Multiomic spatial landscape of innate immune cells at human central nervous system borders

Welcome to the tidyverse

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Hierarchical Grouping to Optimize an Objective Function

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Integrated analysis of multimodal single-cell data

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clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

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

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

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SCANPY: large-scale single-cell gene expression data analysis

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A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease

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Cellpose: a generalist algorithm for cellular segmentation

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Microglia Function in the Central Nervous System During Health and Neurodegeneration

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An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

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A Lineage of Myeloid Cells Independent of Myb and Hematopoietic Stem Cells

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

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A molecular atlas of cell types and zonation in the brain vasculature

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Complex heatmap visualization

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A molecular cell atlas of the human lung from single-cell RNA sequencing

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Iron and cancer: more ore to be mined

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Microglia Biology: One Century of Evolving Concepts

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

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Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution

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

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

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Squidpy: a scalable framework for spatial omics analysis

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CEL-seq2: sensitive highly-multiplexed single-cell RNA-Seq

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UCell: robust and scalable single-cell gene signature scoring

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MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

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Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge

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

Mrdjen, D., Pavlovic, A., Hartmann, F. J., Schreiner, B., Utz, S. G., Leung, B. P., Lelios, I., Heppner, F. L., Kipnis, J., Merkler, D., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.01.011 · Cited by 1,010 · see citing works

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

Darmanis, S., Sloan, S. A., Croote, D., Mignardi, M., Chernikova, S. B., Samghababi, P., Zhang, Y., Neff, N. F., Kowarsky, M., Caneda, C., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.10.030 · Cited by 1,004 · see citing works

Single-cell genomics identifies cell type–specific molecular changes in autism

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

Jordão, M. J. C., Sankowski, R., Brendecke, S. M., Sagar, Locatelli, G., Tai, Y.-H., Tay, T. L., Schramm, E., Armbruster, S., Hagemeyer, N., et al. (2019) · Science · doi:10.1126/science.aat7554 · Cited by 843 · see citing works

Microglia: Scapegoat, saboteur, or something else?

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Transcriptomic diversity of cell types across the adult human brain

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A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk

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Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

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A lymphocyte–microglia–astrocyte axis in chronic active multiple sclerosis

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Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

Pombo Antunes, A. R., Scheyltjens, I., Lodi, F., Messiaen, J., Antoranz, A., Duerinck, J., Kancheva, D., Martens, L., De Vlaminck, K., Van Hove, H., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00789-y · Cited by 704 · see citing works

Neuronal vulnerability and multilineage diversity in multiple sclerosis

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Dysregulation of brain and choroid plexus cell types in severe COVID-19

Yang, A. C., Kern, F., Losada, P. M., Agam, M. R., Maat, C. A., Schmartz, G. P., Fehlmann, T., Stein, J. A., Schaum, N., Lee, D. P., et al. (2021) · Nature · doi:10.1038/s41586-021-03710-0 · Cited by 620 · see citing works

A new fate mapping system reveals context-dependent random or clonal expansion of microglia

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De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

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Microglia and Central Nervous System–Associated Macrophages—From Origin to Disease Modulation

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A combination of ontogeny and CNS environment establishes microglial identity

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Mapping microglia states in the human brain through the integration of high-dimensional techniques

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Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry

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STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq dataPreprint

Kaminow, B., Yunusov, D., & Dobin, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.05.442755 · Cited by 426 · see citing works

Macrophages at CNS interfaces: Ontogeny and function in health and disease

Kierdorf, K., Masuda, T., Jordão, M. J. C., & Prinz, M. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-019-0201-x · Cited by 416 · see citing works

Cell segmentation in imaging-based spatial transcriptomics

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Ontogeny and homeostasis of CNS myeloid cells

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FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

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Perivascular macrophages mediate the neurovascular and cognitive dysfunction associated with hypertension

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Meningeal Immunity and Its Function in Maintenance of the Central Nervous System in Health and Disease

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Myeloid Cells in the Central Nervous System

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Parenchymal border macrophages regulate the flow dynamics of the cerebrospinal fluid

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Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis.

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A single-cell atlas of the normal and malformed human brain vasculature

Winkler, E. A., Kim, C. N., Ross, J. M., Garcia, J. H., Gil, E., Oh, I., Chen, L. Q., Wu, D., Catapano, J. S., Raygor, K. P., et al. (2022) · Science · doi:10.1126/science.abi7377 · Cited by 318 · see citing works

Novel Hexb-based tools for studying microglia in the CNS

Masuda, T., Amann, L., Sankowski, R., Staszewski, O., Lenz, M., d´Errico, P., Snaidero, N., Costa Jordão, M. J., Böttcher, C., Kierdorf, K., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0707-4 · Cited by 317 · see citing works

Specification of CNS macrophage subsets occurs postnatally in defined niches

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Zero-preserving imputation of single-cell RNA-seq data

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Comprehensive cell atlas of the first-trimester developing human brain

Braun, E., Danan-Gotthold, M., Borm, L. E., Vinsland, E., Lee, K. W., Lönnerberg, P., Hu, L., Li, X., He, X., Andrusivová, Ž., et al. (2023) · Science · doi:10.1126/science.adf1226 · Cited by 275 · see citing works

Entry and distribution of microglial cells in human embryonic and fetal cerebral cortex

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Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas

Friedrich, M., Sankowski, R., Bunse, L., Kilian, M., Green, E., Guevara, C. R., Pusch, S., Poschet, G., Sanghvi, K., Hahn, M., et al. (2021) · Nature Cancer · doi:10.1038/s43018-021-00201-z · Cited by 232 · see citing works

Probabilistic cell typing enables fine mapping of closely related cell types in situ

Qian, X., Harris, K. D., Hauling, T., Nicoloutsopoulos, D., Muñoz‐Manchado, A. B., Skene, N., Hjerling‐Leffler, J., & Nilsson, M. F. (2019) · Nature Methods · doi:10.1038/s41592-019-0631-4 · Cited by 230 · see citing works

A molecular cell atlas of the human lung from single cell RNA sequencingPreprint

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Human fetal microglia acquire homeostatic immune-sensing properties early in development

Kracht, L., Borggrewe, M., Eskandar, S., Brouwer, N., Lopes, S. M. C. D. S., Laman, J. D., Scherjon, S. A., Prins, J. R., Kooistra, S. M., & Eggen, B. J. L. (2020) · Science · doi:10.1126/science.aba5906 · Cited by 208 · see citing works

Endothelium-Macrophage Crosstalk Mediates Blood-Brain Barrier Dysfunction in Hypertension

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Efficient Strategies for Microglia Replacement in the Central Nervous System

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Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES

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Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response

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Improvement in Middle Cerebral Artery Structure and Endothelial Function in Stroke‐Prone Spontaneously Hypertensive Rats after Macrophage Depletion

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Macrophage compartmentalization in the brain and cerebrospinal fluid system

Munro, D. A. D., Movahedi, K., & Priller, J. (2022) · Science Immunology · doi:10.1126/sciimmunol.abk0391 · Cited by 55 · see citing works

Commensal microbiota divergently affect myeloid subsets in the mammalian central nervous system during homeostasis and disease

Sankowski, R., Ahmari, J., Mezö, C., Hrabě de Angelis, A. L., Fuchs, V., Utermöhlen, O., Buch, T., Blank, T., Gomez de Agüero, M., Macpherson, A. J., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2021108605 · Cited by 32 · see citing works

Evaluating microglial phenotypes using single-cell technologies

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Sex-dependent APOE4 neutrophil–microglia interactions drive cognitive impairment in Alzheimer’s disease

Rosenzweig, N., Kleemann, K. L., Rust, T., Carpenter, M., Grucci, M., Aronchik, M., Brouwer, N., Valenbreder, I., Cooper-Hohn, J., Iyer, M., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03122-3 · Cited by 90 · see citing works

The contribution of β-amyloid, Tau and α-synuclein to blood–brain barrier damage in neurodegenerative disorders

Wu, Y., Bogale, T. A., Koıstınaho, J., Pizzi, M., Rõlova, T., & Bellucci, A. (2024) · Acta Neuropathologica · doi:10.1007/s00401-024-02696-z · Cited by 81 · see citing works

Border-associated macrophages as gatekeepers of brain homeostasis and immunity

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The niche matters: Origin, function and fate of CNS-associated macrophages during health and disease

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Cranioencephalic functional lymphoid units in glioblastoma

Dobersalske, C., Rauschenbach, L., Hua, Y., Berliner, C., Steinbach, A., Grüneboom, A., Kokkaliaris, K. D., Heiland, D. H., Berger, P., Langer, S., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03152-x · Cited by 56 · see citing works

Central Nervous System Macrophages in Health and Disease

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Microglia dysfunction, neurovascular inflammation and focal neuropathologies are linked to IL-1- and IL-6-related systemic inflammation in COVID-19

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Injectable Trojan Horse Hydrogel Unleashing Penetrable and Immunostimulatory Nanomicelles for Postoperative Treatment of Glioblastoma

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