ArticleScientific reports2021
Deep learning identifies antigenic determinants of severe SARS-CoV-2 infection within T-cell repertoires.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Medical software for precision diagnostics of infection with immunoprofiling and artificial intelligence.Journal of translational medicine · 2026Review
- Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification.PLoS computational biology · 2026Article
- A multi-branch ensemble learning framework for detection of non-small cell lung cancer via T-cell receptor sequencing.BMC cancer · 2026Article
- Article
- Integration of T cell repertoire, CyTOF, genotyping and symptomatology data reveals subphenotypic variability in COVID-19 patients.Computational and structural biotechnology journal · 2025Article
- The T-cell repertoire of Spanish patients with COVID-19 as a strategy to link T-cell characteristics to the severity of the disease.Human genomics · 2024Article
- Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors.Briefings in bioinformatics · 2024Article
- TCellR2Vec: efficient feature selection for TCR sequences for cancer classification.PeerJ. Computer science · 2024Article
- The molecular mechanisms of CD8Frontiers in immunology · 2024Review
- Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities.Cell systems · 2023Article
- Architecture of the SARS-CoV-2-specific T cell repertoire.Frontiers in immunology · 2023Review
- Article
- Deep learning reveals predictive sequence concepts within immune repertoires to immunotherapy.Science advances · 2022Article
- Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19.Diagnostics (Basel, Switzerland) · 2022Review
- T cell repertoire profiling in allografts and native tissues in recipients with COVID-19 after solid organ transplantation: Insight into T cell-mediated allograft protection from viral infection.Frontiers in immunology · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 infection is characterized by a highly variable clinical course with patients experiencing asymptomatic infection all the way to requiring critical care support. This variation in clinical course has led physicians and scientists to study factors that may predispose certain individuals to more severe clinical presentations in hopes of either identifying these individuals early in their illness or improving their medical management. We sought to understand immunogenomic differences that may result in varied clinical outcomes through analysis of T-cell receptor sequencing (TCR-Seq) data in the open access ImmuneCODE database. We identified two cohorts within the database that had clinical outcomes data reflecting severity of illness and utilized DeepTCR, a multiple-instance deep learning repertoire classifier, to predict patients with severe SARS-CoV-2 infection from their repertoire sequencing. We demonstrate that patients with severe infection have repertoires with higher T-cell responses associated with SARS-CoV-2 epitopes and identify the epitopes that result in these responses. Our results provide evidence that the highly variable clinical course seen in SARS-CoV-2 infection is associated to certain antigen-specific responses.
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