ArticleNature methods2021
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed, 106 citations in OpenAlex.
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- Gliadin-specific CD4Science advances · 2026Article
- scXpand: Pan-cancer detection of T cell clonal expansion from single-cell RNA sequencing without paired single-cell TCR sequencing.Cell genomics · 2026Article
- TransTCR: Integrating TCRs and Transcriptomes Through Optimal Transport for Antigen Specificity Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
- The Role of the T Cell Receptor Sequence in Shaping T Cell Functional Fate.Immunological reviews · 2026Review
- The T Cell Receptor: Molecular Sensor, Therapeutic Mediator and Probabilistic Driver of Adaptive Immunity.Immunological reviews · 2026Review
- Computational prediction of TCR cross-reactivity: principles, challenges and translational opportunities.Journal of translational medicine · 2026Review
- Deciphering small sequence differences in T cell receptor-antigen pairing.Nature communications · 2026Article
- crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis.BMC genomics · 2026Article
- Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.Nature communications · 2026Article
- Clinical application of single-cell RNA sequencing in disease and therapy.Clinical and translational medicine · 2025Review
- A pan-disease and population-level single-cell TCRαβ repertoire reference.Cell discovery · 2025Article
- Umbilical cord blood-derived cytotoxic T lymphocytes target melanoma via HLA-A2-restricted tumour antigens.Clinical and translational medicine · 2025Article
- Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.Research square · 2025Article
- Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.bioRxiv : the preprint server for biology · 2025Article
- Profiling antigen-binding affinity of B cell repertoires in tumors by deep learning predicts immune-checkpoint inhibitor treatment outcomes.Nature cancer · 2025Article
- PepTCR-Net: prediction of multi-class antigen peptides by T-cell receptor sequences with deep learning.Briefings in bioinformatics · 2025Article
- Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline.NAR genomics and bioinformatics · 2025Article
- LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt.Briefings in bioinformatics · 2025Article
- Memory T Cells in Respiratory Virus Infections: Protective Potential and Persistent Vulnerabilities.Medical sciences (Basel, Switzerland) · 2025Review
6 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
5 authors at 3 institutions in 1 country.
Funding
Abstract
Many experimental and bioinformatics approaches have been developed to characterize the human T cell receptor (TCR) repertoire. However, the unknown functional relevance of TCR profiling hinders unbiased interpretation of the biology of T cells. To address this inadequacy, we developed tessa, a tool to integrate TCRs with gene expression of T cells to estimate the effect that TCRs confer on the phenotypes of T cells. Tessa leveraged techniques combining single-cell RNA-sequencing with TCR sequencing. We validated tessa and showed its superiority over existing approaches that investigate only the TCR sequences. With tessa, we demonstrated that TCR similarity constrains the phenotypes of T cells to be similar and dictates a gradient in antigen targeting efficiency of T cell clonotypes with convergent TCRs. We showed this constraint could predict a functional dichotomization of T cells postimmunotherapy treatment and is weakened in tumor contexts.
Indexed as
Identifiers
What OpenQuestion holds
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.