ReviewFrontiers in immunology2023
Current annotation strategies for T cell phenotyping of single-cell RNA-seq data.
Review in Frontiers in immunology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Peripheral Immune Alterations and T Cell Clonal Dynamics Across the Parkinson's Disease Spectrum.medRxiv : the preprint server for health sciences · 2026Article
- celltypeEnrich: a consensus-based scRNA-seq cluster annotation tool.bioRxiv : the preprint server for biology · 2026Article
- Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States.bioRxiv : the preprint server for biology · 2026Article
- Single-cell analysis of follicular fluid reveals dysregulation of ovulatory immune function in Polycystic Ovary Syndrome patients undergoing ovarian stimulation†.Biology of reproduction · 2026Article
- Immune cell annotation in the single-cell studies: technologies, challenges, and integrative solutions.Immunologic research · 2026Review
- Endothelial cell senescence shapes T cell activity in late-stage of chronic obstructive pulmonary disease.Cell death discovery · 2026Article
- Subcellular transcriptome sequencing with single cell APEX-seq identifies regulators of cell-cell interactions.bioRxiv : the preprint server for biology · 2026Article
- Single-cell analysis of matched FFPE and frozen tissue samples reveals comparable resolution of intratumoural heterogeneity.Frontiers in genetics · 2026Article
- CD8⁺ T cell heterogeneity in aging: insights from single-cell profiling.Immunity & ageing : I & A · 2025Review
- Robust CD4medRxiv : the preprint server for health sciences · 2025Article
- Single-cell insights into the role of T cells in B-cell malignancies.FEBS letters · 2025Review
- HIV-1 manipulates CD96 on CD4Science advances · 2025Article
- Reproducible annotation of T cell subsets and activation states with gene expression programs.Nature methods · 2025Article
- Article
- The Application of Single-Cell Technologies for Vaccine Development Against Viral Infections.Vaccines · 2025Review
- Type I interferon drives T cell cytotoxicity by upregulation of interferon regulatory factor 7 in autoimmune kidney diseases in mice.Nature communications · 2025Article
- Enhanced interpretation of immune cell phenotype and function through a rhesus macaque single-cell atlas.Cell genomics · 2025Article
- Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy.Science immunology · 2025Article
- T cell receptor-centric perspective to multimodal single-cell data analysis.Science advances · 2024Article
- Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice.Nature reviews. Immunology · 2024Review
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a popular technique for interrogating the diversity and dynamic nature of cellular gene expression and has numerous advantages in immunology. For example, scRNA-seq, in contrast to bulk RNA sequencing, can discern cellular subtypes within a population, which is important for heterogenous populations such as T cells. Moreover, recent advancements in the technology allow the parallel capturing of the highly diverse T-cell receptor (TCR) sequence with the gene expression. However, the field of single-cell RNA sequencing data analysis is still hampered by a lack of gold-standard cell phenotype annotation. This problem is particularly evident in the case of T cells due to the heterogeneity in both their gene expression and their TCR. While current cell phenotype annotation tools can differentiate major cell populations from each other, labelling T-cell subtypes remains problematic. In this review, we identify the common automated strategy for annotating T cells and their subpopulations, and also describe what crucial information is still missing from these tools.
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