{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T23:03:09Z","timestamp":1793833389852,"version":"4.6.1"},"reference-count":108,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T00:00:00Z","timestamp":1766966400000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Parkinsons Dis."],"abstract":"<jats:title>\n                    <jats:bold>Abstract<\/jats:bold>\n                  <\/jats:title>\n                  <jats:p>\n                    Epigenetic mechanisms mediate interactions between aging, genetics, and environmental factors in sporadic Parkinson\u2019s disease (PD). While multiple studies have explored DNA modifications in PD, few focus on 5-hydroxymethylcytosine (5hmc), which is important in the central nervous system and sensitive to environmental exposures. Existing studies have not differentiated between 5-methylcytosine (5mc) and 5hmc or have analyzed them separately. In this study, we modeled 5mc and 5hmc data simultaneously. We identified 108 cytosines with significant PD-associated shifts between these marks in an enriched neuronal population from PD postmortem parietal cortex, within 83 genes and 34 enhancers associated with 67 genes. These data potentially link epigenetic regulation of genes related to LRRK2 and endolysosomal sorting (\n                    <jats:italic>RAB32<\/jats:italic>\n                    and\n                    <jats:italic>AGAP1<\/jats:italic>\n                    ), and genes involved in neuroinflammation, the inflammasome, and neurodevelopment with early changes in PD and suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes not captured by standard methods.\n                  <\/jats:p>","DOI":"10.1038\/s41531-025-01209-3","type":"journal-article","created":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T11:07:54Z","timestamp":1766401674000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Parkinson\u2019s disease-associated alterations in DNA methylation and hydroxymethylation in human brain"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7038-9750","authenticated-orcid":false,"given":"Juliana I.","family":"Choza","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6094-4478","authenticated-orcid":false,"given":"Mahek","family":"Virani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan C.","family":"Kuhn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7909-2339","authenticated-orcid":false,"given":"Marie","family":"Adams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8472-3032","authenticated-orcid":false,"given":"Joseph","family":"Kochmanski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5589-4318","authenticated-orcid":false,"given":"Alison I.","family":"Bernstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,22]]},"reference":[{"key":"1209_CR1","doi-asserted-by":"publisher","first-page":"4996","DOI":"10.1093\/hmg\/dds335","volume":"21","author":"MF Keller","year":"2012","unstructured":"Keller, M. F. et al. Using genome-wide complex trait analysis to quantify \u2018missing heritability\u2019 in Parkinson\u2019s disease. Hum. Mol. Genet. 21, 4996\u20135009 (2012).","journal-title":"Hum. Mol. Genet."},{"key":"1209_CR2","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.3233\/JPD-181474","volume":"8","author":"ER Dorsey","year":"2018","unstructured":"Dorsey, E. R., Sherer, T., Okun, M. S. & Bloem, B. R. The emerging evidence of the Parkinson pandemic. J. Parkinson\u2019s Dis. 8, S3\u2013S8 (2018).","journal-title":"J. Parkinson\u2019s Dis."},{"key":"1209_CR3","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1146\/annurev-pharmtox-011613-135937","volume":"54","author":"SM Goldman","year":"2014","unstructured":"Goldman, S. M. Environmental toxins and Parkinson\u2019s disease. Annu. Rev. Pharmacol. Toxicol. 54, 141\u2013164 (2014).","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"key":"1209_CR4","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1038\/s41586-019-1411-0","volume":"571","author":"G Cavalli","year":"2019","unstructured":"Cavalli, G. & Heard, E. Advances in epigenetics link genetics to the environment and disease. Nature 571, 489\u2013499 (2019).","journal-title":"Nature"},{"key":"1209_CR5","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/s41576-022-00569-3","volume":"24","author":"H Wu","year":"2023","unstructured":"Wu, H., Eckhardt, C. M. & Baccarelli, A. A. Molecular mechanisms of environmental exposures and human disease. Nat. Rev.Genet. 24, 332\u2013344 (2023).","journal-title":"Nat. Rev.Genet."},{"key":"1209_CR6","doi-asserted-by":"publisher","first-page":"23235","DOI":"10.1073\/pnas.2016710117","volume":"117","author":"WT Boyce","year":"2020","unstructured":"Boyce, W. T., Sokolowski, M. B. & Robinson, G. E. Genes and environments, development and time. Proc. Natl. Acad. Sci. USA 117, 23235\u201323241 (2020).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"1209_CR7","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/bs.pmbts.2018.04.008","volume":"158","author":"R Lardenoije","year":"2018","unstructured":"Lardenoije, R., Pishva, E., Lunnon, K. & van den Hove, D. L. Neuroepigenetics of aging and age-related neurodegenerative disorders. Prog. Mol. Biol. Transl. Sci. 158, 49\u201382 (2018).","journal-title":"Prog. Mol. Biol. Transl. Sci."},{"key":"1209_CR8","doi-asserted-by":"publisher","first-page":"971298","DOI":"10.3389\/fgene.2022.971298","volume":"13","author":"SL Schaffner","year":"2022","unstructured":"Schaffner, S. L. & Kobor, M. S. DNA methylation as a mediator of genetic and environmental influences on Parkinson\u2019s disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front. Genet. 13, 971298 (2022).","journal-title":"Front. Genet."},{"key":"1209_CR9","doi-asserted-by":"publisher","first-page":"277","DOI":"10.3389\/fnins.2019.00277","volume":"13","author":"HJ van Heesbeen","year":"2019","unstructured":"van Heesbeen, H. J. & Smidt, M. P. Entanglement of genetics and epigenetics in Parkinson\u2019s disease. Front. Neurosci. 13, 277 (2019).","journal-title":"Front. Neurosci."},{"key":"1209_CR10","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/s41531-023-00568-z","volume":"9","author":"M Tsalenchuk","year":"2023","unstructured":"Tsalenchuk, M., Gentleman, S. M. & Marzi, S. J. Linking environmental risk factors with epigenetic mechanisms in Parkinson\u2019s disease. npj Parkinson\u2019s Dis. 9, 123 (2023).","journal-title":"npj Parkinson\u2019s Dis."},{"key":"1209_CR11","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.expneurol.2014.05.008","volume":"268","author":"Y Cheng","year":"2014","unstructured":"Cheng, Y., Bernstein, A. I., Chen, D. & Jin, P. 5-Hydroxymethylcytosine: A new player in brain disorders?. Exp. Neurol. 268, 3\u20139 (2014).","journal-title":"Exp. Neurol."},{"key":"1209_CR12","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1007\/s40572-020-00268-3","volume":"7","author":"J Kochmanski","year":"2020","unstructured":"Kochmanski, J. & Bernstein, A. I. The impact of environmental factors on 5-hydroxymethylcytosine in the brain. Curr. Envir Health Rpt. 7, 109\u2013120 (2020).","journal-title":"Curr. Envir Health Rpt."},{"key":"1209_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fnins.2014.00397","volume":"8","author":"S Al-mahdawi","year":"2014","unstructured":"Al-mahdawi, S., Virmouni, S. A., Pook, M. A. & Evans-galea, M. The emerging role of 5-hydroxymethylcytosine in neurodegenerative diseases. Front Neurosci. 8, 1\u20138 (2014).","journal-title":"Front Neurosci."},{"key":"1209_CR14","doi-asserted-by":"publisher","first-page":"e125","DOI":"10.1093\/nar\/gkq223","volume":"38","author":"S Jin","year":"2010","unstructured":"Jin, S., Kadam, S. & Pfeifer, G. P. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 38, e125 (2010).","journal-title":"Nucleic Acids Res."},{"key":"1209_CR15","unstructured":"Bernstein, A. I. & Jin, P. Epigenetic Technological Applications 1st edn (Elsevier, 2015)."},{"key":"1209_CR16","doi-asserted-by":"publisher","first-page":"242.e13","DOI":"10.1016\/j.neurobiolaging.2019.02.025","volume":"84","author":"L Shu","year":"2019","unstructured":"Shu, L. et al. Genetic analysis of DNA methylation and hydroxymethylation genes in Parkinson\u2019s disease. Neurobiol. Aging 84, 242.e13\u2013242.e16 (2019).","journal-title":"Neurobiol. Aging"},{"key":"1209_CR17","doi-asserted-by":"publisher","first-page":"3494","DOI":"10.1093\/hmg\/ddac122","volume":"31","author":"S Min","year":"2022","unstructured":"Min, S. et al. Altered hydroxymethylome in the substantia nigra of Parkinson\u2019s disease. Hum. Mol. Genet. 31, 3494\u20133503 (2022).","journal-title":"Hum. Mol. Genet."},{"key":"1209_CR18","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41593-020-0690-y","volume":"23","author":"LL Marshall","year":"2020","unstructured":"Marshall, L. L. et al. Epigenomic analysis of Parkinson\u2019s disease neurons identifies Tet2 loss as neuroprotective. Nat. Neurosci. 23, 1203\u20131214 (2020).","journal-title":"Nat. Neurosci."},{"key":"1209_CR19","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41531-022-00355-2","volume":"8","author":"J Kochmanski","year":"2022","unstructured":"Kochmanski, J., Kuhn, N. C. & Bernstein, A. I. Parkinson\u2019s disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2\u03b2), and NR4A2 (NURR1) in cortical neurons. npj Parkinson\u2019s Dis. 8, 120 (2022).","journal-title":"npj Parkinson\u2019s Dis."},{"key":"1209_CR20","doi-asserted-by":"publisher","first-page":"801","DOI":"10.3389\/fgene.2019.00801","volume":"10","author":"J Kochmanski","year":"2019","unstructured":"Kochmanski, J., Savonen, C. & Bernstein, A. I. A novel application of mixed effects models for reconciling base-pair resolution 5-methylcytosine and 5-hydroxymethylcytosine data in neuroepigenetics. Frontiers in Genetics 10, 801 (2019).","journal-title":"Frontiers in Genetics"},{"key":"1209_CR21","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1126\/science.1220671","volume":"336","author":"MJ Booth","year":"2012","unstructured":"Booth, M. J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934\u2013937 (2012).","journal-title":"Science"},{"key":"1209_CR22","first-page":"2505","volume":"32","author":"EA Houseman","year":"2016","unstructured":"Houseman, E. A., Johnson, K. C. & Christensen, B. C. OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA. Bioinformatics (Oxford, England) 32, 2505\u20132507 (2016).","journal-title":"Bioinformatics (Oxford, England)"},{"key":"1209_CR23","doi-asserted-by":"publisher","DOI":"10.1186\/s13148-019-0636-y","volume":"11","author":"AR Smith","year":"2019","unstructured":"Smith, A. R. et al. Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer\u2019s disease. Clin. Epigenet. 11, 52 (2019).","journal-title":"Clin. Epigenet."},{"key":"1209_CR24","doi-asserted-by":"publisher","first-page":"dvy020","DOI":"10.1093\/eep\/dvy020","volume":"4","author":"X Zhang","year":"2018","unstructured":"Zhang, X. et al. Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. Environ. Epigenet. 4, dvy020 (2018).","journal-title":"Environ. Epigenet."},{"key":"1209_CR25","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1007\/s00401-018-1821-3","volume":"135","author":"WK Glowacka","year":"2018","unstructured":"Glowacka, W. K. et al. 5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma. Acta Neuropathol. 135, 617\u2013634 (2018).","journal-title":"Acta Neuropathol."},{"key":"1209_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms13177","volume":"7","author":"KC Johnson","year":"2016","unstructured":"Johnson, K. C. et al. 5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients. Nat. Commun. 7, 13177 (2016).","journal-title":"Nat. Commun."},{"key":"1209_CR27","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1080\/15592294.2017.1344803","volume":"13","author":"JR Hernandez Mora","year":"2018","unstructured":"Hernandez Mora, J. R. et al. Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci. Epigenetics 13, 182\u2013191 (2018).","journal-title":"Epigenetics"},{"key":"1209_CR28","doi-asserted-by":"publisher","first-page":"2874","DOI":"10.1096\/fj.201600310R","volume":"30","author":"BB Green","year":"2016","unstructured":"Green, B. B. et al. Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression. FASEB J. 30, 2874\u20132884 (2016).","journal-title":"FASEB J."},{"key":"1209_CR29","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.498","volume":"11","author":"Y Han","year":"2021","unstructured":"Han, Y. et al. An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome. Clin. Transl. Med. 11, e498 (2021).","journal-title":"Clin. Transl. Med."},{"key":"1209_CR30","doi-asserted-by":"publisher","first-page":"1345410","DOI":"10.3389\/fgene.2024.1345410","volume":"15","author":"DE Andrade-Brito","year":"2024","unstructured":"Andrade-Brito, D. E. et al. Neuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder. Front. Genet. 15, 1345410 (2024).","journal-title":"Front. Genet."},{"key":"1209_CR31","doi-asserted-by":"publisher","DOI":"10.1186\/s13148-023-01461-5","volume":"15","author":"RL Petroff","year":"2023","unstructured":"Petroff, R. L. et al. Mediation effects of DNA methylation and hydroxymethylation on birth outcomes after prenatal per- and polyfluoroalkyl substances (PFAS) exposure in the Michigan mother-infant Pairs cohort. Clin. Epigenet. 15, 49 (2023).","journal-title":"Clin. Epigenet."},{"key":"1209_CR32","doi-asserted-by":"publisher","first-page":"67002","DOI":"10.1289\/EHP8507","volume":"129","author":"CA Rygiel","year":"2021","unstructured":"Rygiel, C. A. et al. Prenatal lead (Pb) exposure and peripheral blood DNA methylation (5mC) and hydroxymethylation (5hmC) in mexican adolescents from the ELEMENT birth cohort. Environ. Health Perspect. 129, 67002 (2021).","journal-title":"Environ. Health Perspect."},{"key":"1209_CR33","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1001\/jamaneurol.2020.5257","volume":"78","author":"DA Kia","year":"2021","unstructured":"Kia, D. A. et al. Identification of candidate parkinson disease genes by integrating genome-wide association study, expression, and epigenetic data sets. JAMA Neurol 78, 464\u2013472 (2021).","journal-title":"JAMA Neurol"},{"key":"1209_CR34","doi-asserted-by":"publisher","first-page":"1030","DOI":"10.4161\/epi.25865","volume":"8","author":"E Masliah","year":"2013","unstructured":"Masliah, E., Dumaop, W., Galasko, D. & Desplats, P. Distinctive patterns of DNA methylation associated with Parkinson disease: identification of concordant epigenetic changes in brain and peripheral blood leukocytes. Epigenetics 8, 1030\u20131038 (2013).","journal-title":"Epigenetics"},{"key":"1209_CR35","doi-asserted-by":"publisher","first-page":"e342","DOI":"10.1212\/NXG.0000000000000342","volume":"5","author":"JI Young","year":"2019","unstructured":"Young, J. I. et al. Genome-wide brain DNA methylation analysis suggests epigenetic reprogramming in Parkinson's disease. Neurol. Genet. 5, e342 (2019).","journal-title":"Neurol. Genet."},{"key":"1209_CR36","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1093\/toxsci\/kfae091","volume":"201","author":"J Kochmanski","year":"2024","unstructured":"Kochmanski, J. et al. Developmental origins of Parkinson\u2019s disease risk: perinatal exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain. Toxicol Sci 201, 263\u2013281 (2024).","journal-title":"Toxicol Sci"},{"key":"1209_CR37","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/toxsci\/kfz069","volume":"169","author":"J Kochmanski","year":"2019","unstructured":"Kochmanski, J., VanOeveren, S. E., Patterson, J. R. & Bernstein, A. I. Developmental dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and parkinson\u2019s disease in mouse midbrain. Toxicol. Sci. 169, 593\u2013607 (2019).","journal-title":"Toxicol. Sci."},{"key":"1209_CR38","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/s41531-023-00594-x","volume":"9","author":"MS Andersen","year":"2023","unstructured":"Andersen, M. S. et al. Epigenome-wide association study of peripheral immune cell populations in Parkinson\u2019s disease. NPJ Parkinsons Dis. 9, 149 (2023).","journal-title":"NPJ Parkinsons Dis."},{"key":"1209_CR39","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/S1474-4422(24)00121-2","volume":"23","author":"EK Gustavsson","year":"2024","unstructured":"Gustavsson, E. K. et al. RAB32 Ser71Arg in autosomal dominant Parkinson\u2019s disease: linkage, association, and functional analyses. Lancet Neurol. 23, 603\u2013614 (2024).","journal-title":"Lancet Neurol."},{"key":"1209_CR40","doi-asserted-by":"publisher","first-page":"1371","DOI":"10.1038\/s41588-024-01787-7","volume":"56","author":"PJ Hop","year":"2024","unstructured":"Hop, P. J. et al. Systematic rare variant analyses identify RAB32 as a susceptibility gene for familial Parkinson\u2019s disease. Nat. Genet 56, 1371\u20131376 (2024).","journal-title":"Nat. Genet"},{"key":"1209_CR41","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1016\/S1474-4422(24)00323-5","volume":"23","author":"C Beetz","year":"2024","unstructured":"Beetz, C., Radefeldt, M., Tripolszki, K., Kandaswamy, K. K. & Bauer, P. RAB32 mutation in Parkinson\u2019s disease. Lancet Neurol 23, 961 (2024).","journal-title":"Lancet Neurol"},{"key":"1209_CR42","doi-asserted-by":"crossref","unstructured":"Radefeldt, M. et al. Genetic and epidemiological insights into RAB32-linked parkinson\u2019s disease. Mov. Disord. 40, 147\u2212151 (2024).","DOI":"10.1002\/mds.30041"},{"key":"1209_CR43","doi-asserted-by":"crossref","unstructured":"Magistrelli, L. et al. The RAB32 p.Ser71Arg variant in Parkinsonisms: insights from a large Italian cohort. Mov. Disord. 40, 511\u2212516 (2024).","DOI":"10.1002\/mds.30103"},{"key":"1209_CR44","doi-asserted-by":"publisher","first-page":"1920","DOI":"10.1080\/15592294.2022.2091815","volume":"17","author":"DD Jima","year":"2022","unstructured":"Jima, D. D. et al. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 17, 1920\u20131943 (2022).","journal-title":"Epigenetics"},{"key":"1209_CR45","doi-asserted-by":"publisher","first-page":"218","DOI":"10.3389\/fncel.2016.00218","volume":"10","author":"M Arnold","year":"2016","unstructured":"Arnold, M. et al. The endosome localized Arf-GAP AGAP1modulates dendritic spine morphology downstream of the neurodevelopmental disorder factor dysbindin. Front Cell Neurosci 10, 218 (2016).","journal-title":"Front Cell Neurosci"},{"key":"1209_CR46","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1080\/21541248.2017.1308850","volume":"10","author":"R Luo","year":"2019","unstructured":"Luo, R. et al. Arf GAPs and molecular motors. Small GTPases 10, 196\u2013209 (2019).","journal-title":"Small GTPases"},{"key":"1209_CR47","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/S1534-5807(03)00234-X","volume":"5","author":"Z Nie","year":"2003","unstructured":"Nie, Z. et al. Specific regulation of the adaptor protein complex AP-3 by the Arf GAP AGAP1. Dev. Cell 5, 513\u2013521 (2003).","journal-title":"Dev. Cell"},{"key":"1209_CR48","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.1016\/j.bbalip.2015.09.005","volume":"1851","author":"RM Bradley","year":"2015","unstructured":"Bradley, R. M. et al. Acylglycerophosphate acyltransferase 4 (AGPAT4) is a mitochondrial lysophosphatidic acid acyltransferase that regulates brain phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol levels. Biochim. Biophys. Acta 1851, 1566\u20131576 (2015).","journal-title":"Biochim. Biophys. Acta"},{"key":"1209_CR49","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1159\/000090830","volume":"113","author":"A Plagge","year":"2006","unstructured":"Plagge, A. & Kelsey, G. Imprinting the Gnas locus. Cytogenet. Genome Res. 113, 178\u2013187 (2006).","journal-title":"Cytogenet. Genome Res."},{"key":"1209_CR50","doi-asserted-by":"publisher","first-page":"109027","DOI":"10.1016\/j.neuropharm.2022.109027","volume":"210","author":"MA Cenci","year":"2022","unstructured":"Cenci, M. A., Skovg\u00e5rd, K. & Odin, P. Non-dopaminergic approaches to the treatment of motor complications in Parkinson\u2019s disease. Neuropharmacology 210, 109027 (2022).","journal-title":"Neuropharmacology"},{"key":"1209_CR51","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41420-024-01955-y","volume":"10","author":"S Zhao","year":"2024","unstructured":"Zhao, S. et al. Role of RB1 in neurodegenerative diseases: inhibition of post-mitotic neuronal apoptosis via Kmt5b. Cell Death Discov. 10, 1\u201313 (2024).","journal-title":"Cell Death Discov."},{"key":"1209_CR52","doi-asserted-by":"publisher","first-page":"100074","DOI":"10.1016\/j.crneur.2023.100074","volume":"4","author":"S Omais","year":"2023","unstructured":"Omais, S., El Atie, Y. E. & Ghanem, N. Rb deficiency, neuronal survival and neurodegeneration: In search of the perfect mouse model. Curr. Res. Neurobiol. 4, 100074 (2023).","journal-title":"Curr. Res. Neurobiol."},{"key":"1209_CR53","doi-asserted-by":"publisher","first-page":"3585","DOI":"10.1073\/pnas.0611671104","volume":"104","author":"GU H\u00f6glinger","year":"2007","unstructured":"H\u00f6glinger, G. U. et al. The pRb\/E2F cell-cycle pathway mediates cell death in Parkinson\u2019s disease | PNAS. Proc. Natl. Acad. Sci. 104, 3585\u20133590 (2007).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"1209_CR54","doi-asserted-by":"publisher","first-page":"67003","DOI":"10.1289\/EHP14074","volume":"132","author":"RK Morgan","year":"2024","unstructured":"Morgan, R. K. et al. Effects of developmental lead and phthalate exposures on DNA methylation in adult mouse blood, brain, and liver: a focus on genomic imprinting by tissue and sex. Environ. Health Perspect. 132, 67003 (2024).","journal-title":"Environ. Health Perspect."},{"key":"1209_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-05124-5","volume":"9","author":"OI Kahn","year":"2018","unstructured":"Kahn, O. I. et al. APC2 controls dendrite development by promoting microtubule dynamics. Nat. Commun. 9, 2773 (2018).","journal-title":"Nat. Commun."},{"key":"1209_CR56","doi-asserted-by":"publisher","first-page":"6468","DOI":"10.1523\/JNEUROSCI.0590-12.2012","volume":"32","author":"T Shintani","year":"2012","unstructured":"Shintani, T., Takeuchi, Y., Fujikawa, A. & Noda, M. Directional neuronal migration is impaired in mice lacking adenomatous polyposis coli 2. J. Neurosci. 32, 6468\u20136484 (2012).","journal-title":"J. Neurosci."},{"key":"1209_CR57","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1038\/nrn2898","volume":"11","author":"A Dityatev","year":"2010","unstructured":"Dityatev, A., Schachner, M. & Sonderegger, P. The dual role of the extracellular matrix in synaptic plasticity and homeostasis. Nat. Rev. Neurosci. 11, 735\u2013746 (2010).","journal-title":"Nat. Rev. Neurosci."},{"key":"1209_CR58","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1007\/s10571-021-01140-0","volume":"42","author":"KA Szychowski","year":"2022","unstructured":"Szychowski, K. A., Sk\u00f3ra, B. & W\u00f3jtowicz, A. K. Elastin-derived peptides in the central nervous system: friend or foe. Cell Mol. Neurobiol. 42, 2473\u20132487 (2022).","journal-title":"Cell Mol. Neurobiol."},{"key":"1209_CR59","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1177\/1535370220924618","volume":"245","author":"K Ko\u015bla","year":"2020","unstructured":"Ko\u015bla, K., Ka\u0142uzi\u0144ska, \u017b & Bednarek, A. K. The WWOX gene in brain development and pathology. Exp. Biol. Med. (Maywood) 245, 1122\u20131129 (2020).","journal-title":"Exp. Biol. Med. (Maywood)"},{"key":"1209_CR60","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/bs.pbr.2020.02.001","volume":"252","author":"LA Cunningham","year":"2020","unstructured":"Cunningham, L. A. & Moore, D. J. Endosomal sorting pathways in the pathogenesis of Parkinson\u2019s disease. Prog. Brain Res. 252, 271\u2013306 (2020).","journal-title":"Prog. Brain Res."},{"key":"1209_CR61","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.3233\/JPD-202138","volume":"10","author":"ML Erb","year":"2020","unstructured":"Erb, M. L. & Moore, D. J. LRRK2 and the endolysosomal system in Parkinson\u2019s disease. J. Parkinsons Dis. 10, 1271\u20131291 (2020).","journal-title":"J. Parkinsons Dis."},{"key":"1209_CR62","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1016\/j.tins.2021.12.002","volume":"45","author":"EM Rocha","year":"2022","unstructured":"Rocha, E. M., Keeney, M. T., Maio, R. D., Miranda, B. R. D. & Greenamyre, J. T. LRRK2 and idiopathic Parkinson\u2019s disease. Trend Neurosci. 45, 224\u2013236 (2022).","journal-title":"Trend Neurosci."},{"key":"1209_CR63","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1002\/mds.27270","volume":"33","author":"Y Gao","year":"2018","unstructured":"Gao, Y. et al. The emerging role of Rab GTPases in the pathogenesis of Parkinson\u2019s disease. Mov. Disord. 33, 196\u2013207 (2018).","journal-title":"Mov. Disord."},{"key":"1209_CR64","doi-asserted-by":"publisher","first-page":"e1000902","DOI":"10.1371\/journal.pgen.1000902","volume":"6","author":"Y Xiong","year":"2010","unstructured":"Xiong, Y. et al. GTPase activity plays a key role in the pathobiology of LRRK2. PLoS Genet. 6, e1000902 (2010).","journal-title":"PLoS Genet."},{"key":"1209_CR65","doi-asserted-by":"publisher","first-page":"e0157852","DOI":"10.1371\/journal.pone.0157852","volume":"11","author":"R Pinho","year":"2016","unstructured":"Pinho, R. et al. Gene expression differences in peripheral blood of parkinson\u2019s disease patients with distinct progression profiles. PLoS ONE 11, e0157852 (2016).","journal-title":"PLoS ONE"},{"key":"1209_CR66","doi-asserted-by":"publisher","DOI":"10.1242\/dmm.049838","volume":"16","author":"SA Lewis","year":"2023","unstructured":"Lewis, S. A. et al. AGAP1-associated endolysosomal trafficking abnormalities link gene-environment interactions in neurodevelopmental disorders. Dis. Model Mech. 16, dmm049838 (2023).","journal-title":"Dis. Model Mech."},{"key":"1209_CR67","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/s41586-023-06812-z","volume":"624","author":"Z Yao","year":"2023","unstructured":"Yao, Z. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317\u2013332 (2023).","journal-title":"Nature"},{"key":"1209_CR68","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2200544119","volume":"119","author":"I Rimann","year":"2022","unstructured":"Rimann, I. et al. The solute carrier SLC15A4 is required for optimal trafficking of nucleic acid-sensing TLRs and ligands to endolysosomes. Proc. Natl. Acad. Sci. USA 119, e2200544119 (2022).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"1209_CR69","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2022111161","volume":"41","author":"C L\u00f3pez-Haber","year":"2022","unstructured":"L\u00f3pez-Haber, C. et al. The phagosomal solute transporter SLC15A4 promotes inflammasome activity via mTORC1 signaling and autophagy restraint in dendritic cells. EMBO J. 41, e111161 (2022).","journal-title":"EMBO J."},{"key":"1209_CR70","doi-asserted-by":"publisher","DOI":"10.1111\/bpa.13142","volume":"33","author":"RT Vontell","year":"2023","unstructured":"Vontell, R. T. et al. Identification of inflammasome signaling proteins in neurons and microglia in early and intermediate stages of Alzheimer\u2019s disease. Brain Pathol. 33, e13142 (2023).","journal-title":"Brain Pathol."},{"key":"1209_CR71","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1038\/cdd.2015.16","volume":"22","author":"V Kaushal","year":"2015","unstructured":"Kaushal, V. et al. Neuronal NLRP1 inflammasome activation of Caspase-1 coordinately regulates inflammatory interleukin-1-beta production and axonal degeneration-associated Caspase-6 activation. Cell Death Differ 22, 1676\u20131686 (2015).","journal-title":"Cell Death Differ"},{"key":"1209_CR72","doi-asserted-by":"publisher","DOI":"10.1186\/s12974-020-01866-6","volume":"17","author":"KM von Herrmann","year":"2020","unstructured":"von Herrmann, K. M., Anderson, F. L., Martinez, E. M., Young, A. L. & Havrda, M. C. Slc6a3-dependent expression of a CAPS-associated Nlrp3 allele results in progressive behavioral abnormalities and neuroinflammation in aging mice. J. Neuroinflam. 17, 213 (2020).","journal-title":"J. Neuroinflam."},{"key":"1209_CR73","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/s41531-018-0061-5","volume":"4","author":"KM von Herrmann","year":"2018","unstructured":"von Herrmann, K. M. et al. NLRP3 expression in mesencephalic neurons and characterization of a rare NLRP3 polymorphism associated with decreased risk of Parkinson\u2019s disease. NPJ Parkinson\u2019s Dis. 4, 24\u201329 (2018).","journal-title":"NPJ Parkinson\u2019s Dis."},{"key":"1209_CR74","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.trsl.2022.08.006","volume":"252","author":"FL Anderson","year":"2023","unstructured":"Anderson, F. L., Biggs, K. E., Rankin, B. E. & Havrda, M. C. NLRP3 inflammasome in neurodegenerative disease. Transl. Res. 252, 21\u201333 (2023).","journal-title":"Transl. Res."},{"key":"1209_CR75","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1093\/toxsci\/kfy219","volume":"166","author":"FL Anderson","year":"2018","unstructured":"Anderson, F. L., Coffey, M. M., Berwin, B. L. & Havrda, M. C. Inflammasomes: an emerging mechanism translating environmental toxicant exposure into neuroinflammation in parkinson\u2019s disease. Toxicol. Sci. 166, 3\u201315 (2018).","journal-title":"Toxicol. Sci."},{"key":"1209_CR76","doi-asserted-by":"publisher","first-page":"2117","DOI":"10.3233\/JPD-223290","volume":"12","author":"LTN Nguyen","year":"2022","unstructured":"Nguyen, L. T. N. et al. Role of NLRP3 inflammasome in Parkinson\u2019s disease and therapeutic considerations. J. Parkinson\u2019s Dis. 12, 2117\u20132133 (2022).","journal-title":"J. Parkinson\u2019s Dis."},{"key":"1209_CR77","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2021.643254","volume":"12","author":"JA Holbrook","year":"2021","unstructured":"Holbrook, J. A. et al. Neurodegenerative disease and the NLRP3 inflammasome. Front Pharmacol. 12, 643254 (2021).","journal-title":"Front Pharmacol."},{"key":"1209_CR78","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1242\/dev.101428","volume":"141","author":"RN Plasschaert","year":"2014","unstructured":"Plasschaert, R. N. & Bartolomei, M. S. Genomic imprinting in development, growth, behavior and stem cells. Development 141, 1805\u20131813 (2014).","journal-title":"Development"},{"key":"1209_CR79","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/s41576-018-0092-0","volume":"20","author":"D Monk","year":"2019","unstructured":"Monk, D., Mackay, D. J. G., Eggermann, T., Maher, E. R. & Riccio, A. Genomic imprinting disorders: lessons on how genome, epigenome and environment interact. Nat. Rev. Genet. 20, 235\u2013248 (2019).","journal-title":"Nat. Rev. Genet."},{"key":"1209_CR80","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-022-04007-2","volume":"5","author":"X Wen","year":"2022","unstructured":"Wen, X. et al. Interruption of aberrant chromatin looping is required for regenerating RB1 function and suppressing tumorigenesis. Commun. Biol. 5, 1\u201311 (2022).","journal-title":"Commun. Biol."},{"key":"1209_CR81","doi-asserted-by":"publisher","first-page":"e3002559","DOI":"10.1371\/journal.pbio.3002559","volume":"22","author":"D Wu","year":"2024","unstructured":"Wu, D., Sun, J. K. & Chow, K. H. Neuronal cell cycle reentry events in the aging brain are more prevalent in neurodegeneration and lead to cellular senescence. PLoS Biol. 22, e3002559 (2024).","journal-title":"PLoS Biol."},{"key":"1209_CR82","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1111\/ane.12796","volume":"136","author":"D Georgiev","year":"2017","unstructured":"Georgiev, D., Hamberg, K., Hariz, M., Forsgren, L. & Hariz, G. Gender differences in Parkinson\u2019s disease: A clinical perspective. Acta Neurol. Scand. 136, 570\u2013584 (2017).","journal-title":"Acta Neurol. Scand."},{"key":"1209_CR83","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1016\/j.yfrne.2014.02.002","volume":"35","author":"GE Gillies","year":"2014","unstructured":"Gillies, G. E., Pienaar, I. S., Vohra, S. & Qamhawi, Z. Sex differences in Parkinson\u2019s disease. Front. Neuroendocrinol. 35, 370\u2013384 (2014).","journal-title":"Front. Neuroendocrinol."},{"key":"1209_CR84","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbd.2020.104947","volume":"141","author":"AO Gezer","year":"2020","unstructured":"Gezer, A. O. et al. Developmental exposure to the organochlorine pesticide dieldrin causes male-specific exacerbation of \u03b1-synuclein-preformed fibril-induced toxicity and motor deficits. Neurobiol. Dis. 141, 104947 (2020).","journal-title":"Neurobiol. Dis."},{"key":"1209_CR85","doi-asserted-by":"publisher","first-page":"501","DOI":"10.3233\/JPD-191683","volume":"9","author":"S Cerri","year":"2019","unstructured":"Cerri, S., Mus, L. & Blandini, F. Parkinson\u2019s disease in women and men: what\u2019s the difference? J. Parkinson\u2019s Dis. 9, 501\u2013515 (2019).","journal-title":"J. Parkinson\u2019s Dis."},{"key":"1209_CR86","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1093\/toxsci\/kfad086","volume":"196","author":"SL Boyd","year":"2023","unstructured":"Boyd, S. L. et al. Developmental exposure to the Parkinson\u2019s disease-associated organochlorine pesticide dieldrin alters dopamine neurotransmission in \u03b1-synuclein pre-formed fibril (PFF)-injected mice. Toxicological Sci. 196, 99\u2013111 (2023).","journal-title":"Toxicological Sci."},{"key":"1209_CR87","doi-asserted-by":"crossref","unstructured":"Kochmanski, J. & Bernstein, A. I. In Rigor and Reproducibility in Genetics and Genomics 261\u2013284 (Academic Press, 2024).","DOI":"10.1016\/B978-0-12-817218-6.00006-1"},{"key":"1209_CR88","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/978-1-0716-2140-0_2","volume":"2458","author":"B Bhat","year":"2022","unstructured":"Bhat, B. & Jones, G. T. Data analysis of DNA methylation epigenome-wide association studies (EWAS): a guide to the principles of best practice. Methods Mol. Biol. 2458, 23\u201345 (2022).","journal-title":"Methods Mol. Biol."},{"key":"1209_CR89","doi-asserted-by":"publisher","first-page":"139","DOI":"10.2217\/epi-2021-0490","volume":"14","author":"Z Zhang","year":"2022","unstructured":"Zhang, Z. et al. Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays. Epigenomics 14, 139\u2013152 (2022).","journal-title":"Epigenomics"},{"key":"1209_CR90","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1131-9","volume":"18","author":"M van Iterson","year":"2017","unstructured":"van Iterson, M., van Zwet, E. W. & Heijmans, B. T. Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution. Genome Biol. 18, 19 (2017).","journal-title":"Genome Biol."},{"key":"1209_CR91","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1111\/neup.12189","volume":"35","author":"TG Beach","year":"2015","unstructured":"Beach, T. G. et al. Arizona study of aging and neurodegenerative disorders and brain and body donation program. Neuropathology 35, 354\u2013389 (2015).","journal-title":"Neuropathology"},{"key":"1209_CR92","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1007\/s00401-009-0538-8","volume":"117","author":"TG Beach","year":"2009","unstructured":"Beach, T. G. et al. Unified staging system for Lewy body disorders: correlation with nigrostriatal degeneration, cognitive impairment and motor dysfunction. Acta Neuropathol. 117, 613\u2013634 (2009).","journal-title":"Acta Neuropathol."},{"key":"1209_CR93","doi-asserted-by":"publisher","first-page":"3667","DOI":"10.1093\/bioinformatics\/btw527","volume":"32","author":"Z Xu","year":"2016","unstructured":"Xu, Z., Taylor, J. A., Leung, Y. K., Ho, S. M. & Niu, L. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics 32, 3667\u20133669 (2016).","journal-title":"Bioinformatics"},{"key":"1209_CR94","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1093\/bioinformatics\/btw691","volume":"33","author":"J Fortin","year":"2017","unstructured":"Fortin, J., Triche, T. J., Hansen, K. D. & Hansen, K. D. Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics 33, 558\u2013560 (2017).","journal-title":"Bioinformatics"},{"key":"1209_CR95","doi-asserted-by":"publisher","first-page":"1363","DOI":"10.1093\/bioinformatics\/btu049","volume":"30","author":"MJ Aryee","year":"2014","unstructured":"Aryee, M. J. et al. Minfi: A flexible and comprehensive bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30, 1363\u20131369 (2014).","journal-title":"Bioinformatics"},{"key":"1209_CR96","doi-asserted-by":"publisher","first-page":"3982","DOI":"10.1093\/bioinformatics\/btx513","volume":"33","author":"Y Tian","year":"2017","unstructured":"Tian, Y. et al. ChAMP: updated methylation analysis pipeline for Illumina BeadChips. Bioinformatics 33, 3982\u20133984 (2017).","journal-title":"Bioinformatics"},{"key":"1209_CR97","doi-asserted-by":"publisher","first-page":"643","DOI":"10.2217\/epi-2017-0105","volume":"10","author":"C Jiao","year":"2018","unstructured":"Jiao, C. et al. Positional effects revealed in Illumina methylation array and the impact on analysis. Epigenomics 10, 643\u2013659 (2018).","journal-title":"Epigenomics"},{"key":"1209_CR98","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2022.100144","volume":"2","author":"W Zhou","year":"2022","unstructured":"Zhou, W. et al. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genomics 2, 100144 (2022).","journal-title":"Cell Genomics"},{"key":"1209_CR99","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5761-7","volume":"20","author":"G Mansell","year":"2019","unstructured":"Mansell, G. et al. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics 20, 366 (2019).","journal-title":"BMC Genomics"},{"key":"1209_CR100","doi-asserted-by":"publisher","first-page":"vbaf150","DOI":"10.1093\/bioadv\/vbaf150","volume":"5","author":"J Barth","year":"2025","unstructured":"Barth, J. & Reynolds, A. W. EpipwR: efficient power analysis for EWAS with continuous outcomes. Bioinform. Adv. 5, vbaf150 (2025).","journal-title":"Bioinform. Adv."},{"key":"1209_CR101","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23243-4","volume":"12","author":"RG Smith","year":"2021","unstructured":"Smith, R. G. et al. A meta-analysis of epigenome-wide association studies in Alzheimer\u2019s disease highlights novel differentially methylated loci across cortex. Nat. Commun. 12, 3517 (2021).","journal-title":"Nat. Commun."},{"key":"1209_CR102","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-232","volume":"15","author":"S Wahl","year":"2014","unstructured":"Wahl, S. et al. On the potential of models for location and scale for genome-wide DNA methylation data. BMC Bioinform. 15, 232 (2014).","journal-title":"BMC Bioinform."},{"key":"1209_CR103","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02572-z","volume":"23","author":"H Vu","year":"2022","unstructured":"Vu, H. & Ernst, J. Universal annotation of the human genome through integration of over a thousand epigenomic datasets. Genome Biol. 23, 9 (2022).","journal-title":"Genome Biol."},{"key":"1209_CR104","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","volume":"33","author":"JR Conway","year":"2017","unstructured":"Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938\u20132940 (2017).","journal-title":"Bioinformatics"},{"key":"1209_CR105","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nbt.1630","volume":"28","author":"CY McLean","year":"2010","unstructured":"McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28, 495\u2013501 (2010).","journal-title":"Nat Biotechnol"},{"key":"1209_CR106","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1093\/bioinformatics\/btp101","volume":"25","author":"G Bindea","year":"2009","unstructured":"Bindea, G. et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25, 1091\u20131093 (2009).","journal-title":"Bioinformatics"},{"key":"1209_CR107","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","volume":"27","author":"ME Smoot","year":"2011","unstructured":"Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. & Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431\u2013432 (2011).","journal-title":"Bioinformatics"},{"key":"1209_CR108","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","volume":"51","author":"D Szklarczyk","year":"2023","unstructured":"Szklarczyk, D. et al. The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638\u2013D646 (2023).","journal-title":"Nucleic Acids Res."}],"container-title":["npj Parkinson's Disease"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41531-025-01209-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41531-025-01209-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41531-025-01209-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T21:03:57Z","timestamp":1767042237000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41531-025-01209-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,22]]},"references-count":108,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["1209"],"URL":"https:\/\/doi.org\/10.1038\/s41531-025-01209-3","relation":{},"ISSN":["2373-8057"],"issn-type":[{"value":"2373-8057","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,22]]},"assertion":[{"value":"5 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 December 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":"363"}}