A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

(2019) Marta Joana Costa Jordão et al.   SCIENCE

Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

(2018) Aleksandra Deczkowska et al.   CELL

High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease

(2018) Dunja Mrdjen et al.   IMMUNITY

Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia

(2018) James C. Cronk et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies

(2018) Zhana Haimon et al.   NATURE IMMUNOLOGY

Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models

(2018) Bahareh Ajami et al.   NATURE NEUROSCIENCE

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

(2018) Charlotte L. Scott et al.   IMMUNITY

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases

(2017) Susanne Krasemann et al.   IMMUNITY

Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C − Cells

(2017) Alexander Mildner et al.   IMMUNITY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

High-dimensional, single-cell characterization of the brain's immune compartment

(2017) Ben Korin et al.   NATURE NEUROSCIENCE

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

(2017) Ye Emily Wu et al.   NEURON

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Transcriptome‐based profiling of yolk sac‐derived macrophages reveals a role for Irf8 in macrophage maturation

(2016) Nora Hagemeyer et al.   EMBO JOURNAL

IRF8 Transcription Factor Controls Survival and Function of Terminally Differentiated Conventional and Plasmacytoid Dendritic Cells, Respectively

(2016) Dorine Sichien et al.   IMMUNITY

Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species

(2016) Martin Guilliams et al.   IMMUNITY

Tissue-Resident Macrophage Ontogeny and Homeostasis

(2016) Florent Ginhoux et al.   IMMUNITY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Sall1 is a transcriptional regulator defining microglia identity and function

(2016) Anne Buttgereit et al.   NATURE IMMUNOLOGY

Tissue biology perspective on macrophages

(2016) Yasutaka Okabe et al.   NATURE IMMUNOLOGY

Origin, fate and dynamics of macrophages at central nervous system interfaces

(2016) Tobias Goldmann et al.   NATURE IMMUNOLOGY

TREM2 Binds to Apolipoproteins, Including APOE and CLU/APOJ, and Thereby Facilitates Uptake of Amyloid-Beta by Microglia

(2016) Felix L. Yeh et al.   NEURON

Microglia development follows a stepwise program to regulate brain homeostasis

(2016) O. Matcovitch-Natan et al.   SCIENCE

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

TREM2 Lipid Sensing Sustains the Microglial Response in an Alzheimer’s Disease Model

(2015) Yaming Wang et al.   CELL

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

(2015) Jacob H. Levine et al.   CELL

Regulation of myelopoiesis by the transcription factor IRF8

(2015) Tomohiko Tamura et al.   INTERNATIONAL JOURNAL OF HEMATOLOGY

A dural lymphatic vascular system that drains brain interstitial fluid and macromolecules

(2015) Aleksanteri Aspelund et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Structural and functional features of central nervous system lymphatic vessels

(2015) Antoine Louveau et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice

(2014) Oleg Butovsky et al.   ANNALS OF NEUROLOGY

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors

(2014) Elisa Gomez Perdiguero et al.   NATURE

Microglia and brain macrophages in the molecular age: from origin to neuropsychiatric disease

(2014) Marco Prinz et al.   NATURE REVIEWS NEUROSCIENCE

Colony-Stimulating Factor 1 Receptor Signaling Is Necessary for Microglia Viability, Unmasking a Microglia Progenitor Cell in the Adult Brain

(2014) Monica R.P. Elmore et al.   NEURON

IRF8 is a transcriptional determinant for microglial motility

(2014) Takahiro Masuda et al.   Purinergic Signalling

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

A new type of microglia gene targeting shows TAK1 to be pivotal in CNS autoimmune inflammation

(2013) Tobias Goldmann et al.   NATURE NEUROSCIENCE

Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways

(2013) Katrin Kierdorf et al.   NATURE NEUROSCIENCE

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

The microglial sensome revealed by direct RNA sequencing

(2013) Suzanne E Hickman et al.   NATURE NEUROSCIENCE

Fate Mapping Reveals Origins and Dynamics of Monocytes and Tissue Macrophages under Homeostasis

(2012) Simon Yona et al.   IMMUNITY

Deciphering the transcriptional network of the dendritic cell lineage

(2012) Jennifer C Miller et al.   NATURE IMMUNOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

IRF8 Is a Critical Transcription Factor for Transforming Microglia into a Reactive Phenotype

(2012) Takahiro Masuda et al.   Cell Reports

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Choroid plexus: biology and pathology

(2009) Hartwig Wolburg et al.   ACTA NEUROPATHOLOGICA

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

(2009) Linda Madisen et al.   NATURE NEUROSCIENCE

The stream of precursors that colonizes the thymus proceeds selectively through the early T lineage precursor stage of T cell development

(2008) Claudia Benz et al.   JOURNAL OF EXPERIMENTAL MEDICINE