Cait Harrigan, MSc.
Cait Harrigan, MSc.
charrigan@cs.toronto.edu caitharrigan.ca harrig12
I am a PhD candidate at the University of Toronto supervised by Quaid Morris and Kieran Campbell. I am a Doctoral Fellow at the UofT Data Sciences Institute and a graduate researcher at the Vector Institute and Ontario Institute for Cancer Research. I use machine learning to understand cancer genomics by modelling the evolutionary constraints that underlie how mutations occur in DNA. I’m passionate about open science, and promoting great mentorship in the sciences.
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
Undergraduate research assistant
SickKids Hospital, Toronto, Canada
Supervised by Michael Wilson and Anna Goldenberg
Intern - Pharmacoeconomics
Eviviz, Vancouver, Canada
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
Peer reviewed publications
* Indicates joint first authorship, † co-corresponding authorship
Regional Mutational Signature Activities in Cancer Genomes
Caitlin Timmons, Quaid Morris†, and Caitlin F. Harrigan†
PLOS Computational Biology, 2022
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
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
Other publications
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
Workshop paper at ICML 2025
Evolutionary characterisation of lung cancer metastasis
Sonya Hessey*, Abigail Bunkum*, Ariana Huebner*, Kristiana Grigoriadis*, Kerstin Haase*, Cristina Naceur-Lombardelli*, Wing Liu, Caitlin F. Harrigan, Daniele Marinelli, Boyue Ding, Corentin Richard, Carlos Martinez-Ruiz, Mark Hill, Olivia Lucas, Oriol Pich, Kerstin Thol, Piotr Pawlik, Takahiro Karasaki, Sophia Ward, Foteini Athanasopoulou, Monica Sivakumar, Selvaraju Veeriah, Antonia Toncheva, Andrew Rowan, Paulina Prymas, Hayley Bridger, Miriam Mitchinson, Elaine Borg, Mary Falzon, Ian Proctor, Ula Mahadeva, Anna Green, Martin Forster, Sarah Benafif, Tanya Ahmad, Siow Lee, Dionysis Papadatos-Pastos, Babu Naidu, Gerald Langman, Matthew Krebs, Pedro Oliveira, Fiona Blackhall, Yvonne Summers, Jamie Weaver, John Le Quesne, Anne Thomas, Cathy Richards, Dean Fennell, Sanjay Jogai, Judith Cave, Patricia Roxburgh, Sioban Fraser, Alan Kirk, Kevin Blyth, Peter Russell, Crispin Hiley, Allan Hackshaw, The TRACERx consortium, TRACERx EVO Consortium, PEACE Consortium, Simone Zaccaria, Nicholas McGranahan†, Charles Swanton†, Mariam Jamal-Hanjani†
Under consideration at Nature
Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes
Caitlin F. Harrigan, Kieran R. Campbell, Quaid Morris†, Tyler Funnell†
Under consideration at Nature Communications
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
Under consideration at Cell Systems
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
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
Considerations for Visualizing Uncertainty in Clinical Machine Learning Models
Caitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier
Workshop paper at CHI 2021
Posters
Mapping the Evolution of Mutational Signatures on Tumour Phylogenies, ISMB 2024
Dirichlet Allocation of Mutations Captures the Action of DNA Damage and Misrepair Processes, ISMB 2022
TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies, MLCB 2021
Academic awards
NSERC Postgraduate Scholarship - Doctoral
Natural Sciences and Engineering Research Council of Canada
Doctoral Student Fellowship Award
Data Science Institute, University of Toronto
Graduate Research Award
Mitacs, in partnership with UKRI
Queen Elizabeth II Graduate Scholarship in Science & Technology
Province of Ontario
Respectfully declined
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
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 anual 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
Professional training
The Carpentries certified instructor
Oxford ML summer school (Health track)
Teaching assistant positions
Unless otherwise noted, school is University of Toronto
CSC2541: Topics in Machine Learning: Al for Drug Discovery, Head prep TA
CrossTALK drug discovery bootcamp, Head TA
JSC370: Data Science II
JSC270: Data Science I
STA313: Data Visualization
PRISM: Preparation for Research through Immersion, Skills, and Mentorship
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 2024
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