ArticleProceedings of the National Academy of Sciences of the United States of America2023
Measures of epitope binding degeneracy from T cell receptor repertoires.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 36 citations in OpenAlex.
- Unsupervised identification of low-frequency antigen-specific TCRs using distance-based anomaly scoring.Briefings in bioinformatics · 2026Article
- Systematic analysis of CDR contacts and pairing constraints between T cell receptor αβ chains.Bioinformatics (Oxford, England) · 2026Article
- The challenge and promise of studying human antigen-specific T cells.Nature reviews. Immunology · 2026Review
- Machine Learning for TCR Repertoire Epitope Annotation and Pattern Discovery.Immunological reviews · 2026Review
- Diversity, Equality, and Inclusion in the naïve T Cell Receptor Repertoire.Immunological reviews · 2026Review
- Deciphering antigen-driven T cell responses through vectorized TCRdist sequence neighborhood quantification.bioRxiv : the preprint server for biology · 2026Article
- Evolution of the tuberculin skin test reveals generalisable Mtb-reactive T cell metaclones.Nature communications · 2026Article
- TCR representation learning with protein language models: a comprehensive review.International immunology · 2026Review
- Contrasting effects of SARS-CoV-2 vaccination vs. infection on antibody and TCR repertoires.PloS one · 2026Article
- TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.PLoS computational biology · 2026Article
- Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils.Immunity · 2025Article
- T-cell receptor insights: Determinants of Major Histocompatibility Complex class I versus class II recognition.Protein science : a publication of the Protein Society · 2025Article
- TCR2HLA: calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.bioRxiv : the preprint server for biology · 2025Article
- Contrasting Effects of SARS-CoV-2 Vaccination vs. Infection on Antibody and TCR Repertoires.bioRxiv : the preprint server for biology · 2025Article
- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- Identification of immunogenic KIF5B-RET fusion neopeptides driving immune stimulation in tumor specific CD8+ T cells.Frontiers in immunology · 2025Article
- tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs.Briefings in bioinformatics · 2024Article
- Limits on inferring T cell specificity from partial information.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tissue determinants of the human T cell receptor repertoire.bioRxiv : the preprint server for biology · 2024Article
- Combining mutation and recombination statistics to infer clonal families in antibody repertoires.eLife · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Adaptive immunity is driven by specific binding of hypervariable receptors to diverse molecular targets. The sequence diversity of receptors and targets are both individually known but because multiple receptors can recognize the same target, a measure of the effective "functional" diversity of the human immune system has remained elusive. Here, we show that sequence near-coincidences within T cell receptors that bind specific epitopes provide a new window into this problem and allow the quantification of how binding probability covaries with sequence. We find that near-coincidence statistics within epitope-specific repertoires imply a measure of binding degeneracy to amino acid changes in receptor sequence that is consistent across disparate experiments. Paired data on both chains of the heterodimeric receptor are particularly revealing since simultaneous near-coincidences are rare and we show how they can be exploited to estimate the number of epitope responses that created the memory compartment. In addition, we find that paired-chain coincidences are strongly suppressed across donors with different human leukocyte antigens, evidence for a central role of antigen-driven selection in making paired chain receptors public. These results demonstrate the power of coincidence analysis to reveal the sequence determinants of epitope binding in receptor repertoires.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.