{
  "abstract": "T cell receptor (TCR) sequencing is crucial when studying antigen-specific T cell responses and clonal dynamics. A key objective of TCR repertoire analysis is to identify recurring clonotypes across timepoints or different disease states, providing insight into the evolution of immune response. Bulk-TCR sequencing enables high-throughput profiling of TCR and {beta} sequences but lacks pairing information, while single cell TCR sequencing (scTCR-seq) retains pairing information but is limited by sensitivity, throughput, and costs. We present ClonoDeconv, a computational framework to deconvolute paired TCR {beta} ; clonotype frequency from bulk TCR sequencing experiments using a paired scTCR-seq reference. ClonoDeconv robustly estimated shared clonotype abundances from 5' RACE bulk-TCR datasets using a scTCR-seq reference from the same donor. Applied to longitudinal samples, ClonoDeonv successfully captured the expansion and contraction of rare virus-specific clones across timepoints. Taken together, ClonoDeconv provides a cost-effective and scalable approach for studying the longitudinal T-cell clonal dynamics.",
  "abstract_shown": true,
  "affiliations": [
    "Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "name": "Y. Zhou"
    },
    {
      "affs": [
        0
      ],
      "name": "E. Antoun"
    },
    {
      "name": "M. Pereira Pinho"
    },
    {
      "name": "J. Zheng"
    },
    {
      "name": "Y. Wu"
    },
    {
      "name": "G. Adigbli"
    },
    {
      "name": "F. Issa"
    },
    {
      "name": "Y. Peng"
    },
    {
      "name": "J. Knight"
    },
    {
      "name": "T. Dong"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/28rgmf7gnf7d8.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.13.758550",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.13.758550v1.full",
  "id": "28rgmf7gnf7d8",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.13.758550v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "2403|T-cell and B-cell Immunology"
    ]
  ],
  "openalex": "W7222987738",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.13.758550v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-13",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/28rgmf7gnf7d8.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:28:37Z",
      "native_id": "10.64898/2026.10.13.758550",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.13.758550v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "ClonoDeconv: reference-based α - β paired recurrent clonotype proportion estimation from bulk-TCR sequencing",
  "title_text": "ClonoDeconv: reference-based α - β paired recurrent clonotype proportion estimation from bulk-TCR sequencing",
  "type": "preprint",
  "updated_at": "2026-10-30T12:28:37Z",
  "url": "https://research.draconitic.com/paper/28rgmf7gnf7d8",
  "venue": "bioRxiv",
  "versions": []
}