{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T22:57:02Z","timestamp":1791413822050,"version":"4.3.3"},"reference-count":78,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T00:00:00Z","timestamp":1726185600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Ministero della Salute","doi-asserted-by":"publisher","award":["GR-2018-12365280"],"award-info":[{"award-number":["GR-2018-12365280"]}],"id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020581","name":"Fondazione AIRC per la ricerca sul cancro ETS","doi-asserted-by":"publisher","award":["IG 2022 27066"],"award-info":[{"award-number":["IG 2022 27066"]}],"id":[{"id":"10.13039\/100020581","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002803","name":"Fondazione Cariplo","doi-asserted-by":"publisher","award":["2019-3416"],"award-info":[{"award-number":["2019-3416"]}],"id":[{"id":"10.13039\/501100002803","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100022720","name":"Fondazione Regionale per la Ricerca Biomedica","doi-asserted-by":"publisher","award":["CP2_12\/2018"],"award-info":[{"award-number":["CP2_12\/2018"]}],"id":[{"id":"10.13039\/501100022720","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["PNRR PE00000007"],"award-info":[{"award-number":["PNRR PE00000007"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["2022PKF9S"],"award-info":[{"award-number":["2022PKF9S"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002803","name":"Fondazione Cariplo","doi-asserted-by":"publisher","award":["2019-1788"],"award-info":[{"award-number":["2019-1788"]}],"id":[{"id":"10.13039\/501100002803","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Progetti di Rilevante Interesse Nazionale"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transposable elements (TEs) are mobile DNA repeats known to shape the evolution of eukaryotic genomes. In complex organisms, they exhibit tissue-specific transcription. However, understanding their role in cellular diversity across most tissues remains a challenge, when employing single-cell RNA sequencing (scRNA-seq), due to their widespread presence and genetic similarity. To address this, we present IRescue (Interspersed Repeats single-cell quantifier), a software capable of estimating the expression of TE subfamilies at the single-cell level. IRescue incorporates a unique UMI deduplication algorithm to rectify sequencing errors and employs an Expectation-Maximization procedure to effectively redistribute the counts of multi-mapping reads. Our study showcases the precision of IRescue through analysis of both simulated and real single cell and nuclei RNA-seq data from human colorectal cancer, brain, skin aging, and PBMCs during SARS-CoV-2 infection and recovery. By linking the expression patterns of TE signatures to specific conditions and biological contexts, we unveil insights into their potential roles in cellular heterogeneity and disease progression.<\/jats:p>","DOI":"10.1093\/nar\/gkae793","type":"journal-article","created":{"date-parts":[[2024,9,14]],"date-time":"2024-09-14T08:13:00Z","timestamp":1726301580000},"page":"e93-e93","source":"Crossref","is-referenced-by-count":11,"title":["IRescue: uncertainty-aware quantification of transposable elements expression at single cell level"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7064-7294","authenticated-orcid":false,"given":"Benedetto","family":"Polimeni","sequence":"first","affiliation":[{"name":"INGM, Istituto Nazionale di Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Milan ,","place":["Italy"]},{"name":"Department of Biosciences, University of Milan , Milan ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Marasca","sequence":"additional","affiliation":[{"name":"INGM, Istituto Nazionale di Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Milan ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0602-5335","authenticated-orcid":false,"given":"Valeria","family":"Ranzani","sequence":"additional","affiliation":[{"name":"INGM, Istituto Nazionale di Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Milan ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0527-9234","authenticated-orcid":false,"given":"Beatrice","family":"Bodega","sequence":"additional","affiliation":[{"name":"INGM, Istituto Nazionale di Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Milan ,","place":["Italy"]},{"name":"Department of Biosciences, University of Milan , Milan ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,9,13]]},"reference":[{"key":"2024102814480447400_B1","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2024102814480447400_B2","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s13059-018-1577-z","article-title":"Ten things you should know about transposable elements","volume":"19","author":"Bourque","year":"2018","journal-title":"Genome Biol."},{"key":"2024102814480447400_B3","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mob. DNA"},{"key":"2024102814480447400_B4","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1093\/gbe\/evw264","article-title":"Evolution and Diversity of Transposable Elements in Vertebrate Genomes","volume":"9","author":"Sotero-Caio","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"2024102814480447400_B5","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1038\/s41576-020-0251-y","article-title":"Measuring and interpreting transposable element expression","volume":"21","author":"Lanciano","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"2024102814480447400_B6","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: from conflicts to benefits","volume":"18","author":"Chuong","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"2024102814480447400_B7","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/j.cell.2018.07.001","article-title":"Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing","volume":"174","author":"Attig","year":"2018","journal-title":"Cell"},{"key":"2024102814480447400_B8","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/ng.368","article-title":"The regulated retrotransposon transcriptome of mammalian cells","volume":"41","author":"Faulkner","year":"2009","journal-title":"Nat. Genet."},{"key":"2024102814480447400_B9","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/s41588-021-00989-7","article-title":"LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion","volume":"54","author":"Marasca","year":"2022","journal-title":"Nat. Genet."},{"key":"2024102814480447400_B10","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.cell.2018.05.043","article-title":"A LINE1-nucleolin partnership regulates early development and ESC identity","volume":"174","author":"Percharde","year":"2018","journal-title":"Cell"},{"key":"2024102814480447400_B11","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nrg3117","article-title":"Repetitive DNA and next-generation sequencing: computational challenges and solutions","volume":"13","author":"Treangen","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2024102814480447400_B12","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/s13100-019-0172-5","article-title":"Paired-end mappability of transposable elements in the human genome","volume":"10","author":"Sexton","year":"2019","journal-title":"Mob. DNA"},{"key":"2024102814480447400_B13","doi-asserted-by":"crossref","first-page":"3201","DOI":"10.3390\/ijms21093201","article-title":"The sophisticated transcriptional response governed by transposable elements in human health and disease","volume":"21","author":"Marasca","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"2024102814480447400_B14","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/s41576-018-0050-x","article-title":"Computational tools to unmask transposable elements","volume":"19","author":"Goerner-Potvin","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"2024102814480447400_B15","doi-asserted-by":"crossref","first-page":"3593","DOI":"10.1093\/bioinformatics\/btv422","article-title":"TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets","volume":"31","author":"Jin","year":"2015","journal-title":"Bioinforma."},{"key":"2024102814480447400_B16","doi-asserted-by":"crossref","first-page":"e27","DOI":"10.1093\/nar\/gky1301","article-title":"SQuIRE reveals locus-specific regulation of interspersed repeat expression","volume":"47","author":"Yang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2024102814480447400_B17","doi-asserted-by":"crossref","first-page":"5228","DOI":"10.1038\/s41467-019-13035-2","article-title":"Transposable element expression in tumors is associated with immune infiltration and increased antigenicity","volume":"10","author":"Kong","year":"2019","journal-title":"Nat. Commun."},{"key":"2024102814480447400_B18","doi-asserted-by":"crossref","first-page":"e1006453","DOI":"10.1371\/journal.pcbi.1006453","article-title":"Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression","volume":"15","author":"Bendall","year":"2019","journal-title":"PLoS Comput. Biol."},{"key":"2024102814480447400_B19","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1038\/s41467-021-21808-x","article-title":"Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE","volume":"12","author":"He","year":"2021","journal-title":"Nat. Commun."},{"key":"2024102814480447400_B20","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/s42003-022-04020-5","article-title":"SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression","volume":"5","author":"Rodr\u00edguez-Quiroz","year":"2022","journal-title":"Commun. Biol."},{"key":"2024102814480447400_B21","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13100-022-00276-0","article-title":"SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution","volume":"13","author":"Stow","year":"2022","journal-title":"Mob. DNA"},{"key":"2024102814480447400_B22","doi-asserted-by":"crossref","first-page":"baaa073","DOI":"10.1093\/database\/baaa073","article-title":"A curated database reveals trends in single-cell transcriptomics","volume":"2020","author":"Svensson","year":"2020","journal-title":"Database"},{"key":"2024102814480447400_B23","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res."},{"key":"2024102814480447400_B24","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1093\/nar\/gkad049","article-title":"LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5\u2032 single-cell RNA-Seq","volume":"51","author":"McKerrow","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024102814480447400_B25","doi-asserted-by":"crossref","first-page":"eadf8838","DOI":"10.1126\/sciimmunol.adf8838","article-title":"Selective control of transposable element expression during T cell exhaustion and anti\u2013PD-1 treatment","volume":"8","author":"Bont\u00e9","year":"2023","journal-title":"Sci. Immunol."},{"key":"2024102814480447400_B26","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024102814480447400_B27","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"2024102814480447400_B28","doi-asserted-by":"crossref","DOI":"10.1101\/2021.05.05.442755","article-title":"STARsolo: accurate, fast and versatile mapping\/quantification of single-cell and single-nucleus RNA-seq data","author":"Kaminow","year":"2021"},{"key":"2024102814480447400_B29","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2024102814480447400_B30","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The Human Genome Browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2024102814480447400_B31","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2024102814480447400_B32","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"2024102814480447400_B33","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2024102814480447400_B34","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"2024102814480447400_B35","doi-asserted-by":"crossref","unstructured":"Bonfield J.K., Marshall J., Danecek P., Li H., Ohan V., Whitwham A., Keane T., Davies R.M. HTSlib: C library for reading\/writing high-throughput sequencing data. GigaScience. 2021; 10:giab007.","DOI":"10.1093\/gigascience\/giab007"},{"key":"2024102814480447400_B36","doi-asserted-by":"crossref","DOI":"10.25080\/TCWV9851","article-title":"Exploring network structure, dynamics, and function using NetworkX","volume-title":"Proc. 7th Python Sci. Conf. SciPy 2008","author":"Hagberg","year":"2008"},{"key":"2024102814480447400_B37","doi-asserted-by":"crossref","first-page":"D916","DOI":"10.1093\/nar\/gkaa1087","article-title":"GENCODE 2021","volume":"49","author":"Frankish","year":"2021","journal-title":"Nucleic. Acids. Res."},{"key":"2024102814480447400_B38","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/s13059-019-1662-y","article-title":"EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data","volume":"20","author":"Lun","year":"2019","journal-title":"Genome Biol."},{"key":"2024102814480447400_B39","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013"},{"key":"2024102814480447400_B40","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"2024102814480447400_B41","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/s41592-018-0254-1","article-title":"A test metric for assessing single-cell RNA-seq batch correction","volume":"16","author":"B\u00fcttner","year":"2019","journal-title":"Nat. Methods"},{"key":"2024102814480447400_B42","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di\u00a0Tommaso","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2024102814480447400_B43","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2024102814480447400_B44","doi-asserted-by":"crossref","first-page":"eadh9543","DOI":"10.1126\/sciadv.adh9543","article-title":"LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification","volume":"9","author":"Garza","year":"2023","journal-title":"Sci. Adv."},{"key":"2024102814480447400_B45","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/s42003-020-0922-4","article-title":"Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming","volume":"3","author":"Sol\u00e9-Boldo","year":"2020","journal-title":"Commun. Biol."},{"key":"2024102814480447400_B46","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2024102814480447400_B47","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.tig.2003.08.004","article-title":"Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions","volume":"19","author":"van\u00a0de\u00a0Lagemaat","year":"2003","journal-title":"Trends Genet."},{"key":"2024102814480447400_B48","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1101\/gr.265173.120","article-title":"Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data","volume":"31","author":"Shao","year":"2021","journal-title":"Genome Res."},{"key":"2024102814480447400_B49","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.ejca.2021.08.003","article-title":"Overexpression of transposable elements is associated with immune evasion and poor outcome in colorectal cancer","volume":"157","author":"Zhu","year":"2021","journal-title":"Eur. J. Cancer"},{"key":"2024102814480447400_B50","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1038\/s41588-019-0373-3","article-title":"Transposable elements drive widespread expression of oncogenes in human cancers","volume":"51","author":"Jang","year":"2019","journal-title":"Nat. Genet."},{"key":"2024102814480447400_B51","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1038\/s41588-020-0636-z","article-title":"Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer","volume":"52","author":"Lee","year":"2020","journal-title":"Nat. Genet."},{"key":"2024102814480447400_B52","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nrc.2017.35","article-title":"Transposable elements in cancer","volume":"17","author":"Burns","year":"2017","journal-title":"Nat. Rev. Cancer"},{"key":"2024102814480447400_B53","doi-asserted-by":"crossref","first-page":"974","DOI":"10.3390\/ijms18050974","article-title":"Transposable Elements in Human Cancer: Causes and Consequences of Deregulation","volume":"18","author":"Anwar","year":"2017","journal-title":"Int. J. Mol. Sci."},{"key":"2024102814480447400_B54","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/nature08248","article-title":"L1 retrotransposition in human neural progenitor cells","volume":"460","author":"Coufal","year":"2009","journal-title":"Nature"},{"key":"2024102814480447400_B55","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.neuron.2014.12.028","article-title":"Cell lineage analysis in human brain using endogenous retroelements","volume":"85","author":"Evrony","year":"2015","journal-title":"Neuron"},{"key":"2024102814480447400_B56","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/j.molcel.2019.05.024","article-title":"LINE-1 Evasion of Epigenetic Repression in Humans","volume":"75","author":"Sanchez-Luque","year":"2019","journal-title":"Mol. Cell"},{"key":"2024102814480447400_B57","doi-asserted-by":"crossref","first-page":"101881","DOI":"10.1016\/j.arr.2023.101881","article-title":"Transposable elements and their role in aging","volume":"86","author":"Yushkova","year":"2023","journal-title":"Ageing Res. Rev."},{"key":"2024102814480447400_B58","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1016\/j.cmet.2019.02.014","article-title":"LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation","volume":"29","author":"Simon","year":"2019","journal-title":"Cell Metab."},{"key":"2024102814480447400_B59","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/s41586-018-0784-9","article-title":"L1 drives IFN in senescent cells and promotes age-associated inflammation","volume":"566","author":"De\u00a0Cecco","year":"2019","journal-title":"Nature"},{"key":"2024102814480447400_B60","doi-asserted-by":"crossref","first-page":"eabl6057","DOI":"10.1126\/scitranslmed.abl6057","article-title":"LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes","volume":"14","author":"Della\u00a0Valle","year":"2022","journal-title":"Sci. Transl. Med."},{"key":"2024102814480447400_B61","doi-asserted-by":"crossref","first-page":"3016","DOI":"10.4161\/cc.10.17.17543","article-title":"Inhibition of activated pericentromeric SINE\/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal","volume":"10","author":"Wang","year":"2011","journal-title":"Cell Cycle"},{"key":"2024102814480447400_B62","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.mad.2014.03.004","article-title":"The hallmarks of fibroblast ageing","volume":"138","author":"Tigges","year":"2014","journal-title":"Mech. Ageing Dev."},{"key":"2024102814480447400_B63","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1101\/gr.277511.122","article-title":"Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells","volume":"33","author":"Senapati","year":"2023","journal-title":"Genome Res."},{"key":"2024102814480447400_B64","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1101\/gr.081737.108","article-title":"Active Alu retrotransposons in the human genome","volume":"18","author":"Bennett","year":"2008","journal-title":"Genome Res."},{"key":"2024102814480447400_B65","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1134\/S0022093018010040","article-title":"Changes in gene expression and DNA methylation of evolutionarily young AluY repeats during apoptosis of human K562 erythro-myeloblastic leukemia cells","volume":"54","author":"Kabanov","year":"2018","journal-title":"J. Evol. Biochem. Physiol."},{"key":"2024102814480447400_B66","doi-asserted-by":"crossref","first-page":"e01260-21","DOI":"10.1128\/Spectrum.01260-21","article-title":"Upregulation of human endogenous retroviruses in bronchoalveolar lavage fluid of COVID-19 patients","volume":"9","author":"Kitsou","journal-title":"Microbiol. Spectr."},{"key":"2024102814480447400_B67","doi-asserted-by":"crossref","first-page":"e147170","DOI":"10.1172\/jci.insight.147170","article-title":"SARS-CoV-2 infection mediates differential expression of human endogenous retroviruses and long interspersed nuclear elements","volume":"6","author":"Marston","year":"2021","journal-title":"JCI Insight"},{"key":"2024102814480447400_B68","doi-asserted-by":"crossref","first-page":"e55101","DOI":"10.15252\/embr.202255101","article-title":"Impaired activation of transposable elements in SARS-CoV-2 infection","volume":"23","author":"Sorek","year":"2022","journal-title":"EMBO Rep."},{"key":"2024102814480447400_B69","doi-asserted-by":"crossref","first-page":"1001558","DOI":"10.3389\/fcell.2022.1001558","article-title":"Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-months recovery of COVID-19","volume":"10","author":"Yin","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"key":"2024102814480447400_B70","doi-asserted-by":"crossref","first-page":"eabg5021","DOI":"10.1126\/sciimmunol.abg5021","article-title":"Integrated longitudinal immunophenotypic, transcriptional and repertoire analyses delineate immune responses in COVID-19 patients","volume":"6","author":"Notarbartolo","year":"2021","journal-title":"Sci. Immunol."},{"key":"2024102814480447400_B71","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"2024102814480447400_B72","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2024102814480447400_B73","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinf."},{"key":"2024102814480447400_B74","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1093\/bioinformatics\/btz724","article-title":"L1EM: A tool for accurate locus specific LINE-1 RNA quantification","volume":"36","author":"McKerrow","year":"2020","journal-title":"Bioinformatics"},{"key":"2024102814480447400_B75","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1158\/2159-8290.CD-23-0331","article-title":"Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer","volume":"13","author":"Grillo","year":"2023","journal-title":"Cancer Discov."},{"key":"2024102814480447400_B76","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nn.3368","article-title":"Activation of transposable elements during aging and neuronal decline in Drosophila","volume":"16","author":"Li","year":"2013","journal-title":"Nat. Neurosci."},{"key":"2024102814480447400_B77","doi-asserted-by":"crossref","first-page":"101911","DOI":"10.1016\/j.gde.2022.101911","article-title":"Cancer-associated chromatin variants uncover the oncogenic role of transposable elements","volume":"74","author":"Grillo","year":"2022","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2024102814480447400_B78","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.conb.2020.01.012","article-title":"Awakening the dark side: retrotransposon activation in neurodegenerative disorders","volume":"61","author":"Ochoa\u00a0Thomas","year":"2020","journal-title":"Curr. Opin. Neurobiol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/19\/e93\/60142398\/gkae793.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/19\/e93\/60142398\/gkae793.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T14:50:43Z","timestamp":1730127043000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/52\/19\/e93\/7756585"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,13]]},"references-count":78,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2024,9,13]]},"published-print":{"date-parts":[[2024,10,28]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkae793","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,10,28]]},"published":{"date-parts":[[2024,9,13]]}}}