Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

(2019) Imran Siddiqui et al.   IMMUNITY

Oxysterol Sensing through the Receptor GPR183 Promotes the Lymphoid-Tissue-Inducing Function of Innate Lymphoid Cells and Colonic Inflammation

(2018) Johanna Emgård et al.   IMMUNITY

A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade

(2018) Daniela S. Thommen et al.   NATURE MEDICINE

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors

(2018) Thomas Duhen et al.   Nature Communications

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

CD49a Expression Defines Tissue-Resident CD8 + T Cells Poised for Cytotoxic Function in Human Skin

(2017) Stanley Cheuk et al.   IMMUNITY

Maintenance of PD-1 on brain-resident memory CD8 T cells is antigen independent

(2017) Shwetank et al.   IMMUNOLOGY AND CELL BIOLOGY

IL-2hightissue-resident T cells in the human liver: Sentinels for hepatotropic infection

(2017) Laura J. Pallett et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The PD-1: PD-L1 pathway promotes development of brain-resident memory T cells following acute viral encephalitis

(2017) Sujata Prasad et al.   Journal of Neuroinflammation

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours

(2017) J. Justin Milner et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Is autoimmunity the Achilles' heel of cancer immunotherapy?

(2017) Carl H June et al.   NATURE MEDICINE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Glucocorticoid receptor in T cells mediates protection from autoimmunity in pregnancy

(2017) Jan Broder Engler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of resident memory T cells enhances the efficacy of cancer vaccine

(2017) Mevyn Nizard et al.   Nature Communications

PD-1 expression on tumor-specific T cells: Friend or foe for immunotherapy?

(2017) Sylvain Simon et al.   OncoImmunology

Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis

(2016) Massimiliano Mellone et al.   Aging-US

Upregulated Glucose Metabolism Correlates Inversely with CD8 + T-cell Infiltration and Survival in Squamous Cell Carcinoma

(2016) Christian H. Ottensmeier et al.   CANCER RESEARCH

Regulatory T Cell Specificity Directs Tolerance versus Allergy against Aeroantigens in Humans

(2016) Petra Bacher et al.   CELL

T Cell Factor 1-Expressing Memory-like CD8 + T Cells Sustain the Immune Response to Chronic Viral Infections

(2016) Daniel T. Utzschneider et al.   IMMUNITY

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

(2016) Se Jin Im et al.   NATURE

Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells

(2016) Pleun Hombrink et al.   NATURE IMMUNOLOGY

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

(2016) Isaac Engel et al.   NATURE IMMUNOLOGY

T cell fate and clonality inference from single-cell transcriptomes

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

Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes

(2016) L. K. Mackay et al.   SCIENCE

Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors

(2016) Oliver Wood et al.   Oncotarget

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

(2015) Evan Z. Macosko et al.   CELL

The Inhibitory Receptor NKG2A Sustains Virus-Specific CD8+ T Cells in Response to a Lethal Poxvirus Infection

(2015) Aaron S. Rapaport et al.   IMMUNITY

The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection

(2015) Claudia X. Dominguez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Protein Tyrosine Phosphatase SHP-1 Modulates T Cell Responses by Controlling Cbl-b Degradation

(2015) Yun Xiao et al.   JOURNAL OF IMMUNOLOGY

CD8+CD103+Tumor–Infiltrating Lymphocytes Are Tumor-Specific Tissue-Resident Memory T Cells and a Prognostic Factor for Survival in Lung Cancer Patients

(2015) Fayçal Djenidi et al.   JOURNAL OF IMMUNOLOGY

Pembrolizumab versus Ipilimumab in Advanced Melanoma

(2015) Caroline Robert et al.   NEW ENGLAND JOURNAL OF MEDICINE

HHLA2 and TMIGD2: new immunotherapeutic targets of the B7 and CD28 families

(2015) Murali Janakiram et al.   OncoImmunology

snpqc- an R pipeline for quality control of Illumina SNP genotyping array data

(2014) Cedric Gondro et al.   ANIMAL GENETICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

Tissue-Resident Memory T Cells

(2014) Jason M. Schenkel et al.   IMMUNITY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The receptors CD96 and CD226 oppose each other in the regulation of natural killer cell functions

(2014) Christopher J Chan et al.   NATURE IMMUNOLOGY

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

The developmental pathway for CD103+CD8+ tissue-resident memory T cells of skin

(2013) Laura K Mackay et al.   NATURE IMMUNOLOGY

GPR15-Mediated Homing Controls Immune Homeostasis in the Large Intestine Mucosa

(2013) S. V. Kim et al.   SCIENCE

CD103 or LFA-1 Engagement at the Immune Synapse between Cytotoxic T Cells and Tumor Cells Promotes Maturation and Regulates T-cell Effector Functions

(2012) K. Franciszkiewicz et al.   CANCER RESEARCH

The cellular function of srGAP3 and its role in neuronal morphogenesis

(2012) Claire Bacon et al.   MECHANISMS OF DEVELOPMENT

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Regulation of CD4+ and CD8+ Effector Responses by Sprouty-1

(2012) Sam Collins et al.   PLoS One

DUSP4 deficiency enhances CD25 expression and CD4+T-cell proliferation without impeding T-cell development

(2011) Ching-Yu Huang et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

An Interleukin-21- Interleukin-10-STAT3 Pathway Is Critical for Functional Maturation of Memory CD8+ T Cells

(2011) Weiguo Cui et al.   IMMUNITY

MYADM regulates Rac1 targeting to ordered membranes required for cell spreading and migration

(2011) Juan F. Aranda et al.   MOLECULAR BIOLOGY OF THE CELL

The transcriptional regulators Id2 and Id3 control the formation of distinct memory CD8+ T cell subsets

(2011) Cliff Y Yang et al.   NATURE IMMUNOLOGY

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

AMP kinase-related kinase NUAK2 affects tumor growth, migration, and clinical outcome of human melanoma

(2011) T. Namiki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Junctional Adhesion Molecule JAML Is a Costimulatory Receptor for Epithelial    T Cell Activation

(2010) D. A. Witherden et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The significance of OX40 and OX40L to T-cell biology and immune disease

(2009) Michael Croft et al.   IMMUNOLOGICAL REVIEWS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Ankyrin repeat domain 28 (ANKRD28), a novel binding partner of DOCK180, promotes cell migration by regulating focal adhesion formation

(2008) Mitsuhiro Tachibana et al.   EXPERIMENTAL CELL RESEARCH