Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

Regulatory T Cells and Human Disease

(2020) Shimon Sakaguchi et al.   Annual Review of Immunology

Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF

(2020) Michael Delacher et al.   IMMUNITY

Distinct microbial and immune niches of the human colon

(2020) Kylie R. James et al.   NATURE IMMUNOLOGY

IRF4 instructs effector Treg differentiation and immune suppression in human cancer

(2020) Giorgia Alvisi et al.   JOURNAL OF CLINICAL INVESTIGATION

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

(2019) Johan Henriksson et al.   CELL

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation

(2019) Ricardo J. Miragaia et al.   IMMUNITY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Connecting blood and intratumoral Treg cell activity in predicting future relapse in breast cancer

(2019) Lei Wang et al.   NATURE IMMUNOLOGY

Rbpj expression in regulatory T cells is critical for restraining TH2 responses

(2019) Michael Delacher et al.   Nature Communications

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

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Reepithelialization in focus: Non-invasive monitoring of epidermal wound healing in vitro

(2019) Lisa Kiesewetter et al.   BIOSENSORS & BIOELECTRONICS

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

(2019) Andrea Cossarizza et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

(2019) Peter A. Szabo et al.   Nature Communications

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

TCR Transgenic Mice Reveal Stepwise, Multi-site Acquisition of the Distinctive Fat-Treg Phenotype

(2018) Chaoran Li et al.   CELL

Cancer: the dark side of wound healing

(2018) Gopinath M. Sundaram et al.   FEBS Journal

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

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

Insights Into the Molecular Mechanisms of T Follicular Helper-Mediated Immunity and Pathology

(2018) Lei Qin et al.   Frontiers in Immunology

Characterization of regulatory T cells in obese omental adipose tissue in humans

(2018) Dan Wu et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Brain regulatory T cells suppress astrogliosis and potentiate neurological recovery

(2018) Minako Ito et al.   NATURE

Human retinoic acid–regulated CD161+ regulatory T cells support wound repair in intestinal mucosa

(2018) Giovanni A. M. Povoleri et al.   NATURE IMMUNOLOGY

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

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Regulatory T cells promote myelin regeneration in the central nervous system

(2017) Yvonne Dombrowski et al.   NATURE NEUROSCIENCE

JunB is essential for IL-23-dependent pathogenicity of Th17 cells

(2017) Zafrul Hasan et al.   Nature Communications

Regulatory T cells in cancer immunotherapy

(2016) Atsushi Tanaka et al.   CELL RESEARCH

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells

(2016) Marco De Simone et al.   IMMUNITY

Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer

(2016) George Plitas et al.   IMMUNITY

Early dissemination seeds metastasis in breast cancer

(2016) Hedayatollah Hosseini et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Catch-up validation study of an in vitro skin irritation test method based on an open source reconstructed epidermis (phase II)

(2016) F. Groeber et al.   TOXICOLOGY IN VITRO

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

A Distinct Function of Regulatory T Cells in Tissue Protection

(2015) Nicholas Arpaia et al.   CELL

The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells

(2015) Ajithkumar Vasanthakumar et al.   NATURE IMMUNOLOGY

Individual intestinal symbionts induce a distinct population of ROR + regulatory T cells

(2015) E. Sefik et al.   SCIENCE

Tumors: Wounds That Do Not Heal--Redux

(2015) H. F. Dvorak   Cancer Immunology Research

An Emerging Approach for Parallel Quantification of Intracellular Protozoan Parasites and Host Cell Characterization Using TissueFAXS Cytometry

(2015) Maximilian Schmid et al.   PLoS One

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

The alarmin IL-33 promotes regulatory T-cell function in the intestine

(2014) Chris Schiering et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Impedance Spectroscopy for the Non-Destructive Evaluation of In Vitro Epidermal Models

(2014) F. Groeber et al.   PHARMACEUTICAL RESEARCH

A Special Population of Regulatory T Cells Potentiates Muscle Repair

(2013) Dalia Burzyn et al.   CELL

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

PPAR-γ is a major driver of the accumulation and phenotype of adipose tissue Treg cells

(2012) Daniela Cipolletta et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells

(2011) Wataru Ise et al.   NATURE IMMUNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Expression of Helios, an Ikaros Transcription Factor Family Member, Differentiates Thymic-Derived from Peripherally Induced Foxp3+ T Regulatory Cells

(2010) A. M. Thornton et al.   JOURNAL OF IMMUNOLOGY

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

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Functional Delineation and Differentiation Dynamics of Human CD4+ T Cells Expressing the FoxP3 Transcription Factor

(2009) Makoto Miyara et al.   IMMUNITY

Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters

(2009) Markus Feuerer et al.   NATURE MEDICINE

Regulatory T cells are key cerebroprotective immunomodulators in acute experimental stroke

(2009) Arthur Liesz et al.   NATURE MEDICINE

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Heterogeneity of natural Foxp3+T cells: A committed regulatory T-cell lineage and an uncommitted minor population retaining plasticity

(2009) Noriko Komatsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA