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

01/21 - present

MSc. in Computer Science, University of Toronto

Supervised by Quaid Morris

09/19 - 03/21

Honours BSc. in Computational Biology, University of Toronto

Awarded with distinction

09/15 - 06/19

Research experience

Visiting graduate researcher

The Francis Crick Institute, London, England

Hosted by Nicholas McGranahan

03/24 - 05/24

Visiting graduate researcher

Memorial Sloan Kettering Cancer Center, New York, USA

Hosted by Quaid Morris

05/21 - 09/21

Undergraduate research assistant

SickKids Hospital, Toronto, Canada

Supervised by Michael Wilson and Anna Goldenberg

05/17 - 09/17

Intern - Pharmacoeconomics

Eviviz, Vancouver, Canada

05/16 - 09/16

Academic talks

Mutational Signatures for DNA Damage and Misrepair, BIRS: Mathematical Methods in Cancer Biology, Evolution and Therapy, Invited talk

05/23 view

DAMUTA: Dirichlet allocation of mutations as a function of both damage and DNA repair, Cold Spring Harbour Laboratory Meeting: Genome Informatics, Selected Talk

11/21

TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies, Pacific Symposium on Biocomputing, Selected Talk, Poster

01/20

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

TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies

Caitlin F. Harrigan, Yulia Rubanova, Quaid Morris, and Alina Selega

Pacific Symposium on Biocomputing, 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

07/24

Dirichlet Allocation of Mutations Captures the Action of DNA Damage and Misrepair Processes, ISMB 2022

07/22

TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies, MLCB 2021

12/19

Academic awards

NSERC Postgraduate Scholarship - Doctoral

Natural Sciences and Engineering Research Council of Canada

09/22 - present

Doctoral Student Fellowship Award

Data Science Institute, University of Toronto

09/22 - present

Graduate Research Award

Mitacs, in partnership with UKRI

03/24 - 05/24

Queen Elizabeth II Graduate Scholarship in Science & Technology

Province of Ontario

Respectfully declined

09/22

Ontario Graduate Scholarship

Province of Ontario

09/21 - 09/22

ACM SIGHPC Computational & Data Science Fellowship

Special Interest Group on High Performance Computing of the Association for Computing Machinery

07/20 - 07/22

JXTX foundation Genome Informatics Scholarship

James P. Taylor Foundation for Open Science

08/21

General Motors Women in Science and Mathematics Award

University of Toronto

09/20

NIH Conference Travel Fellowship

International Society for Computational Biology

11/19

The Audrey Taylor Award for co-curricular contribution to the New College community

University of Toronto

07/17

Grants

Emergent Data Sciences Program Grant

Data Science Institute, University of Toronto

Awarded for CrossTALK drug discovery bootcamp

09/24

Student initiative fund

University of Toronto

Awarded for Bioinformatics and Computational Biology Hackathon

02/18

Event grant

New College Student council

Awarded for Bioinformatics and Computational Biology Hackathon

02/18

Academic service

Jouranl peer review: Genome Biology (2023), Genome Medicine (2021), Nature Cancer (2024), PLOS Computational Biology (2023, 2023), iScience (2021)
Conference referee: ICML 2025 workshop CODEML (2025)
Conference program committee: Machine Learning in Computational Biology (2019), Pacific Symposium on Biocomputing (2020)

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

06/23 - 08/23 view

Fedir Zhydok, BS Student; Computer Science. Artificial intelligence in medicine, global classroom program at University of Toronto, Topic: Identifying metastatic tumours from mutational signatures

09/22 - 12/22 view

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.

05/21 - 08/22 view

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

05/20 - 11/20 view

Guest lectures

Feature engineering & data loaders, CrossTALK drug discovery bootcamp

06/25 code

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

03/23 view code

Data Collection & Analysis, PRISM research & mentorship program, University of Toronto, Invited by Prof. Sadia Sharmin

02/22 pdf

Environmental & Life Sciences Workshop Series, STEMHub Foundation

01/20

R for bioinformatics workshop, Global Society for Genetics and Genome Biology

01/20 code

Other talks

Machine Learning for Cancer Genomics, Artificial Intelligence in Healthcare Society Case Competition, York University, Invited keynote

03/24 pdf

Finding the ‘I’ in science, ACM Canadian Celebration of  Women in Computing, Selected Workshop

10/22 pdf

Undergraduate research opportunities: how to find them and make them work for you, UofT Bioinformatics and Computational Biology Student Union, Invited by the BCBSU

02/20

How to hack your degree, Computer Science Student Union, University of Toronto, Invited by the CSSU

05/19

Progam & event organization

Program Organizer

UofT Graduate Application Assistance Program

09/21 - 01/25

Project Manager

STEMHub Foundation, Toronto, Canada

10/20 - 05/21

Volunteer Coordinator

Computer science grad visit day, University of Toronto

03/20

Founder and treasurer

Bioinformatics and Computational Biology Student Union, University of Toronto

05/18 - 05/19

Program information session

UofT Bioinformatics and Computational Biology Student Union

06/17 - 06/19

Planning executive

Bioinformatics and Computational Biology Hackathon 2018

03/18

Professional training

The Carpentries certified instructor

10/23

Oxford ML summer school (Health track)

07/23

Teaching assistant positions

Unless otherwise noted, school is University of Toronto

CSC2541: Topics in Machine Learning: Al for Drug Discovery, Head prep TA

04/25 - present

CrossTALK drug discovery bootcamp, Head TA

01/25 - present

JSC370: Data Science II

01/23 - 05/23

JSC270: Data Science I

01/23 - 05/23

STA313: Data Visualization

09/22 - 12/22

PRISM: Preparation for Research through Immersion, Skills, and Mentorship

01/22 - 05/22

JSC370: Data Science II

01/22 - 05/22

CSC197: Privacy in the Age of Big Data Collection

09/21 - 12/21

STA4273: Minimizing Expectations

01/21 - 05/21

CSC197: Privacy in the Age of Big Data Collection

09/20 - 12/20

JSC270: Data Science I

01/20 - 05/20

CSC373: Algorithm Design, Analysis & Complexity

09/19 - 12/19

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

09/21 - 01/25

Computer Science Alumni Mentorship Program, University of Toronto

01/23 - 05/23

Statistical Science Alumni Mentorship Program, University of Toronto

10/21 - 05/22

ProjectX machine learning research competition, UofT AI club

09/20 - 02/21

Her Code Camp, Toronto, Canada

08/20 - 08/21

Department of Statistics Mentorship Program, University of Toronto

10/18 - 05/19

SPROUT Peer Mentorship Program, University of Toronto

09/16 - 05/19

New College E-Mentorship Program, University of Toronto

09/16 - 05/19

Hackathons

Silver medal, Toronto Bioinformatics Hackathon 2024

09/24

Silver medal, American Statistical Association DataFest Competition

05/18

Community activities

Webmaster, Project Galiwatch

03/20 - present

Graduate student ambassador, Computer science grad visit day, University of Toronto

03/25

Judge, Lunenfeld-Tanenbaum Research Institute Summer Poster Session

07/24

Webmaster, IMERSS Xetthecum ecocultural digital mapping project

10/23 - 12/24

Volunteer, Meals on wheels

06/23 - 09/23

Volunteer, Billion oysters project

05/21 - 09/21

Communications and Marketing Executive, UofT Women in Computer Science

09/16 - 05/17


Last updated: Jul 2025