Redefining Microglial Identity in Health and Disease at Single-Cell Resolution

Neurotoxic reactive astrocytes are induced by activated microglia

Liddelow, S. A., Guttenplan, K. A., Clarke, L. E., Bennett, F. C., Bohlen, C. J., Schirmer, L., Bennett, M. L., Münch, A. E., Chung, W.-S., Peterson, T. C., et al. (2017) · Nature · doi:10.1038/nature21029 · Cited by 7,971 · see citing works

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

Keren-Shaul, H., Spinrad, A., Weiner, A., Matcovitch-Natan, O., Dvir-Szternfeld, R., Ulland, T. K., David, E., Baruch, K., Lara-Astaiso, D., Toth, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.018 · Cited by 5,493 · see citing works

Synaptic Pruning by Microglia Is Necessary for Normal Brain Development

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Microglia Sculpt Postnatal Neural Circuits in an Activity and Complement-Dependent Manner

Schafer, D. P., Lehrman, E. K., Kautzman, A. G., Koyama, R., Mardinly, A. R., Yamasaki, R., Ransohoff, R. M., Greenberg, M. E., Barres, B. A., & Stevens, B. (2012) · Neuron · doi:10.1016/j.neuron.2012.03.026 · Cited by 4,089 · see citing works

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Ståhl, P. L., Salmén, F., Vickovic, S., Lundmark, A., Navarro, J. F., Magnusson, J., Giacomello, S., Asp, M., Westholm, J. O., Huss, M., et al. (2016) · Science · doi:10.1126/science.aaf2403 · Cited by 3,834 · see citing works

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

Efremova, M., Vento-Tormo, M., Teichmann, S. A., & Vento-Tormo, R. (2020) · Nature Protocols · doi:10.1038/s41596-020-0292-x · Cited by 3,449 · see citing works

Molecular Architecture of the Mouse Nervous System

Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.021 · Cited by 2,995 · see citing works

Microglia promote learning-dependent synapse formation through brain-derived neurotrophic factor

Parkhurst, C. N., Yang, G., Ninan, I., Savas, J. N., Yates, J. R., Lafaille, J. J., Hempstead, B. L., Littman, D. R., & Gan, W.-B. (2013) · Cell · doi:10.1016/j.cell.2013.11.030 · Cited by 2,599 · see citing works

Single-cell transcriptomic analysis of Alzheimer’s disease

Mathys, H., Davila-Velderrain, J., Peng, Z., Gao, F., Mohammadi, S., Young, J. Z., Menon, M., He, L., Abdurrob, F., Jiang, X., et al. (2019) · Nature · doi:10.1038/s41586-019-1195-2 · Cited by 2,568 · see citing works

The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232 · see citing works

Current best practices in single-cell RNA-seq analysis: a tutorial

Luecken, M. D., & Theis, F. J. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188746 · Cited by 2,231 · see citing works

Complex cell-state changes revealed by single cell RNA sequencing of 76,149 microglia throughout the mouse lifespan and in the injured brain

Hammond, T. R., Dufort, C., Dissing-Olesen, L., Giera, S., Young, A., Wysoker, A., Walker, A. J., Segel, M., Nemesh, J., Saunders, A., et al. (2018) · doi:10.1101/406140 · Cited by 2,225 · see citing works

Differential Roles of M1 and M2 Microglia in Neurodegenerative Diseases

Tang, Y., & Le, W. (2016) · Molecular Neurobiology · doi:10.1007/s12035-014-9070-5 · Cited by 2,190 · see citing works

Heterogeneity in the distribution and morphology of microglia in the normal adult mouse brain

Lawson, L. J., Perry, V. H., Dri, P., & Gordon, S. (1990) · Neuroscience · doi:10.1016/0306-4522(90)90229-w · Cited by 2,045 · see citing works

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

Initiative, T. A. D. N., Hollingworth, P., CHARGE consortium, EADI1 consortium, Harold, D., Sims, R., Gerrish, A., Lambert, J.-C., Carrasquillo, M. M., Abraham, R., et al. (2011) · Nature Genetics · doi:10.1038/ng.803 · Cited by 1,997 · see citing works

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease

Naj, A. C., Jun, G., Beecham, G. W., Wang, L.-S., Vardarajan, B. N., Buros, J., Gallins, P. J., Buxbaum, J. D., Jarvik, G. P., Crane, P. K., et al. (2011) · Nature Genetics · doi:10.1038/ng.801 · Cited by 1,901 · see citing works

Single-cell RNA sequencing technologies and bioinformatics pipelines

Hwang, B., Lee, J. H., & Bang, D. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0071-8 · Cited by 1,793 · see citing works

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH

Eng, C.-H. L., Lawson, M., Zhu, Q., Dries, R., Koulena, N., Takei, Y., Yun, J., Cronin, C., Karp, C., Yuan, G.-C., et al. (2019) · Nature · doi:10.1038/s41586-019-1049-y · Cited by 1,754 · see citing works

A comparison of single-cell trajectory inference methods

Saelens, W., Cannoodt, R., Todorov, H., & Saeys, Y. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0071-9 · Cited by 1,670 · see citing works

A polarizing question: do M1 and M2 microglia exist?

Ransohoff, R. M. (2016) · Nature Neuroscience · doi:10.1038/nn.4338 · Cited by 1,573 · see citing works

The Human Cell Atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457 · see citing works

Using Raman spectroscopy to characterize biological materials

Butler, H. J., Ashton, L., Bird, B., Cinque, G., Curtis, K., Dorney, J., Esmonde-White, K., Fullwood, N. J., Gardner, B., Martin-Hirsch, P. L., et al. (2016) · Nature Protocols · doi:10.1038/nprot.2016.036 · Cited by 1,309 · see citing works

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

Marques, S., Zeisel, A., Codeluppi, S., van Bruggen, D., Mendanha Falcão, A., Xiao, L., Li, H., Häring, M., Hochgerner, H., Romanov, R. A., et al. (2016) · Science · doi:10.1126/science.aaf6463 · Cited by 1,246 · see citing works

Deficient neuron-microglia signaling results in impaired functional brain connectivity and social behavior

Zhan, Y., Paolicelli, R. C., Sforazzini, F., Weinhard, L., Bolasco, G., Pagani, F., Vyssotski, A. L., Bifone, A., Gozzi, A., Ragozzino, D., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3641 · Cited by 1,236 · see citing works

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

Goldmann, T., Wieghofer, P., Jordão, M. J. C., Prutek, F., Hagemeyer, N., Frenzel, K., Amann, L., Staszewski, O., Kierdorf, K., Krueger, M., et al. (2016) · Nature Immunology · doi:10.1038/ni.3423 · Cited by 1,209 · see citing works

Microglia development follows a stepwise program to regulate brain homeostasis

Matcovitch-Natan, O., Winter, D. R., Giladi, A., Vargas Aguilar, S., Spinrad, A., Sarrazin, S., Ben-Yehuda, H., David, E., Zelada González, F., Perrin, P., et al. (2016) · Science · doi:10.1126/science.aad8670 · Cited by 1,180 · see citing works

iPSC-derived human microglia-like cells to study neurological diseases

Abud, E. M., Ramirez, R. N., Martinez, E. S., Healy, L. M., Nguyen, C. H. H., Newman, S. A., Yeromin, A. V., Scarfone, V. M., Marsh, S. E., Fimbres, C., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.03.042 · Cited by 1,154 · see citing works

Microglial brain region-dependent diversity and selective regional sensitivities to aging

Grabert, K., Michoel, T., Karavolos, M. H., Clohisey, S., Baillie, J. K., Stevens, M. P., Freeman, T. C., Summers, K. M., & McColl, B. W. (2016) · Nature Neuroscience · doi:10.1038/nn.4222 · Cited by 1,151 · see citing works

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

Zhou, Y., Song, W. M., Andhey, P. S., Swain, A., Levy, T., Miller, K. R., Poliani, P. L., Cominelli, M., Grover, S., Gilfillan, S., et al. (2020) · Nature Medicine · doi:10.1038/s41591-019-0695-9 · Cited by 1,150 · see citing works

Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing

Li, Q., Cheng, Z., Zhou, L., Darmanis, S., Neff, N. F., Okamoto, J., Gulati, G., Bennett, M. L., Sun, L. O., Clarke, L. E., et al. (2019) · Neuron · doi:10.1016/j.neuron.2018.12.006 · Cited by 1,129 · see citing works

Clearance of apoptotic neurons without inflammation by microglial triggering receptor expressed on myeloid cells-2

Takahashi, K., Rochford, C. D. P., & Neumann, H. (2005) · The Journal of Experimental Medicine · doi:10.1084/jem.20041611 · Cited by 1,124 · see citing works

Microglial control of astrocytes in response to microbial metabolites

Rothhammer, V., Borucki, D. M., Tjon, E. C., Takenaka, M. C., Chao, C.-C., Ardura-Fabregat, A., de Lima, K. A., Gutiérrez-Vázquez, C., Hewson, P., Staszewski, O., et al. (2018) · Nature · doi:10.1038/s41586-018-0119-x · Cited by 1,051 · see citing works

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

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

Venteicher, A. S., Tirosh, I., Hebert, C. M., Yizhak, K., Neftel, C., Filbin, M. G., Hovestadt, V., Escalante, L. E., Shaw, M. L., Rodman, C., et al. (2017) · Science · doi:10.1126/science.aai8478 · Cited by 975 · see citing works

Highly Multiplexed Subcellular RNA Sequencing in Situ

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S. F., Li, C., Amamoto, R., et al. (2014) · Science · doi:10.1126/science.1250212 · Cited by 973 · see citing works

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

Grubman, A., Chew, G., Ouyang, J. F., Sun, G., Choo, X. Y., McLean, C., Simmons, R. K., Buckberry, S., Vargas-Landin, D. B., Poppe, D., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0539-4 · Cited by 956 · see citing works

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

Chen, W.-T., Lu, A., Craessaerts, K., Pavie, B., Sala Frigerio, C., Corthout, N., Qian, X., Laláková, J., Kühnemund, M., Voytyuk, I., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.038 · Cited by 949 · see citing works

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

Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., Bhaduri, A., Goyal, N., Rowitch, D. H., & Kriegstein, A. R. (2019) · Science · doi:10.1126/science.aav8130 · Cited by 927 · see citing works

Cell type- and brain region-resolved mouse brain proteome

Sharma, K., Schmitt, S., Bergner, C. G., Tyanova, S., Kannaiyan, N., Manrique-Hoyos, N., Kongi, K., Cantuti, L., Hanisch, U.-K., Philips, M.-A., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4160 · Cited by 871 · see citing works

Altered human oligodendrocyte heterogeneity in multiple sclerosis

Jäkel, S., Agirre, E., Mendanha Falcão, A., van Bruggen, D., Lee, K. W., Knuesel, I., Malhotra, D., ffrench-Constant, C., Williams, A., & Castelo-Branco, G. (2019) · Nature · doi:10.1038/s41586-019-0903-2 · Cited by 854 · see citing works

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

Identification of region-specific astrocyte subtypes at single cell resolution

Batiuk, M. Y., Martirosyan, A., Wahis, J., de Vin, F., Marneffe, C., Kusserow, C., Koeppen, J., Viana, J. F., Oliveira, J. F., Voet, T., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14198-8 · Cited by 805 · see citing works

Microglia Heterogeneity in the Single-Cell Era

Masuda, T., Sankowski, R., Staszewski, O., & Prinz, M. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.010 · Cited by 784 · see citing works

Transcriptomic analysis of purified human cortical microglia reveals age-associated changes

Galatro, T. F., Holtman, I. R., Lerario, A. M., Vainchtein, I. D., Brouwer, N., Sola, P. R., Veras, M. M., Pereira, T. F., Leite, R. E. P., Möller, T., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4597 · Cited by 741 · see citing works

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

Mathys, H., Adaikkan, C., Gao, F., Young, J. Z., Manet, E., Hemberg, M., De Jager, P. L., Ransohoff, R. M., Regev, A., & Tsai, L.-H. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.09.039 · Cited by 740 · see citing works

Single-cell transcriptomic profiling of the aging mouse brain

Ximerakis, M., Lipnick, S. L., Innes, B. T., Simmons, S. K., Adiconis, X., Dionne, D., Mayweather, B. A., Nguyen, L., Niziolek, Z., Ozek, C., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0491-3 · Cited by 736 · see citing works

Classification of low quality cells from single-cell RNA-seq data

Ilicic, T., Kim, J. K., Kolodziejczyk, A. A., Bagger, F. O., McCarthy, D. J., Marioni, J. C., & Teichmann, S. A. (2016) · Genome Biology · doi:10.1186/s13059-016-0888-1 · Cited by 693 · see citing works

Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer’s Disease Not Evident in Mouse Models

Friedman, B. A., Srinivasan, K., Ayalon, G., Meilandt, W. J., Lin, H., Huntley, M. A., Cao, Y., Lee, S.-H., Haddick, P. C. G., Ngu, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2017.12.066 · Cited by 662 · see citing works

Astrocyte-derived interleukin-33 promotes microglial synapse engulfment and neural circuit development

Vainchtein, I. D., Chin, G., Cho, F. S., Kelley, K. W., Miller, J. G., Chien, E. C., Liddelow, S. A., Nguyen, P. T., Nakao-Inoue, H., Dorman, L. C., et al. (2018) · Science · doi:10.1126/science.aal3589 · Cited by 657 · see citing works

Efficient derivation of microglia-like cells from human pluripotent stem cells

Muffat, J., Li, Y., Yuan, B., Mitalipova, M., Omer, A., Corcoran, S., Bakiasi, G., Tsai, L.-H., Aubourg, P., Ransohoff, R. M., et al. (2016) · Nature Medicine · doi:10.1038/nm.4189 · Cited by 651 · see citing works

A 3D human triculture system modeling neurodegeneration and neuroinflammation in Alzheimer’s disease

Park, J., Wetzel, I., Marriott, I., Dréau, D., D’Avanzo, C., Kim, D. Y., Tanzi, R. E., & Cho, H. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0175-4 · Cited by 644 · see citing works

Neuronal vulnerability and multilineage diversity in multiple sclerosis

Schirmer, L., Velmeshev, D., Holmqvist, S., Kaufmann, M., Werneburg, S., Jung, D., Vistnes, S., Stockley, J. H., Young, A., Steindel, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1404-z · Cited by 638 · see citing works

A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Yang, L., Han, Y., Nilsson-Payant, B. E., Gupta, V., Wang, P., Duan, X., Tang, X., Zhu, J., Zhao, Z., Jaffré, F., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.06.015 · Cited by 632 · see citing works

Mitochondrial double-stranded RNA triggers antiviral signalling in humans

Dhir, A., Dhir, S., Borowski, L. S., Jimenez, L., Teitell, M., Rötig, A., Crow, Y. J., Rice, G. I., Duffy, D., Tamby, C., et al. (2018) · Nature · doi:10.1038/s41586-018-0363-0 · Cited by 631 · see citing works

Microglia innately develop within cerebral organoids

Ormel, P. R., de Sá, R. V., van Bodegraven, E. J., Karst, H., Harschnitz, O., Sneeboer, M. A. M., Johansen, L. E., van Dijk, R. E., Scheefhals, N., van Berlekom, A. B., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06684-2 · Cited by 624 · see citing works

A highly efficient human pluripotent stem cell microglia model displays a neuronal-co-culture-specific expression profile and inflammatory response

Haenseler, W., Sansom, S. N., Buchrieser, J., Newey, S. E., Moore, C. S., Nicholls, F. J., Chintawar, S., Schnell, C., Antel, J. P., Allen, N. D., et al. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.05.017 · Cited by 593 · see citing works

Microglia contribute to normal myelinogenesis and to oligodendrocyte progenitor maintenance during adulthood

Hagemeyer, N., Hanft, K.-M., Akriditou, M.-A., Unger, N., Park, E. S., Stanley, E. R., Staszewski, O., Dimou, L., & Prinz, M. (2017) · Acta Neuropathologica · doi:10.1007/s00401-017-1747-1 · Cited by 558 · see citing works

Multiplexed protein maps link subcellular organization to cellular states

Gut, G., Herrmann, M. D., & Pelkmans, L. (2018) · Science · doi:10.1126/science.aar7042 · Cited by 510 · see citing works

A transcriptomic atlas of aged human microglia

Olah, M., Patrick, E., Villani, A.-C., Xu, J., White, C. C., Ryan, K. J., Piehowski, P., Kapasi, A., Nejad, P., Cimpean, M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-02926-5 · Cited by 482 · see citing works

Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program

Geirsdottir, L., David, E., Keren-Shaul, H., Weiner, A., Bohlen, S. C., Neuber, J., Balic, A., Giladi, A., Sheban, F., Dutertre, C.-A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.11.010 · Cited by 461 · see citing works

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

Sankowski, R., Böttcher, C., Masuda, T., Geirsdottir, L., Sagar, Sindram, E., Seredenina, T., Muhs, A., Scheiwe, C., Shah, M. J., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0532-y · Cited by 449 · see citing works

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

NBB-Psy, Böttcher, C., Schlickeiser, S., Sneeboer, M. A. M., Kunkel, D., Knop, A., Paza, E., Fidzinski, P., Kraus, L., Snijders, G. J. L., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0290-2 · Cited by 436 · see citing works

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Maniatis, S., Äijö, T., Vickovic, S., Braine, C., Kang, K., Mollbrink, A., Fagegaltier, D., Andrusivová, Ž., Saarenpää, S., Saiz-Castro, G., et al. (2019) · Science · doi:10.1126/science.aav9776 · Cited by 429 · see citing works

Directed differentiation of human pluripotent stem cells to microglia

Douvaras, P., Sun, B., Wang, M., Kruglikov, I., Lallos, G., Zimmer, M., Terrenoire, C., Zhang, B., Gandy, S., Schadt, E., et al. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.04.023 · Cited by 381 · see citing works

Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo

Hasselmann, J., Coburn, M. A., England, W., Figueroa Velez, D. X., Kiani Shabestari, S., Tu, C. H., McQuade, A., Kolahdouzan, M., Echeverria, K., Claes, C., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.07.002 · Cited by 380 · see citing works

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

Ajami, B., Samusik, N., Wieghofer, P., Ho, P. P., Crotti, A., Bjornson, Z., Prinz, M., Fantl, W. J., Nolan, G. P., & Steinman, L. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0100-x · Cited by 338 · see citing works

Microglia-Mediated Inflammation and Neurodegenerative Disease

Xu, L., Dan, H., & Bai, Y. (2015) · Molecular Neurobiology · doi:10.1007/s12035-015-9593-4 · Cited by 332 · see citing works

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Menon, M., Mohammadi, S., Davila-Velderrain, J., Goods, B. A., Cadwell, T. D., Xing, Y., Stemmer-Rachamimov, A., Shalek, A. K., Love, J. C., Kellis, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12780-8 · Cited by 331 · 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

Transcriptional profiling of human microglia reveals grey–white matter heterogeneity and multiple sclerosis-associated changes

van der Poel, M., Ulas, T., Mizee, M. R., Hsiao, C.-C., Miedema, S. S. M., Adelia, Schuurman, K. G., Helder, B., Tas, S. W., Schultze, J. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08976-7 · Cited by 306 · see citing works

Stem-cell-derived human microglia transplanted in mouse brain to study human disease

Mancuso, R., Van Den Daele, J., Fattorelli, N., Wolfs, L., Balusu, S., Burton, O., Liston, A., Sierksma, A., Fourne, Y., Poovathingal, S., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0525-x · Cited by 295 · see citing works

Novel Alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology

Sierksma, A., Lu, A., Mancuso, R., Fattorelli, N., Thrupp, N., Salta, E., Zoco, J., Blum, D., Buée, L., De Strooper, B., et al. (2020) · EMBO Molecular Medicine · doi:10.15252/emmm.201910606 · Cited by 291 · see citing works

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development

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Single‐cell transcriptomics reveals distinct inflammation‐induced microglia signatures

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Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

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Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis

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Human mitochondrial RNA decay mediated by PNPase–hSuv3 complex takes place in distinct foci

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Microglia response following acute demyelination is heterogeneous and limits infiltrating macrophage dispersion

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

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Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain

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Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain

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Transcriptomic profiling of microglia and astrocytes throughout aging

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Functionalization of Brain Region-specific Spheroids with Isogenic Microglia-like Cells

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A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain

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Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV

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Human glioblastoma‐associated microglia/monocytes express a distinct RNA profile compared to human control and murine samples

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Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina

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Molecular Profiling of Resident and Infiltrating Mononuclear Phagocytes during Rapid Adult Retinal Degeneration Using Single-Cell RNA Sequencing

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Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis

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A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis

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MIC‐MAC: An automated pipeline for high‐throughput characterization and classification of three‐dimensional microglia morphologies in mouse and human postmortem brain samples

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Microglia influence host defense, disease, and repair following murine coronavirus infection of the central nervous system

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Human iPSC-Derived Neurons and Cerebral Organoids Establish Differential Effects of Germline NF1 Gene Mutations

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Developmental trajectory of oligodendrocyte progenitor cells in the human brain revealed by single cell RNA sequencing

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Neuroinflammation and EIF2 Signaling Persist despite Antiretroviral Treatment in an hiPSC Tri-culture Model of HIV Infection

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Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions

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Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo

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Early activation of Egr-1 promotes neuroinflammation and dopaminergic neurodegeneration in an experimental model of Parkinson's disease

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Microglia in Neurodegenerative Disorders

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Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses

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Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial dataPreprint

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Quality assessment of single-cell RNA sequencing data by coverage skewness analysisPreprint

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Topographic organization of connections between the hypothalamus and prefrontal cortex in the rhesus monkey

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Microglia in neurodegenerative diseases: mechanism and potential therapeutic targets

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Cholesterol Metabolism in Aging and Age-Related Disorders

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Microglia in Parkinson’s Disease

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The meninges host a distinct compartment of regulatory T cells that preserves brain homeostasis

Marin-Rodero, M., Cintado, E., Walker, A. J., Jayewickreme, T., Pinho-Ribeiro, F. A., Richardson, Q., Jackson, R. P., Chiu, I. M., Benoist, C. O., Stevens, B., et al. (2025) · Science Immunology · doi:10.1126/sciimmunol.adu2910 · Cited by 70 · see citing works

Microglia Heterogeneity in Alzheimer’s Disease: Insights From Single-Cell Technologies

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Microglia in Health and Disease: The Strength to Be Diverse and Reactive

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Epigenetic Modulation of Microglia Function and Phenotypes in Neurodegenerative Diseases

Wang, L., Yu, C.-C., Liu, X., Deng, X., Tian, Q., & Du, Y. (2021) · Neural Plasticity · doi:10.1155/2021/9912686 · Cited by 37 · see citing works

Microglia-Mediated Phagocytosis in Alzheimer’s Disease: Mechanisms, Heterogeneity, and Therapeutic Insights

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Ensheathing glia promote increased lifespan and healthy brain aging

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Microglia across evolution: from conserved origins to functional divergence

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Single-cell RNA sequencing in dissecting microenvironment of age-related macular degeneration: Challenges and perspectives

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Novel cell-based analysis reveals region-dependent changes in microglial dynamics in grey matter in a cuprizone model of demyelination

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Cell competition for neuron-derived trophic factor controls the turnover and lifespan of microglia

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Type I interferon signalling and interferon‐responsive microglia in health and disease

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Pathogenesis and therapeutic applications of microglia receptors in Alzheimer’s disease

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Microglia signaling in health and disease – Implications in sex-specific brain development and plasticity

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Upregulation of adenosine A2A receptor in astrocytes is sufficient to trigger hippocampal multicellular dysfunctions and memory deficits

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Targeting glial cells: Unveiling the neuroprotective mechanisms of Ginseng in the brain microenvironment

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Excessive Alcohol Use as a Risk Factor for Alzheimer’s Disease: Epidemiological and Preclinical Evidence

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Glial Cells in Spinal Muscular Atrophy: Speculations on Non-Cell-Autonomous Mechanisms and Therapeutic Implications

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Microglial reprogramming by Hv1 antagonism protects neurons from inflammatory and glutamate toxicity

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Hematopoietic stem cell gene therapy to halt neurodegeneration

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The Prospect of Nanoparticle Systems for Modulating Immune Cell Polarization During Central Nervous System Infection

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Beyond Quiescent and Active: Intermediate Microglial Transcriptomic States in a Mouse Model of Down Syndrome

Fernández‐Blanco, Á., Sierra, C., Tejido, C., & Dierssen, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25063289 · Cited by 6 · see citing works

Minimizing the ex vivo confounds of cell-isolation techniques on transcriptomic -profiles of purified microgliaPreprint

Ocañas, S. R., Pham, K. D., Blankenship, H. E., Machalinski, A. H., Chucair‐Elliott, A. J., & Freeman, W. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.15.452509 · Cited by 8 · see citing works

Inflammation associated microglial expansion disrupts hippocampal glial network communication, driving postoperative neurocognitive impairment

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Specificity and efficiency of tamoxifen-mediated Cre induction is equivalent regardless of age

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Autophagy-NLRP3 Inflammasome Crosstalk in Microglia: A Therapeutic Target for Multiple Sclerosis

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Potential key pathophysiological participant and treatment target in autism spectrum disorder: Microglia

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Microglia heterogeneity and therapeutic strategies in Parkinson’s disease

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Applications of single‐cell multi‐omics sequencing in deep understanding of brain diseases

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Neuroimmune interactions in sleep regulation: Epigenetic interfaces between microglia and T cells in brain homeostasis and dysfunction

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Post-traumatic Neuroinflammation: Relevance to Pediatrics

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Targeting Wnt signaling in Alzheimer’s disease: mechanisms and therapeutic opportunities

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Multiscale Approximations to Understand the Complex Role of Microglia in Alzheimer's Disease

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Cholinergic regulation of neuroinflammation: linking microglia, immunometabolism, and neuromodulation

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Acupuncture regulating microglial activation in Alzheimer's disease: Research progress in its neuroinflammation mechanism

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Consistent specificity and efficiency of tamoxifen-mediated cre induction across agesPreprint

Kellogg, C. M., Pham, K. D., Ko, S., Cox, J. E. J., Machalinski, A. H., Stout, M. B., Sharpe, A. L., Beckstead, M. J., Chucair‐Elliott, A. J., Ocañas, S. R., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.19.558482 · Cited by 1 · see citing works

Microglial reprogramming by Hv1 antagonism provides protection from inflammatory neurotoxicityPreprint

Hernández-Espinosa, D. R., Gale, J. R., Scrabis, M. G., & Aizenman, E. (2022) · Research Square · doi:10.21203/rs.3.rs-1527316/v1

Étude du rôle de la microglie dans la propagation de la protéine Tau : mise en place de nouveaux modèles

Duwat, C. (2021) · theses.fr (ABES) · doi:10.70675/b4d3f614ze4bdz4745zb73cz5c7e662402bb

Caractérisation du récepteur Smoothened en tant que régulateur majeur des états fonctionnels des cellules microgliales

Mesaoudi, A. E. (2024) · theses.fr (ABES) · doi:10.70675/f339157ez1688z4acaz87fcz0ecae062a7cc

Targeting microglia: A new strategy for the treatment of Alzheimer's disease

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Microglial advances in psychiatric disorders

de Jesus, J. R., Ribeiro, I. S., Pereira, M. V. S., Aquino, W. C. P., & Alfredo, L. H. M. (2026) · Advances in immunology · doi:10.1016/bs.ai.2026.04.007

CD11c + microglia promote dysfunctional T cell activation in diffuse midline gliomaPreprint

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The role of IRF5 as an immune regulator

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Microglia heterogeneity, modeling and cell-state annotation in development and neurodegeneration

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A single cell-based atlas of human microglial states reveals associations with neurological disorders and histopathological features of the aging brainPreprint

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

Sankowski, R., Böttcher, C., Masuda, T., Geirsdóttir, L., Sagar, S., Sindram, E., Seredenina, T., Muhs, A., Scheiwe, C. F., Shah, M., et al. (2019) · MPG.PuRe (Max Planck Society)

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Wang, H. (2021) · Frontiers in Synaptic Neuroscience · doi:10.3389/fnsyn.2021.773590 · Cited by 61 · see citing works

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

Sankowski, R., Böttcher, C., Masuda, T., Geirsdottir, L., Sagar, Sindram, E., Seredenina, T., Muhs, A., Scheiwe, C., Shah, M. J., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0532-y · Cited by 449 · see citing works