ArticleNature communications2021
GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 88 papers, 1 of them a synthesis that pooled it.
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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
88 citing papers in PubMed, 1 synthesis or guideline pooled it, 116 citations in OpenAlex.
- Anchor Clustering for million-scale immune repertoire sequencing data.BMC bioinformatics · 2024Pooled it
- Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy.Journal for immunotherapy of cancer · 2023Trial
- T cell repertoire in peripheral blood as a potential biomarker for predicting response to concurrent cetuximab and nivolumab in head and neck squamous cell carcinoma.Journal for immunotherapy of cancer · 2022Trial
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- Machine Learning of Personal Repertoires From Public T Cell Receptors.Immunological reviews · 2026Review
- The Role of the T Cell Receptor Sequence in Shaping T Cell Functional Fate.Immunological reviews · 2026Review
- The challenge and promise of studying human antigen-specific T cells.Nature reviews. Immunology · 2026Review
- A comparative and exploratory analysis of computational methods for TCR structural prediction and antigen-specific TCR discovery.Briefings in bioinformatics · 2026Article
- BenchRep-T: A Systematic Evaluation of T-Cell Repertoire-Based Disease Diagnostics.bioRxiv : the preprint server for biology · 2026Article
- A lightweight TcrLM model predicts T cell receptor and epitope binding specificity.Cell reports methods · 2026Article
- AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity.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
- Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification.PLoS computational biology · 2026Article
- Quantifying Cross-Attention Interaction in Transformers for Interpreting TCR-pMHC Binding.ArXiv · 2026Article
- Article
- Quantitative V gene-targeted T cell receptor sequencing as a biomarker in type 1 diabetes.JCI insight · 2026Article
- NeoTCRseek: an integrated platform for high-sensitivity identification of neoantigen-specific TCR clonotypes to track clinical T-cell dynamics.Frontiers in immunology · 2026Article
- TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.PLoS computational biology · 2026Article
- Immunogenetics and TCR expression patterns together predict future T1D onset from multi-omic datasets.Frontiers in genetics · 2026Article
- Identification of Sjögren's disease-associated T cell receptor motifs through deep sequencing.JCI insight · 2025Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Similarity in T-cell receptor (TCR) sequences implies shared antigen specificity between receptors, and could be used to discover novel therapeutic targets. However, existing methods that cluster T-cell receptor sequences by similarity are computationally inefficient, making them impractical to use on the ever-expanding datasets of the immune repertoire. Here, we developed GIANA (Geometric Isometry-based TCR AligNment Algorithm) a computationally efficient tool for this task that provides the same level of clustering specificity as TCRdist at 600 times its speed, and without sacrificing accuracy. GIANA also allows the rapid query of large reference cohorts within minutes. Using GIANA to cluster large-scale TCR datasets provides candidate disease-specific receptors, and provides a new solution to repertoire classification. Querying unseen TCR-seq samples against an existing reference differentiates samples from patients across various cohorts associated with cancer, infectious and autoimmune disease. Our results demonstrate how GIANA could be used as the basis for a TCR-based non-invasive multi-disease diagnostic platform.
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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.