Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

(2020) Cédric R Weber et al.   BIOINFORMATICS

Genesis of the αβ T-cell receptor

(2019) Thomas Dupic et al.   PLoS Computational Biology

Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

(2019) Henrik Knecht et al.   LEUKEMIA

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

(2019) Monika Brüggemann et al.   LEUKEMIA

Tools for fundamental analysis functions of TCR repertoires: a systematic comparison

(2019) Yanfang Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Immunoglobulin gene analysis as a tool for investigating human immune responses

(2018) Deborah Dunn-Walters et al.   IMMUNOLOGICAL REVIEWS

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories

(2018) Brian D. Corrie et al.   IMMUNOLOGICAL REVIEWS

Human adaptive immune receptor repertoire analysis-Past, present, and future

(2018) Sandra C. A. Nielsen et al.   IMMUNOLOGICAL REVIEWS

Quantitative profiling reveals minor changes of T cell receptor repertoire in response to subunit inactivated influenza vaccine

(2018) Anastasiia L. Sycheva et al.   VACCINE

MAIT cell clonal expansion and TCR repertoire shaping in human volunteers challenged with Salmonella Paratyphi A

(2018) Lauren J. Howson et al.   Nature Communications

RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy

(2018) Wahiba Chaara et al.   Frontiers in Immunology

T cell receptor sequencing of activated CD8 T cells in the blood identifies tumor-infiltrating clones that expand after PD-1 therapy and radiation in a melanoma patient

(2018) Andreas Wieland et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

TCR repertoire profiling of tumors, adjacent normal tissues, and peripheral blood predicts survival in nasopharyngeal carcinoma

(2018) Ya-bin Jin et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins

(2018) Mikhail V. Pogorelyy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma

(2018) Sabrina A. Hogan et al.   Cancer Immunology Research

T cell receptor repertoire usage in cancer as a surrogate marker for immune responses

(2017) David Schrama et al.   Seminars in Immunopathology

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

(2017) Felix Breden et al.   Frontiers in Immunology

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

(2016) Olga V. Britanova et al.   JOURNAL OF IMMUNOLOGY

A Leukocyte Immune-Type Receptor Subset Is a Marker of Antiviral Cytotoxic Cells in Channel Catfish,Ictalurus punctatus

(2016) Erin B. Taylor et al.   JOURNAL OF IMMUNOLOGY

Systematic Comparative Evaluation of Methods for Investigating the TCRβ Repertoire

(2016) Xiao Liu et al.   PLoS One

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

(2015) Wei Zhang et al.   GENETICS

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

(2015) Victor Greiff et al.   TRENDS IN IMMUNOLOGY

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

(2015) Wei Zhang et al.   GENETICS

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

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

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine

(2013) N. Thomas et al.   BIOINFORMATICS

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Measuring T cell receptor and T cell gene expression diversity in antigen-responsive human CD4+ T cells

(2013) Anne Eugster et al.   JOURNAL OF IMMUNOLOGICAL METHODS

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

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

(2012) A. Murugan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

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

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

(2009) H. S. Robins et al.   BLOOD