ArticleeLife2023
Improved T cell receptor antigen pairing through data-driven filtering of sequencing information from single cells.
Article in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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
20 citing papers in PubMed.
- T Cell Thoughts.Immunological reviews · 2026Review
- The challenge and promise of studying human antigen-specific T cells.Nature reviews. Immunology · 2026Review
- Revised Adaptive Immune Receptor Data in the Immune Epitope Database.bioRxiv : the preprint server for biology · 2026Article
- TCRBinder: Unified pre-trained language model with paired-chain synergy for predicting T-cell receptor binding specificity.PLoS computational biology · 2026Article
- A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions.bioRxiv : the preprint server for biology · 2026Article
- Duration of Initial Viremia Modulates Functional Properties of HIV-specific T Cell Receptors.Research square · 2026Article
- Duration of Initial Viremia Modulates Functional Properties of HIV-specific T Cell Receptors.bioRxiv : the preprint server for biology · 2026Article
- nuTCRacker: Predicting the Recognition of HLA-I-Peptide Complexes by αβTCRs for Unseen Peptides.European journal of immunology · 2025Article
- Phage display enables machine learning discovery of cancer antigen-specific TCRs.Science advances · 2025Article
- TCRCluster: a novel approach to T-cell receptor latent featurization and clustering using contrastive learning-guided two-stage variational autoencoders.NAR genomics and bioinformatics · 2025Article
- A functionally validated TCR-pMHC database for TCR specificity model development.bioRxiv : the preprint server for biology · 2025Article
- NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions.Frontiers in immunology · 2025Article
- TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data.Bioinformatics (Oxford, England) · 2024Article
- Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells.Nature communications · 2024Article
- Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set.Science advances · 2024Article
- Article
- Herpes Virus Infections in Kidney Transplant Patients (HINT) - a prospective observational cohort study.BMC infectious diseases · 2023Observational
- Benchmarking data-driven filtering for denoising of TCRpMHC single-cell data.Scientific reports · 2023Article
- Article
- Herpesvirus immunology in solid organ transplant recipients - liver transplant study (HISTORY): a retrospective and prospective observational cohort study.BMC infectious diseases · 2023Observational
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Novel single-cell-based technologies hold the promise of matching T cell receptor (TCR) sequences with their cognate peptide-MHC recognition motif in a high-throughput manner. Parallel capture of TCR transcripts and peptide-MHC is enabled through the use of reagents labeled with DNA barcodes. However, analysis and annotation of such single-cell sequencing (SCseq) data are challenged by dropout, random noise, and other technical artifacts that must be carefully handled in the downstream processing steps. We here propose a rational, data-driven method termed ITRAP (improved T cell Receptor Antigen Paring) to deal with these challenges, filtering away likely artifacts, and enable the generation of large sets of TCR-pMHC sequence data with a high degree of specificity and sensitivity, thus outputting the most likely pMHC target per T cell. We have validated this approach across 10 different virus-specific T cell responses in 16 healthy donors. Across these samples, we have identified up to 1494 high-confident TCR-pMHC pairs derived from 4135 single cells.
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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.