Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota

Mapping the developing human immune system across organs

(2022) Chenqu Suo et al.   SCIENCE

Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells

(2022) Daniel A. Michelson et al.   CELL

ZBTB46 defines and regulates ILC3s that protect the intestine

(2022) Wenqing Zhou et al.   NATURE

Extrathymic expression of Aire controls the induction of effective TH17 cell-mediated immune response to Candida albicans

(2022) Jan Dobeš et al.   NATURE IMMUNOLOGY

A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation

(2022) Ranit Kedmi et al.   NATURE

ILC3s select microbiota-specific regulatory T cells to establish tolerance in the gut

(2022) Mengze Lyu et al.   NATURE

Environmental signals rather than layered ontogeny imprint the function of type 2 conventional dendritic cells in young and adult mice

(2021) Nikos E. Papaioannou et al.   Nature Communications

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Cells of the human intestinal tract mapped across space and time

(2021) Rasa Elmentaite et al.   NATURE

Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity

(2021) Rémi Fiancette et al.   NATURE IMMUNOLOGY

T-bet and RORα control lymph node formation by regulating embryonic innate lymphoid cell differentiation

(2021) Christina Stehle et al.   NATURE IMMUNOLOGY

Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium

(2021) Jiaxi Wang et al.   Science Immunology

A cell atlas of human thymic development defines T cell repertoire formation

(2020) Jong-Eun Park et al.   SCIENCE

An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint

(2020) Deepshika Ramanan et al.   CELL

αvβ8 integrin-expression by BATF3-dependent dendritic cells facilitates early IgA responses to Rotavirus

(2020) J. Nakawesi et al.   Mucosal Immunology

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens

(2019) Joannah R. Fergusson et al.   Frontiers in Immunology

Aire-expressing ILC3-like cells in the lymph node display potent APC features

(2019) Tomoyoshi Yamano et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult

(2019) Ziad Al Nabhani et al.   IMMUNITY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage

(2019) Christelle Harly et al.   NATURE IMMUNOLOGY

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity

(2019) Chrysothemis C. Brown et al.   CELL

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Clec9a-Mediated Ablation of Conventional Dendritic Cells Suggests a Lymphoid Path to Generating Dendritic Cells In Vivo

(2018) Johanna Salvermoser et al.   Frontiers in Immunology

Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

(2018) Chamutal Bornstein et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

(2018) Mo Xu et al.   NATURE

Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans

(2018) Jarny Choi et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Alicia N Schep et al.   NATURE METHODS

Visualizing the structure of RNA-seq expression data using grade of membership models

(2017) Kushal K. Dey et al.   PLoS Genetics

Aire Enforces Immune Tolerance by Directing Autoreactive T Cells into the Regulatory T Cell Lineage

(2016) Sven Malchow et al.   IMMUNITY

Absence of MHC class II on cDCs results in microbial-dependent intestinal inflammation

(2016) Jakob Loschko et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcriptional programs that control expression of the autoimmune regulator gene Aire

(2016) Yonatan Herzig et al.   NATURE IMMUNOLOGY

Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine

(2016) K. S. Kim et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance

(2015) S. Yang et al.   SCIENCE

The microbiota regulates type 2 immunity through ROR t+ T cells

(2015) C. Ohnmacht et al.   SCIENCE

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

(2015) E. Sefik et al.   SCIENCE

Tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs

(2015) G. Gasteiger et al.   SCIENCE

Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4+ T cells

(2015) M. R. Hepworth et al.   SCIENCE

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Distinct Contributions of Aire and Antigen-Presenting-Cell Subsets to the Generation of Self-Tolerance in the Thymus

(2014) Justin S.A. Perry et al.   IMMUNITY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Genetic Tracing via DNGR-1 Expression History Defines Dendritic Cells as a Hematopoietic Lineage

(2013) Barbara U. Schraml et al.   CELL

Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria

(2013) Matthew R. Hepworth et al.   NATURE

Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits

(2013) Andreas Zembrzycki et al.   NATURE NEUROSCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

(2012) T. Olszak et al.   SCIENCE

Delayed protection by ESAT-6–specific effector CD4+T cells after airborneM. tuberculosisinfection

(2008) Alena M. Gallegos et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells

(2008) J. M. Gardner et al.   SCIENCE