Research

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

Publications

*, ^† Indicates equal contribution

Damage and misrepair signatures: compact representations of pan-cancer mutational processes

Caitlin F. Harrigan, Kieran R. Campbell, Quaid Morris^†, Tyler Funnell^†

biorxiv

view

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

view code

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

view code

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

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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

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Regional mutational signature activities in cancer genomes

Caitlin Timmons, Quaid Morris^†, and Caitlin F. Harrigan^†

PLOS Computational Biology, 2022

view code

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

view code

Considerations for visualizing uncertainty in clinical machine learning models

Caitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier

Workshop paper at CHI 2021

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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

view code

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

view code

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