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Methods for diversity and overlap analysis in T-cell receptor populations

https://doi.org/10.1007/s00285-012-0589-7

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Categorical Data Analysis

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Efficient characterization of the TCR repertoire in lymph nodes by flow cytometry

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Convergence properties of functional estimates for discrete distributions

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Coverage‐adjusted entropy estimation

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Through the Jungle of Biological Diversity

inferredcites →https://doi.org/10.1016/j.coi.2007.12.001openalex-snapshot

T-cell receptor bias and immunity

inferredcites →https://doi.org/10.1016/j.cub.2005.02.006openalex-snapshot

Biological diversity

inferredcites →https://doi.org/10.1016/j.immuni.2006.05.016openalex-snapshot

Origin and T Cell Receptor Diversity of Foxp3+CD4+CD25+ T Cells

inferredcites →https://doi.org/10.1016/j.immuni.2007.07.019openalex-snapshot

Nonself-Antigens Are the Cognate Specificities of Foxp3+ Regulatory T Cells

inferredcites →https://doi.org/10.1016/j.jim.2011.09.012openalex-snapshot

Quantitative analysis of T cell receptor diversity in clinical samples of human peripheral blood

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Model for comparative analysis of antigen receptor repertoires

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Massive Expansion of Antigen-Specific CD8+ T Cells during an Acute Virus Infection

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Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample

inferredcites →https://doi.org/10.1038/334395a0openalex-snapshot

T-cell antigen receptor genes and T-cell recognition

inferredcites →https://doi.org/10.1038/ni1318openalex-snapshot

An intersection between the self-reactive regulatory and nonregulatory T cell receptor repertoires

inferredcites →https://doi.org/10.1038/nmeth949openalex-snapshot

Direct measurement of T-cell receptor repertoire diversity with AmpliCot

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Genotype and SNP calling from next-generation sequencing data

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Selection of regulatory T cells in the thymus

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A tribute to Claude Shannon (1916–2001) and a plea for more rigorous use of species richness, species diversity and the ‘Shannon–Wiener’ Index

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Heterogeneity of natural Foxp3 + T cells: A committed regulatory T-cell lineage and an uncommitted minor population retaining plasticity

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Induction of antigen-specific T cell anergy: An early event in the course of tumor progression

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Conversion of Peripheral CD4+CD25− Naive T Cells to CD4+CD25+ Regulatory T Cells by TGF-β Induction of Transcription Factor Foxp3

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THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS

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A Poisson model for the coverage problem with a genomic application

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Always Good Turing: asymptotically optimal probability estimation

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Universal Compression of Memoryless Sources Over Unknown Alphabets

inferredcites →https://doi.org/10.1111/j.0030-1299.2005.13735.xopenalex-snapshot

Simpson diversity and the Shannon–Wiener index as special cases of a generalized entropy

inferredcites →https://doi.org/10.1111/j.1461-0248.2004.00707.xopenalex-snapshot

A new statistical approach for assessing similarity of species composition with incidence and abundance data

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Entropy and diversity

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Always Good Turing: Asymptotically Optimal Probability Estimation

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A Direct Estimate of the Human αβ T Cell Receptor Diversity

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Testing Symmetric Properties of Distributions

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A Pilot Study of MUC-1/CEA/TRICOM Poxviral-Based Vaccine in Patients with Metastatic Breast and Ovarian Cancer

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Asymptotic normality of a nonparametric estimator of sample coverage

inferredcites →https://doi.org/10.1214/aos/1176346256openalex-snapshot

A Normal Limit Law for a Nonparametric Estimator of the Coverage of a Random Sample

inferredcites →https://doi.org/10.1214/aos/1176350066openalex-snapshot

The Efficiency of Good's Nonparametric Coverage Estimator

inferredcites →https://doi.org/10.2307/3236223openalex-snapshot

Comparison of different methods for diversity ordering

inferredcites →https://doi.org/10.3184/003685011x13139280383942openalex-snapshot

Specific T-cell Activation in an Unspecific T-cell Repertoire

inferredcites →https://doi.org/10.5860/choice.32-3876openalex-snapshot

Immunobiology: the immune system in health and disease

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Mathematical Characterization of Private and Public Immune Receptor Sequences

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Limit theorems for empirical Rényi entropy and divergence with applications to molecular diversity analysis

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Dynamic changes of T cell receptor repertoires in patients with hepatitis B virus-related acute-on-chronic liver failure

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Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes

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Pipeline to characterize antigen-specific TCR repertoires in tumors: Examples from an HPV16 tumor model

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Gene expression profiling of brain samples from patients with Lewy body dementia

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T Cell Receptor Is Required for Differentiation, but Not Maintenance, of Intestinal CD4+ Intraepithelial Lymphocytes

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Exercise-associated epigenetic remodeling and TCR repertoire dynamics in Lynch syndrome carriers

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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

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Sequencing the peripheral blood B and T cell repertoire – Quantifying robustness and limitations

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How many TCR clonotypes does a body maintain?

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Spike-specific T cells are enriched in breastmilk following SARS-CoV-2 mRNA vaccination

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Protocol for the isolation of CD8+ tumor-infiltrating lymphocytes from human tumors and their characterization by single-cell immune profiling and multiome

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

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Radiation and dual checkpoint blockade activate non-redundant immune mechanisms in cancer

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The same self-peptide selects conventional and regulatory CD4+ T cells with identical antigen receptors

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Genetic T-cell receptor diversity at 1 year following allogeneic hematopoietic stem cell transplantation

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Self and microbiota-derived epitopes induce CD4+ T cell anergy and conversion into CD4+Foxp3+ regulatory cells

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Antitumor efficacy and potential mechanism of FAP-targeted radioligand therapy combined with immune checkpoint blockade

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Single-cell landscape of primary central nervous system diffuse large B-cell lymphoma

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Dormant pathogenic CD4+ T cells are prevalent in the peripheral repertoire of healthy mice

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Converging and evolving immuno-genomic routes toward immune escape in breast cancer

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Reverse TCR repertoire evolution toward dominant low-affinity clones during chronic CMV infection

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Tissue adaptation and clonal segregation of human memory T cells in barrier sites

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mRNA-based influenza vaccine expands the B cell response breadth in humans

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A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma

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Neoadjuvant atezolizumab for resectable non-small cell lung cancer: an open-label, single-arm phase II trial

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Non-canonicaly recruited TCRαβCD8αα IELs recognize microbial antigens

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Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR-seq

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Deciphering cell to cell spatial relationship for pathology images using SpatialQPFs

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Association of CD8+ T lymphocyte repertoire spreading with the severity of DRESS syndrome

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Glimpse of natural selection of long-lived T-cell clones in healthy life

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Immune correlates of clinical benefit in a phase I study of hyperthermia with adoptive T cell immunotherapy in patients with solid tumors

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Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer

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The impact of CTLA-4 blockade and interferon-α on clonality of T-cell repertoire in the tumor microenvironment and peripheral blood of metastatic melanoma patients

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Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq

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Shopping Local and Trusted Traders: Identifying Production Zones and Trade Routes of Northern Italian Terra Sigillata Using Similarity Indices

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Converging evolution leads to near maximal junction diversity through parallel mechanisms in B and T cell receptors

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Exploring Indicators of Subcutaneous Tissue Fluid Accumulation in Breast Cancer-Related Lymphedema Patients Using Fractal Analysis with Virtual Volume

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Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing

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Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging

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CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching

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Immediate and substantial evolution of T-cell repertoire in peripheral blood and tumor microenvironment of patients with esophageal squamous cell carcinoma treated with preoperative chemotherapy

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Mathematics in modern immunology

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Predicting developmental relationships of tumor resident and circulating T cells in ovarian cancer

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mRNA-based influenza vaccine expands breadth of B cell response in humans

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Multiple interaction networks reveal that Lepidoptera larvae and adults prefer various host plants for diet and pollination

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Human CD45RA− FoxP3hi Memory-Type Regulatory T Cells Show Distinct TCR Repertoires With Conventional T Cells and Play an Important Role in Controlling Early Immune Activation

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T‐cell receptor sequencing demonstrates persistence of virus‐specific T cells after antiviral immunotherapy

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Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico

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A circulating reservoir of pathogenic-like CD4+ T cells shares a genetic and phenotypic signature with the inflamed synovial micro-environment

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Severe acute myositis and myocarditis on initiation of 6-weekly pembrolizumab post-COVID-19 mRNA vaccination

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TCR sequencing in cancer immunology and immunotherapy: what, when, where, why, and how

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Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer

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CDK4/6 Inhibition Sensitizes Intracranial Tumors to PD-1 Blockade in Preclinical Models of Brain Metastasis

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Combination immunotherapy with TLR agonists and checkpoint inhibitors suppresses head and neck cancer

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Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment

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Single-cell characterisation of tissue homing CD4 + and CD8 + T cell clones in immune-mediated refractory arthritis

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RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

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Non-linear interactions between candidate genes of myocardial infarction revealed in mRNA expression profiles

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Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

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An artificial intelligence-based ecological index for prognostic evaluation of colorectal cancer

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A comprehensive evaluation of diversity measures for TCR repertoire profiling

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TCRcloud: a global visualization tool for T-cell and B-cell receptor transcripts

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Profile of dorsal root ganglion neurons: study of oxytocin expression

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T-cell repertoire diversity: friend or foe for protective antitumor response?

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A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

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The Extracellular Domains of IgG1 and T Cell-Derived IL-4/IL-13 Are Critical for the Polyclonal Memory IgE Response In Vivo

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Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms

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Differences in Expression Level of Helios and Neuropilin-1 Do Not Distinguish Thymus-Derived from Extrathymically-Induced CD4+Foxp3+ Regulatory T Cells

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Generation of antigen-specific memory CD4 T cells by heterologous immunization enhances the magnitude of the germinal center response upon influenza infection

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Graph-based data structure for enumeration of all possible generation scenarios of immune receptor sequences

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Characteristics of profiling the peripheral blood T‐cell receptor repertoire in patients with diffuse large B-cell lymphoma

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Intratumor heterogeneity and clonal distribution of tumor-infiltrating lymphocytes revealed by multiregional T and B cell receptor repertoires in gastric cancer

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Serial Assessment of Circulating T lymphocyte Phenotype and Receptor Repertoire During Treatment of Non-Muscle Invasive Bladder Cancer with Adoptive T Cell Immunotherapy

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A circulating reservoir of pathogenic-like CD4+ T cells shares a genetic and phenotypic signature with the inflamed synovial micro-environment

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Evaluating simple measures of spatial-temporal overlap as a proxy for encounter risk between a protected species and commercial fishery

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Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires

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Lineage Tracking the Generation of T Regulatory Cells From Microbial Activated T Effector Cells in Naïve Mice

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Characteristics of TCR Repertoire Associated With Successful Immune Checkpoint Therapy Responses

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Immune Recovery Following Autologous Hematopoietic Stem Cell Transplantation in HIV-Related Lymphoma Patients on the BMT CTN 0803/AMC 071 Trial

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CGAT: Cell Graph ATtention Network for Grading of Pancreatic Disease Histology Images

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Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform

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Clonal Distribution and Intratumor Heterogeneity of the TCR Repertoire in Papillary Thyroid Cancer With or Without Coexistent Hashimoto’s Thyroiditis

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Restored CD8+PD-1+ T Cells Facilitate the Response to Anti-PD-1 for Patients With Pancreatic Ductal Adenocarcinoma

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Machine Learning-Guided Prediction of Antigen-Reactive In Silico Clonotypes Based on Changes in Clonal Abundance through Bio-Panning

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Characterization of Circulating T Cell Receptor Repertoire Provides Information about Clinical Outcome after PD-1 Blockade in Advanced Non-Small Cell Lung Cancer Patients

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Challenges and Opportunities in the Statistical Analysis of Multiplex Immunofluorescence Data

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T-Cell Receptor Repertoire Analysis with Computational Tools—An Immunologist’s Perspective

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Local Variation in Ground Arthropod Diversity Rises as Distance to Residential Areas Decreases in a Mature Evergreen Forest

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T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer

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Shared T-Cell Receptor Repertoire in the Tonsils of Patients with IgA Nephropathy

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The relationship between naturalized alien and native plant species: insights from oceanic islands of the south-east Pacific over the last 200 years

inferred← citeshttps://doi.org/10.4049/jimmunol.2100404openalex-snapshot

Evolution of Cytomegalovirus-Responsive T Cell Clonality following Solid Organ Transplantation

inferred← citeshttps://doi.org/10.4049/jimmunol.2200061openalex-snapshot

Proteogenomic and V(D)J Analysis of Human Decidual T Cells Highlights Unique Transcriptional Programming and Clonal Distribution

inferred← citeshttps://doi.org/10.48550/arxiv.1505.03220openalex-snapshot

Limit Theorems for Empirical Rényi Entropy and Divergence with Applications to Molecular Diversity Analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.25572505openalex-snapshot

Additional file 1 of Single-cell characterisation of tissue homing CD4 + and CD8 + T cell clones in immune-mediated refractory arthritis

inferred← citeshttps://doi.org/10.6084/m9.figshare.25572689openalex-snapshot

Additional file 2 of Single-cell characterisation of tissue homing CD4 + and CD8 + T cell clones in immune-mediated refractory arthritis

inferred← citeshttps://doi.org/10.61186/jibs.9.4.623openalex-snapshot

Biodiversity of butterflies (Lepidoptera, Papilionoidea) in Mountain Koritnik in the Republic of Kosovo

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