T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

(2019) Zachary Sethna et al.   BIOINFORMATICS

Commonality despite exceptional diversity in the baseline human antibody repertoire

(2019) Bryan Briney et al.   NATURE

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

(2018) Simone Rizzetto et al.   BIOINFORMATICS

Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection

(2018) Ian Setliff et al.   Cell Host & Microbe

Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

(2018) Yuval Elhanati et al.   IMMUNOLOGICAL REVIEWS

Neoadjuvant PD-1 Blockade in Resectable Lung Cancer

(2018) Patrick M. Forde et al.   NEW ENGLAND JOURNAL OF MEDICINE

CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients

(2018) Ekaterina A Komech et al.   RHEUMATOLOGY

Hematopoietic stem cell transplantation in its 60s: A platform for cellular therapies

(2018) Christian Chabannon et al.   Science Translational Medicine

High-throughput immune repertoire analysis with IGoR

(2018) Quentin Marcou et al.   Nature Communications

Method for identification of condition-associated public antigen receptor sequences

(2018) Mikhail V Pogorelyy et al.   eLife

RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy

(2018) Wahiba Chaara et al.   Frontiers in Immunology

Computational Evaluation of B-Cell Clone Sizes in Bulk Populations

(2018) Aaron M. Rosenfeld et al.   Frontiers in Immunology

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

(2018) Enkelejda Miho et al.   Frontiers in Immunology

Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges

(2018) Marco De Simone et al.   Frontiers in Immunology

Robust B Cell Responses Predict Rapid Resolution of Lyme Disease

(2018) Lisa K. Blum et al.   Frontiers in Immunology

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

T cell receptor alpha repertoire of CD8+ T cells following allogeneic stem cell transplantation using next-generation sequencing

(2018) Cornelia S. Link-Rachner et al.   HAEMATOLOGICA

Urine-derived lymphocytes as a non-invasive measure of the bladder tumor immune microenvironment

(2018) Yien Ning Sophia Wong et al.   JOURNAL OF EXPERIMENTAL MEDICINE

T cells in patients with narcolepsy target self-antigens of hypocretin neurons

(2018) Daniela Latorre et al.   NATURE

Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity

(2018) William S DeWitt et al.   eLife

High-throughput determination of the antigen specificities of T cell receptors in single cells

(2018) Shu-Qi Zhang et al.   NATURE BIOTECHNOLOGY

Publisher Correction: Neoadjuvant immune checkpoint blockade in high-risk resectable melanoma

(2018) Rodabe N. Amaria et al.   NATURE MEDICINE

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

Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation

(2018) Athina Soragia Gkazi et al.   Frontiers in Immunology

On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition

(2017) Nicolas De Neuter et al.   IMMUNOGENETICS

Clinically resolved psoriatic lesions contain psoriasis-specific IL-17–producing αβ T cell clones

(2017) Tiago R. Matos et al.   JOURNAL OF CLINICAL INVESTIGATION

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads

(2017) Alexander Shlemov et al.   JOURNAL OF IMMUNOLOGY

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

(2017) Victor Greiff et al.   JOURNAL OF IMMUNOLOGY

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Public antibodies to malaria antigens generated by two LAIR1 insertion modalities

(2017) Kathrin Pieper et al.   NATURE

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

An atlas of B-cell clonal distribution in the human body

(2017) Wenzhao Meng et al.   NATURE BIOTECHNOLOGY

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire

(2017) Ryan O Emerson et al.   NATURE GENETICS

Haematopoietic stem cell transplantation for autoimmune diseases

(2017) Joost F. Swart et al.   Nature Reviews Rheumatology

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

(2017) Shaked Afik et al.   NUCLEIC ACIDS RESEARCH

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

(2017) Whijae Roh et al.   Science Translational Medicine

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

(2017) David Schrama et al.   Seminars in Immunopathology

Dynamics of B Cell Recovery In Kidney/Bone Marrow Transplant Recipients

(2017) Baoshan Gao et al.   TRANSPLANTATION

Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires

(2017) Simon Friedensohn et al.   TRENDS IN BIOTECHNOLOGY

Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8 + TCR Repertoires to Immunodominant Viral Antigens

(2017) Guobing Chen et al.   Cell Reports

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

(2017) Mikhail V. Pogorelyy et al.   PLoS Computational Biology

Discovery of T Cell Receptor β Motifs Specific to HLA-B27-Positive Ankylosing Spondylitis by Deep Repertoire Sequence Analysis

(2017) Malek Faham et al.   Arthritis & Rheumatology

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

(2017) Theres Oakes et al.   Frontiers in Immunology

A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains

(2016) Kazutaka Kitaura et al.   BMC IMMUNOLOGY

Allogeneic Stem Cell Transplantation: A Historical and Scientific Overview

(2016) Anurag K. Singh et al.   CANCER RESEARCH

Immune Toxicities Elicted by CTLA-4 Blockade in Cancer Patients Are Associated with Early Diversification of the T-cell Repertoire

(2016) David Y. Oh et al.   CANCER RESEARCH

Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8+T cell receptor alpha repertoire following allogeneic transplantation

(2016) C. S. Link et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Deep sequencing and human antibody repertoire analysis

(2016) Scott D Boyd et al.   CURRENT OPINION IN IMMUNOLOGY

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

(2016) Auda A Eltahla et al.   IMMUNOLOGY AND CELL BIOLOGY

Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon Assembly

(2016) Charles Cole et al.   JOURNAL OF IMMUNOLOGY

Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children

(2016) I V Zvyagin et al.   LEUKEMIA

Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination

(2016) Jiwon Lee et al.   NATURE MEDICINE

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

(2016) Alena Gros et al.   NATURE MEDICINE

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

High-quality full-length immunoglobulin profiling with unique molecular barcoding

(2016) M A Turchaninova et al.   Nature Protocols

Clonal expansion of CD8 T cells in the systemic circulation precedes development of ipilimumab-induced toxicities

(2016) Sumit K. Subudhi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly sensitive and unbiased approach for elucidating antibody repertoires

(2016) Sherry G. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversification of the antigen-specific T cell receptor repertoire after varicella zoster vaccination

(2016) Qian Qi et al.   Science Translational Medicine

T cell repertoire following kidney transplantation revealed by high-throughput sequencing

(2016) Liusheng Lai et al.   TRANSPLANT IMMUNOLOGY

Quantitative characterization of T-cell repertoire and biomarkers in kidney transplant rejection

(2016) Houda Alachkar et al.   BMC Nephrology

Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples

(2016) Joseph Kaplinsky et al.   Nature Communications

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

(2016) David Redmond et al.   Genome Medicine

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

(2016) Marc Duez et al.   PLoS One

Donor CD4 T Cell Diversity Determines Virus Reactivation in Patients After HLA-Matched Allogeneic Stem Cell Transplantation

(2015) J. Ritter et al.   AMERICAN JOURNAL OF TRANSPLANTATION

IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

(2015) Leon Kuchenbecker et al.   BIOINFORMATICS

Generation of human memory stem T cells after haploidentical T-replete hematopoietic stem cell transplantation

(2015) Nicoletta Cieri et al.   BLOOD

CMV reactivation drives posttransplant T-cell reconstitution and results in defects in the underlying TCRβ repertoire

(2015) Yvonne Suessmuth et al.   BLOOD

Autologous stem cell transplantation aids autoimmune patients by functional renewal and TCR diversification of regulatory T cells

(2015) E. M. Delemarre et al.   BLOOD

ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data

(2015) Susanne Schaller et al.   BMC BIOINFORMATICS

tcR: an R package for T cell receptor repertoire advanced data analysis

(2015) Vadim I. Nazarov et al.   BMC BIOINFORMATICS

Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients

(2015) P Y Yew et al.   BONE MARROW TRANSPLANTATION

Direct high-throughput amplification and sequencing of immunoglobulin genes from single human B cells

(2015) Rajagopal Murugan et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

High Diversity in the TCR Repertoire of GAD65 Autoantigen-Specific Human CD4+T Cells

(2015) Anne Eugster et al.   JOURNAL OF IMMUNOLOGY

Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection

(2015) William S. DeWitt et al.   JOURNAL OF VIROLOGY

A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens

(2015) Joshua Tan et al.   NATURE

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients

(2015) Heather Morris et al.   Science Translational Medicine

Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing

(2015) Dharma R Thapa et al.   ARTHRITIS RESEARCH & THERAPY

High-resolution analysis of the human T-cell receptor repertoire

(2015) Eliana Ruggiero et al.   Nature Communications

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

(2015) Katharine Best et al.   Scientific Reports

Profiling tissue-resident T cell repertoires by RNA sequencing

(2015) Scott D. Brown et al.   Genome Medicine

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

(2015) Mikhail Shugay et al.   PLoS Computational Biology

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire

(2015) Jacob D. Galson et al.   Frontiers in Immunology

Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

(2014) Katherine J.L. Jackson et al.   Cell Host & Microbe

CTLA4 Blockade Broadens the Peripheral T-Cell Receptor Repertoire

(2014) L. Robert et al.   CLINICAL CANCER RESEARCH

Hematopoietic Stem Cell Transplantation for Primary Immunodeficiencies

(2014) Elizabeth Kang et al.   HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

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

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Defining the Alloreactive T Cell Repertoire Using High-Throughput Sequencing of Mixed Lymphocyte Reaction Culture

(2014) Ryan O. Emerson et al.   PLoS One

Quantification of HTLV-1 Clonality and TCR Diversity

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

Convergent Antibody Signatures in Human Dengue

(2013) Poornima Parameswaran et al.   Cell Host & Microbe

Pairing of T-cell receptor chains via emulsion PCR

(2013) Maria A. Turchaninova et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes

(2013) Christian E. Busse et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

(2013) Brandon J DeKosky et al.   NATURE BIOTECHNOLOGY

High-throughput identification of antigen-specific TCRs by TCR gene capture

(2013) Carsten Linnemann et al.   NATURE MEDICINE

Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation

(2013) Jeroen W J van Heijst et al.   NATURE MEDICINE

Using synthetic templates to design an unbiased multiplex PCR assay

(2013) Christopher S. Carlson et al.   Nature Communications

CD4+ T Cell-Receptor Repertoire Diversity is Compromised in the Spleen but Not in the Bone Marrow of Aged Mice Due to Private and Sporadic Clonal Expansions

(2013) Eric Shifrut et al.   Frontiers in Immunology

Preparing Unbiased T-Cell Receptor and Antibody cDNA Libraries for the Deep Next Generation Sequencing Profiling

(2013) Ilgar Z. Mamedov et al.   Frontiers in Immunology

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

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

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

Immunoglobulin Analysis Tool: A Novel Tool for the Analysis of Human and Mouse Heavy and Light Chain Transcripts

(2012) Tobias Rogosch et al.   Frontiers in Immunology

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

Antigen-Driven Patterns of TCR Bias Are Shared across Diverse Outcomes of Human Hepatitis C Virus Infection

(2010) J. J. Miles et al.   JOURNAL OF IMMUNOLOGY

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

The Yellow Fever Virus Vaccine Induces a Broad and Polyfunctional Human Memory CD8+ T Cell Response

(2009) R. S. Akondy et al.   JOURNAL OF IMMUNOLOGY

Human Effector and Memory CD8+ T Cell Responses to Smallpox and Yellow Fever Vaccines

(2008) Joseph D. Miller et al.   IMMUNITY