Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification

Hannah Kockelbergh; Shelley C. Evans; Liam Brierley; Peter L. Green; Andrea L. Jorgensen; Elizabeth J. Soilleux; Anna Fowler

doi:10.1371/journal.pcbi.1014211

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Open Access

Peer-reviewed

Research Article

Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification

Hannah Kockelbergh,

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

Affiliations Department of Health Data Science, University of Liverpool, Liverpool, United Kingdom, The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom

https://orcid.org/0000-0002-1196-1195

⨯
Shelley C. Evans,

Roles Data curation, Resources, Writing – review & editing

Affiliations Department of Pathology, University of Cambridge, Cambridge, United Kingdom, Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom

https://orcid.org/0000-0003-3242-6017

⨯
Liam Brierley,

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

Affiliations Department of Health Data Science, University of Liverpool, Liverpool, United Kingdom, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom

https://orcid.org/0000-0002-3026-4723

⨯
Peter L. Green,

Roles Conceptualization, Supervision, Writing – review & editing

Affiliation School of Engineering, University of Liverpool, Liverpool, United Kingdom
⨯
Andrea L. Jorgensen,

Roles Conceptualization, Supervision, Writing – review & editing

Affiliation Department of Health Data Science, University of Liverpool, Liverpool, United Kingdom
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Elizabeth J. Soilleux,

Roles Conceptualization, Funding acquisition, Resources, Supervision, Writing – review & editing

Affiliation Department of Pathology, University of Cambridge, Cambridge, United Kingdom
⨯
Anna Fowler

Roles Conceptualization, Formal analysis, Funding acquisition, Methodology, Supervision, Writing – review & editing

* E-mail: a.fowler@liverpool.ac.uk

Affiliation Department of Health Data Science, University of Liverpool, Liverpool, United Kingdom

https://orcid.org/0000-0003-1793-0047

⨯

Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification

Hannah Kockelbergh,
Shelley C. Evans,
Liam Brierley,
Peter L. Green,
Andrea L. Jorgensen,
Elizabeth J. Soilleux,
Anna Fowler

Published: April 30, 2026
https://doi.org/10.1371/journal.pcbi.1014211

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T cell receptors
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Sequence motif analysis
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Optimization
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Amino acid substitution
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Autoimmune diseases
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Biopsy
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Protein sequencing
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