RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data

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

(2015) Leon Kuchenbecker et al.   BIOINFORMATICS

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

(2015) Yvonne Suessmuth et al.   BLOOD

Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers

(2015) Evgeny S. Egorov et al.   JOURNAL OF IMMUNOLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Screening Mutations of MYBPC3 in 114 Unrelated Patients with Hypertrophic Cardiomyopathy by Targeted Capture and Next-generation Sequencing

(2015) Xuxia Liu et al.   Scientific Reports

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

TCRklass: A New K-String–Based Algorithm for Human and Mouse TCR Repertoire Characterization

(2014) Xi Yang et al.   JOURNAL OF IMMUNOLOGY

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

Characterizing immune repertoires by high throughput sequencing: strategies and applications

(2014) Jorg J.A. Calis et al.   TRENDS IN IMMUNOLOGY

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

(2013) N. Thomas et al.   BIOINFORMATICS

MiTCR: software for T-cell receptor sequencing data analysis

(2013) Dmitriy A Bolotin et al.   NATURE METHODS

Sequence analysis of T-cell repertoires in health and disease

(2013) Daniel J Woodsworth et al.   Genome Medicine

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

Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors

(2012) Paul D. Baum et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Chromatin conformation governs T-cell receptor J  gene segment usage

(2012) W. Ndifon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

(2011) Phuong Nguyen et al.   BMC GENOMICS

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

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

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human T-cell memory consists mainly of unexpanded clones

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

Maximum entropy models for antibody diversity

(2010) T. Mora 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

Profiling model T-cell metagenomes with short reads

(2009) René L. Warren et al.   BIOINFORMATICS

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 new paradigm of flow cell sequencing

(2008) R. A. Holt et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY