal integration to large cohorts, Caitlin F. Harrigan, Ching Yeung Lam, Danian Chen, Christian Lai, Rod Bremner, Hartland W. Jackson, Kieran R. Campbell, biorxiv
3. Measuring scientific capabilities of language models with a systems biology dry lab, Haonan Duan*, Stephen Zhewen Lu*, Caitlin F. Harrigan, Nishkrit Desai, Jiarui Lu, Michał Koziarski, Leonardo Cotta, Chris J. Maddison, biorxiv, Workshop paper at ICML 2025, Poster at NeurIPS 2025
4. Bacterial ADP-heptose initiates a revival stem cell program in the intestinal epithelium, Shawn Goyal, Cynthia X. Guo, Adrienne Ranger, Derek K. Tsang, Ojas Singh, Caitlin F. Harrigan, Olga Zaslaver, Hannes L. Rost, Herbert Y. Gaisano, Scott A. Yuzwa, Nan Gao, Jeffrey L. Wrana, Dana J. Philpott, Scott D. Gray-Owen and Stephen E. Girardin, Cell Stem Cell, 2025
5. Whole slide Imaging Mass Cytometry allows the rapid profiling of the immune landscape of histopathologically aggressive prostate tumors, Jennifer L. Gorman, Lydia Y. Liu, Jordan P. Hartig, Nikesh Parsotam, Amanda Khoo, Vladimir Ignatchenko, Sarah Asbury, Somi Afiuni, Ricardo Gonzalez, Michael J. Geuenich, Caitlin F. Harrigan, Yuju Lee, Jianan Chen, Liang Lim, Qanber Raza, Peggi M. Angel, Kieran Campbell, Stanley K. Liu, Michelle R. Downes, Richard R. Drake, Thomas Kislinger, David King, Hartland W. Jackson, AACR annual meeting proceedings, 2024
6. Regional mutational signature activities in cancer genomes, Caitlin Timmons, Quaid Morris†, and Caitlin F. Harrigan†, PLOS Computational Biology, 2022
7. Activating mTOR mutations are detrimental in nutrient-poor conditions, Agata A. Bielska, Caitlin F. Harrigan, Yeon Ju Kyung, Quaid Morris, Wilhelm Palm, and Craig B. Thompson, Cancer Research, 2022
8. Considerations for visualizing uncertainty in clinical machine learning models, Caitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier, Workshop paper at CHI 2021
9. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig, Yulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, and Quaid Morris, Nature Communications, 2020
Academic talks
Mutational Signatures for DNA Damage and Misrepair, BIRS: Mathematical Methods in Cancer Biology, Evolution and Therapy, Invited talk
DAMUTA: Dirichlet allocation of mutations as a function of both damage and DNA repair, Cold Spring Harbour Laboratory Meeting: Genome Informatics, Selected Talk
TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies, Pacific Symposium on Biocomputing, Selected Talk, Poster
Academic awards
Doctoral Student Fellowship Award
Data Science Institute, University of Toronto
NSERC Postgraduate Scholarship - Doctoral
Natural Sciences and Engineering Research Council of Canada
Graduate Research Award
Mitacs, in partnership with UKRI
Queen Elizabeth II Graduate Scholarship in Science & Technology
Province of Ontario
Ontario Graduate Scholarship
Province of Ontario
ACM SIGHPC Computational & Data Science Fellowship
Special Interest Group on High Performance Computing of the Association for Computing Machinery
JXTX foundation Genome Informatics Scholarship
James P. Taylor Foundation for Open Science
General Motors Women in Science and Mathematics Award
University of Toronto
NIH Conference Travel Fellowship
International Society for Computational Biology
The Audrey Taylor Award for co-curricular contribution to the New College community
University of Toronto
Grants
Emergent Data Sciences Program Grant
Data Science Institute, University of Toronto
Awarded for CrossTALK drug discovery bootcamp
Student initiative fund
University of Toronto
Awarded for Bioinformatics and Computational Biology Hackathon
Event grant
New College Student council
Awarded for Bioinformatics and Computational Biology Hackathon
Academic service
Professional training
The Carpentries certified instructor
Oxford ML summer school (health track)
Student supervision
Kiki Zhang, Combined BS/MSE Student; Biomedical Engineering. Research internship via Computational Biology Student Program at MSKCC, Topic: Mutational signatures in the context of branching evolution
Fedir Zhydok, BS Student; Computer Science. Artificial intelligence in medicine, global classroom program at University of Toronto, Topic: Identifying metastatic tumours from mutational signatures
Caitlin Timmons, BA Student; Statistical and Datasciences, Biology. Research internship via Computational Biology Student Program at MSKCC. Went on to a Research Technician position at Dana-Farber Cancer Institute., Topic: Modelling spatial distribution of mutational signatures in cancer genomes.
Haritha Lakshmanan, Highschool Student. Independent study at MSKCC. Went on to a combined BA/MD at Brooklyn College., Topic: Automatic discovery of mutations predictive of survival in breast cancer patients
Guest lectures
Feature engineering & data loaders, CrossTALK drug discovery bootcamp
Exploring & Explaining Data in the Wild, AI & Data Science Post-Graduate Program, Loyalist College, Invited by Prof. Peter Papadakos as an annual guest lecturer in 2023 & 2024
Data Collection & Analysis, PRISM research & mentorship program, University of Toronto, Invited by Prof. Sadia Sharmin
Environmental & Life Sciences Workshop Series, STEMHub Foundation
R for bioinformatics workshop, Global Society for Genetics and Genome Biology
Other talks
Machine Learning for Cancer Genomics, Artificial Intelligence in Healthcare Society Case Competition, York University, Invited keynote
Finding the ‘I’ in science, ACM Canadian Celebration of Women in Computing, Selected Workshop
Undergraduate research opportunities: how to find them and make them work for you, UofT Bioinformatics and Computational Biology Student Union, Invited by the BCBSU
How to hack your degree, Computer Science Student Union, University of Toronto, Invited by the CSSU
Progam & event organization
Program Organizer
UofT Graduate Application Assistance Program
Project Manager
STEMHub Foundation, Toronto, Canada
Volunteer Coordinator
Computer science grad visit day, University of Toronto
Founder and treasurer
Bioinformatics and Computational Biology Student Union, University of Toronto
Program information session
UofT Bioinformatics and Computational Biology Student Union
Planning executive
Bioinformatics and Computational Biology Hackathon 2018
Teaching assistant positions
Unless otherwise noted, school is University of Toronto
CSC2541: Topics in Machine Learning: AI for Drug Discovery, Head prep TA
CrossTALK drug discovery bootcamp, Head TA
JSC370: Data Science II
JSC270: Data Science I
STA313: Data Visualization
JSC370: Data Science II
CSC197: Privacy in the Age of Big Data Collection
STA4273: Minimizing Expectations
CSC197: Privacy in the Age of Big Data Collection
JSC270: Data Science I
CSC373: Algorithm Design, Analysis & Complexity
Mentorship activities
As part of my ongoing commitment to supporting students at all levels and background in engaging with computational biology, I make an effort to be available to provide guidance and resources to students, with a particular focus on creating an inclusive environment that fosters diverse perspectives and experiences. In addition to being a mentor through the organized programs listed here, I set aside ~2h/month for by-request 30 minute meetings.
Graduate Application Assistance Program, University of Toronto
Computer Science Alumni Mentorship Program, University of Toronto
Statistical Science Alumni Mentorship Program, University of Toronto
ProjectX machine learning research competition, UofT AI club
Her Code Camp, Toronto, Canada
Department of Statistics Mentorship Program, University of Toronto
SPROUT Peer Mentorship Program, University of Toronto
New College E-Mentorship Program, University of Toronto
Hackathons
Silver medal, Toronto Bioinformatics Hackathon
Silver medal, American Statistical Association DataFest Competition
Community activities
Webmaster, Project Galiwatch
Graduate student ambassador, Computer science grad visit day, University of Toronto
Judge, Lunenfeld-Tanenbaum Research Institute Summer Poster Session
Webmaster, IMERSS Xetthecum ecocultural digital mapping project
Volunteer, Meals on wheels
Volunteer, Billion oysters project
Communications and Marketing Executive, UofT Women in Computer Science