{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T04:54:14Z","timestamp":1775624054592,"version":"3.50.1"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"DOI":"10.1038\/s41467-025-56124-1","type":"journal-article","created":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T11:31:25Z","timestamp":1737027085000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":65,"title":["The Human Microglia Atlas (HuMicA) unravels changes in disease-associated microglia subsets across neurodegenerative conditions"],"prefix":"10.1038","volume":"16","author":[{"given":"Ricardo","family":"Martins-Ferreira","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0173-8221","authenticated-orcid":false,"given":"Josep","family":"Calafell-Segura","sequence":"additional","affiliation":[]},{"given":"B\u00e1rbara","family":"Leal","sequence":"additional","affiliation":[]},{"given":"Javier","family":"Rodr\u00edguez-Ubreva","sequence":"additional","affiliation":[]},{"given":"Elena","family":"Mart\u00ednez-Saez","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6101-8472","authenticated-orcid":false,"given":"Elisabetta","family":"Mereu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6125-7000","authenticated-orcid":false,"given":"Paulo","family":"Pinho E Costa","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9732-6677","authenticated-orcid":false,"given":"Ariadna","family":"Laguna","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1400-2440","authenticated-orcid":false,"given":"Esteban","family":"Ballestar","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,1,16]]},"reference":[{"key":"56124_CR1","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1126\/science.1194637","volume":"330","author":"F Ginhoux","year":"2010","unstructured":"Ginhoux, F. et al. Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 330, 841\u2013845 (2010).","journal-title":"Science"},{"key":"56124_CR2","doi-asserted-by":"publisher","first-page":"45","DOI":"10.3389\/fncel.2013.00045","volume":"7","author":"F Ginhoux","year":"2013","unstructured":"Ginhoux, F., Lim, S., Hoeffel, G., Low, D. & Huber, T. Origin and differentiation of microglia. Front Cell Neurosci. 7, 45 (2013).","journal-title":"Front Cell Neurosci."},{"key":"56124_CR3","doi-asserted-by":"publisher","unstructured":"Martins-Ferreira, R., Leal, B., Costa, P. P. E. & Ballestar, E. Microglial Innate Memory and Epigenetic Reprogramming in Neurological Disorders. Prog. Neurobiol. 101971. https:\/\/doi.org\/10.1016\/j.pneurobio.2020.101971 (2020).","DOI":"10.1016\/j.pneurobio.2020.101971"},{"key":"56124_CR4","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/nri.2017.125","volume":"18","author":"Q Li","year":"2018","unstructured":"Li, Q. & Barres, B. A. Microglia and macrophages in brain homeostasis and disease. Nat. Rev. Immunol. 18, 225\u2013242 (2018).","journal-title":"Nat. Rev. Immunol."},{"key":"56124_CR5","doi-asserted-by":"publisher","DOI":"10.1186\/s12974-021-02309-6","volume":"18","author":"SC Woodburn","year":"2021","unstructured":"Woodburn, S. C., Bollinger, J. L. & Wohleb, E. S. The semantics of microglia activation: neuroinflammation, homeostasis, and stress. J. Neuroinflammation 18, 258 (2021).","journal-title":"J. Neuroinflammation"},{"key":"56124_CR6","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.semcdb.2019.05.004","volume":"94","author":"CS Subhramanyam","year":"2019","unstructured":"Subhramanyam, C. S., Wang, C., Hu, Q. & Dheen, S. T. Microglia-mediated neuroinflammation in neurodegenerative diseases. Semin Cell Dev. Biol. 94, 112\u2013120 (2019).","journal-title":"Semin Cell Dev. Biol."},{"key":"56124_CR7","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.celrep.2013.06.018","volume":"4","author":"IM Chiu","year":"2013","unstructured":"Chiu, I. M. et al. A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep. 4, 385\u2013401 (2013).","journal-title":"Cell Rep."},{"key":"56124_CR8","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1016\/j.cell.2017.05.018","volume":"169","author":"H Keren-Shaul","year":"2017","unstructured":"Keren-Shaul, H. et al. A Unique Microglia Type Associated with Restricting Development of Alzheimer\u2019s Disease. Cell 169, 1276\u20131290.e17 (2017).","journal-title":"Cell"},{"key":"56124_CR9","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1038\/nmeth.4407","volume":"14","author":"N Habib","year":"2017","unstructured":"Habib, N. et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods 14, 955\u2013958 (2017).","journal-title":"Nat. Methods"},{"key":"56124_CR10","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/s41586-019-1195-2","volume":"570","author":"H Mathys","year":"2019","unstructured":"Mathys, H. et al. Single-cell transcriptomic analysis of Alzheimer\u2019s disease. Nature 570, 332\u2013337 (2019).","journal-title":"Nature"},{"key":"56124_CR11","doi-asserted-by":"publisher","first-page":"2087","DOI":"10.1038\/s41593-019-0539-4","volume":"22","author":"A Grubman","year":"2019","unstructured":"Grubman, A. et al. A single-cell atlas of entorhinal cortex from individuals with Alzheimer\u2019s disease reveals cell-type-specific gene expression regulation. Nat. Neurosci. 22, 2087\u20132097 (2019).","journal-title":"Nat. Neurosci."},{"key":"56124_CR12","doi-asserted-by":"publisher","first-page":"25800","DOI":"10.1073\/pnas.2008762117","volume":"117","author":"S-F Lau","year":"2020","unstructured":"Lau, S.-F., Cao, H., Fu, A. K. Y. & Ip, N. Y. Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer\u2019s disease. Proc. Natl Acad. Sci. USA 117, 25800\u201325809 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"56124_CR13","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41593-020-00764-7","volume":"24","author":"K Leng","year":"2021","unstructured":"Leng, K. et al. Molecular characterization of selectively vulnerable neurons in Alzheimer\u2019s disease. Nat. Neurosci. 24, 276\u2013287 (2021).","journal-title":"Nat. Neurosci."},{"key":"56124_CR14","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1038\/s41588-021-00894-z","volume":"53","author":"S Morabito","year":"2021","unstructured":"Morabito, S. et al. Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer\u2019s disease. Nat. Genet 53, 1143\u20131155 (2021).","journal-title":"Nat. Genet"},{"key":"56124_CR15","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1038\/s41591-019-0695-9","volume":"26","author":"Y Zhou","year":"2020","unstructured":"Zhou, Y. et al. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer\u2019s disease. Nat. Med 26, 131\u2013142 (2020).","journal-title":"Nat. Med"},{"key":"56124_CR16","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/s41586-019-0903-2","volume":"566","author":"S J\u00e4kel","year":"2019","unstructured":"J\u00e4kel, S. et al. Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature 566, 543\u2013547 (2019).","journal-title":"Nature"},{"key":"56124_CR17","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/s41586-019-1404-z","volume":"573","author":"L Schirmer","year":"2019","unstructured":"Schirmer, L. et al. Neuronal vulnerability and multilineage diversity in multiple sclerosis. Nature 573, 75\u201382 (2019).","journal-title":"Nature"},{"key":"56124_CR18","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1126\/science.aav8130","volume":"364","author":"D Velmeshev","year":"2019","unstructured":"Velmeshev, D. et al. Single-cell genomics identifies cell type-specific molecular changes in autism. Science 364, 685\u2013689 (2019).","journal-title":"Science"},{"key":"56124_CR19","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1007\/s00401-021-02343-x","volume":"142","author":"R Feleke","year":"2021","unstructured":"Feleke, R. et al. Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases. Acta Neuropathol. 142, 449\u2013474 (2021).","journal-title":"Acta Neuropathol."},{"key":"56124_CR20","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1038\/s41586-019-0924-x","volume":"566","author":"T Masuda","year":"2019","unstructured":"Masuda, T. et al. Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution. Nature 566, 388\u2013392 (2019).","journal-title":"Nature"},{"key":"56124_CR21","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1016\/j.molmed.2019.08.013","volume":"25","author":"EC Wright-Jin","year":"2019","unstructured":"Wright-Jin, E. C. & Gutmann, D. H. Microglia as Dynamic Cellular Mediators of Brain Function. Trends Mol. Med 25, 967\u2013979 (2019).","journal-title":"Trends Mol. Med"},{"key":"56124_CR22","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/s41586-021-03710-0","volume":"595","author":"AC Yang","year":"2021","unstructured":"Yang, A. C. et al. Dysregulation of brain and choroid plexus cell types in severe COVID-19. Nature 595, 565\u2013571 (2021).","journal-title":"Nature"},{"key":"56124_CR23","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-021-00933-8","volume":"13","author":"JF Fullard","year":"2021","unstructured":"Fullard, J. F. et al. Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19. Genome Med 13, 118 (2021).","journal-title":"Genome Med"},{"key":"56124_CR24","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-95565-8","volume":"11","author":"S Lopez-Leon","year":"2021","unstructured":"Lopez-Leon, S. et al. More than 50 long-term effects of COVID-19: a systematic review and meta-analysis. Sci. Rep. 11, 16144 (2021).","journal-title":"Sci. Rep."},{"key":"56124_CR25","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1016\/S0140-6736(21)01755-4","volume":"398","author":"L Huang","year":"2021","unstructured":"Huang, L. et al. 1-year outcomes in hospital survivors with COVID-19: a longitudinal cohort study. Lancet 398, 747\u2013758 (2021).","journal-title":"Lancet"},{"key":"56124_CR26","doi-asserted-by":"publisher","unstructured":"Douaud, G. et al. SARS-CoV-2 is associated with changes in brain structure in UK Biobank. Nature. https:\/\/doi.org\/10.1038\/s41586-022-04569-5 (2022).","DOI":"10.1038\/s41586-022-04569-5"},{"key":"56124_CR27","doi-asserted-by":"crossref","unstructured":"Zappia, L. & Oshlack, A. Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience 7, 1\u20139 (2018).","DOI":"10.1093\/gigascience\/giy083"},{"key":"56124_CR28","doi-asserted-by":"publisher","first-page":"3088","DOI":"10.1016\/j.neuron.2021.09.001","volume":"109","author":"MN Tran","year":"2021","unstructured":"Tran, M. N. et al. Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain. Neuron 109, 3088\u20133103.e5 (2021).","journal-title":"Neuron"},{"key":"56124_CR29","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1016\/j.immuni.2018.01.011","volume":"48","author":"D Mrdjen","year":"2018","unstructured":"Mrdjen, D. et al. High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease. Immunity 48, 380\u2013395.e6 (2018).","journal-title":"Immunity"},{"key":"56124_CR30","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1006\/exnr.2000.7618","volume":"168","author":"I Bechmann","year":"2001","unstructured":"Bechmann, I. et al. Turnover of rat brain perivascular cells. Exp. Neurol. 168, 242\u2013249 (2001).","journal-title":"Exp. Neurol."},{"key":"56124_CR31","doi-asserted-by":"crossref","unstructured":"Gosselin, D. et al. An environment-dependent transcriptional network specifies human microglia identity. Science 356, eaal3222 (2017).","DOI":"10.1126\/science.aal3222"},{"key":"56124_CR32","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1038\/nn.4597","volume":"20","author":"TF Galatro","year":"2017","unstructured":"Galatro, T. F. et al. Transcriptomic analysis of purified human cortical microglia reveals age-associated changes. Nat. Neurosci. 20, 1162\u20131171 (2017).","journal-title":"Nat. Neurosci."},{"key":"56124_CR33","doi-asserted-by":"publisher","first-page":"1448","DOI":"10.1016\/j.immuni.2022.07.004","volume":"55","author":"A Silvin","year":"2022","unstructured":"Silvin, A. et al. Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration. Immunity 55, 1448\u20131465.e6 (2022).","journal-title":"Immunity"},{"key":"56124_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19737-2","volume":"11","author":"M Olah","year":"2020","unstructured":"Olah, M. et al. Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer\u2019s disease. Nat. Commun. 11, 6129 (2020).","journal-title":"Nat. Commun."},{"key":"56124_CR35","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s00401-021-02263-w","volume":"141","author":"E Gerrits","year":"2021","unstructured":"Gerrits, E. et al. Distinct amyloid-\u03b2 and tau-associated microglia profiles in Alzheimer\u2019s disease. Acta Neuropathol. 141, 681\u2013696 (2021).","journal-title":"Acta Neuropathol."},{"key":"56124_CR36","doi-asserted-by":"publisher","first-page":"4386","DOI":"10.1016\/j.cell.2023.08.037","volume":"186","author":"N Sun","year":"2023","unstructured":"Sun, N. et al. Human microglial state dynamics in Alzheimer\u2019s disease progression. Cell 186, 4386\u20134403.e29 (2023).","journal-title":"Cell"},{"key":"56124_CR37","doi-asserted-by":"publisher","first-page":"10934","DOI":"10.1093\/nar\/gkad841","volume":"51","author":"S M\u00fcller-Dott","year":"2023","unstructured":"M\u00fcller-Dott, S. et al. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Res 51, 10934\u201310949 (2023).","journal-title":"Nucleic Acids Res"},{"key":"56124_CR38","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1038\/s41421-022-00377-3","volume":"8","author":"W Tan","year":"2022","unstructured":"Tan, W. et al. Distinct phases of adult microglia proliferation: a Myc-mediated early phase and a Tnfaip3-mediated late phase. Cell Discov. 8, 34 (2022).","journal-title":"Cell Discov."},{"key":"56124_CR39","doi-asserted-by":"publisher","first-page":"3438","DOI":"10.1021\/acschemneuro.2c00440","volume":"13","author":"J Miao","year":"2022","unstructured":"Miao, J., Chen, Z., Wu, Y., Hu, Q. & Ji, T. Sp1 Inhibits PGC-1\u03b1 via HDAC2-Catalyzed Histone Deacetylation in Chronic Constriction Injury-Induced Neuropathic Pain. ACS Chem. Neurosci. 13, 3438\u20133452 (2022).","journal-title":"ACS Chem. Neurosci."},{"key":"56124_CR40","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.abb.2019.05.011","volume":"669","author":"E Butturini","year":"2019","unstructured":"Butturini, E., Boriero, D., Carcereri de Prati, A. & Mariotto, S. STAT1 drives M1 microglia activation and neuroinflammation under hypoxia. Arch. Biochem Biophys. 669, 22\u201330 (2019).","journal-title":"Arch. Biochem Biophys."},{"key":"56124_CR41","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1002\/glia.21178","volume":"59","author":"S Jayadev","year":"2011","unstructured":"Jayadev, S. et al. Transcription factor p53 influences microglial activation phenotype. Glia 59, 1402\u20131413 (2011).","journal-title":"Glia"},{"key":"56124_CR42","doi-asserted-by":"publisher","first-page":"136283","DOI":"10.1016\/j.neulet.2021.136283","volume":"765","author":"M Chen","year":"2021","unstructured":"Chen, M., Chen, X., Hu, X., Dai, J. & Sun, J. Androgen receptor contributes to microglial\/macrophage activation in rats with intracranial hemorrhage by mediating the JMJD3\/Botch\/Notch1 axis. Neurosci. Lett. 765, 136283 (2021).","journal-title":"Neurosci. Lett."},{"key":"56124_CR43","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1002\/eji.201948299","volume":"50","author":"Q Li","year":"2020","unstructured":"Li, Q. et al. Bcl6 modulates innate immunity by controlling macrophage activity and plays critical role in experimental autoimmune encephalomyelitis. Eur. J. Immunol. 50, 525\u2013536 (2020).","journal-title":"Eur. J. Immunol."},{"key":"56124_CR44","doi-asserted-by":"publisher","first-page":"108189","DOI":"10.1016\/j.celrep.2020.108189","volume":"32","author":"N Thrupp","year":"2020","unstructured":"Thrupp, N. et al. Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans. Cell Rep. 32, 108189 (2020).","journal-title":"Cell Rep."},{"key":"56124_CR45","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1038\/s41590-023-01558-2","volume":"24","author":"M-J Dolan","year":"2023","unstructured":"Dolan, M.-J. et al. Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat. Immunol. 24, 1382\u20131390 (2023).","journal-title":"Nat. Immunol."},{"key":"56124_CR46","doi-asserted-by":"publisher","first-page":"e2203828120","DOI":"10.1073\/pnas.2203828120","volume":"120","author":"S Mangiola","year":"2023","unstructured":"Mangiola, S. et al. sccomp: Robust differential composition and variability analysis for single-cell data. Proc. Natl Acad. Sci. USA 120, e2203828120 (2023).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"56124_CR47","doi-asserted-by":"publisher","first-page":"4365","DOI":"10.1016\/j.cell.2023.08.039","volume":"186","author":"H Mathys","year":"2023","unstructured":"Mathys, H. et al. Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer\u2019s disease pathology. Cell 186, 4365\u20134385.e27 (2023).","journal-title":"Cell"},{"key":"56124_CR48","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.immuni.2018.11.004","volume":"50","author":"TR Hammond","year":"2019","unstructured":"Hammond, T. R. et al. Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes. Immunity 50, 253\u2013271.e6 (2019).","journal-title":"Immunity"},{"key":"56124_CR49","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.neuron.2018.12.006","volume":"101","author":"Q Li","year":"2019","unstructured":"Li, Q. et al. Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing. Neuron 101, 207\u2013223.e10 (2019).","journal-title":"Neuron"},{"key":"56124_CR50","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.1016\/j.freeradbiomed.2008.09.002","volume":"45","author":"S Ramanan","year":"2008","unstructured":"Ramanan, S., Kooshki, M., Zhao, W., Hsu, F.-C. & Robbins, M. E. PPARalpha ligands inhibit radiation-induced microglial inflammatory responses by negatively regulating NF-kappaB and AP-1 pathways. Free Radic. Biol. Med 45, 1695\u20131704 (2008).","journal-title":"Free Radic. Biol. Med"},{"key":"56124_CR51","doi-asserted-by":"crossref","unstructured":"Yuan, T. et al. The Protective Role of Microglial PPAR\u03b1 in Diabetic Retinal Neurodegeneration and Neurovascular Dysfunction. Cells 11, 3869 (2022).","DOI":"10.3390\/cells11233869"},{"key":"56124_CR52","doi-asserted-by":"crossref","unstructured":"Pappalardo, J. L. et al. Transcriptomic and clonal characterization of T cells in the human central nervous system. Sci. Immunol. 5, eabb8786 (2020).","DOI":"10.1126\/sciimmunol.abb8786"},{"key":"56124_CR53","doi-asserted-by":"publisher","first-page":"2111","DOI":"10.1038\/s41593-019-0525-x","volume":"22","author":"R Mancuso","year":"2019","unstructured":"Mancuso, R. et al. Stem-cell-derived human microglia transplanted in mouse brain to study human disease. Nat. Neurosci. 22, 2111\u20132116 (2019).","journal-title":"Nat. Neurosci."},{"key":"56124_CR54","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1093\/brain\/awab446","volume":"145","author":"S Smaji\u0107","year":"2022","unstructured":"Smaji\u0107, S. et al. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain 145, 964\u2013978 (2022).","journal-title":"Brain"},{"key":"56124_CR55","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1016\/j.neuron.2021.10.036","volume":"110","author":"D Franjic","year":"2022","unstructured":"Franjic, D. et al. Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells. Neuron 110, 452\u2013469.e14 (2022).","journal-title":"Neuron"},{"key":"56124_CR56","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049","volume":"8","author":"GXY Zheng","year":"2017","unstructured":"Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).","journal-title":"Nat. Commun."},{"key":"56124_CR57","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573\u20133587.e29 (2021).","journal-title":"Cell"},{"key":"56124_CR58","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-05882-0","volume":"7","author":"Y Zhu","year":"2017","unstructured":"Zhu, Y., Wang, L., Yin, Y. & Yang, E. Systematic analysis of gene expression patterns associated with postmortem interval in human tissues. Sci. Rep. 7, 5435 (2017).","journal-title":"Sci. Rep."},{"key":"56124_CR59","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","volume":"8","author":"CS McGinnis","year":"2019","unstructured":"McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors. Cell Syst. 8, 329\u2013337.e4 (2019).","journal-title":"Cell Syst."},{"key":"56124_CR60","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1874-1","volume":"20","author":"C Hafemeister","year":"2019","unstructured":"Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).","journal-title":"Genome Biol."},{"key":"56124_CR61","first-page":"1888","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive Integration of Single-. Cell Data. Cell 177, 1888\u20131902.e21 (2019).","journal-title":"Cell Data. Cell"},{"key":"56124_CR62","doi-asserted-by":"publisher","unstructured":"Hao, Y. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol. https:\/\/doi.org\/10.1038\/s41587-023-01767-y (2023).","DOI":"10.1038\/s41587-023-01767-y"},{"key":"56124_CR63","first-page":"275","volume":"18","author":"M Stephens","year":"2017","unstructured":"Stephens, M. False discovery rates: a new deal. Biostatistics 18, 275\u2013294 (2017).","journal-title":"Biostatistics"},{"key":"56124_CR64","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","volume":"33","author":"DJ McCarthy","year":"2017","unstructured":"McCarthy, D. J., Campbell, K. R., Lun, A. T. L. & Wills, Q. F. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 33, 1179\u20131186 (2017).","journal-title":"Bioinformatics"},{"key":"56124_CR65","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847\u20132849 (2016).","journal-title":"Bioinformatics"},{"key":"56124_CR66","unstructured":"Leek, J. T. et al. sva: Surrogate Variable Analysis. R package version 3.44.0. (2022)."},{"key":"56124_CR67","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"56124_CR68","unstructured":"Shen, L. & ISoMaM, S. GeneOverlap: Test and visualize gene overlaps. R package version 1.34.0 http:\/\/shenlab-sinai.github.io\/shenlab-sinai\/ (2022)."},{"key":"56124_CR69","first-page":"100141","volume":"2","author":"T Wu","year":"2021","unstructured":"Wu, T. et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innov. (Camb. (Mass.)) 2, 100141 (2021).","journal-title":"Innov. (Camb. (Mass.))"},{"key":"56124_CR70","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1038\/ng.3593","volume":"48","author":"MJ Alvarez","year":"2016","unstructured":"Alvarez, M. J. et al. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat. Genet 48, 838\u2013847 (2016).","journal-title":"Nat. Genet"},{"key":"56124_CR71","doi-asserted-by":"publisher","first-page":"vbac016","DOI":"10.1093\/bioadv\/vbac016","volume":"2","author":"P Badia-I-Mompel","year":"2022","unstructured":"Badia-I-Mompel, P. et al. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinforma. Adv. 2, vbac016 (2022).","journal-title":"Bioinforma. Adv."},{"key":"56124_CR72","doi-asserted-by":"publisher","unstructured":"Korotkevich, G. et al. Fast gene set enrichment analysis. bioRxiv 60012. https:\/\/doi.org\/10.1101\/060012 (2021).","DOI":"10.1101\/060012"},{"key":"56124_CR73","doi-asserted-by":"publisher","first-page":"3374","DOI":"10.1093\/bioinformatics\/btab209","volume":"37","author":"JF Ouyang","year":"2021","unstructured":"Ouyang, J. F., Kamaraj, U. S., Cao, E. Y. & Rackham, O. J. L. ShinyCell: simple and sharable visualization of single-cell gene expression data. Bioinformatics 37, 3374\u20133376 (2021).","journal-title":"Bioinformatics"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-56124-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-56124-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-56124-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T12:24:59Z","timestamp":1737030299000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-56124-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,16]]},"references-count":73,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["56124"],"URL":"https:\/\/doi.org\/10.1038\/s41467-025-56124-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-3227213\/v1","asserted-by":"object"},{"id-type":"doi","id":"10.1101\/2023.08.01.550767","asserted-by":"object"}]},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,16]]},"assertion":[{"value":"2 August 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 January 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"739"}}