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Chem."},{"key":"10.1016\/j.neuron.2025.10.001_bib71","article-title":"Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1","volume":"11","author":"Minderjahn","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2025.10.001_bib72","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1242\/dev.029538","article-title":"Kruppel-like factor 2 cooperates with the ETS family protein ERG to activate Flk1 expression during vascular development","volume":"136","author":"Meadows","year":"2009","journal-title":"Development"},{"key":"10.1016\/j.neuron.2025.10.001_bib73","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1038\/s41590-023-01528-8","article-title":"SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity","volume":"24","author":"Fixsen","year":"2023","journal-title":"Nat. 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Neurodegener."},{"key":"10.1016\/j.neuron.2025.10.001_bib76","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1093\/brain\/awab432","article-title":"Gene-mapping study of extremes of cerebral small vessel disease reveals TRIM47 as a strong candidate","volume":"145","author":"Mishra","year":"2022","journal-title":"Brain"},{"key":"10.1016\/j.neuron.2025.10.001_bib77","article-title":"Cerebral Small Vessel Disease genetic determinant TRIM47 controls brain homeostasis via the NRF2 antioxidant system","author":"Dupl\u00e0a","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2025.10.001_bib78","doi-asserted-by":"crossref","first-page":"4365","DOI":"10.1016\/j.cell.2023.08.039","article-title":"Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology","volume":"186","author":"Mathys","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.10.001_bib79","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/s41588-024-02050-9","article-title":"Cell state-dependent allelic effects and contextual Mendelian randomization analysis for human brain phenotypes","volume":"57","author":"Haglund","year":"2025","journal-title":"Nat. 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Alzheimers Dis."},{"key":"10.1016\/j.neuron.2025.10.001_bib86","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.neuint.2017.04.014","article-title":"Poly(ADP-ribose) polymerase-1 regulates microglia mediated decrease of endothelial tight junction integrity","volume":"108","author":"Mehrabadi","year":"2017","journal-title":"Neurochem. Int."},{"key":"10.1016\/j.neuron.2025.10.001_bib87","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1042\/CS20160618","article-title":"Endothelial cell-oligodendrocyte interactions in small vessel disease and aging","volume":"131","author":"Rajani","year":"2017","journal-title":"Clin. Sci. (Lond.)"},{"key":"10.1016\/j.neuron.2025.10.001_bib88","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.neuroscience.2023.10.018","article-title":"Oligodendrocytes Play a Critical Role in White Matter Damage of Vascular Dementia","volume":"538","author":"Zhang","year":"2024","journal-title":"Neuroscience"},{"key":"10.1016\/j.neuron.2025.10.001_bib89","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1172\/JCI39733","article-title":"Cerebrovascular dysfunction and microcirculation rarefaction precede white matter lesions in a mouse genetic model of cerebral ischemic small vessel disease","volume":"120","author":"Joutel","year":"2010","journal-title":"J. Clin. Invest."},{"key":"10.1016\/j.neuron.2025.10.001_bib90","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1111\/nan.12116","article-title":"Differential gene expression in multiple neurological, inflammatory and connective tissue pathways in a spontaneous model of human small vessel stroke","volume":"40","author":"Bailey","year":"2014","journal-title":"Neuropathol. Appl. Neurobiol."},{"key":"10.1016\/j.neuron.2025.10.001_bib91","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1111\/j.1747-4949.2011.00659.x","article-title":"Is the spontaneously hypertensive stroke prone rat a pertinent model of sub cortical ischemic stroke? A systematic review","volume":"6","author":"Bailey","year":"2011","journal-title":"Int. J. Stroke"},{"key":"10.1016\/j.neuron.2025.10.001_bib92","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3003748","article-title":"A Paravascular Pathway Facilitates CSF Flow Through the Brain Parenchyma and the Clearance of Interstitial Solutes, Including Amyloid \u03b2","volume":"4","author":"Iliff","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.neuron.2025.10.001_bib93","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.conb.2021.07.006","article-title":"Cerebral small vessel disease: A glymphopathy?","volume":"72","author":"Benveniste","year":"2022","journal-title":"Curr. Opin. Neurobiol."},{"key":"10.1016\/j.neuron.2025.10.001_bib94","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.jneuroim.2016.01.015","article-title":"Vitamin D3 alters microglia immune activation by an IL-10 dependent SOCS3 mechanism","volume":"292","author":"Boontanrart","year":"2016","journal-title":"J. Neuroimmunol."},{"key":"10.1016\/j.neuron.2025.10.001_bib95","doi-asserted-by":"crossref","DOI":"10.1186\/s12974-023-02705-0","article-title":"Microglia\/macrophages require vitamin D signaling to restrain neuroinflammation and brain injury in a murine ischemic stroke model","volume":"20","author":"Cui","year":"2023","journal-title":"J. Neuroinflammation"},{"key":"10.1016\/j.neuron.2025.10.001_bib96","doi-asserted-by":"crossref","first-page":"51","DOI":"10.3233\/JAD-2012-110560","article-title":"Genomic and nongenomic signaling induced by 1\u03b1,25(OH)2-vitamin D3 promotes the recovery of amyloid-\u03b2 phagocytosis by Alzheimer's disease macrophages","volume":"29","author":"Mizwicki","year":"2012","journal-title":"J. Alzheimers Dis."},{"key":"10.1016\/j.neuron.2025.10.001_bib97","doi-asserted-by":"crossref","first-page":"703","DOI":"10.3233\/JAD-2009-1080","article-title":"1alpha,25-dihydroxyvitamin D3 interacts with curcuminoids to stimulate amyloid-beta clearance by macrophages of Alzheimer's disease patients","volume":"17","author":"Masoumi","year":"2009","journal-title":"J. Alzheimers Dis."},{"key":"10.1016\/j.neuron.2025.10.001_bib98","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1212\/WNL.0000000000000755","article-title":"Vitamin D and the risk of dementia and Alzheimer disease","volume":"83","author":"Littlejohns","year":"2014","journal-title":"Neurology"},{"key":"10.1016\/j.neuron.2025.10.001_bib99","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.jalz.2013.05.1765","article-title":"Reduced 25-hydroxyvitamin D and risk of Alzheimer's disease and vascular dementia","volume":"10","author":"Afzal","year":"2014","journal-title":"Alzheimers Dement."},{"key":"10.1016\/j.neuron.2025.10.001_bib100","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-025-60099-4","article-title":"The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia xenografted into a mouse model of Alzheimer's disease","volume":"16","author":"Murphy","year":"2025","journal-title":"Nat. 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Neurochem."},{"key":"10.1016\/j.neuron.2025.10.001_bib103","doi-asserted-by":"crossref","first-page":"5294","DOI":"10.1523\/JNEUROSCI.2427-21.2022","article-title":"Microglial mTOR Activation Upregulates Trem2 and Enhances \u03b2-Amyloid Plaque Clearance in the 5XFAD Alzheimer's Disease Model","volume":"42","author":"Shi","year":"2022","journal-title":"J. Neurosci."},{"key":"10.1016\/j.neuron.2025.10.001_bib104","article-title":"Rapamycin treatment for Alzheimer's disease and related dementias: a pilot phase 1 clinical trial","volume":"5","author":"Gonzales","year":"2025","journal-title":"Commun. Med. (Lond)"},{"key":"10.1016\/j.neuron.2025.10.001_bib105","doi-asserted-by":"crossref","DOI":"10.1186\/s12883-024-03596-1","article-title":"Evaluating the effect of rapamycin treatment in Alzheimer's disease and aging using in vivo imaging: the ERAP phase IIa clinical study protocol","volume":"24","author":"Svensson","year":"2024","journal-title":"BMC Neurol."},{"key":"10.1016\/j.neuron.2025.10.001_bib106","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1038\/npp.2009.197","article-title":"Inhibitors of class 1 histone deacetylases reverse contextual memory deficits in a mouse model of Alzheimer's disease","volume":"35","author":"Kilgore","year":"2010","journal-title":"Neuropsychopharmacology"},{"key":"10.1016\/j.neuron.2025.10.001_bib107","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature07925","article-title":"HDAC2 negatively regulates memory formation and synaptic plasticity","volume":"459","author":"Guan","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2025.10.001_bib108","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature10849","article-title":"An epigenetic blockade of cognitive functions in the neurodegenerating brain","volume":"483","author":"Gr\u00e4ff","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2025.10.001_bib109","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1038\/s41588-020-0696-0","article-title":"An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease","volume":"52","author":"Nativio","year":"2020","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2025.10.001_bib110","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/s41593-018-0101-9","article-title":"Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease","volume":"21","author":"Nativio","year":"2018","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.10.001_bib111","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1038\/s41593-018-0253-7","article-title":"A histone acetylome-wide association study of Alzheimer's disease identifies disease-associated H3K27ac differences in the entorhinal cortex","volume":"21","author":"Marzi","year":"2018","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.10.001_bib112","article-title":"Cell type-specific histone acetylation profiling of Alzheimer\u2019s disease subjects and integration with genetics","volume":"15","author":"Ramamurthy","year":"2022","journal-title":"Front. Mol. Neurosci."},{"key":"10.1016\/j.neuron.2025.10.001_bib113","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.bbi.2025.05.027","article-title":"HDAC inhibitors engage MITF and the disease-associated microglia signature to enhance amyloid \u03b2 uptake","volume":"129","author":"Haage","year":"2025","journal-title":"Brain Behav. Immun."},{"key":"10.1016\/j.neuron.2025.10.001_bib114","doi-asserted-by":"crossref","DOI":"10.1186\/alzrt230","article-title":"Adjusting the compass: new insights into the role of angiogenesis in Alzheimer's disease","volume":"5","author":"Jefferies","year":"2013","journal-title":"Alzheimers Res. Ther."},{"key":"10.1016\/j.neuron.2025.10.001_bib115","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/s00702-009-0226-9","article-title":"Evidence of angiogenic vessels in Alzheimer's disease","volume":"116","author":"Desai","year":"2009","journal-title":"J. Neural Transm. (Vienna)"},{"key":"10.1016\/j.neuron.2025.10.001_bib116","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1038\/s41380-019-0458-5","article-title":"Brain expression of the vascular endothelial growth factor gene family in cognitive aging and alzheimer's disease","volume":"26","author":"Mahoney","year":"2021","journal-title":"Mol. Psychiatry"},{"key":"10.1016\/j.neuron.2025.10.001_bib117","article-title":"Association of ten VEGF family genes with Alzheimer's disease endophenotypes at single cell resolution","volume":"21","author":"Wu","year":"2025","journal-title":"Alzheimers Dement."},{"key":"10.1016\/j.neuron.2025.10.001_bib118","doi-asserted-by":"crossref","DOI":"10.1186\/s40035-023-00388-4","article-title":"Blockage of VEGF function by bevacizumab alleviates early-stage cerebrovascular dysfunction and improves cognitive function in a mouse model of Alzheimer's disease","volume":"13","author":"Zhang","year":"2024","journal-title":"Transl. Neurodegener."},{"key":"10.1016\/j.neuron.2025.10.001_bib119","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1523\/JNEUROSCI.2888-08.2009","article-title":"Microglial VEGF receptor response is an integral chemotactic component in Alzheimer's disease pathology","volume":"29","author":"Ryu","year":"2009","journal-title":"J. Neurosci."},{"key":"10.1016\/j.neuron.2025.10.001_bib120","doi-asserted-by":"crossref","first-page":"3264","DOI":"10.1038\/s41596-020-0373-x","article-title":"Efficient low-cost chromatin profiling with CUT&Tag","volume":"15","author":"Kaya-Okur","year":"2020","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.neuron.2025.10.001_bib121","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single-cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"Buenrostro","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2025.10.001_bib122","unstructured":"Cheshire, C., Charlotte-west, R\u00f6nkk\u00f6, T., nf-core bot, Patel, H., Tamara-hodgetts, Ladd, D., Thiery, A., Fields, C., Deu-Pons, J., et al. (2024). nf-core\/cutandrun: nf-core\/cutandrun v3.2.2 Iridium Ibis (3.2.2). Zenodo. https:\/\/doi.org\/10.5281\/zenodo.10606804."},{"key":"10.1016\/j.neuron.2025.10.001_bib123","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2025.10.001_bib124","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based Analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2025.10.001_bib125","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","article-title":"ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2025.10.001_bib126","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2025.10.001_bib127","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-016-0992-2","article-title":"CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data","volume":"17","author":"Cairns","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2025.10.001_bib128","doi-asserted-by":"crossref","first-page":"4764","DOI":"10.1093\/bioinformatics\/btz450","article-title":"Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data","volume":"35","author":"Cairns","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2025.10.001_bib129","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.7334.1","article-title":"HiCUP: pipeline for mapping and processing Hi-C data","volume":"4","author":"Wingett","year":"2015","journal-title":"F1000Res"},{"key":"10.1016\/j.neuron.2025.10.001_bib130","doi-asserted-by":"crossref","first-page":"4593","DOI":"10.1093\/bioinformatics\/btab665","article-title":"MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics","volume":"37","author":"Murphy","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2025.10.001_bib131","doi-asserted-by":"crossref","DOI":"10.3389\/fnins.2016.00016","article-title":"Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment","volume":"10","author":"Skene","year":"2016","journal-title":"Front. Neurosci."},{"key":"10.1016\/j.neuron.2025.10.001_bib132","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gks461","article-title":"Camera: a competitive gene set test accounting for inter-gene correlation","volume":"40","author":"Wu","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2025.10.001_bib133","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf018","article-title":"edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets","volume":"53","author":"Chen","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2025.10.001_bib134","article-title":"Fast gene set enrichment analysis","author":"Korotkevich","year":"2019","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2025.10.001_bib135","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/ng.3211","article-title":"LD Score regression distinguishes confounding from polygenicity in genome-wide association studies","volume":"47","author":"Bulik-Sullivan","year":"2015","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2025.10.001_bib136","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.24956.2","article-title":"gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler","volume":"9","author":"Kolberg","year":"2020","journal-title":"F1000Res"},{"key":"10.1016\/j.neuron.2025.10.001_bib137","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. 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