{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:53:43Z","timestamp":1782280423514,"version":"3.54.5"},"posted":{"date-parts":[[2024,6,29]]},"group-title":"Neuroscience","reference-count":90,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,12,29]],"date-time":"2024-12-29T00:00:00Z","timestamp":1735430400000},"content-version":"vor","delay-in-days":183,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,6,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Sporadic early-onset Alzheimer\u2019s disease (sEOAD) represents a significant but less-studied subtype of Alzheimer\u2019s disease (AD). Here, we generated a single-nucleus multiome atlas derived from the postmortem prefrontal cortex, entorhinal cortex, and hippocampus of nine individuals with or without sEOAD. Comprehensive analyses were conducted to delineate cell type-specific transcriptomic changes and linked candidate\n                  <jats:italic>cis-<\/jats:italic>\n                  regulatory elements (cCREs) across brain regions. We prioritized seven conservative transcription factors in glial cells in multiple brain regions, including RFX4 in astrocytes and IKZF1 in microglia, which are implicated in regulating sEOAD-associated genes. Moreover, we identified the top 25 altered intercellular signaling between glial cells and neurons, highlighting their regulatory potential on gene expression in receiver cells. We reported 38 cCREs linked to sEOAD-associated genes overlapped with late-onset AD risk loci, and sEOAD cCREs enriched in neuropsychiatric disorder risk loci. This atlas helps dissect transcriptional and chromatin dynamics in sEOAD, providing a key resource for AD research.\n                <\/jats:p>","DOI":"10.1101\/2024.06.25.600720","type":"posted-content","created":{"date-parts":[[2024,6,29]],"date-time":"2024-06-29T20:25:16Z","timestamp":1719692716000},"source":"Crossref","is-referenced-by-count":1,"title":["Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer\u2019s disease"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9193-6319","authenticated-orcid":false,"given":"Andi","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7624-3195","authenticated-orcid":false,"given":"Citu","family":"Citu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0255-706X","authenticated-orcid":false,"given":"Nitesh","family":"Enduru","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xian","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8303-8116","authenticated-orcid":false,"given":"Astrid M.","family":"Manuel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7138-0907","authenticated-orcid":false,"given":"Tirthankar","family":"Sinha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damian","family":"Gorski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3797-7582","authenticated-orcid":false,"given":"Brisa S.","family":"Fernandes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meifang","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul E.","family":"Schulz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6148-8861","authenticated-orcid":false,"given":"Lukas M.","family":"Simon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudio","family":"Soto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3477-0914","authenticated-orcid":false,"given":"Zhongming","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2024070208150652000_2024.06.25.600720v1.1","doi-asserted-by":"crossref","unstructured":"Ayodele, T. , Rogaeva, E. , Kurup, J.T. , Beecham, G. & Reitz, C . Early-onset Alzheimer\u2019s Disease: what is missing in research? Curr. Neurol. Neurosci. Rep. 21, 4 (2021).","DOI":"10.1007\/s11910-020-01090-y"},{"key":"2024070208150652000_2024.06.25.600720v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41380-022-01531-9"},{"key":"2024070208150652000_2024.06.25.600720v1.3","doi-asserted-by":"crossref","first-page":"fcad280","DOI":"10.1093\/braincomms\/fcad280","article-title":"Longitudinal clinical, cognitive and biomarker profiles in dominantly inherited versus sporadic early-onset Alzheimer\u2019s disease","volume":"5","year":"2023","journal-title":"Brain Commun"},{"key":"2024070208150652000_2024.06.25.600720v1.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.adf7044"},{"key":"2024070208150652000_2024.06.25.600720v1.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.add7046"},{"key":"2024070208150652000_2024.06.25.600720v1.6","doi-asserted-by":"crossref","unstructured":"Yan, F. et al. Single-cell multiomics decodes regulatory programs for mouse secondary palate development. Nat. Commun. 15, 821 (2024).","DOI":"10.1038\/s41467-024-45199-x"},{"key":"2024070208150652000_2024.06.25.600720v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00894-z"},{"key":"2024070208150652000_2024.06.25.600720v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.08.040"},{"key":"2024070208150652000_2024.06.25.600720v1.9","doi-asserted-by":"crossref","unstructured":"Anderson, A.G. et al. Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer\u2019s disease-specific cis-regulatory elements. Cell Genom. 3, 100263 (2023).","DOI":"10.1016\/j.xgen.2023.100263"},{"key":"2024070208150652000_2024.06.25.600720v1.10","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.tins.2022.11.006","article-title":"Entorhinal cortex dysfunction in Alzheimer\u2019s disease","volume":"46","year":"2023","journal-title":"Trends Neurosci"},{"key":"2024070208150652000_2024.06.25.600720v1.11","doi-asserted-by":"crossref","unstructured":"Mu, Y. & Gage, F.H . Adult hippocampal neurogenesis and its role in Alzheimer\u2019s disease. Mol. Neurodegener. 6, 85 (2011).","DOI":"10.1186\/1750-1326-6-85"},{"key":"2024070208150652000_2024.06.25.600720v1.12","doi-asserted-by":"publisher","DOI":"10.1212\/NXG.0000000000000512"},{"key":"2024070208150652000_2024.06.25.600720v1.13","doi-asserted-by":"publisher","DOI":"10.1001\/archneurol.2011.221"},{"key":"2024070208150652000_2024.06.25.600720v1.14","first-page":"e12155","article-title":"Insight into the genetic etiology of Alzheimer\u2019s disease: a comprehensive review of the role of rare variants","volume":"13","year":"2021","journal-title":"Alzheimer\u2019s Dement. Diagn. Assess. Dis. Monit"},{"key":"2024070208150652000_2024.06.25.600720v1.15","doi-asserted-by":"crossref","first-page":"8368","DOI":"10.1038\/s41598-019-44848-2","article-title":"Genetic analyses of early-onset Alzheimer\u2019s disease using next generation sequencing","volume":"9","year":"2019","journal-title":"Sci. Rep"},{"key":"2024070208150652000_2024.06.25.600720v1.16","first-page":"e12482","article-title":"Early-onset Alzheimer\u2019s disease explained by polygenic risk of late-onset disease?","volume":"15","year":"2023","journal-title":"Alzheimer\u2019s Dement. Diagn. Assess. Dis. Monit"},{"key":"2024070208150652000_2024.06.25.600720v1.17","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1038\/s41588-018-0311-9","article-title":"Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer\u2019s disease risk","volume":"51","year":"2019","journal-title":"Nat. Genet"},{"key":"2024070208150652000_2024.06.25.600720v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0358-2"},{"key":"2024070208150652000_2024.06.25.600720v1.19","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/s41588-020-00776-w","article-title":"Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer\u2019s disease risk genes","volume":"53","year":"2021","journal-title":"Nat. Genet"},{"key":"2024070208150652000_2024.06.25.600720v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00921-z"},{"key":"2024070208150652000_2024.06.25.600720v1.21","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1038\/s41588-022-01024-z","article-title":"New insights into the genetic etiology of Alzheimer\u2019s disease and related dementias","volume":"54","year":"2022","journal-title":"Nat. Genet"},{"key":"2024070208150652000_2024.06.25.600720v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/nrneurol.2012.263"},{"key":"2024070208150652000_2024.06.25.600720v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2018.04.002"},{"key":"2024070208150652000_2024.06.25.600720v1.24","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/s41586-019-1195-2","article-title":"Single-cell transcriptomic analysis of Alzheimer\u2019s disease","volume":"570","year":"2019","journal-title":"Nature"},{"key":"2024070208150652000_2024.06.25.600720v1.25","unstructured":"Gabitto, M.I. , et al. Integrated multimodal cell atlas of Alzheimer\u2019s disease. bioRxiv, 2023.2005.2008.539485 (2024)."},{"key":"2024070208150652000_2024.06.25.600720v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-019-0539-4"},{"key":"2024070208150652000_2024.06.25.600720v1.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27150-6"},{"key":"2024070208150652000_2024.06.25.600720v1.28","doi-asserted-by":"crossref","unstructured":"Arendt, T. , Br\u00fcckner, M.K. , Morawski, M. , J\u00e4ger, C. & Gertz, H.-J . Early neurone loss in Alzheimer\u2019s disease: cortical or subcortical? Acta Neuropathol. Commun. 3, 10 (2015).","DOI":"10.1186\/s40478-015-0187-1"},{"key":"2024070208150652000_2024.06.25.600720v1.29","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awv236"},{"key":"2024070208150652000_2024.06.25.600720v1.30","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-021-02263-w"},{"key":"2024070208150652000_2024.06.25.600720v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.jalz.2016.10.003"},{"key":"2024070208150652000_2024.06.25.600720v1.32","doi-asserted-by":"crossref","unstructured":"Reed, M.J. , Damodarasamy, M. & Banks, W.A . The extracellular matrix of the blood-brain barrier: structural and functional roles in health, aging, and Alzheimer\u2019s disease. Tissue Barriers 7, 1651157 (2019).","DOI":"10.1080\/21688370.2019.1651157"},{"key":"2024070208150652000_2024.06.25.600720v1.33","doi-asserted-by":"crossref","unstructured":"Wang, X.L. & Li, L . Cell type-specific potential pathogenic genes and functional pathways in Alzheimer\u2019s disease. BMC Neurol. 21, 381 (2021).","DOI":"10.1186\/s12883-021-02407-1"},{"key":"2024070208150652000_2024.06.25.600720v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24232-3"},{"key":"2024070208150652000_2024.06.25.600720v1.35","doi-asserted-by":"crossref","unstructured":"Satarker, S. et al. Astrocytic glutamatergic transmission and its implications in neurodegenerative disorders. Cells 11 (2022).","DOI":"10.3390\/cells11071139"},{"key":"2024070208150652000_2024.06.25.600720v1.36","doi-asserted-by":"crossref","unstructured":"Bell, S.M. et al. Mitochondrial dysfunction in Alzheimer\u2019s disease: a biomarker of the future? Biomedicines 9 (2021).","DOI":"10.3390\/biomedicines9010063"},{"key":"2024070208150652000_2024.06.25.600720v1.37","doi-asserted-by":"crossref","first-page":"5702","DOI":"10.1038\/s41380-021-01068-3","article-title":"Brain cells derived from Alzheimer\u2019s disease patients have multiple specific innate abnormalities in energy metabolism","volume":"26","year":"2021","journal-title":"Mol. Psychiatry"},{"key":"2024070208150652000_2024.06.25.600720v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2493-4"},{"key":"2024070208150652000_2024.06.25.600720v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10101-7"},{"key":"2024070208150652000_2024.06.25.600720v1.40","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.01.029"},{"key":"2024070208150652000_2024.06.25.600720v1.41","doi-asserted-by":"crossref","first-page":"3996","DOI":"10.1038\/s41467-024-48484-x","article-title":"Effects of SPI1-mediated transcriptome remodeling on Alzheimer\u2019s disease-related phenotypes in mouse models of Abeta amyloidosis","volume":"15","year":"2024","journal-title":"Nat. Commun"},{"key":"2024070208150652000_2024.06.25.600720v1.42","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1038\/s41592-023-01938-4","article-title":"SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks","volume":"20","year":"2023","journal-title":"Nat. Methods"},{"key":"2024070208150652000_2024.06.25.600720v1.43","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.molcel.2020.11.015","article-title":"Molecular co-occupancy identifies transcription factor binding vooperativity in vivo","volume":"81","year":"2021","journal-title":"Mol. Cell"},{"key":"2024070208150652000_2024.06.25.600720v1.44","doi-asserted-by":"crossref","first-page":"D306","DOI":"10.1093\/nar\/gkac849","article-title":"TFSyntax: a database of transcription factors binding syntax in mammalian genomes","volume":"51","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024070208150652000_2024.06.25.600720v1.45","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4401"},{"key":"2024070208150652000_2024.06.25.600720v1.46","doi-asserted-by":"crossref","unstructured":"Choi, W. et al. RFX4 is an intrinsic factor for neuronal differentiation through induction of proneural genes POU3F2 and NEUROD1. Cell. Mol. Life Sci. 81, 99 (2024).","DOI":"10.1007\/s00018-024-05129-y"},{"key":"2024070208150652000_2024.06.25.600720v1.47","doi-asserted-by":"crossref","unstructured":"Dai, D.L. , Li, M. & Lee, E.B . Human Alzheimer\u2019s disease reactive astrocytes exhibit a loss of homeostastic gene expression. Acta Neuropathol. Commun. 11, 127 (2023).","DOI":"10.1186\/s40478-023-01624-8"},{"key":"2024070208150652000_2024.06.25.600720v1.48","doi-asserted-by":"crossref","unstructured":"Liu, A. , Fernandes, B.S. , Citu, C. & Zhao, Z . Unraveling the intercellular communication disruption and key pathways in Alzheimer\u2019s disease: an integrative study of single-nucleus transcriptomes and genetic association. Alzheimers Res. Ther. 16, 3 (2024).","DOI":"10.1186\/s13195-023-01372-w"},{"key":"2024070208150652000_2024.06.25.600720v1.49","doi-asserted-by":"crossref","unstructured":"Browaeys, R. , et al. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data. bioRxiv, 2023.2006.2013.544751 (2023).","DOI":"10.1101\/2023.06.13.544751"},{"key":"2024070208150652000_2024.06.25.600720v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/nrm.2015.16"},{"key":"2024070208150652000_2024.06.25.600720v1.51","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1093\/jnen\/nlab056","article-title":"Loss of lysosomal proteins progranulin and prosaposin associated with increased neurofibrillary tangle development in Alzheimer disease","volume":"80","year":"2021","journal-title":"J. Neuropathol. Exp. Neurol"},{"key":"2024070208150652000_2024.06.25.600720v1.52","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20181290"},{"key":"2024070208150652000_2024.06.25.600720v1.53","doi-asserted-by":"crossref","unstructured":"Leung, H.W. , Foo, G. & VanDongen, A . Arc regulates transcription of genes for plasticity, excitability and Alzheimer\u2019s disease. Biomedicines 10 (2022).","DOI":"10.3390\/biomedicines10081946"},{"key":"2024070208150652000_2024.06.25.600720v1.54","doi-asserted-by":"crossref","first-page":"e064268","DOI":"10.1002\/alz.064268","article-title":"A large-scale genome-wide association study of early-onset Alzheimer disease","volume":"18","year":"2022","journal-title":"Alzheimer\u2019s & Dementia"},{"key":"2024070208150652000_2024.06.25.600720v1.55","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-022-01128-z"},{"key":"2024070208150652000_2024.06.25.600720v1.56","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3211"},{"key":"2024070208150652000_2024.06.25.600720v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/ng.543"},{"key":"2024070208150652000_2024.06.25.600720v1.58","doi-asserted-by":"publisher","DOI":"10.1038\/nature12873"},{"key":"2024070208150652000_2024.06.25.600720v1.59","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3434"},{"key":"2024070208150652000_2024.06.25.600720v1.60","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3424"},{"key":"2024070208150652000_2024.06.25.600720v1.61","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3680"},{"key":"2024070208150652000_2024.06.25.600720v1.62","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3760."},{"key":"2024070208150652000_2024.06.25.600720v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3745"},{"key":"2024070208150652000_2024.06.25.600720v1.64","doi-asserted-by":"crossref","unstructured":"Nagel, M. , Watanabe, K. , Stringer, S. , Posthuma, D. & van der Sluis, S . Item-level analyses reveal genetic heterogeneity in neuroticism. Nat. Commun. 9, 905 (2018).","DOI":"10.1038\/s41467-018-03242-8"},{"key":"2024070208150652000_2024.06.25.600720v1.65","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0090-3"},{"key":"2024070208150652000_2024.06.25.600720v1.66","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0344-8"},{"key":"2024070208150652000_2024.06.25.600720v1.67","doi-asserted-by":"publisher","DOI":"10.1038\/S41593-018-0326-7"},{"key":"2024070208150652000_2024.06.25.600720v1.68","unstructured":"International Multiple Sclerosis Genetics, C. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science 365 (2019)."},{"key":"2024070208150652000_2024.06.25.600720v1.69","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12576-w"},{"key":"2024070208150652000_2024.06.25.600720v1.70","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0481-0"},{"key":"2024070208150652000_2024.06.25.600720v1.71","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00857-4"},{"key":"2024070208150652000_2024.06.25.600720v1.72","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-022-04434-5"},{"key":"2024070208150652000_2024.06.25.600720v1.73","doi-asserted-by":"publisher","DOI":"10.1038\/S41588-022-01285-8"},{"key":"2024070208150652000_2024.06.25.600720v1.74","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1038\/s41562-023-01579-9","article-title":"Participation bias in the UK Biobank distorts genetic associations and downstream analyses. Nat","volume":"7","year":"2023","journal-title":"Hum. Behav"},{"key":"2024070208150652000_2024.06.25.600720v1.75","doi-asserted-by":"crossref","unstructured":"Enduru, N. et al. Genetic overlap between Alzheimer\u2019s disease and immune-mediated diseases: an atlas of shared genetic determinants and biological convergence. Mol. Psychiatry (2024).","DOI":"10.1038\/s41380-024-02510-y"},{"key":"2024070208150652000_2024.06.25.600720v1.76","doi-asserted-by":"crossref","unstructured":"Hunker, A.C. & Zweifel, L.S . Protocol to design, clone, and validate sgRNAs for in vivo reverse genetic studies. STAR Protoc. 1 (2020).","DOI":"10.1016\/j.xpro.2020.100070"},{"key":"2024070208150652000_2024.06.25.600720v1.77","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01943-7"},{"key":"2024070208150652000_2024.06.25.600720v1.78","doi-asserted-by":"crossref","unstructured":"Wang, M. et al. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer\u2019s disease: review, recommendation, implementation and application. Mol. Neurodegener. 17, 17 (2022).","DOI":"10.1186\/s13024-022-00517-z"},{"key":"2024070208150652000_2024.06.25.600720v1.79","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01282-5"},{"key":"2024070208150652000_2024.06.25.600720v1.80","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors","volume":"8","year":"2019","journal-title":"Cell Syst"},{"key":"2024070208150652000_2024.06.25.600720v1.81","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41587-021-01206-w","article-title":"A Python library for probabilistic analysis of single-cell omics data","volume":"40","year":"2022","journal-title":"Nat. Biotechnol"},{"key":"2024070208150652000_2024.06.25.600720v1.82","doi-asserted-by":"crossref","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","DOI":"10.1186\/gb-2008-9-9-r137"},{"key":"2024070208150652000_2024.06.25.600720v1.83","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0"},{"key":"2024070208150652000_2024.06.25.600720v1.84","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25960-2"},{"key":"2024070208150652000_2024.06.25.600720v1.85","doi-asserted-by":"publisher","DOI":"10.1089\/omi.2011.0118"},{"key":"2024070208150652000_2024.06.25.600720v1.86","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv145"},{"key":"2024070208150652000_2024.06.25.600720v1.87","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.056"},{"key":"2024070208150652000_2024.06.25.600720v1.88","doi-asserted-by":"crossref","unstructured":"Myers, T.A. , Chanock, S.J. & Machiela, M.J . LDlinkR: an R package for rapidly calculating linkage disequilibrium statistics in diverse populations. Front. Genet. 11, 157 (2020).","DOI":"10.3389\/fgene.2020.00157"},{"key":"2024070208150652000_2024.06.25.600720v1.89","doi-asserted-by":"publisher","DOI":"10.1038\/nature15394"},{"key":"2024070208150652000_2024.06.25.600720v1.90","doi-asserted-by":"crossref","unstructured":"Zimmerman, K.D. & Langefeld, C.D . Hierarchicell: an R-package for estimating power for tests of differential expression with single-cell data. BMC Genomics 22, 319 (2021).","DOI":"10.1186\/s12864-021-07635-w"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.06.25.600720","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:01:15Z","timestamp":1782277275000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.06.25.600720"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,29]]},"references-count":90,"URL":"https:\/\/doi.org\/10.1101\/2024.06.25.600720","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1126\/sciadv.adw4917","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2024,6,29]]},"subtype":"preprint"}}