{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T05:06:29Z","timestamp":1790139989527,"version":"4.0.1"},"reference-count":64,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T00:00:00Z","timestamp":1754265600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["U01DA053625-01"],"award-info":[{"award-number":["U01DA053625-01"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["2T32DA039080"],"award-info":[{"award-number":["2T32DA039080"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01AG079291"],"award-info":[{"award-number":["R01AG079291"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01AG074541"],"award-info":[{"award-number":["R01AG074541"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01AG054214"],"award-info":[{"award-number":["R01AG054214"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01AG072758"],"award-info":[{"award-number":["R01AG072758"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["1RF1MH121267-01"],"award-info":[{"award-number":["1RF1MH121267-01"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["U54NS100717"],"award-info":[{"award-number":["U54NS100717"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIH National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM152101"],"award-info":[{"award-number":["R35GM152101"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100024743","name":"Suez Canal University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100024743","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["GRFP2139291"],"award-info":[{"award-number":["GRFP2139291"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100023835","name":"BRAIN Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100023835","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020424","name":"Weill Cornell Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020424","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.celrep.2025.116198","type":"journal-article","created":{"date-parts":[[2025,9,5]],"date-time":"2025-09-05T18:30:32Z","timestamp":1757097032000},"page":"116198","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"title":["A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain"],"prefix":"10.1016","volume":"44","author":[{"given":"Natan","family":"Belchikov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anoushka","family":"Joglekar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Careen","family":"Foord","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Jarroux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justine","family":"Hsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaun","family":"Pollard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadaf","family":"Amin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrey D.","family":"Prjibelski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiaoching","family":"Gong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sai","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta","family":"Giannelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harro","family":"Seelaar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandru I.","family":"Tomescu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Elizabeth","family":"Ross","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alissa Nana","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lea T.","family":"Grinberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salvatore","family":"Spina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce L.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johnathan","family":"Cooper-Knock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael P.","family":"Snyder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William W.","family":"Seeley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priyanka","family":"Rao-Ruiz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabine","family":"Spijker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"August B.","family":"Smit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire D.","family":"Clelland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Gan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7058-3606","authenticated-orcid":false,"given":"Hagen U.","family":"Tilgner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2025.116198_bib1","doi-asserted-by":"crossref","first-page":"1672","DOI":"10.1016\/S0140-6736(15)00461-4","article-title":"Frontotemporal dementia","volume":"386","author":"Bang","year":"2015","journal-title":"Lancet"},{"key":"10.1016\/j.celrep.2025.116198_bib2","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/nature05016","article-title":"Mutations in progranulin cause tau-negative frontotemporal dementia linked to chromosome 17","volume":"442","author":"Baker","year":"2006","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib3","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1038\/nature05017","article-title":"Null mutations in progranulin cause ubiquitin-positive frontotemporal dementia linked to chromosome 17q21","volume":"442","author":"Cruts","year":"2006","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib4","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1126\/science.1134108","article-title":"Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis","volume":"314","author":"Neumann","year":"2006","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116198_bib5","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1038\/ng.2434","article-title":"Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models","volume":"44","author":"Armakola","year":"2012","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2025.116198_bib6","doi-asserted-by":"crossref","first-page":"E736","DOI":"10.1073\/pnas.1222809110","article-title":"ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43","volume":"110","author":"Arnold","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116198_bib7","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/s41586-022-04436-3","article-title":"TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A","volume":"603","author":"Brown","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib8","doi-asserted-by":"crossref","first-page":"4680","DOI":"10.1016\/j.cell.2021.07.018","article-title":"TDP-43 condensation properties specify its RNA-binding and regulatory repertoire","volume":"184","author":"Hallegger","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116198_bib9","doi-asserted-by":"crossref","first-page":"6889","DOI":"10.1093\/nar\/gkaa410","article-title":"FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention","volume":"48","author":"Humphrey","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116198_bib10","doi-asserted-by":"crossref","first-page":"4857","DOI":"10.1038\/s41598-020-61676-x","article-title":"Extensive splicing changes in an ALS\/FTD transgenic mouse model overexpressing cytoplasmic fused in sarcoma","volume":"10","author":"Ito","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2025.116198_bib11","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1093\/hmg\/ddq137","article-title":"TDP-43 and FUS\/TLS: emerging roles in RNA processing and neurodegeneration","volume":"19","author":"Lagier-Tourenne","year":"2010","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.celrep.2025.116198_bib12","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41586-022-04424-7","article-title":"TDP-43 represses cryptic exon inclusion in the FTD-ALS gene UNC13A","volume":"603","author":"Ma","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib13","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.neuron.2019.03.014","article-title":"Disruption of RNA metabolism in neurological diseases and emerging therapeutic interventions","volume":"102","author":"Nussbacher","year":"2019","journal-title":"Neuron"},{"key":"10.1016\/j.celrep.2025.116198_bib14","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/nn.2779","article-title":"Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43","volume":"14","author":"Polymenidou","year":"2011","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib15","doi-asserted-by":"crossref","first-page":"6171","DOI":"10.1038\/ncomms7171","article-title":"ALS-causative mutations in FUS\/TLS confer gain and loss of function by altered association with SMN and U1-snRNP","volume":"6","author":"Sun","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116198_bib16","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1101\/gr.265298.120","article-title":"Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains","volume":"30","author":"Wang","year":"2020","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116198_bib17","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/s41586-020-2709-7","article-title":"Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency","volume":"588","author":"Zhang","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib18","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1016\/j.celrep.2019.04.003","article-title":"Loss of nuclear TDP-43 is associated with decondensation of LINE retrotransposons","volume":"27","author":"Liu","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116198_bib19","doi-asserted-by":"crossref","first-page":"11929","DOI":"10.1523\/JNEUROSCI.1860-14.2014","article-title":"An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex","volume":"34","author":"Zhang","year":"2014","journal-title":"J. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib20","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.neuron.2015.11.013","article-title":"Purification and characterization of progenitor and mature human astrocytes reveals transcriptional and functional differences with mouse","volume":"89","author":"Zhang","year":"2016","journal-title":"Neuron"},{"key":"10.1016\/j.celrep.2025.116198_bib21","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1038\/s41593-024-01616-4","article-title":"Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain","volume":"27","author":"Joglekar","year":"2024","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib22","doi-asserted-by":"crossref","first-page":"E4821","DOI":"10.1073\/pnas.1320101110","article-title":"Characterization of the human ESC transcriptome by hybrid sequencing","volume":"110","author":"Au","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116198_bib23","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/nbt.2280","article-title":"Hybrid error correction and de novo assembly of single-molecule sequencing reads","volume":"30","author":"Koren","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib24","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nbt.2705","article-title":"A single-molecule long-read survey of the human transcriptome","volume":"31","author":"Sharon","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib25","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1038\/nbt.4259","article-title":"Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells","volume":"36","author":"Gupta","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib26","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/s41467-020-20343-5","article-title":"A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain","volume":"12","author":"Joglekar","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116198_bib27","doi-asserted-by":"crossref","first-page":"3120","DOI":"10.1038\/s41467-019-11049-4","article-title":"High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes","volume":"10","author":"Singh","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116198_bib28","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1038\/s41587-022-01231-3","article-title":"Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue","volume":"40","author":"Hardwick","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib29","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":"10.1016\/j.celrep.2025.116198_bib30","article-title":"Combined single-cell profiling of chromatin\u2013transcriptome and splicing across brain cell types, regions and disease state","author":"Hu","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib31","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1038\/nn.3357","article-title":"Degeneration and impaired regeneration of gray matter oligodendrocytes in amyotrophic lateral sclerosis","volume":"16","author":"Kang","year":"2013","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib32","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1093\/brain\/aws339","article-title":"Oligodendrocyte dysfunction in the pathogenesis of amyotrophic lateral sclerosis","volume":"136","author":"Philips","year":"2013","journal-title":"Brain"},{"key":"10.1016\/j.celrep.2025.116198_bib33","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-015-0844-5","article-title":"MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data","volume":"16","author":"Finak","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116198_bib34","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"10.1016\/j.celrep.2025.116198_bib35","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/nn.2778","article-title":"Characterizing the RNA targets and position-dependent splicing regulation by TDP-43","volume":"14","author":"Tollervey","year":"2011","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib36","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.neuron.2019.05.002","article-title":"SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse","volume":"103","author":"Koopmans","year":"2019","journal-title":"Neuron"},{"key":"10.1016\/j.celrep.2025.116198_bib37","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1038\/s41588-018-0238-1","article-title":"Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer\u2019s disease susceptibility","volume":"50","author":"Raj","year":"2018","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2025.116198_bib38","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.gde.2020.03.007","article-title":"Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder","volume":"65","author":"Gonatopoulos-Pournatzis","year":"2020","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.celrep.2025.116198_bib39","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1016\/j.cell.2014.11.035","article-title":"A highly conserved program of neuronal microexons is misregulated in autistic brains","volume":"159","author":"Irimia","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116198_bib40","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nature20612","article-title":"Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism","volume":"540","author":"Parikshak","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib41","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14519","article-title":"Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci","volume":"8","author":"Takata","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116198_bib42","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1214\/aos\/1013699998","article-title":"The control of the false discovery rate in multiple testing under dependency","volume":"29","author":"Benjamini","year":"2001","journal-title":"Ann. Stat."},{"key":"10.1016\/j.celrep.2025.116198_bib43","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1101\/gr.276405.121","article-title":"Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns","volume":"32","author":"Mikheenko","year":"2022","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116198_bib44","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/s41587-022-01565-y","article-title":"Accurate isoform discovery with IsoQuant using long reads","volume":"41","author":"Prjibelski","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib45","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1007\/s00415-024-12758-7","article-title":"Two novel variants in GRN: the relevance of CNV analysis and genetic screening in FTLD patients with a negative family history","volume":"272","author":"De Houwer","year":"2024","journal-title":"J. Neurol."},{"key":"10.1016\/j.celrep.2025.116198_bib46","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.neuron.2021.10.036","article-title":"Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells","volume":"110","author":"Franjic","year":"2022","journal-title":"Neuron"},{"key":"10.1016\/j.celrep.2025.116198_bib47","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/s41586-019-1506-7","article-title":"Conserved cell types with divergent features in human versus mouse cortex","volume":"573","author":"Hodge","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib48","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1038\/s42003-021-02517-z","article-title":"Comprehensive in situ mapping of human cortical transcriptomic cell types","volume":"4","author":"Langseth","year":"2021","journal-title":"Commun. Biol."},{"key":"10.1016\/j.celrep.2025.116198_bib49","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1007\/s00401-021-02402-3","article-title":"Signature laminar distributions of pathology in frontotemporal lobar degeneration","volume":"143","author":"Ohm","year":"2022","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.celrep.2025.116198_bib50","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1261\/rna.7100104","article-title":"Multiple links between transcription and splicing","volume":"10","author":"Kornblihtt","year":"2004","journal-title":"RNA"},{"key":"10.1016\/j.celrep.2025.116198_bib51","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1101\/gr.134445.111","article-title":"Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs","volume":"22","author":"Tilgner","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116198_bib52","doi-asserted-by":"crossref","first-page":"11456","DOI":"10.1073\/pnas.94.21.11456","article-title":"Functional association between promoter structure and transcript alternative splicing","volume":"94","author":"Cramer","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116198_bib53","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41593-020-00764-7","article-title":"Molecular characterization of selectively vulnerable neurons in Alzheimer\u2019s disease","volume":"24","author":"Leng","year":"2021","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib63","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116198_bib64","doi-asserted-by":"crossref","first-page":"3474","DOI":"10.1093\/bioinformatics\/btac340","article-title":"ScisorWiz: Visualizing Differential Isoform Expression in Single-Cell Long-Read Data","volume":"38","author":"Stein","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116198_bib58","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116198_bib54","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s00401-018-1942-8","article-title":"Neurons selectively targeted in frontotemporal dementia reveal early stage TDP-43 pathobiology","volume":"137","author":"Nana","year":"2019","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.celrep.2025.116198_bib55","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1038\/s41593-019-0539-4","article-title":"A single-cell atlas of entorhinal cortex from individuals with Alzheimer\u2019s disease reveals cell-type-specific gene expression regulation","volume":"22","author":"Grubman","year":"2019","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2025.116198_bib56","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/nmeth.4407","article-title":"Massively parallel single-nucleus RNA-seq with DroNc-seq","volume":"14","author":"Habib","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116198_bib57","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.24192","article-title":"The AMPA receptor-associated protein Shisa7 regulates hippocampal synaptic function and contextual memory","volume":"6","author":"Schmitz","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.celrep.2025.116198_bib59","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nbt.4038","article-title":"Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain","volume":"36","author":"Lake","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116198_bib60","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/s41586-018-0654-5","article-title":"Shared and distinct transcriptomic cell types across neocortical areas","volume":"563","author":"Tasic","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116198_bib61","doi-asserted-by":"crossref","first-page":"3222","DOI":"10.1016\/j.cell.2021.04.021","article-title":"A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation","volume":"184","author":"Yao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116198_bib62","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."}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725009696?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725009696?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T04:41:19Z","timestamp":1790138479000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124725009696"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":64,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9]]}},"alternative-id":["S2211124725009696"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116198","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116198","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"116198"}}