Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection

Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1−CD8+ Tumor-Infiltrating T Cells

(2019) Sema Kurtulus et al.   IMMUNITY

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

The transcription factor c-Myb regulates CD8+ T cell stemness and antitumor immunity

(2019) Sanjivan Gautam et al.   NATURE IMMUNOLOGY

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

CD8 T Cell Exhaustion in Chronic Infection and Cancer: Opportunities for Interventions

(2018) Masao Hashimoto et al.   Annual Review of Medicine

T Cell Dysfunction in Cancer

(2018) Daniela S. Thommen et al.   CANCER CELL

Expression of the DNA-Binding Factor TOX Promotes the Encephalitogenic Potential of Microbe-Induced Autoreactive CD8 + T Cells

(2018) Nicolas Page et al.   IMMUNITY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

CD8+ T Cell Priming in Established Chronic Viral Infection Preferentially Directs Differentiation of Memory-like Cells for Sustained Immunity

(2018) Laura M. Snell et al.   IMMUNITY

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

Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8 + T Cell Terminal Differentiation and Loss of Multipotency

(2017) Simon M. Gray et al.   IMMUNITY

Effector CD8 T cells dedifferentiate into long-lived memory cells

(2017) Ben Youngblood et al.   NATURE

T memory stem cells in health and disease

(2017) Luca Gattinoni et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

CD8 + T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections

(2016) Bing He et al.   IMMUNITY

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

Follicular CXCR5-expressing CD8+ T cells curtail chronic viral infection

(2016) Ran He et al.   NATURE

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

(2016) Se Jin Im et al.   NATURE

CXCR5+ follicular cytotoxic T cells control viral infection in B cell follicles

(2016) Yew Ann Leong et al.   NATURE IMMUNOLOGY

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

(2015) Evan Z. Macosko et al.   CELL

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

(2015) Gustavo J. Martinez et al.   IMMUNITY

The development of innate lymphoid cells requires TOX-dependent generation of a common innate lymphoid cell progenitor

(2015) Corey R Seehus et al.   NATURE IMMUNOLOGY

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

Adoptive cell transfer as personalized immunotherapy for human cancer

(2015) S. A. Rosenberg et al.   SCIENCE

A Critical Role of IL-21-Induced BATF in Sustaining CD8-T-Cell-Mediated Chronic Viral Control

(2015) Gang Xin et al.   Cell Reports

TCF1 Is Required for the T Follicular Helper Cell Response to Viral Infection

(2015) Tuoqi Wu et al.   Cell Reports

The Transcription Factor FoxO1 Sustains Expression of the Inhibitory Receptor PD-1 and Survival of Antiviral CD8+ T Cells during Chronic Infection

(2014) Matthew M. Staron 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

Myeloid Cells Limit Production of Antibody-Secreting Cells after Immunization in the Lymph Node

(2013) D. R. Fooksman et al.   JOURNAL OF IMMUNOLOGY

Hypoxia-inducible factors enhance the effector responses of CD8+ T cells to persistent antigen

(2013) Andrew L Doedens et al.   NATURE IMMUNOLOGY

Network Analysis Reveals Centrally Connected Genes and Pathways Involved in CD8+ T Cell Exhaustion versus Memory

(2012) Travis A. Doering et al.   IMMUNITY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Anti-viral CD8 T cells and the cytokines that they love

(2012) Maureen A. Cox et al.   VIROLOGY

Pathogenic virus-specific T cells cause disease during treatment with the calcineurin inhibitor FK506: implications for transplantation

(2010) Koichi Araki et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Wnt signaling arrests effector T cell differentiation and generates CD8+ memory stem cells

(2009) Luca Gattinoni et al.   NATURE MEDICINE

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

Development of all CD4 T lineages requires nuclear factor TOX

(2008) Parinaz Aliahmad et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Selective expansion of a subset of exhausted CD8 T cells by  PD-L1 blockade

(2008) S. D. Blackburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY