{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T10:00:32Z","timestamp":1790244032138,"version":"4.1.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000062","name":"U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["U54DK134301"],"award-info":[{"award-number":["U54DK134301"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["U54DK134301"],"award-info":[{"award-number":["U54DK134301"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Aging"],"DOI":"10.1038\/s43587-026-01221-z","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T09:02:23Z","timestamp":1790240543000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A cross-species single-cell kidney epigenome atlas reveals epithelial-dominant aging-like states in disease"],"prefix":"10.1038","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5565-2685","authenticated-orcid":false,"given":"Hyeonsoo","family":"Jeong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8637-9044","authenticated-orcid":false,"given":"Blue B.","family":"Lake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dinh","family":"Diep","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2963-0834","authenticated-orcid":false,"given":"Xuwen","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9087-4585","authenticated-orcid":false,"given":"Debora L.","family":"Gisch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madhurima","family":"Kaushal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7871-0999","authenticated-orcid":false,"given":"Stephanie","family":"Reinert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3066-2876","authenticated-orcid":false,"given":"Michael T.","family":"Eadon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph P.","family":"Gaut","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2804-127X","authenticated-orcid":false,"given":"Sanjay","family":"Jain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7596-5224","authenticated-orcid":false,"given":"Kun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"1221_CR1","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/S0140-6736(13)60647-9","volume":"382","author":"NH Lameire","year":"2013","unstructured":"Lameire, N. H. et al. Acute kidney injury: an increasing global concern. Lancet 382, 170\u2013179 (2013).","journal-title":"Lancet"},{"key":"1221_CR2","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1146\/annurev-med-050214-013407","volume":"67","author":"A Zuk","year":"2016","unstructured":"Zuk, A. & Bonventre, J. V. Acute kidney injury. Annu. Rev. Med. 67, 293\u2013307 (2016).","journal-title":"Annu. Rev. Med."},{"key":"1221_CR3","doi-asserted-by":"publisher","first-page":"15874","DOI":"10.1073\/pnas.2005477117","volume":"117","author":"Y Kirita","year":"2020","unstructured":"Kirita, Y., Wu, H., Uchimura, K., Wilson, P. C. & Humphreys, B. D. Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury. Proc. Natl Acad. Sci. USA 117, 15874\u201315883 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1221_CR4","doi-asserted-by":"publisher","first-page":"569322","DOI":"10.3389\/fphys.2020.569322","volume":"11","author":"L Sheng","year":"2020","unstructured":"Sheng, L. & Zhuang, S. New insights into the role and mechanism of partial epithelial-mesenchymal transition in kidney fibrosis. Front. Physiol. 11, 569322 (2020).","journal-title":"Front. Physiol."},{"key":"1221_CR5","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1126\/science.aar2131","volume":"360","author":"J Park","year":"2018","unstructured":"Park, J. et al. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. Science 360, 758\u2013763 (2018).","journal-title":"Science"},{"key":"1221_CR6","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1681\/ASN.2018121251","volume":"30","author":"M-H Docherty","year":"2019","unstructured":"Docherty, M.-H., O\u2019Sullivan, E. D., Bonventre, J. V. & Ferenbach, D. A. Cellular senescence in the kidney. J. Am. Soc. Nephrol. 30, 726\u2013736 (2019).","journal-title":"J. Am. Soc. Nephrol."},{"key":"1221_CR7","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.ado2849","volume":"10","author":"Y Muto","year":"2024","unstructured":"Muto, Y. et al. Epigenetic reprogramming driving successful and failed repair in acute kidney injury. Sci. Adv. 10, eado2849 (2024).","journal-title":"Sci. Adv."},{"key":"1221_CR8","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/s41581-018-0103-6","volume":"15","author":"C Guo","year":"2019","unstructured":"Guo, C., Dong, G., Liang, X. & Dong, Z. Epigenetic regulation in AKI and kidney repair: mechanisms and therapeutic implications. Nat. Rev. Nephrol. 15, 220\u2013239 (2019).","journal-title":"Nat. Rev. Nephrol."},{"key":"1221_CR9","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s41586-023-05769-3","volume":"619","author":"BB Lake","year":"2023","unstructured":"Lake, B. B. et al. An atlas of healthy and injured cell states and niches in the human kidney. Nature 619, 585\u2013594 (2023).","journal-title":"Nature"},{"key":"1221_CR10","doi-asserted-by":"publisher","unstructured":"Lake, B. B. et al. Cellular and spatial drivers of unresolved injury and functional decline in the human kidney. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2025.09.26.678707 (2025).","DOI":"10.1101\/2025.09.26.678707"},{"key":"1221_CR11","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1038\/s41588-024-01802-x","volume":"56","author":"A Abedini","year":"2024","unstructured":"Abedini, A. et al. Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression. Nat. Genet. 56, 1712\u20131724 (2024).","journal-title":"Nat. Genet."},{"key":"1221_CR12","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1101\/gad.947102","volume":"16","author":"A Bird","year":"2002","unstructured":"Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6\u201321 (2002).","journal-title":"Genes Dev."},{"key":"1221_CR13","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nrg3354","volume":"14","author":"ZD Smith","year":"2013","unstructured":"Smith, Z. D. & Meissner, A. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 14, 204\u2013220 (2013).","journal-title":"Nat. Rev. Genet."},{"key":"1221_CR14","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nrg.2016.112","volume":"17","author":"B Bonev","year":"2016","unstructured":"Bonev, B. & Cavalli, G. Organization and function of the 3D genome. Nat. Rev. Genet. 17, 661\u2013678 (2016).","journal-title":"Nat. Rev. Genet."},{"key":"1221_CR15","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SSP Rao","year":"2014","unstructured":"Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665\u20131680 (2014).","journal-title":"Cell"},{"key":"1221_CR16","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1681\/ASN.2015121308","volume":"28","author":"ED O\u2019Sullivan","year":"2017","unstructured":"O\u2019Sullivan, E. D., Hughes, J. & Ferenbach, D. A. Renal aging: causes and consequences. J. Am. Soc. Nephrol. 28, 407\u2013420 (2017).","journal-title":"J. Am. Soc. Nephrol."},{"key":"1221_CR17","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1038\/s41592-019-0502-z","volume":"16","author":"G Li","year":"2019","unstructured":"Li, G. et al. Joint profiling of DNA methylation and chromatin architecture in single cells. Nat. Methods 16, 991\u2013993 (2019).","journal-title":"Nat. Methods"},{"key":"1221_CR18","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35374-3","volume":"13","author":"RV Nichols","year":"2022","unstructured":"Nichols, R. V. et al. High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nat. Commun. 13, 7627 (2022).","journal-title":"Nat. Commun."},{"key":"1221_CR19","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/s41586-022-05580-6","volume":"613","author":"N Loyfer","year":"2023","unstructured":"Loyfer, N. et al. A DNA methylation atlas of normal human cell types. Nature 613, 355\u2013364 (2023).","journal-title":"Nature"},{"key":"1221_CR20","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/nature10716","volume":"480","author":"MB Stadler","year":"2011","unstructured":"Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490\u2013495 (2011).","journal-title":"Nature"},{"key":"1221_CR21","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"1221_CR22","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1016\/j.devcel.2024.02.010","volume":"59","author":"Y Zhang","year":"2024","unstructured":"Zhang, Y., Kang, Z., Liu, M., Wang, L. & Liu, F. Single-cell omics identifies inflammatory signaling as a trans-differentiation trigger in mouse embryos. Dev. Cell 59, 961\u2013978.e7 (2024).","journal-title":"Dev. Cell"},{"key":"1221_CR23","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":"1221_CR24","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1681\/ASN.0000000000000057","volume":"34","author":"LMS Gerhardt","year":"2023","unstructured":"Gerhardt, L. M. S. et al. Lineage tracing and single-nucleus multiomics reveal novel features of adaptive and maladaptive repair after acute kidney injury. J. Am. Soc. Nephrol. 34, 554\u2013571 (2023).","journal-title":"J. Am. Soc. Nephrol."},{"key":"1221_CR25","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/s43587-022-00248-2","volume":"2","author":"AT Higgins-Chen","year":"2022","unstructured":"Higgins-Chen, A. T. et al. A computational solution for bolstering reliability of epigenetic clocks: implications for clinical trials and longitudinal tracking. Nat. Aging 2, 644\u2013661 (2022).","journal-title":"Nat. Aging"},{"key":"1221_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44467-6","volume":"15","author":"DL Gisch","year":"2024","unstructured":"Gisch, D. L. et al. The chromatin landscape of healthy and injured cell types in the human kidney. Nat. Commun. 15, 433 (2024).","journal-title":"Nat. Commun."},{"key":"1221_CR27","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1038\/ng.3211","volume":"47","author":"Schizophrenia Working Group of the Psychiatric Genomics Consortium","year":"2015","unstructured":"Schizophrenia Working Group of the Psychiatric Genomics Consortium et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291\u2013295 (2015).","journal-title":"Nat. Genet."},{"key":"1221_CR28","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/ng.3805","volume":"49","author":"S Guo","year":"2017","unstructured":"Guo, S. et al. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat. Genet. 49, 635\u2013642 (2017).","journal-title":"Nat. Genet."},{"key":"1221_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34854-w","volume":"13","author":"X Cao","year":"2022","unstructured":"Cao, X. et al. Chromatin accessibility dynamics dictate renal tubular epithelial cell response to injury. Nat. Commun. 13, 7322 (2022).","journal-title":"Nat. Commun."},{"key":"1221_CR30","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abj9111","volume":"7","author":"J-Y Lee","year":"2021","unstructured":"Lee, J.-Y. et al. Misexpression of genes lacking CpG islands drives degenerative changes during aging. Sci. Adv. 7, eabj9111 (2021).","journal-title":"Sci. Adv."},{"key":"1221_CR31","doi-asserted-by":"publisher","first-page":"4382","DOI":"10.1093\/nar\/gky147","volume":"46","author":"S Beck","year":"2018","unstructured":"Beck, S. et al. Implications of CpG islands on chromosomal architectures and modes of global gene regulation. Nucleic Acids Res. 46, 4382\u20134391 (2018).","journal-title":"Nucleic Acids Res"},{"key":"1221_CR32","doi-asserted-by":"publisher","DOI":"10.1126\/science.add6371","volume":"383","author":"S Aggarwal","year":"2024","unstructured":"Aggarwal, S. et al. SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys. Science 383, eadd6371 (2024).","journal-title":"Science"},{"key":"1221_CR33","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545\u201315550 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1221_CR34","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","volume":"485","author":"JR Dixon","year":"2012","unstructured":"Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376\u2013380 (2012).","journal-title":"Nature"},{"key":"1221_CR35","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/s41586-023-06592-6","volume":"622","author":"BB Sun","year":"2023","unstructured":"Sun, B. B. et al. Plasma proteomic associations with genetics and health in the UK Biobank. Nature 622, 329\u2013338 (2023).","journal-title":"Nature"},{"key":"1221_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-10-r115","volume":"14","author":"S Horvath","year":"2013","unstructured":"Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, 3156 (2013).","journal-title":"Genome Biol."},{"key":"1221_CR37","doi-asserted-by":"publisher","first-page":"e679","DOI":"10.1212\/WNL.0000000000207489","volume":"101","author":"V Maltby","year":"2023","unstructured":"Maltby, V. et al. Evaluation of cell-specific epigenetic age acceleration in people with multiple sclerosis. Neurology 101, e679\u2013e689 (2023).","journal-title":"Neurology"},{"key":"1221_CR38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29801-8","volume":"13","author":"X Cao","year":"2022","unstructured":"Cao, X. et al. Accelerated biological aging in COVID-19 patients. Nat. Commun. 13, 2135 (2022).","journal-title":"Nat. Commun."},{"key":"1221_CR39","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s43856-023-00250-8","volume":"3","author":"VM Vetter","year":"2023","unstructured":"Vetter, V. M. et al. DNA methylation age acceleration is associated with risk of diabetes complications. Commun. Med. 3, 21 (2023).","journal-title":"Commun. Med."},{"key":"1221_CR40","first-page":"429","volume":"10","author":"DL McCartney","year":"2018","unstructured":"McCartney, D. L. et al. Investigating the relationship between DNA methylation age acceleration and risk factors for Alzheimer\u2019s disease. Alzheimers Dement. Diagn. Assess. Dis. Monit. 10, 429\u2013437 (2018).","journal-title":"Alzheimers Dement. Diagn. Assess. Dis. Monit."},{"key":"1221_CR41","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1038\/nrneph.2017.107","volume":"13","author":"P Bhargava","year":"2017","unstructured":"Bhargava, P. & Schnellmann, R. G. Mitochondrial energetics in the kidney. Nat. Rev. Nephrol. 13, 629\u2013646 (2017).","journal-title":"Nat. Rev. Nephrol."},{"key":"1221_CR42","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1038\/nri3523","volume":"13","author":"C Kurts","year":"2013","unstructured":"Kurts, C., Panzer, U., Anders, H.-J. & Rees, A. J. The immune system and kidney disease: basic concepts and clinical implications. Nat. Rev. Immunol. 13, 738\u2013753 (2013).","journal-title":"Nat. Rev. Immunol."},{"key":"1221_CR43","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1016\/j.devcel.2019.10.005","volume":"51","author":"A Ransick","year":"2019","unstructured":"Ransick, A. et al. Single-cell profiling reveals sex, lineage, and regional diversity in the mouse kidney. Dev. Cell 51, 399\u2013413.e7 (2019).","journal-title":"Dev. Cell"},{"key":"1221_CR44","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1681\/ASN.0000000000000089","volume":"34","author":"L Chen","year":"2023","unstructured":"Chen, L., Chou, C.-L., Yang, C.-R. & Knepper, M. A. Multiomics analyses reveal sex differences in mouse renal proximal subsegments. J. Am. Soc. Nephrol. 34, 829\u2013845 (2023).","journal-title":"J. Am. Soc. Nephrol."},{"key":"1221_CR45","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s41581-023-00757-2","volume":"20","author":"AA McDonough","year":"2024","unstructured":"McDonough, A. A., Harris, A. N., Xiong, L. I. & Layton, A. T. Sex differences in renal transporters: assessment and functional consequences. Nat. Rev. Nephrol. 20, 21\u201336 (2024).","journal-title":"Nat. Rev. Nephrol."},{"key":"1221_CR46","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","volume":"27","author":"F Krueger","year":"2011","unstructured":"Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27, 1571\u20131572 (2011).","journal-title":"Bioinformatics"},{"key":"1221_CR47","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"1221_CR48","doi-asserted-by":"publisher","first-page":"861","DOI":"10.21105\/joss.00861","volume":"3","author":"L McInnes","year":"2018","unstructured":"McInnes, L., Healy, J., Saul, N. & Gro\u00dfberger, L. UMAP: uniform manifold approximation and projection. J. Open Source Softw. 3, 861 (2018).","journal-title":"J. Open Source Softw."},{"key":"1221_CR49","doi-asserted-by":"publisher","first-page":"1458","DOI":"10.1038\/s41587-022-01284-4","volume":"40","author":"Z-J Cao","year":"2022","unstructured":"Cao, Z.-J. & Gao, G. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding. Nat. Biotechnol. 40, 1458\u20131466 (2022).","journal-title":"Nat. Biotechnol."},{"key":"1221_CR50","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0","volume":"19","author":"FA Wolf","year":"2018","unstructured":"Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).","journal-title":"Genome Biol."},{"key":"1221_CR51","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1093\/bioinformatics\/17.6.520","volume":"17","author":"O Troyanskaya","year":"2001","unstructured":"Troyanskaya, O. et al. Missing value estimation methods for DNA microarrays. Bioinformatics 17, 520\u2013525 (2001).","journal-title":"Bioinformatics"},{"key":"1221_CR52","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt599","volume":"41","author":"L Burger","year":"2013","unstructured":"Burger, L., Gaidatzis, D., Sch\u00fcbeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155\u2013e155 (2013).","journal-title":"Nucleic Acids Res."},{"key":"1221_CR53","doi-asserted-by":"publisher","first-page":"e202503514","DOI":"10.26508\/lsa.202503514","volume":"9","author":"N Loyfer","year":"2026","unstructured":"Loyfer, N., Rosenski, J. & Kaplan, T. wgbstools: a computational suite for DNA methylation sequencing data analysis. Life Sci. Alliance 9, e202503514 (2026).","journal-title":"Life Sci. Alliance"},{"key":"1221_CR54","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1093\/biostatistics\/kxs033","volume":"14","author":"H Wu","year":"2013","unstructured":"Wu, H., Wang, C. & Wu, Z. A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics 14, 232\u2013243 (2013).","journal-title":"Biostatistics"},{"key":"1221_CR55","doi-asserted-by":"publisher","first-page":"5141","DOI":"10.1093\/bioinformatics\/btac650","volume":"38","author":"Y Ding","year":"2022","unstructured":"Ding, Y. et al. mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes. Bioinformatics 38, 5141\u20135143 (2022).","journal-title":"Bioinformatics"},{"key":"1221_CR56","doi-asserted-by":"publisher","first-page":"vbad003","DOI":"10.1093\/bioadv\/vbad003","volume":"3","author":"Z Li","year":"2023","unstructured":"Li, Z., Nagai, J. S., Kuppe, C., Kramann, R. & Costa, I. G. scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference. Bioinform. Adv. 3, vbad003 (2023).","journal-title":"Bioinform. Adv."},{"key":"1221_CR57","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41586-020-03182-8","volume":"598","author":"H Liu","year":"2021","unstructured":"Liu, H. et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature 598, 120\u2013128 (2021).","journal-title":"Nature"},{"key":"1221_CR58","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34626-6","volume":"13","author":"A Chakraborty","year":"2022","unstructured":"Chakraborty, A., Wang, J. G. & Ay, F. dcHiC detects differential compartments across multiple Hi-C datasets. Nat. Commun. 13, 6827 (2022).","journal-title":"Nat. Commun."}],"container-title":["Nature Aging"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01221-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01221-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01221-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T09:02:25Z","timestamp":1790240545000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01221-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,24]]},"references-count":58,"alternative-id":["1221"],"URL":"https:\/\/doi.org\/10.1038\/s43587-026-01221-z","relation":{},"ISSN":["2662-8465"],"issn-type":[{"value":"2662-8465","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,24]]},"assertion":[{"value":"9 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"H.J. and X.L. were full-time employees of Altos Labs. B.B.L., D.D. and Q.Y. are full-time employees of Altos Labs. S.J. has consulted with Athenium, receives royalties from Elsevier and has an intellectual property invention disclosure on FUSION histology-omics software tool and may receive royalties from commercial use. K.Z. is a full-time employee of Altos Labs and cofounder, equity holder and serves on the scientific advisory board of Singlera Genomics. The other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}