A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections

scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets

(2022) Massimo Andreatta et al.   BIOINFORMATICS

The Era of Cytotoxic CD4 T Cells

(2022) Mara Cenerenti et al.   Frontiers in Immunology

Tissue-resident CD4+ T helper cells assist the development of protective respiratory B and CD8+ T cell memory responses

(2021) Young Min Son et al.   Science Immunology

T resident helper cells promote humoral responses in the lung

(2021) Nivedya Swarnalekha et al.   Science Immunology

Opposing effects of T cell receptor signal strength on CD4 T cells responding to acute versus chronic viral infection

(2021) Marco Künzli et al.   eLife

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Interpretation of T cell states from single-cell transcriptomics data using reference atlases

(2021) Massimo Andreatta et al.   Nature Communications

Dependence on Bcl6 and Blimp1 drive distinct differentiation of murine memory and follicular helper CD4+ T cells

(2021) Thomas Ciucci et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Dynamic CD4+ T cell heterogeneity defines subset-specific suppression and PD-L1-blockade-driven functional restoration in chronic infection

(2021) Laura M. Snell et al.   NATURE IMMUNOLOGY

Long-lived T follicular helper cells retain plasticity and help sustain humoral immunity

(2020) Marco Künzli et al.   Science Immunology

STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data

(2020) Massimo Andreatta et al.   BIOINFORMATICS

Transcription tipping points for T follicular helper cell and T-helper 1 cell fate commitment

(2020) Amania A. Sheikh et al.   Cellular & Molecular Immunology

Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory

(2020) Megan S. F. Soon et al.   NATURE IMMUNOLOGY

Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population

(2020) J. Justin Milner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development

(2020) Laura B. Chopp et al.   IMMUNITY

Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire

(2020) Achia Khatun et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok

(2019) Thomas Ciucci et al.   IMMUNITY

Origins of CD 4 + circulating and tissue‐resident memory T cells

(2019) Quynh P. Nguyen et al.   IMMUNOLOGY

TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8+ T cell exhaustion

(2019) Hyungseok Seo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation

(2019) Melanie S. Vacchio et al.   IMMUNITY

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

(2019) Assaf Magen et al.   Cell Reports

CD4 Helper and CD8 Cytotoxic T Cell Differentiation

(2018) Ichiro Taniuchi   Annual Review of Immunology

The transcription factors Runx3 and ThPOK cross-regulate acquisition of cytotoxic function by human Th1 lymphocytes

(2018) Yasmina Serroukh et al.   eLife

Epigenetic control of innate and adaptive immune memory

(2018) Colleen M. Lau et al.   NATURE IMMUNOLOGY

Lactobacillus reuteriinduces gut intraepithelial CD4+CD8αα+T cells

(2017) Luisa Cervantes-Barragan et al.   SCIENCE

TCR Signal Quality Modulates Fate Decisions of Single CD4 + T Cells in a Probabilistic Manner

(2017) Yi-Li Cho et al.   Cell Reports

T Cell Fate at the Single-Cell Level

(2016) Veit R. Buchholz et al.   Annual Review of Immunology

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

TGF-β receptor maintains CD4 T helper cell identity during chronic viral infections

(2016) Gavin M. Lewis et al.   JOURNAL OF CLINICAL INVESTIGATION

Most microbe-specific naive CD4+ T cells produce memory cells during infection

(2016) N. J. Tubo et al.   SCIENCE

Transcription Factor T-bet Regulates Intraepithelial Lymphocyte Functional Maturation

(2014) Bernardo S. Reis et al.   IMMUNITY

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

(2014) Alison Crawford et al.   IMMUNITY

Molecular regulation of effector and memory T cell differentiation

(2014) John T Chang et al.   NATURE IMMUNOLOGY

Single Naive CD4+ T Cells from a Diverse Repertoire Produce Different Effector Cell Types during Infection

(2013) Noah J. Tubo et al.   CELL

Distinct Memory CD4+ T Cells with Commitment to T Follicular Helper- and T Helper 1-Cell Lineages Are Generated after Acute Viral Infection

(2013) J. Scott Hale et al.   IMMUNITY

Transcriptional reprogramming of mature CD4+ helper T cells generates distinct MHC class II–restricted cytotoxic T lymphocytes

(2013) Daniel Mucida et al.   NATURE IMMUNOLOGY

Disparate Individual Fates Compose Robust CD8+ T Cell Immunity

(2013) V. R. Buchholz et al.   SCIENCE

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

(2012) Travis A. Doering et al.   IMMUNITY

Follicular Helper CD4 T Cells (TFH)

(2011) Shane Crotty   Annual Review of Immunology

Opposing Signals from the Bcl6 Transcription Factor and the Interleukin-2 Receptor Generate T Helper 1 Central and Effector Memory Cells

(2011) Marion Pepper et al.   IMMUNITY

Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4+ Cell Properties during Viral Infection

(2011) Heather D. Marshall et al.   IMMUNITY

Viral persistence redirects CD4 T cell differentiation toward T follicular helper cells

(2011) Laura M. Fahey et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Origins of CD4+ effector and central memory T cells

(2011) Marion Pepper et al.   NATURE IMMUNOLOGY

Differentiation of Effector CD4 T Cell Populations

(2010) Jinfang Zhu et al.   Annual Review of 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

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology