TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

Comprehensive Phenotyping of T Cells Using Flow Cytometry

(2019) Charlotte M. Mousset et al.   CYTOMETRY PART A

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

(2019) Mandeep Singh et al.   Nature Communications

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

(2018) David Zemmour et al.   NATURE IMMUNOLOGY

Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors

(2018) Erika J. Crosby et al.   OncoImmunology

High-resolution repertoire analysis reveals a major bystander activation of Tfh and Tfr cells

(2018) Paul-Gydeon Ritvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

(2018) Mridusmita Saikia et al.   NATURE METHODS

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

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

(2017) David Schrama et al.   Seminars in Immunopathology

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

CD4+T cell effector commitment coupled to self-renewal by asymmetric cell divisions

(2016) Simone A. Nish et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcriptional Profiling of Th2 Cells Identifies Pathogenic Features Associated with Asthma

(2016) Grégory Seumois et al.   JOURNAL OF IMMUNOLOGY

T cell fate and clonality inference from single-cell transcriptomes

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

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL

(2015) Ilan R. Kirsch et al.   Science Translational Medicine

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

High-throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV-reactive CD8+T cells

(2014) Andreas Lossius et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

The signaling symphony: T cell receptor tunes cytokine-mediated T cell differentiation

(2014) Weishan Huang et al.   JOURNAL OF LEUKOCYTE BIOLOGY

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

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Flow-cytometric analysis of rare antigen-specific T cells

(2013) Petra Bacher et al.   CYTOMETRY PART A

Food allergy diagnosis and therapy: where are we now?

(2013) Aleena Syed et al.   Immunotherapy

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Using synthetic templates to design an unbiased multiplex PCR assay

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

Memory T Cell Subsets, Migration Patterns, and Tissue Residence

(2012) Scott N. Mueller et al.   Annual Review of Immunology

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Lack of IL-4 receptor expression on T helper cells reduces T helper 2 cell polyfunctionality and confers resistance in allergic bronchopulmonary mycosis

(2012) U Müller et al.   Mucosal Immunology

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Hierarchical IL-5 Expression Defines a Subpopulation of Highly Differentiated Human Th2 Cells

(2011) B. Upadhyaya et al.   JOURNAL OF IMMUNOLOGY

Polyfunctional responses by human T cells result from sequential release of cytokines

(2011) Q. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paired analysis of TCRα and TCRβ chains at the single-cell level in mice

(2010) Pradyot Dash et al.   JOURNAL OF CLINICAL INVESTIGATION

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

(2009) Gang Wei et al.   IMMUNITY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL