{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:33:04Z","timestamp":1790836384577,"version":"4.1.0"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover previously uncharacterized genomic dynamics in 18 cells from three human brains utilizing single cell long-read whole genome sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements, but requires validation in larger studies.<\/jats:p>","DOI":"10.1038\/s42003-025-08805-2","type":"journal-article","created":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T18:15:59Z","timestamp":1763662559000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Single cell long read whole genome sequencing reveals somatic transposon activity in human brain"],"prefix":"10.1038","volume":"8","author":[{"given":"Michal B.","family":"Izydorczyk","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1297-3315","authenticated-orcid":false,"given":"Ester","family":"Kalef-Ezra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1988-3838","authenticated-orcid":false,"given":"Dominic W.","family":"Horner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinchang","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadine","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3255-9648","authenticated-orcid":false,"given":"Marco","family":"Toffoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeliha","family":"Sahin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7605-8979","authenticated-orcid":false,"given":"Yi","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heer H.","family":"Mehta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6623-0429","authenticated-orcid":false,"given":"Sonja W.","family":"Scholz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2025-8239","authenticated-orcid":false,"given":"Clifton L.","family":"Dalgard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donna M.","family":"Muzny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6085-6749","authenticated-orcid":false,"given":"Adam","family":"Ameur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6040-2691","authenticated-orcid":false,"given":"Fritz J.","family":"Sedlazeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6423-6539","authenticated-orcid":false,"given":"Christos","family":"Proukakis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,20]]},"reference":[{"key":"8805_CR1","doi-asserted-by":"publisher","first-page":"1058","DOI":"10.1038\/nmeth.3578","volume":"12","author":"T Garvin","year":"2015","unstructured":"Garvin, T. et al. Interactive analysis and assessment of single-cell copy-number variations. Nat. Methods 12, 1058\u20131060 (2015).","journal-title":"Nat. Methods"},{"key":"8805_CR2","doi-asserted-by":"publisher","first-page":"6119","DOI":"10.1093\/nar\/gkt345","volume":"41","author":"T Voet","year":"2013","unstructured":"Voet, T. et al. Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res. 41, 6119\u20136138 (2013).","journal-title":"Nucleic Acids Res."},{"key":"8805_CR3","unstructured":"Lander, E. S. et al. Initial sequencing and analysis of the human genome (2001). Nature 409, 860\u2013921."},{"key":"8805_CR4","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1038\/nature03663","volume":"435","author":"AR Muotri","year":"2005","unstructured":"Muotri, A. R. et al. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435, 903\u2013910 (2005).","journal-title":"Nature"},{"key":"8805_CR5","doi-asserted-by":"publisher","first-page":"307ra153","DOI":"10.1126\/scitranslmed.aac8201","volume":"7","author":"W Li","year":"2015","unstructured":"Li, W. et al. Human endogenous retrovirus-K contributes to motor neuron disease. Sci. Transl. Med. 7, 307ra153 (2015).","journal-title":"Sci. Transl. Med."},{"key":"8805_CR6","doi-asserted-by":"publisher","unstructured":"Bushman, D. M. et al. Genomic mosaicism with increased amyloid precursor protein (APP) gene copy number in single neurons from sporadic Alzheimer\u2019s disease brains. Elife 4. https:\/\/doi.org\/10.7554\/eLife.05116 (2015).","DOI":"10.7554\/eLife.05116"},{"key":"8805_CR7","doi-asserted-by":"publisher","first-page":"1680","DOI":"10.1177\/15353702221117147","volume":"247","author":"S K\u00f5ks","year":"2022","unstructured":"K\u00f5ks, S., Pfaff, A. L., Singleton, L. M., Bubb, V. J. & Quinn, J. P. Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson\u2019s disease. Exp. Biol. Med. 247, 1680\u20131690 (2022).","journal-title":"Exp. Biol. Med."},{"key":"8805_CR8","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1016\/j.molcel.2020.10.024","volume":"80","author":"AD Ewing","year":"2020","unstructured":"Ewing, A. D. et al. Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Mol. Cell 80, 915\u2013928.e5 (2020).","journal-title":"Mol. Cell"},{"key":"8805_CR9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40898-3","volume":"14","author":"J H\u00e5rd","year":"2023","unstructured":"H\u00e5rd, J. et al. Long-read whole-genome analysis of human single cells. Nat. Commun. 14, 5164 (2023).","journal-title":"Nat. Commun."},{"key":"8805_CR10","doi-asserted-by":"publisher","first-page":"2142","DOI":"10.1016\/j.neuron.2024.04.002","volume":"112","author":"R Chia","year":"2024","unstructured":"Chia, R. et al. Genome sequence analyses identify novel risk loci for multiple system atrophy. Neuron 112, 2142\u20132156.e5 (2024).","journal-title":"Neuron"},{"key":"8805_CR11","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1038\/nrneurol.2017.26","volume":"13","author":"F Krismer","year":"2017","unstructured":"Krismer, F. & Wenning, G. K. Multiple system atrophy: insights into a rare and debilitating movement disorder. Nat. Rev. Neurol. 13, 232\u2013243 (2017).","journal-title":"Nat. Rev. Neurol."},{"key":"8805_CR12","doi-asserted-by":"publisher","first-page":"2419","DOI":"10.1093\/brain\/awy157","volume":"141","author":"K Mokretar","year":"2018","unstructured":"Mokretar, K. et al. Somatic copy number gains of \u03b1-synuclein (SNCA) in Parkinson\u2019s disease and multiple system atrophy brains. Brain 141, 2419\u20132431 (2018).","journal-title":"Brain"},{"key":"8805_CR13","doi-asserted-by":"publisher","first-page":"1288","DOI":"10.1038\/s42003-024-06940-w","volume":"7","author":"E Kalef-Ezra","year":"2024","unstructured":"Kalef-Ezra, E. et al. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. Commun. Biol. 7, 1288 (2024).","journal-title":"Commun. Biol."},{"key":"8805_CR14","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1002\/mds.29291","volume":"38","author":"ME Garcia-Segura","year":"2023","unstructured":"Garcia-Segura, M. E., Perez-Rodriguez, D., Chambers, D., Jaunmuktane, Z. & Proukakis, C. Somatic SNCA copy number variants in multiple system atrophy are related to pathology and inclusions. Mov. Disord. 38, 338\u2013342 (2023).","journal-title":"Mov. Disord."},{"key":"8805_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40478-019-0873-5","volume":"7","author":"D Perez-Rodriguez","year":"2019","unstructured":"Perez-Rodriguez, D. et al. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol. Commun. 7, 1\u201322 (2019).","journal-title":"Acta Neuropathol. Commun."},{"key":"8805_CR16","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/s41586-021-03477-4","volume":"593","author":"F Abascal","year":"2021","unstructured":"Abascal, F. et al. Somatic mutation landscapes at single-molecule resolution. Nature 593, 405\u2013410 (2021).","journal-title":"Nature"},{"key":"8805_CR17","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1038\/s41588-022-01180-2","volume":"54","author":"LJ Luquette","year":"2022","unstructured":"Luquette, L. J. et al. Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements. Nat. Genet. 54, 1564\u20131571 (2022).","journal-title":"Nat. Genet."},{"key":"8805_CR18","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1002\/ana.10113","volume":"51","author":"M Funayama","year":"2002","unstructured":"Funayama, M. et al. A new locus for Parkinson\u2019s disease (PARK8) maps to chromosome 12p11.2\u2013q13.1. Ann. Neurol. 51, 296\u2013301 (2002).","journal-title":"Ann. Neurol."},{"key":"8805_CR19","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1016\/j.neuron.2004.10.023","volume":"44","author":"C Pais\u00e1n-Ru\u00edz","year":"2004","unstructured":"Pais\u00e1n-Ru\u00edz, C. et al. Cloning of the gene containing mutations that cause PARK8-linked Parkinson\u2019s disease. Neuron 44, 595\u2013600 (2004).","journal-title":"Neuron"},{"key":"8805_CR20","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/j.neuron.2004.11.005","volume":"44","author":"A Zimprich","year":"2004","unstructured":"Zimprich, A. et al. Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron 44, 601\u2013607 (2004).","journal-title":"Neuron"},{"key":"8805_CR21","first-page":"287","volume":"2","author":"AI Soto-Ortolaza","year":"2013","unstructured":"Soto-Ortolaza, A. I. et al. GWAS risk factors in Parkinson\u2019s disease: LRRK2 coding variation and genetic interaction with PARK16. Am. J. Neurodegener. Dis. 2, 287\u2013299 (2013).","journal-title":"Am. J. Neurodegener. Dis."},{"key":"8805_CR22","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/S1474-4422(20)30394-X","volume":"20","author":"E Jabbari","year":"2021","unstructured":"Jabbari, E. et al. Genetic determinants of survival in progressive supranuclear palsy: a genome-wide association study. Lancet Neurol. 20, 107\u2013116 (2021).","journal-title":"Lancet Neurol."},{"key":"8805_CR23","doi-asserted-by":"publisher","first-page":"1688","DOI":"10.1016\/j.csbj.2023.02.034","volume":"21","author":"N Lu","year":"2023","unstructured":"Lu, N., Qiao, Y., Lu, Z. & Tu, J. Chimera: the spoiler in multiple displacement amplification. Comput. Struct. Biotechnol. J. 21, 1688\u20131696 (2023).","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"8805_CR24","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1038\/s41587-020-0538-8","volume":"38","author":"JM Zook","year":"2020","unstructured":"Zook, J. M. et al. A robust benchmark for detection of germline large deletions and insertions. Nat. Biotechnol. 38, 1347\u20131355 (2020).","journal-title":"Nat. Biotechnol."},{"key":"8805_CR25","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1038\/s41587-021-01158-1","volume":"40","author":"J Wagner","year":"2022","unstructured":"Wagner, J. et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat. Biotechnol. 40, 672\u2013680 (2022).","journal-title":"Nat. Biotechnol."},{"key":"8805_CR26","doi-asserted-by":"publisher","unstructured":"Smolka, M. et al. Comprehensive structural variant detection: From mosaic to population-level. bioRxiv. https:\/\/doi.org\/10.1101\/2022.04.04.487055 (2022).","DOI":"10.1101\/2022.04.04.487055"},{"key":"8805_CR27","doi-asserted-by":"publisher","unstructured":"Jun, G. et al. Structural variation across 138,134 samples in the TOPMed consortium. bioRxiv.org. https:\/\/doi.org\/10.1101\/2023.01.25.525428 (2023).","DOI":"10.1101\/2023.01.25.525428"},{"key":"8805_CR28","doi-asserted-by":"publisher","first-page":"3025","DOI":"10.1016\/j.cell.2022.06.032","volume":"185","author":"G Pascarella","year":"2022","unstructured":"Pascarella, G. et al. Recombination of repeat elements generates somatic complexity in human genomes. Cell 185, 3025\u20133040.e6 (2022).","journal-title":"Cell"},{"key":"8805_CR29","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1016\/j.molcel.2019.05.024","volume":"75","author":"FJ Sanchez-Luque","year":"2019","unstructured":"Sanchez-Luque, F. J. et al. LINE-1 evasion of epigenetic repression in humans. Mol. Cell 75, 590\u2013604.e12 (2019).","journal-title":"Mol. Cell"},{"key":"8805_CR30","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.neuron.2014.12.028","volume":"85","author":"GD Evrony","year":"2015","unstructured":"Evrony, G. D. et al. Cell lineage analysis in human brain using endogenous retroelements. Neuron 85, 49\u201359 (2015).","journal-title":"Neuron"},{"key":"8805_CR31","doi-asserted-by":"publisher","first-page":"D1188","DOI":"10.1093\/nar\/gkac1072","volume":"51","author":"LR Nassar","year":"2023","unstructured":"Nassar, L. R. et al. The UCSC Genome Browser database: 2023 update. Nucleic Acids Res. 51, D1188\u2013D1195 (2023).","journal-title":"Nucleic Acids Res."},{"key":"8805_CR32","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/cr.2018.8","volume":"28","author":"J Jacob-Hirsch","year":"2018","unstructured":"Jacob-Hirsch, J. et al. Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders. Cell Res. 28, 187\u2013203 (2018).","journal-title":"Cell Res."},{"key":"8805_CR33","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1038\/s41587-023-02024-y","volume":"42","author":"M Smolka","year":"2024","unstructured":"Smolka, M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat. Biotechnol. 42, 1571\u20131580 (2024).","journal-title":"Nat. Biotechnol."},{"key":"8805_CR34","doi-asserted-by":"publisher","unstructured":"Kalef-Ezra, E., Perez-Rodriguez, D. & Proukakis, C. Manual isolation of nuclei from human brain using CellRaft device and single nucleus Whole Genome Amplification v1. https:\/\/doi.org\/10.17504\/protocols.io.kxygxzjjov8j\/v1 (2022).","DOI":"10.17504\/protocols.io.kxygxzjjov8j\/v1"},{"key":"8805_CR35","doi-asserted-by":"publisher","unstructured":"Horner, D., Kalef-Ezra, E., Toffoli, M. & Proukakis, C. Sequencing dMDA products on the MinION using Oxford Nanopore\u2019s Rapid Barcoding kit v1. https:\/\/doi.org\/10.17504\/protocols.io.kxygxy9odl8j\/v1 (2024).","DOI":"10.17504\/protocols.io.kxygxy9odl8j\/v1"},{"key":"8805_CR36","doi-asserted-by":"publisher","unstructured":"Holmes, N. Oxford Nanopore Technologies (ONT) library preparation and sequencing of DNA prepared using droplet Multiple Displacement Amplification (dMDA) v1. https:\/\/doi.org\/10.17504\/protocols.io.q26g71x2qgwz\/v1 (2024).","DOI":"10.17504\/protocols.io.q26g71x2qgwz\/v1"},{"key":"8805_CR37","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"8805_CR38","doi-asserted-by":"publisher","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10. https:\/\/doi.org\/10.1093\/gigascience\/giab008 (2021).","DOI":"10.1093\/gigascience\/giab008"},{"key":"8805_CR39","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/bioinformatics\/btx699","volume":"34","author":"BS Pedersen","year":"2018","unstructured":"Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867\u2013868 (2018).","journal-title":"Bioinformatics"},{"key":"8805_CR40","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1038\/s43588-022-00387-x","volume":"2","author":"Z Zheng","year":"2022","unstructured":"Zheng, Z. et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nat. Comput. Sci. 2, 797\u2013803 (2022).","journal-title":"Nat. Comput. Sci."},{"key":"8805_CR41","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"8805_CR42","doi-asserted-by":"publisher","unstructured":"Cleary, J. G. et al. Comparing Variant Call Files for performance benchmarking of next-generation sequencing variant calling pipelines. bioRxiv. https:\/\/doi.org\/10.1101\/023754 (2015).","DOI":"10.1101\/023754"},{"key":"8805_CR43","doi-asserted-by":"crossref","unstructured":"English, A.C., Menon, V.K. & Gibbs, R.A. Truvari: refined structural variant comparison preserves Allelic diversity. Genome Biol. 23, 271 (2022).","DOI":"10.1186\/s13059-022-02840-6"},{"key":"8805_CR44","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad311","volume":"39","author":"W De Coster","year":"2023","unstructured":"De Coster, W. & Rademakers, R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics 39, btad311 (2023).","journal-title":"Bioinformatics"},{"key":"8805_CR45","doi-asserted-by":"publisher","unstructured":"Lin, M. F. et al. GLnexus: joint variant calling for large cohort sequencing. bioRxiv, 343970. https:\/\/doi.org\/10.1101\/343970 (2018).","DOI":"10.1101\/343970"},{"key":"8805_CR46","doi-asserted-by":"publisher","first-page":"874","DOI":"10.1016\/j.neuron.2020.06.008","volume":"107","author":"H Stroud","year":"2020","unstructured":"Stroud, H. et al. An activity-mediated transition in transcription in early postnatal neurons. Neuron 107, 874\u2013890.e8 (2020).","journal-title":"Neuron"},{"key":"8805_CR47","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","volume":"32","author":"X Chen","year":"2016","unstructured":"Chen, X. et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32, 1220\u20131222 (2016).","journal-title":"Bioinformatics"},{"key":"8805_CR48","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1038\/nmeth.3505","volume":"12","author":"C Chiang","year":"2015","unstructured":"Chiang, C. et al. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat. Methods 12, 966\u2013968 (2015).","journal-title":"Nat. Methods"},{"key":"8805_CR49","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1007\/978-1-61779-603-6_2","volume":"859","author":"S Tempel","year":"2012","unstructured":"Tempel, S. Using and understanding RepeatMasker. Methods Mol. Biol. 859, 29\u201351 (2012).","journal-title":"Methods Mol. Biol."},{"key":"8805_CR50","doi-asserted-by":"publisher","DOI":"10.1186\/1759-8753-5-13","volume":"5","author":"M Bailly-Bechet","year":"2014","unstructured":"Bailly-Bechet, M., Haudry, A. & Lerat, E. One code to find them all\u201d: a Perl tool to conveniently parse RepeatMasker output files. Mob. DNA 5, 13 (2014).","journal-title":"Mob. DNA"},{"key":"8805_CR51","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkad426","volume":"51","author":"V Geoffroy","year":"2023","unstructured":"Geoffroy, V. et al. The AnnotSV webserver in 2023: updated visualization and ranking. Nucleic Acids Res. 51, W39\u2013W45 (2023).","journal-title":"Nucleic Acids Res."},{"key":"8805_CR52","doi-asserted-by":"publisher","first-page":"D916","DOI":"10.1093\/nar\/gkaa1087","volume":"49","author":"A Frankish","year":"2021","unstructured":"Frankish, A. et al. GENCODE 2021. Nucleic Acids Res. 49, D916\u2013D923 (2021).","journal-title":"Nucleic Acids Res."},{"key":"8805_CR53","doi-asserted-by":"publisher","unstructured":"Zheng, X. et al. STIX: Long-reads based accurate structural variation annotation at population scale. bioRxiv https:\/\/doi.org\/10.1101\/2024.09.30.615931 (2024).","DOI":"10.1101\/2024.09.30.615931"},{"key":"8805_CR54","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."},{"key":"8805_CR55","doi-asserted-by":"publisher","unstructured":"Izydorczyk, M. scONT. https:\/\/doi.org\/10.5281\/zenodo.14194549. (2024).","DOI":"10.5281\/zenodo.14194549"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08805-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08805-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08805-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T15:02:27Z","timestamp":1780930947000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08805-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,20]]},"references-count":55,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["8805"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-08805-2","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,20]]},"assertion":[{"value":"16 December 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 August 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"FJS receives research support from PacBio, Illumina, and Oxford Nanopore. SWS receives research support from Cerevel Therapeutics. SWS serves on the scientific advisory boards of Mission MSA, G-Can, and the Lewy Body Dementia Association. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1627"}}