Nucleotide context models outperform protein language models for predicting antibody affinity maturation

• Mackenzie M. Johnson ,

  Contributed equally to this work with: Mackenzie M. Johnson, Kevin Sung, Hugh K. Haddox

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

  Affiliation Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America

  https://orcid.org/0000-0002-3915-2023

  ⨯
• Kevin Sung ,

  Contributed equally to this work with: Mackenzie M. Johnson, Kevin Sung, Hugh K. Haddox

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

  Affiliation Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America

  ⨯
• Hugh K. Haddox ,

  Contributed equally to this work with: Mackenzie M. Johnson, Kevin Sung, Hugh K. Haddox

  Roles Conceptualization, Visualization, Writing – review & editing

  Affiliation Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America

  https://orcid.org/0000-0001-8324-8324

  ⨯
• Ashni A. Vora,

  Roles Data curation, Investigation, Writing – review & editing

  Affiliation Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America

  ⨯
• Tatsuya Araki,

  Roles Data curation, Investigation, Writing – review & editing

  Affiliation Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America

  https://orcid.org/0000-0002-6203-7250

  ⨯
• Gabriel D. Victora,

  Roles Conceptualization, Data curation, Investigation, Methodology, Project administration, Writing – review & editing

  Affiliations Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America

  ⨯
• Yun S. Song,

  Roles Conceptualization, Funding acquisition, Investigation, Writing – review & editing

  Affiliations Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America, Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America

  ⨯
• Julia Fukuyama,

  Roles Conceptualization, Investigation, Methodology, Writing – review & editing

  Affiliation Department of Statistics, Indiana University Bloomington, Bloomington, Indiana, United States of America

  ⨯
• Frederick A. Matsen IV

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

  * E-mail: matsen@fredhutch.org

  Affiliations Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America, Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America, Department of Statistics, University of Washington, Seattle, Washington, United States of America

  https://orcid.org/0000-0003-0607-6025

  ⨯