ArticlePLoS computational biology2014
Quantification of HTLV-1 clonality and TCR diversity.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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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.
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Who cites it
52 citing papers in PubMed.
- Loss of HTLV-1-specific CD8Blood neoplasia · 2026Article
- Integrated TCRγ Clonality Workflow for Molecular Diagnosis in HTLV-1 Carriers and Adult T-Cell Leukemia/Lymphoma.Diagnostics (Basel, Switzerland) · 2026Article
- Clonal expansion and phenotypic alterations of TCR Vβ3Journal of virology · 2026Article
- Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.Molecular ecology resources · 2026Article
- Review
- A comprehensive review and evaluation of species richness estimation.Briefings in bioinformatics · 2025Review
- Article
- Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription.Science advances · 2022Article
- Are homeostatic mechanisms aiding the reconstitution of the T-cell pool during lymphopenia in humans?Frontiers in immunology · 2022Review
- Perturbations in the T cell receptor β repertoire during malaria infection in children: A preliminary study.Frontiers in immunology · 2022Article
- Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells.The Journal of experimental medicine · 2021Article
- Quantification of T cell clonality in human T cell leukaemia virus type-1 carriers can detect the development of adult T cell leukaemia early.Blood cancer journal · 2021Article
- The relative contributions of infectious and mitotic spread to HTLV-1 persistence.PLoS computational biology · 2020Article
- Article
- Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy.International journal of molecular sciences · 2020Review
- Methods for sequence and structural analysis of B and T cell receptor repertoires.Computational and structural biotechnology journal · 2020Review
- Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling.PLoS pathogens · 2019Article
- Comparative virology of HTLV-1 and HTLV-2.Retrovirology · 2019Review
- Major histocompatibility complex class I diversity limits the repertoire of T cell receptors.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Biomarkers and Preclinical Models for Adult T-Cell Leukemia-Lymphoma Treatment.Frontiers in microbiology · 2019Review
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological "species" in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations.
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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.