Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

NR4A transcription factors limit CAR T cell function in solid tumours

(2019) Joyce Chen et al.   NATURE

TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection

(2019) Francesca Alfei et al.   NATURE

TOX is a critical regulator of tumour-specific T cell differentiation

(2019) Andrew C. Scott et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Non-conventional Inhibitory CD4 + Foxp3 − PD-1 hi T Cells as a Biomarker of Immune Checkpoint Blockade Activity

(2018) Roberta Zappasodi et al.   CANCER CELL

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells

(2018) John L. Johnson et al.   IMMUNITY

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells

(2018) Patrick Fernandes Rodrigues et al.   NATURE IMMUNOLOGY

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Pembrolizumab for advanced basal cell carcinoma: an investigator-initiated, proof-of-concept study

(2018) Anne Lynn S. Chang et al.   JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin

(2018) Dian Yang et al.   Cancer Discovery

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

(2018) Hanjie Li et al.   CELL

Organoid Modeling of the Tumor Immune Microenvironment

(2018) James T. Neal et al.   CELL

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis

(2018) Jim G. Castellanos et al.   IMMUNITY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Transcription Factor IRF4 Promotes CD8 + T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection

(2017) Kevin Man et al.   IMMUNITY

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

(2017) J. Justin Milner et al.   NATURE

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer

(2017) Paola A. Betancur et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

(2016) Sarah K. Denny et al.   CELL

Constitutive Glycolytic Metabolism Supports CD8 + T Cell Effector Memory Differentiation during Viral Infection

(2016) Anthony T. Phan et al.   IMMUNITY

Dynamic Changes in Chromatin Accessibility Occur in CD8 + T Cells Responding to Viral Infection

(2016) James P. Scott-Browne et al.   IMMUNITY

Activin A programs the differentiation of human TFH cells

(2016) Michela Locci et al.   NATURE IMMUNOLOGY

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade

(2016) K. E. Pauken et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

The Transcription Factor NFAT Promotes Exhaustion of Activated CD8 + T Cells

(2015) Gustavo J. Martinez et al.   IMMUNITY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Batf3 maintains autoactivation of Irf8 for commitment of a CD8α+ conventional DC clonogenic progenitor

(2015) Gary E Grajales-Reyes et al.   NATURE IMMUNOLOGY

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Erythro-megakaryocytic transcription factors associated with hereditary anemia

(2014) J. D. Crispino et al.   BLOOD

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Molecular and Transcriptional Basis of CD4+ T Cell Dysfunction during Chronic Infection

(2014) Alison Crawford et al.   IMMUNITY

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

c-Myc-induced transcription factor AP4 is required for host protection mediated by CD8+ T cells

(2014) Chun Chou et al.   NATURE IMMUNOLOGY

A sharp T-cell antigen receptor signaling threshold for T-cell proliferation

(2014) B. B. Au-Yeung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Runx1 is essential at two stages of early murine B-cell development

(2013) B. Niebuhr et al.   BLOOD

Persistent Antigen and Germinal Center B Cells Sustain T Follicular Helper Cell Responses and Phenotype

(2013) Dirk Baumjohann et al.   IMMUNITY

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

(2013) Gabriela Bindea et al.   IMMUNITY

CD4+ follicular helper T cell infiltration predicts breast cancer survival

(2013) Chunyan Gu-Trantien et al.   JOURNAL OF CLINICAL INVESTIGATION

GLI activation by atypical protein kinase C ι/λ regulates the growth of basal cell carcinomas

(2013) Scott X. Atwood et al.   NATURE

Integrin-modulating therapy prevents fibrosis and autoimmunity in mouse models of scleroderma

(2013) Elizabeth E. Gerber et al.   NATURE

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

(2013) Laura K Mackay et al.   NATURE IMMUNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

IRF-8 extinguishes neutrophil production and promotes dendritic cell lineage commitment in both myeloid and lymphoid mouse progenitors

(2012) A. M. Becker et al.   BLOOD

Re(de)fining the dendritic cell lineage

(2012) Ansuman T Satpathy et al.   NATURE IMMUNOLOGY

Networking erythropoiesis: Figure 1.

(2010) Marc A. Kerenyi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcriptional analysis of HIV-specific CD8+ T cells shows that PD-1 inhibits T cell function by upregulating BATF

(2010) Michael Quigley et al.   NATURE MEDICINE

CD47 Is Upregulated on Circulating Hematopoietic Stem Cells and Leukemia Cells to Avoid Phagocytosis

(2009) Siddhartha Jaiswal et al.   CELL

Regulation of lymphoid versus myeloid fate 'choice' by the transcription factor Mef2c

(2009) Sandra Stehling-Sun et al.   NATURE IMMUNOLOGY

A Vital Role for Interleukin-21 in the Control of a Chronic Viral Infection

(2009) J. S. Yi et al.   SCIENCE

IL-21 Is Required to Control Chronic Viral Infection

(2009) H. Elsaesser et al.   SCIENCE

IL-21R on T Cells Is Critical for Sustained Functionality and Control of Chronic Viral Infection

(2009) A. Frohlich et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY