Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets

Early precursors and molecular determinants of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing

(2020) Nadia S. Kurd et al.   Science Immunology

CD4+ T cells persist for years in the human small intestine and display a TH1 cytokine profile

(2020) Raquel Bartolomé-Casado et al.   Mucosal Immunology

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

(2020) Daniele Corridoni et al.   NATURE MEDICINE

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Interstitial Migration of CD8αβ T Cells in the Small Intestine Is Dynamic and Is Dictated by Environmental Cues

(2019) Emily A. Thompson et al.   Cell Reports

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

(2019) Maria Gutierrez-Arcelus et al.   Nature Communications

Hobit- and Blimp-1-driven CD4+ tissue-resident memory T cells control chronic intestinal inflammation

(2019) Sebastian Zundler et al.   NATURE IMMUNOLOGY

Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease

(2019) Toufic Mayassi et al.   CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Resident memory CD8 T cells persist for years in human small intestine

(2019) Raquel Bartolomé-Casado et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Functional Requirement for CD69 in Establishment of Resident Memory CD8+ T Cells Varies with Tissue Location

(2019) Daniel A. Walsh et al.   JOURNAL OF IMMUNOLOGY

Characterization of donor and recipient CD8+ tissue-resident memory T cells in transplant nephrectomies

(2019) Kitty de Leur et al.   Scientific Reports

Location, location, location: Tissue resident memory T cells in mice and humans

(2019) Peter A. Szabo et al.   Science Immunology

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

(2019) Jerome C. Martin et al.   CELL

Tissue-Resident Memory T Cells in Cancer Immunosurveillance

(2019) Simone L. Park et al.   TRENDS IN IMMUNOLOGY

TCR and Inflammatory Signals Tune Human MAIT Cells to Exert Specific Tissue Repair and Effector Functions

(2019) Tianqi Leng et al.   Cell Reports

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

T Cells in Nonlymphoid Tissues Give Rise to Lymph-Node-Resident Memory T Cells

(2018) Lalit K. Beura et al.   IMMUNITY

The role of cytokines in T-cell memory in health and disease

(2018) Miro E. Raeber et al.   IMMUNOLOGICAL REVIEWS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Unique and Common Features of Innate-Like Human Vδ2+ γδT Cells and Mucosal-Associated Invariant T Cells

(2018) Nicholas M. Provine et al.   Frontiers in Immunology

High-dimensional immune phenotyping and transcriptional analyses reveal robust recovery of viable human immune and epithelial cells from frozen gastrointestinal tissue

(2018) Liza Konnikova et al.   Mucosal Immunology

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Human Intestinal Allografts Contain Functional Hematopoietic Stem and Progenitor Cells that Are Maintained by a Circulating Pool

(2018) Jianing Fu et al.   Cell Stem Cell

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

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

Trigger-happy resident memory CD4+ T cells inhabit the human lungs

(2017) A E Oja et al.   Mucosal Immunology

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

(2017) J. Justin Milner et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Transcriptional Regulation of Tissue-Resident Lymphocytes

(2017) Laura K. Mackay et al.   TRENDS IN IMMUNOLOGY

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

TGFβ Signaling Intersects with CD103 Integrin Signaling to Promote T-Lymphocyte Accumulation and Antitumor Activity in the Lung Tumor Microenvironment

(2016) Marie Boutet et al.   CANCER RESEARCH

ABC transporters and NR4A1 identify a quiescent subset of tissue-resident memory T cells

(2016) Chandra Sekhar Boddupalli et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2016) Pleun Hombrink et al.   NATURE IMMUNOLOGY

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

(2016) L. K. Mackay et al.   SCIENCE

Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease

(2016) N. T. Ventham et al.   Nature Communications

Macrochimerism in Intestinal Transplantation: Association With Lower Rejection Rates and Multivisceral Transplants, Without GVHD

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

Transcriptional repressor ZEB2 promotes terminal differentiation of CD8 + effector and memory T cell populations during infection

(2015) Kyla D. Omilusik et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CD161intCD8+ T cells: a novel population of highly functional, memory CD8+ T cells enriched within the gut

(2015) J R Fergusson et al.   Mucosal Immunology

Proinflammatory microenvironments within the intestine regulate the differentiation of tissue-resident CD8+ T cells responding to infection

(2015) Tessa Bergsbaken et al.   NATURE IMMUNOLOGY

Hair follicle–derived IL-7 and IL-15 mediate skin-resident memory T cell homeostasis and lymphoma

(2015) Takeya Adachi et al.   NATURE MEDICINE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life

(2014) Joseph J.C. Thome et al.   CELL

DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis

(2014) R Alan Harris et al.   Epigenetics

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

(2014) Simone Picelli et al.   Nature Protocols

Resident memory CD8 T cells trigger protective innate and adaptive immune responses

(2014) J. M. Schenkel et al.   SCIENCE

Skin-resident memory CD8+ T cells trigger a state of tissue-wide pathogen alert

(2014) S. Ariotti et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Evaluation of Responsive Gene Expression as a Sensitive and Specific Biomarker in Patients with Ulcerative Colitis

(2012) Juan Román et al.   INFLAMMATORY BOWEL DISEASES

Leukocyte Function-associated Antigen-1/Intercellular Adhesion Molecule-1 Interaction Induces a Novel Genetic Signature Resulting in T-cells Refractory to Transforming Growth Factor-β Signaling

(2012) Navin K. Verma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Different patterns of peripheral migration by memory CD4+ and CD8+ T cells

(2011) Thomas Gebhardt et al.   NATURE

Autocrine IL-2 is required for secondary population expansion of CD8+ memory T cells

(2011) Sonia Feau et al.   NATURE IMMUNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Integrin-Dependent Organization and Bidirectional Vesicular Traffic at Cytotoxic Immune Synapses

(2009) Dongfang Liu et al.   IMMUNITY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A versatile platform for comprehensive chip-based explorative cytometry

(2008) Christian Hennig et al.   CYTOMETRY PART A