ArticlePLoS biology2019
Detecting T cell receptors involved in immune responses from single repertoire snapshots.
Article in PLoS biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
94 citing papers in PubMed, 1 synthesis or guideline pooled it, 143 citations in OpenAlex.
- Resolving SARS-CoV-2 CD4Cell reports. Medicine · 2022Pooled it
- Long-term Sculpting of the B-cell Repertoire following Cancer Immunotherapy in Patients Treated with Sipuleucel-T.Cancer immunology research · 2020Trial
- Unsupervised identification of low-frequency antigen-specific TCRs using distance-based anomaly scoring.Briefings in bioinformatics · 2026Article
- T Cell Thoughts.Immunological reviews · 2026Review
- Machine Learning of Personal Repertoires From Public T Cell Receptors.Immunological reviews · 2026Review
- replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion.bioRxiv : the preprint server for biology · 2026Article
- Machine Learning for TCR Repertoire Epitope Annotation and Pattern Discovery.Immunological reviews · 2026Review
- T-cell repertoire response in individuals with post-acute sequelae of COVID-19.bioRxiv : the preprint server for biology · 2026Article
- Deciphering antigen-driven T cell responses through vectorized TCRdist sequence neighborhood quantification.bioRxiv : the preprint server for biology · 2026Article
- Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.Genome medicine · 2026Article
- The Abundance of α-Chain-Centric TCRs in the Mouse Repertoire of Primarily Activated Effectors and Reactivated Memory T Cells.Computational and structural biotechnology journal · 2026Article
- T Cell Receptor Sharing in Hypersensitivity Pneumonitis.Computational and structural biotechnology journal · 2026Article
- replicateFest: an R package and shiny app for analysis of T cell receptor repertoire data from the functional expansion.Frontiers in immunology · 2026Article
- Machine learning in AIRR diagnostics: Advances and applications.Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Neighborhood enrichment for the identification of antigen-specific T-cell receptors.Briefings in bioinformatics · 2025Article
- Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target.Nature communications · 2025Article
- Diverse modes of T cell receptor sequence convergence define unique functional and cellular phenotypes.bioRxiv : the preprint server for biology · 2025Article
- Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination.Nucleic acids research · 2025Article
- Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.Nucleic acids research · 2025Article
- TCR and BCR repertoire analysis reveals distinct signatures between benign and malignant ovarian tumors.Frontiers in oncology · 2025Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hypervariable T cell receptors (TCRs) play a key role in adaptive immunity, recognizing a vast diversity of pathogen-derived antigens. Our ability to extract clinically relevant information from large high-throughput sequencing of TCR repertoires (RepSeq) data is limited, because little is known about TCR-disease associations. We present Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE), a statistical approach that identifies TCR sequences actively involved in current immune responses from a single RepSeq sample and apply it to repertoires of patients with a variety of disorders - patients with autoimmune disease (ankylosing spondylitis [AS]), under cancer immunotherapy, or subject to an acute infection (live yellow fever [YF] vaccine). We validate the method with independent assays. ALICE requires no longitudinal data collection nor large cohorts, and it is directly applicable to most RepSeq datasets. Its results facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.
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Registered trials
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.