ArticleFrontiers in immunology2019
Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires.
Article in Frontiers in immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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108 citing papers in PubMed.
- Continuous replenishment of the dysfunctional CD8 T cell axis is associated with response to chemoimmunotherapy in advanced breast cancer.Cell reports. Medicine · 2025Trial
- Randomized trial of neoadjuvant vaccination with tumor-cell lysate induces T cell response in low-grade gliomas.The Journal of clinical investigation · 2022Trial
- Predicting specificity of TCR-pMHC interactions using machine-learning and biophysical models.Cell systems · 2026Article
- DynaTCR: dynamic hard-negative ensemble graph learning improves TCR-epitope binding prediction.Bioinformatics (Oxford, England) · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Mitigating negative data bias to enhance TCR-epitope binding and residue interaction prediction.Briefings in bioinformatics · 2026Article
- Modeling TCR-Epitope Recognition Specificity: What We Should Learn to Succeed.Immunological reviews · 2026Review
- Machine Learning for TCR Repertoire Epitope Annotation and Pattern Discovery.Immunological reviews · 2026Review
- Deciphering small sequence differences in T cell receptor-antigen pairing.Nature communications · 2026Article
- A lightweight TcrLM model predicts T cell receptor and epitope binding specificity.Cell reports methods · 2026Article
- Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery.Nature biotechnology · 2026Article
- Antigen specificity of clonally enriched CD8Nature immunology · 2026Article
- TCR representation learning with protein language models: a comprehensive review.International immunology · 2026Review
- A Biologically Informed Vision-Guided Framework for Interpretable T Cell Receptor-Epitope Binding Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- CD4/CD8 ratio is associated with structural reorganization of vaccine-induced immune responses in people living with HIV.Frontiers in immunology · 2026Article
- Identification of a TCR signature in peripheral blood derived CD4+ T cells, associated with chronic chikungunya disease, suggests a conducive, female-biased, background immune profile.Frontiers in immunology · 2026Article
- Assessing data size requirements for training generalizable sequence-based TCR specificity models via pan-allelic MHC-I point-mutation ligandome evaluation.Scientific reports · 2025Article
- Predicting antigen-specific T-cell immunity against Wilms tumor 1 in hematologic cancer.Leukemia · 2025Article
- Challenges and future directions of AIRR-seq-based diagnostics.Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Self-Contemplating In-Context Learning Enhances T Cell Receptor Generation for Novel Epitopes.Proceedings of machine learning research · 2025Article
48 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
High-throughput T cell receptor (TCR) sequencing allows the characterization of an individual's TCR repertoire and directly queries their immune state. However, it remains a non-trivial task to couple these sequenced TCRs to their antigenic targets. In this paper, we present a novel strategy to annotate full TCR sequence repertoires with their epitope specificities. The strategy is based on a machine learning algorithm to learn the TCR patterns common to the recognition of a specific epitope. These results are then combined with a statistical analysis to evaluate the occurrence of specific epitope-reactive TCR sequences per epitope in repertoire data. In this manner, we can directly study the capacity of full TCR repertoires to target specific epitopes of the relevant vaccines or pathogens. We demonstrate the usability of this approach on three independent datasets related to vaccine monitoring and infectious disease diagnostics by independently identifying the epitopes that are targeted by the TCR repertoire. The developed method is freely available as a web tool for academic use at tcrex.biodatamining.be.
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