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Med. Genet."},{"key":"10.1016\/j.cell.2026.10.027_bib99","doi-asserted-by":"crossref","DOI":"10.3389\/fnhum.2023.1178616","article-title":"Specificity of striatal dopamine D1 system in humans: implications for clinical use of D1 receptor-agonists in Parkinson\u2019s disease","volume":"17","author":"Goto","year":"2023","journal-title":"Front. Hum. Neurosci."},{"key":"10.1016\/j.cell.2026.10.027_bib100","doi-asserted-by":"crossref","DOI":"10.1186\/2047-9158-2-17","article-title":"Evidence of neurodegeneration in autism spectrum disorder","volume":"2","author":"Kern","year":"2013","journal-title":"Transl. Neurodegener."},{"key":"10.1016\/j.cell.2026.10.027_bib101","doi-asserted-by":"crossref","first-page":"2189","DOI":"10.1002\/aur.2590","article-title":"The prevalence and incidence of early-onset dementia among adults with autism spectrum disorder","volume":"14","author":"Vivanti","year":"2021","journal-title":"Autism Res."},{"key":"10.1016\/j.cell.2026.10.027_bib102","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.neuroscience.2007.05.050","article-title":"The immediate early gene early growth response gene 3 mediates adaptation to stress and novelty","volume":"148","author":"Gallitano-Mendel","year":"2007","journal-title":"Neuroscience"},{"key":"10.1016\/j.cell.2026.10.027_bib103","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1523\/JNEUROSCI.1802-22.2022","article-title":"Inducible CRISPR epigenome systems mimic cocaine induced bidirectional regulation of Nab2 and Egr3","volume":"43","author":"Choi","year":"2023","journal-title":"J. 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Res."},{"key":"10.1016\/j.cell.2026.10.027_bib113","doi-asserted-by":"crossref","DOI":"10.1016\/j.conb.2024.102925","article-title":"Astrocyte-neuron crosstalk in neurodevelopmental disorders","volume":"89","author":"S\u00e9journ\u00e9","year":"2024","journal-title":"Curr. Opin. Neurobiol."},{"key":"10.1016\/j.cell.2026.10.027_bib114","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1038\/s41380-022-01486-x","article-title":"Astrocytes derived from ASD individuals alter behavior and destabilize neuronal activity through aberrant Ca2+ signaling","volume":"27","author":"Allen","year":"2022","journal-title":"Mol. Psychiatry"},{"key":"10.1016\/j.cell.2026.10.027_bib115","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms15132","article-title":"Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism","volume":"8","author":"Hasel","year":"2017","journal-title":"Nat. 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Genet."},{"key":"10.1016\/j.cell.2026.10.027_bib127","doi-asserted-by":"crossref","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"10.1016\/j.cell.2026.10.027_bib142","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004219","article-title":"MAGMA: generalized gene-set analysis of GWAS data","volume":"11","author":"de Leeuw","year":"2015","journal-title":"PLoS Comput. 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