Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Developmental plasticity allows outside-in immune responses by resident memory T cells

(2020) Raissa Fonseca et al.   NATURE IMMUNOLOGY

Homeostasis and transitional activation of regulatory T cells require c-Myc

(2020) Jordy Saravia et al.   Science Advances

Heterogenous Populations of Tissue-Resident CD8+ T Cells Are Generated in Response to Infection and Malignancy

(2020) J. Justin Milner et al.   IMMUNITY

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

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

(2019) Sebastian Zundler et al.   NATURE IMMUNOLOGY

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis

(2019) Tomas Castro-Dopico et al.   IMMUNITY

T Follicular Helper Cell Biology: A Decade of Discovery and Diseases

(2019) Shane Crotty   IMMUNITY

Innate lymphoid cells support regulatory T cells in the intestine through interleukin-2

(2019) Lei Zhou et al.   NATURE

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Macrophages in intestinal inflammation and resolution: a potential therapeutic target in IBD

(2019) Yi Rang Na et al.   Nature Reviews Gastroenterology & Hepatology

EOMES interacts with RUNX3 and BRG1 to promote innate memory cell formation through epigenetic reprogramming

(2019) Nicolas Istaces et al.   Nature Communications

Human CD4+CD103+ cutaneous resident memory T cells are found in the circulation of healthy individuals

(2019) Maria M. Klicznik 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

Integrin Activation Controls Regulatory T Cell–Mediated Peripheral Tolerance

(2018) Jane E. Klann et al.   JOURNAL OF IMMUNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

High Levels of Eomes Promote Exhaustion of Anti-tumor CD8+ T Cells

(2018) Jing Li et al.   Frontiers in Immunology

Circulating and Tissue-Resident CD4 + T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation

(2017) Ahmed N. Hegazy et al.   GASTROENTEROLOGY

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

(2017) Stanley Cheuk et al.   IMMUNITY

Survival of tissue-resident memory T cells requires exogenous lipid uptake and metabolism

(2017) Youdong Pan et al.   NATURE

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

(2017) J. Justin Milner et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Transcriptional Regulation of Tissue-Resident Lymphocytes

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

IL-12 drives functional plasticity of human group 2 innate lymphoid cells

(2016) Ai Ing Lim et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment

(2016) Yohko Kitagawa et al.   NATURE IMMUNOLOGY

Tumor Necrosis Factor Receptor 2 Restricts the Pathogenicity of CD8+ T Cells in Mice With Colitis

(2015) Shivesh Punit et al.   GASTROENTEROLOGY

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

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

Resident memory T cells in human health and disease

(2015) R. A. Clark   Science Translational Medicine

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

CD4+ T Cell Help Guides Formation of CD103+ Lung-Resident Memory CD8+ T Cells during Influenza Viral Infection

(2014) Brian J. Laidlaw et al.   IMMUNITY

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses

(2014) Janilyn Arsenio et al.   NATURE IMMUNOLOGY

Molecular regulation of effector and memory T cell differentiation

(2014) John T Chang et al.   NATURE IMMUNOLOGY

KLF2 is a rate-limiting transcription factor that can be targeted to enhance regulatory T-cell production

(2014) Sudheer K. Pabbisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased Th17-Inducing Activity of CD14+ CD163low Myeloid Cells in Intestinal Lamina Propria of Patients With Crohn’s Disease

(2013) Takayuki Ogino et al.   GASTROENTEROLOGY

Characterisation of enterocolitis in the piroxicam-accelerated interleukin-10 knock out mouse — A model mimicking inflammatory bowel disease

(2013) Kristine Holgersen et al.   Journal of Crohns & Colitis

Differentiation of CD8 memory T cells depends on Foxo1

(2013) Rodrigo Hess Michelini et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2013) Laura K Mackay et al.   NATURE IMMUNOLOGY

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Mucosal CXCR4+IgG plasma cells contribute to the pathogenesis of human ulcerative colitis through FcγR-mediated CD14 macrophage activation

(2012) Michihide Uo et al.   GUT

CD8+ TCR Repertoire Formation Is Guided Primarily by the Peptide Component of the Antigenic Complex

(2012) D. Koning et al.   JOURNAL OF IMMUNOLOGY

The Molecular Signature of Tissue Resident Memory CD8 T Cells Isolated from the Brain

(2012) L. M. Wakim et al.   JOURNAL OF IMMUNOLOGY

Progenitor and Terminal Subsets of CD8+ T Cells Cooperate to Contain Chronic Viral Infection

(2012) M. A. Paley et al.   SCIENCE

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation

(2011) Marc Beyer et al.   NATURE IMMUNOLOGY

Cutting Edge: The Transcription Factor Eomesodermin Enables CD8+ T Cells To Compete for the Memory Cell Niche

(2010) A. Banerjee et al.   JOURNAL OF IMMUNOLOGY

Inflammatory Bowel Disease

(2009) Clara Abraham et al.   NEW ENGLAND JOURNAL OF MEDICINE

Unique CD14+ intestinal macrophages contribute to the pathogenesis of Crohn disease via IL-23/IFN-γ axis

(2008) Nobuhiko Kamada et al.   JOURNAL OF CLINICAL INVESTIGATION

Regulatory T Cells: Mechanisms of Differentiation and Function

(2007) Steven Z. Josefowicz et al.   Annual Review of Immunology