Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids.

[1]  Santiago J. Carmona,et al.  UCell: Robust and scalable single-cell gene signature scoring , 2021, bioRxiv.

[2]  Mark Ellisman,et al.  Microglial Gi-dependent dynamics regulate brain network hyperexcitability , 2020, Nature neuroscience.

[3]  Evan Z. Macosko,et al.  Single Cell Sequencing Reveals Glial Specific Responses to Tissue Processing & Enzymatic Dissociation in Mice and Humans , 2020, bioRxiv.

[4]  Ukpong B. Eyo,et al.  Negative feedback control of neuronal activity by microglia , 2020, Nature.

[5]  W. Lee,et al.  Sensory Experience Engages Microglia to Shape Neural Connectivity through a Non-Phagocytic Mechanism , 2020, Neuron.

[6]  S. Lopes,et al.  Human fetal microglia acquire homeostatic immune-sensing properties early in development , 2020, Science.

[7]  D. Bosco,et al.  Microglial depletion aggravates the severity of acute and chronic seizures in mice , 2020, Brain, Behavior, and Immunity.

[8]  B. Stevens,et al.  A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding , 2020, bioRxiv.

[9]  C. Matute,et al.  Functional and Metabolic Characterization of Microglia Culture in a Defined Medium , 2020, Frontiers in Cellular Neuroscience.

[10]  F. Alt,et al.  Increased Neural Progenitor Proliferation in a hiPSC Model of Autism Induces Replication Stress-Associated Genome Instability. , 2020, Cell stem cell.

[11]  F. Tang,et al.  Decoding the development of the human hippocampus , 2020, Nature.

[12]  Maximilian Haeussler,et al.  Cell Stress in Cortical Organoids Impairs Molecular Subtype Specification , 2019, Nature.

[13]  R. Rizzo,et al.  HHV-6A infection induces amyloid-beta expression and activation of microglial cells , 2019, Alzheimer's Research & Therapy.

[14]  I. Amit,et al.  Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program , 2019, Cell.

[15]  R. Jaenisch,et al.  Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain , 2019, Proceedings of the National Academy of Sciences.

[16]  Yunlong Tan,et al.  Microglial regional heterogeneity and its role in the brain , 2019, Molecular Psychiatry.

[17]  David R. Kelley,et al.  Solo: doublet identification via semi-supervised deep learning , 2019, bioRxiv.

[18]  John C. Marioni,et al.  Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender , 2019, bioRxiv.

[19]  Gene W. Yeo,et al.  Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development. , 2019, Cell stem cell.

[20]  Jennifer L Hu,et al.  MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices , 2019, Nature Methods.

[21]  Jeroen A. A. Demmers,et al.  Homozygous Mutations in CSF1R Cause a Pediatric-Onset Leukoencephalopathy and Can Result in Congenital Absence of Microglia. , 2019, American journal of human genetics.

[22]  R. Satija,et al.  Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression , 2019, Genome Biology.

[23]  Ulrich Sure,et al.  Edinburgh Research Explorer Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution , 2022 .

[24]  Evan Z. Macosko,et al.  Single‐Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell‐State Changes , 2019, Immunity.

[25]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[26]  Vincent A. Traag,et al.  From Louvain to Leiden: guaranteeing well-connected communities , 2018, Scientific Reports.

[27]  N. Neff,et al.  Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing , 2018, Neuron.

[28]  Fan Zhang,et al.  Fast, sensitive, and accurate integration of single cell data with Harmony , 2018, bioRxiv.

[29]  R. Kahn,et al.  Microglia innately develop within cerebral organoids , 2018, Nature Communications.

[30]  Emily K. Lehrman,et al.  CD47 Protects Synapses from Excess Microglia-Mediated Pruning during Development , 2018, Neuron.

[31]  Anne E Carpenter,et al.  CellProfiler 3.0: Next-generation image processing for biology , 2018, PLoS biology.

[32]  F. C. Bennett,et al.  A Combination of Ontogeny and CNS Environment Establishes Microglial Identity , 2018, Neuron.

[33]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[34]  S. Pașca,et al.  The rise of three-dimensional human brain cultures , 2018, Nature.

[35]  Alex A. Pollen,et al.  Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex , 2017, Science.

[36]  Markus Glatzel,et al.  The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases. , 2017, Immunity.

[37]  C. Gross,et al.  Microglia remodel synapses by presynaptic trogocytosis and spine head filopodia induction , 2017, Nature Communications.

[38]  Baptiste N. Jaeger,et al.  An environment-dependent transcriptional network specifies human microglia identity , 2017, Science.

[39]  I. Amit,et al.  A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease , 2017, Cell.

[40]  F. C. Bennett,et al.  Diverse Requirements for Microglial Survival, Specification, and Function Revealed by Defined-Medium Cultures , 2017, Neuron.

[41]  Michael D. Cahalan,et al.  iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases , 2017, Neuron.

[42]  Alex A. Pollen,et al.  Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia. , 2017, Cell stem cell.

[43]  Alex A. Pollen,et al.  Zika virus cell tropism in the developing human brain and inhibition by azithromycin , 2016, Proceedings of the National Academy of Sciences.

[44]  F. Alt,et al.  Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells , 2016, Cell.

[45]  Giulio Genovese,et al.  Schizophrenia risk from complex variation of complement component 4 , 2016, Nature.

[46]  A. Planas,et al.  IFN gamma regulates proliferation and neuronal differentiation by STAT1 in adult SVZ niche , 2015, Front. Cell. Neurosci..

[47]  D. Geschwind,et al.  Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture , 2015, Nature Methods.

[48]  P. Linsley,et al.  MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data , 2015, Genome Biology.

[49]  S. Linnarsson,et al.  Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.

[50]  C. Giachino,et al.  Multiple facets of histone variant H2AX: a DNA double-strand-break marker with several biological functions , 2015, Nucleic acids research.

[51]  Yoav Gilad,et al.  A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics , 2014, bioRxiv.

[52]  Francesco Sforazzini,et al.  Deficient neuron-microglia signaling results in impaired functional brain connectivity and social behavior , 2014, Nature Neuroscience.

[53]  J. Yates,et al.  Microglia Promote Learning-Dependent Synapse Formation through Brain-Derived Neurotrophic Factor , 2013, Cell.

[54]  B. Conklin,et al.  Induced pluripotent stem cells from patients with human fibrodysplasia ossificans progressiva show increased mineralization and cartilage formation , 2013, Orphanet Journal of Rare Diseases.

[55]  Jason S. Park,et al.  A robust method to derive functional neural crest cells from human pluripotent stem cells. , 2013, American journal of stem cells.

[56]  Edward Y. Chen,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[57]  V. Martínez‐Cerdeño,et al.  Microglia Regulate the Number of Neural Precursor Cells in the Developing Cerebral Cortex , 2013, The Journal of Neuroscience.

[58]  A. McAllister,et al.  The major histocompatibility complex and autism spectrum disorder , 2012, Developmental neurobiology.

[59]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[60]  Ben A. Barres,et al.  Microglia Sculpt Postnatal Neural Circuits in an Activity and Complement-Dependent Manner , 2012, Neuron.

[61]  R. Petersen,et al.  Mutations in the colony stimulating factor 1 receptor (CSF1R) cause hereditary diffuse leukoencephalopathy with spheroids , 2011, Nature Genetics.

[62]  N. Reich,et al.  The DNA Damage Response Induces IFN , 2011, The Journal of Immunology.

[63]  P. Legendre,et al.  Pattern of invasion of the embryonic mouse spinal cord by microglial cells at the time of the onset of functional neuronal networks , 2011, Glia.

[64]  G. Guillemin,et al.  Metallothionein Treatment Attenuates Microglial Activation and Expression of Neurotoxic Quinolinic Acid Following Traumatic Brain Injury , 2009, Neurotoxicity Research.

[65]  Polina Golland,et al.  CellProfiler Analyst: data exploration and analysis software for complex image-based screens , 2008, BMC Bioinformatics.

[66]  F. Helmchen,et al.  Resting Microglial Cells Are Highly Dynamic Surveillants of Brain Parenchyma in Vivo , 2005, Science.

[67]  G. Garden Microglia in human immunodeficiency virus‐associated neurodegeneration , 2002, Glia.

[68]  J. Hidalgo,et al.  CNS Wound Healing Is Severely Depressed in Metallothionein I- and II-Deficient Mice , 1999, The Journal of Neuroscience.

[69]  V. Perry,et al.  Heterogeneity in the distribution and morphology of microglia in the normal adult mouse brain , 1990, Neuroscience.