ArticleNucleic acids research2020
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 256 papers, 4 of them syntheses that pooled it.
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Who cites it
256 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models.Database : the journal of biological databases and curation · 2025Pooled it
- Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy.Cell genomics · 2025Pooled it
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Resolving SARS-CoV-2 CD4Cell reports. Medicine · 2022Pooled it
- Dynamics of Spinal Fluid Immune Cell Alterations Following Cladribine Tablet Treatment in Multiple Sclerosis.Neurology(R) neuroimmunology & neuroinflammation · 2026Trial
- Durable response to CAR T is associated with elevated activation and clonotypic expansion of the cytotoxic native T cell repertoire.Nature communications · 2025Trial
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- scXpand: Pan-cancer detection of T cell clonal expansion from single-cell RNA sequencing without paired single-cell TCR sequencing.Cell genomics · 2026Article
- T Cell Thoughts.Immunological reviews · 2026Review
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- Systematic analysis of CDR contacts and pairing constraints between T cell receptor αβ chains.Bioinformatics (Oxford, England) · 2026Article
- TcrDesign: de novo design of epitope-specific full-length T cell receptors.Science China. Life sciences · 2026Article
- Machine Learning of Personal Repertoires From Public T Cell Receptors.Immunological reviews · 2026Review
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Computational prediction of TCR cross-reactivity: principles, challenges and translational opportunities.Journal of translational medicine · 2026Review
- Variants in human CD48 lead to impaired T cell immunity and increased inflammation.The Journal of clinical investigation · 2026Article
- Immune landscape of the affected brain in Rasmussen encephalitis.Scientific reports · 2026Article
- Transcriptional landscape of CD4+ T cells in Systemic Sclerosis.bioRxiv : the preprint server for biology · 2026Article
- Quantifying Cross-Attention Interaction in Transformers for Interpreting TCR-pMHC Binding.ArXiv · 2026Article
- Article
196 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https://vdjdb.cdr3.net.
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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.