ArticleNucleic acids research2018
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 372 papers, 2 of them syntheses that pooled it.
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Who cites it
372 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Anchor Clustering for million-scale immune repertoire sequencing data.BMC bioinformatics · 2024Pooled it
- Decade-long persistence of CD19 CAR T cells in B cell lymphomas.Nature medicine · 2026Trial
- Dynamics of Spinal Fluid Immune Cell Alterations Following Cladribine Tablet Treatment in Multiple Sclerosis.Neurology(R) neuroimmunology & neuroinflammation · 2026Trial
- High peripheral T cell diversity is associated with lower risk of toxicity and superior response to dual immune checkpoint inhibitor therapy in patients with metastatic NSCLC.Journal for immunotherapy of cancer · 2024Trial
- Immunologic signatures of response and resistance to nivolumab with ipilimumab in advanced metastatic cancer.The Journal of experimental medicine · 2024Trial
- Toward next-generation therapeutic HPV vaccines: A review on expanding the antigen repertoire and an integrated bioinformatics selection framework.Human vaccines & immunotherapeutics · 2026Review
- Article
- Differential requirements for cytokine signaling and local antigen in upper versus lower respiratory tract CD8+ TRM development.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- Peripheral Immune Alterations and T Cell Clonal Dynamics Across the Parkinson's Disease Spectrum.medRxiv : the preprint server for health sciences · 2026Article
- Unsupervised identification of low-frequency antigen-specific TCRs using distance-based anomaly scoring.Briefings in bioinformatics · 2026Article
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- T Cell Thoughts.Immunological reviews · 2026Review
- Identifying expanding TCR clonotypes with a longitudinal Bayesian mixture model and their associations with cancer patient prognosis, metastasis-directed therapy, and VJ gene enrichment.Bioinformatics (Oxford, England) · 2026Article
- Thymic selection of the T cell receptor repertoire is biased toward autoimmunity in females.eLife · 2026Article
- T-cell receptor repertoires against HLA class I-restricted minor histocompatibility antigens are highly diverse with a small subset of public clonotypes.Journal for immunotherapy of cancer · 2026Article
- Structure-based TCR-pMHC binding prediction and generalization to unseen peptides.npj drug discovery · 2026Article
- Shared CD4+ T cell receptor specificity groups in Crohn's disease and ulcerative colitis.JCI insight · 2026Article
- DynaTCR: dynamic hard-negative ensemble graph learning improves TCR-epitope binding prediction.Bioinformatics (Oxford, England) · 2026Article
- Technical review of artificial intelligence in TCR-T therapy.Journal of the National Cancer Center · 2026Review
312 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
28 authors.
Funding
Abstract
The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises significant advances in the field of translational medicine. Recent developments in high-throughput sequencing methods (immune repertoire sequencing technology, or RepSeq) and single-cell RNA sequencing technology have allowed us to obtain huge numbers of TCR sequences from donor samples and link them to T-cell phenotypes. However, our ability to annotate these TCR sequences still lags behind, owing to the enormous diversity of the TCR repertoire and the scarcity of available data on T-cell specificities. In this paper, we present VDJdb, a database that stores and aggregates the results of published T-cell specificity assays and provides a universal platform that couples antigen specificities with TCR sequences. We demonstrate that VDJdb is a versatile instrument for the annotation of TCR repertoire data, enabling a concatenated view of antigen-specific TCR sequence motifs. VDJdb can be accessed at https://vdjdb.cdr3.net and https://github.com/antigenomics/vdjdb-db.
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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.