Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction

Jeremy Charlier; Zeinab Sherkatghanad; Vladimir Makarenkov

doi:10.1371/journal.pcbi.1013606

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Open Access

Peer-reviewed

Research Article

Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction

Jeremy Charlier ,

Contributed equally to this work with: Jeremy Charlier, Zeinab Sherkatghanad

Roles Conceptualization, Data curation, Formal analysis, Methodology, Software, Validation, Writing – original draft, Writing – review & editing

Affiliation Département d’Informatique, Université du Québec à Montréal, Montreal, Quebec, Canada
⨯
Zeinab Sherkatghanad ,

Contributed equally to this work with: Jeremy Charlier, Zeinab Sherkatghanad

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Writing – original draft, Writing – review & editing

Affiliation Département d’Informatique, Université du Québec à Montréal, Montreal, Quebec, Canada
⨯
Vladimir Makarenkov

Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing

* E-mail: makarenkov.vladimir@uqam.ca

Affiliations Département d’Informatique, Université du Québec à Montréal, Montreal, Quebec, Canada, Mila - Quebec AI Institute, Montreal, Quebec, Canada

https://orcid.org/0000-0003-3753-5925

⨯

Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction

Jeremy Charlier,
Zeinab Sherkatghanad,
Vladimir Makarenkov

Published: October 24, 2025
https://doi.org/10.1371/journal.pcbi.1013606

About the Authors

Jeremy Charlier

Contributed equally to this work with: Jeremy Charlier, Zeinab Sherkatghanad

Roles Conceptualization, Data curation, Formal analysis, Methodology, Software, Validation, Writing – original draft, Writing – review & editing

Affiliation Département d’Informatique, Université du Québec à Montréal, Montreal, Quebec, Canada

Zeinab Sherkatghanad

Contributed equally to this work with: Jeremy Charlier, Zeinab Sherkatghanad

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Writing – original draft, Writing – review & editing

Affiliation Département d’Informatique, Université du Québec à Montréal, Montreal, Quebec, Canada

Vladimir Makarenkov

Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing

* E-mail: makarenkov.vladimir@uqam.ca

Affiliations Département d’Informatique, Université du Québec à Montréal, Montreal, Quebec, Canada, Mila - Quebec AI Institute, Montreal, Quebec, Canada

https://orcid.org/0000-0003-3753-5925

Competing Interests

The authors have declared that no competing interests exist.

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Machine learning
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CRISPR
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Deep learning
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Cosine similarity
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Machine learning algorithms
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Distance measurement
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Genomics
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