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

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

(2016) David DeTomaso et al.   BMC BIOINFORMATICS

Antiviral CD8 + T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion

(2016) Srinika Ranasinghe et al.   IMMUNITY

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

(2016) Jernej Godec et al.   IMMUNITY

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

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses

(2016) Vesna Pulko et al.   NATURE IMMUNOLOGY

T cell fate and clonality inference from single-cell transcriptomes

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

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

A Mine Is a Terrible Thing to Waste: High Content, Single Cell Technologies for Comprehensive Immune Analysis

(2015) P. K. Chattopadhyay et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

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

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccination

(2015) Rama S. Akondy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-lasting stem cell–like memory CD8 + T cells with a naïve-like profile upon yellow fever vaccination

(2015) Silvia A. Fuertes Marraco et al.   Science Translational Medicine

Adenoviral Vector Vaccination Induces a Conserved Program of CD8+ T Cell Memory Differentiation in Mouse and Man

(2015) Beatrice Bolinger et al.   Cell Reports

Statistical significance of variables driving systematic variation in high-dimensional data

(2014) Neo Christopher Chung et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Human syndromes of immunodeficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development

(2014) Xiaomin Yu et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

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

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

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

A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCV-specific T cell memory

(2014) L. Swadling et al.   Science Translational Medicine

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes

(2012) Evan W. Newell et al.   IMMUNITY

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Vanessa Venturi et al.   JOURNAL OF IMMUNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

(2008) X. Brochet et al.   NUCLEIC ACIDS RESEARCH