ArticleBriefings in bioinformatics2020
Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.
Article in Briefings in bioinformatics, 2020. 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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Who cites it
20 citing papers in PubMed, 34 citations in OpenAlex.
- Spatiotemporal single-cell profiling reveals T cell clonal dynamics and phenotypic plasticity in human graft-versus-host disease.Nature immunology · 2026Article
- Mapping the TCR landscape: computational tools empowering translational immunology and therapy design.Journal for immunotherapy of cancer · 2026Review
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- HTGTS-TCR-Seq for Profiling of Mouse and Human T-Cell Receptor α and β Gene Rearrangements and Diversity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Disrupting explicit encoding paradigms: property-interactive transformers decode T-cell receptor specificity beyond dataset biases.Briefings in bioinformatics · 2025Article
- White paper on best practices for translational research in neuroendocrine neoplasms.Journal of neuroendocrinology · 2025Article
- Development and characterization of human T-cell receptor (TCR) alpha and beta clones' library as biological standards and resources for TCR sequencing and engineering.Biology methods & protocols · 2024Article
- GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data.BMC bioinformatics · 2023Article
- Evaluation of the TCR Repertoire as a Predictive and Prognostic Biomarker in Cancer: Diversity or Clonality?Cancers · 2022Review
- Machine Learning Approaches to TCR Repertoire Analysis.Frontiers in immunology · 2022Review
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Data Sharing and Reuse: A Method by the AIRR Community.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases.Nature biotechnology · 2021Article
- Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing.Immunology and cell biology · 2021Review
- TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function.Nucleic acids research · 2021Article
- RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database.Frontiers in immunology · 2021Article
- Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset.Frontiers in immunology · 2021Article
- Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy.International journal of molecular sciences · 2020Review
- Molecular characterization of hypoxanthine guanine phosphoribosyltransferase mutant T cells in human blood: The concept of surrogate selection for immunologically relevant cells.Mutation research. Reviews in mutation researchReview
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.
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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.