Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach

Narrowing of Human Influenza A Virus-Specific T Cell Receptor α and β Repertoires with Increasing Age

(2015) Anna Gil et al.   JOURNAL OF VIROLOGY

Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence

(2014) Niclas Thomas et al.   BIOINFORMATICS

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity

(2014) Asaf Madi et al.   GENOME RESEARCH

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

(2014) Paolo A. Muraro et al.   JOURNAL OF CLINICAL INVESTIGATION

Revealing Individual Signatures of Human T Cell CDR3 Sequence Repertoires with Kidera Factors

(2014) Michael Epstein et al.   PLoS One

Diversity and clonal selection in the human T-cell repertoire

(2014) Q. Qi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding

(2014) Linling He et al.   Scientific Reports

Quantification of HTLV-1 Clonality and TCR Diversity

(2014) Daniel J. Laydon et al.   PLoS Computational Biology

An estimation of the number of cells in the human body

(2013) Eva Bianconi et al.   ANNALS OF HUMAN BIOLOGY

Fractal Organization of the Human T Cell Repertoire in Health and after Stem Cell Transplantation

(2013) Jeremy Meier et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Human lymphocyte repertoires in ageing

(2013) Scott D Boyd et al.   CURRENT OPINION IN IMMUNOLOGY

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

Bayesian multivariate Poisson abundance models for T-cell receptor data

(2013) Joshua Greene et al.   JOURNAL OF THEORETICAL BIOLOGY

Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota

(2013) Anna Cebula et al.   NATURE

Detecting diversity: emerging methods to estimate species diversity

(2013) Kelly J. Iknayan et al.   TRENDS IN ECOLOGY & EVOLUTION

Huge Overlap of Individual TCR Beta Repertoires

(2013) Mikhail Shugay et al.   Frontiers in Immunology

Estimating the Diversity, Completeness, and Cross-Reactivity of the T Cell Repertoire

(2013) Veronika I. Zarnitsyna et al.   Frontiers in Immunology

Estimating abundances of retroviral insertion sites from DNA fragment length data

(2012) Charles C. Berry et al.   BIOINFORMATICS

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms

(2012) Dmitry A. Bolotin et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

(2012) R. K. Colwell et al.   Journal of Plant Ecology

TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection

(2012) Huabiao Chen et al.   NATURE IMMUNOLOGY

Estimating the Richness of a Population When the Maximum Number of Classes Is Fixed: A Nonparametric Solution to an Archaeological Problem

(2012) Metin I. Eren et al.   PLoS One

The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones

(2011) N. A. Gillet et al.   BLOOD

Quantitative tracking of T cell clones after haematopoietic stem cell transplantation

(2011) Ilgar Z. Mamedov et al.   EMBO Molecular Medicine

TCR diversity and Treg cells, sometimes more is more

(2011) James B. Wing et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

(2011) R. L. Warren et al.   GENOME RESEARCH

Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination

(2011) John J Miles et al.   IMMUNOLOGY AND CELL BIOLOGY

A Mechanism for TCR Sharing between T Cell Subsets and Individuals Revealed by Pyrosequencing

(2011) Vanessa Venturi et al.   JOURNAL OF IMMUNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Human T-cell memory consists mainly of unexpanded clones

(2010) Paul L. Klarenbeek et al.   IMMUNOLOGY LETTERS

Primary CTL response magnitude in mice is determined by the extent of naive T cell recruitment and subsequent clonal expansion

(2010) Nicole L. La Gruta et al.   JOURNAL OF CLINICAL INVESTIGATION

Model for comparative analysis of antigen receptor repertoires

(2010) Grzegorz A. Rempala et al.   JOURNAL OF THEORETICAL BIOLOGY

Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire

(2010) M. F. Quigley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets

(2010) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

(2010) H. S. Robins et al.   Science Translational Medicine

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

(2009) J. D. Freeman et al.   GENOME RESEARCH

Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models

(2009) Nuno Sepúlveda et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Estimating the number of unseen variants in the human genome

(2009) I. Ionita-Laza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-obese diabetic mice select a low-diversity repertoire of natural regulatory T cells

(2009) C. Ferreira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

(2009) J. Glanville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

(2009) J. A. Weinstein et al.   SCIENCE

Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus

(2008) Eric J. Yager et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Method for assessing the similarity between subsets of the T cell receptor repertoire

(2007) Vanessa Venturi et al.   JOURNAL OF IMMUNOLOGICAL METHODS