{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:53:31Z","timestamp":1791262411320,"version":"4.1.0"},"reference-count":65,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T00:00:00Z","timestamp":1765324800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["RR210070"],"award-info":[{"award-number":["RR210070"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["U01DK131383"],"award-info":[{"award-number":["U01DK131383"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Institutes of Health National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA230033"],"award-info":[{"award-number":["R01CA230033"]}],"id":[{"id":"10.13039\/100000054","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":[[2026,1]]},"DOI":"10.1016\/j.celrep.2025.116839","type":"journal-article","created":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T17:45:48Z","timestamp":1768326348000},"page":"116839","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["Differentiation in the human urothelia is defined by distinct alternative polyadenylation"],"prefix":"10.1016","volume":"45","author":[{"given":"Ninh B.","family":"Le","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surbhi","family":"Sona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Briana","family":"Santo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosie","family":"Ou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R. Allen","family":"Schweickart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veena","family":"Kochat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William I.","family":"Padron","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunal","family":"Rai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shih-Han","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joo Mi","family":"Yi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Wessely","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byron H.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3214-3968","authenticated-orcid":false,"given":"Angela H.","family":"Ting","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2025.116839_bib1","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1152\/physrev.00041.2019","article-title":"The Urothelium: Life in a Liquid Environment","volume":"100","author":"Dalghi","year":"2020","journal-title":"Physiol. Rev."},{"key":"10.1016\/j.celrep.2025.116839_bib2","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/s41385-022-00565-0","article-title":"The urothelium: a multi-faceted barrier against a harsh environment","volume":"15","author":"Jafari","year":"2022","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.celrep.2025.116839_bib3","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1016\/j.devcel.2022.07.004","article-title":"Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter","volume":"57","author":"Fink","year":"2022","journal-title":"Dev. Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib4","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.molcel.2011.08.017","article-title":"Mechanisms and consequences of alternative polyadenylation","volume":"43","author":"Di Giammartino","year":"2011","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib5","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nrm1488","article-title":"Molecular mechanisms of translational control","volume":"5","author":"Gebauer","year":"2004","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib6","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.molcel.2007.11.018","article-title":"New modes of translational control in development, behavior, and disease","volume":"28","author":"Sonenberg","year":"2007","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib7","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S0968-0004(03)00002-1","article-title":"Translational control by the 3'-UTR: the ends specify the means","volume":"28","author":"Mazumder","year":"2003","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.celrep.2025.116839_bib8","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1101\/gad.349689.122","article-title":"Developmentally regulated alternate 3' end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage","volume":"36","author":"Berry","year":"2022","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2025.116839_bib9","doi-asserted-by":"crossref","first-page":"2005","DOI":"10.1016\/j.celrep.2017.10.095","article-title":"Widespread Translational Remodeling during Human Neuronal Differentiation","volume":"21","author":"Blair","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116839_bib10","doi-asserted-by":"crossref","first-page":"15945","DOI":"10.1073\/pnas.1002929107","article-title":"Distinct 3'UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF)","volume":"107","author":"Lau","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116839_bib11","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1093\/nar\/gkad1151","article-title":"Alternative cleavage and polyadenylation of the Ccnb1 mRNA defines accumulation of cyclin protein during the meiotic cell cycle","volume":"52","author":"Wang","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib12","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1016\/j.cell.2009.06.016","article-title":"Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells","volume":"138","author":"Mayr","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib13","first-page":"D174","article-title":"PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing","volume":"48","author":"Herrmann","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib14","doi-asserted-by":"crossref","first-page":"5101","DOI":"10.1038\/s41467-021-25388-8","article-title":"The landscape of alternative polyadenylation in single cells of the developing mouse embryo","volume":"12","author":"Agarwal","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116839_bib15","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1126\/science.1155390","article-title":"Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites","volume":"320","author":"Sandberg","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116839_bib16","doi-asserted-by":"crossref","first-page":"7028","DOI":"10.1073\/pnas.0900028106","article-title":"Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development","volume":"106","author":"Ji","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116839_bib17","doi-asserted-by":"crossref","first-page":"3182","DOI":"10.1038\/s41467-020-16959-2","article-title":"Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation","volume":"11","author":"Cheng","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116839_bib18","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a034728","article-title":"What Are 3' UTRs Doing?","volume":"11","author":"Mayr","year":"2019","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib19","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1016\/j.molcel.2020.03.024","article-title":"DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex","volume":"78","author":"Nanavaty","year":"2020","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib20","doi-asserted-by":"crossref","first-page":"2709","DOI":"10.1038\/s41467-022-30525-y","article-title":"Enhancers regulate 3' end processing activity to control expression of alternative 3'UTR isoforms","volume":"13","author":"Kwon","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116839_bib21","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2003-4-11-r74","article-title":"Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates","volume":"4","author":"Ohshima","year":"2003","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib22","doi-asserted-by":"crossref","first-page":"4949","DOI":"10.1128\/MCB.01901-05","article-title":"Protein tyrosine kinase 6 negatively regulates growth and promotes enterocyte differentiation in the small intestine","volume":"26","author":"Haegebarth","year":"2006","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib23","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/j.bone.2009.06.019","article-title":"T-cell leukemia translocation-associated gene (TCTA) protein is required for human osteoclastogenesis","volume":"45","author":"Kotake","year":"2009","journal-title":"Bone"},{"key":"10.1016\/j.celrep.2025.116839_bib24","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/s41556-019-0318-1","article-title":"Stage-specific requirement for Mettl3-dependent m(6)A mRNA methylation during haematopoietic stem cell differentiation","volume":"21","author":"Lee","year":"2019","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.redox.2022.102373","article-title":"IFT20 governs mesenchymal stem cell fate through positively regulating TGF-beta-Smad2\/3-Glut1 signaling mediated glucose metabolism","volume":"54","author":"Li","year":"2022","journal-title":"Redox Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib26","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1016\/j.stemcr.2019.01.004","article-title":"Histamine H1 Receptors in Neural Stem Cells Are Required for the Promotion of Neurogenesis Conferred by H3 Receptor Antagonism following Traumatic Brain Injury","volume":"12","author":"Liao","year":"2019","journal-title":"Stem Cell Rep."},{"key":"10.1016\/j.celrep.2025.116839_bib27","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1016\/j.celrep.2015.09.071","article-title":"Optineurin Negatively Regulates Osteoclast Differentiation by Modulating NF-kappaB and Interferon Signaling: Implications for Paget's Disease","volume":"13","author":"Obaid","year":"2015","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116839_bib28","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1007\/s00018-023-04962-x","article-title":"Metabolic and cell cycle shift induced by the deletion of Dnm1l attenuates the dissolution of pluripotency in mouse embryonic stem cells","volume":"80","author":"Seo","year":"2023","journal-title":"Cell. Mol. Life Sci."},{"key":"10.1016\/j.celrep.2025.116839_bib29","doi-asserted-by":"crossref","DOI":"10.1042\/BSR20182152","article-title":"Akirin1 promotes myoblast differentiation by modulating multiple myoblast differentiation factors","volume":"39","author":"Sun","year":"2019","journal-title":"Biosci. Rep."},{"key":"10.1016\/j.celrep.2025.116839_bib30","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-71489-7","article-title":"The short isoform of extended synaptotagmin-2 controls Ca(2+) dynamics in T cells via interaction with STIM1","volume":"10","author":"Woo","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2025.116839_bib31","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1091\/mbc.e10-08-0678","article-title":"DDR1 triggers epithelial cell differentiation by promoting cell adhesion through stabilization of E-cadherin","volume":"22","author":"Yeh","year":"2011","journal-title":"Mol. Biol. Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib32","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s13287-019-1148-6","article-title":"MagT1 regulated the odontogenic differentiation of BMMSCs induced byTGC-CM via ERK signaling pathway","volume":"10","author":"Zheng","year":"2019","journal-title":"Stem Cell Res. Ther."},{"key":"10.1016\/j.celrep.2025.116839_bib33","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.bone.2005.12.008","article-title":"Wnt signaling activation during bone regeneration and the role of Dishevelled in chondrocyte proliferation and differentiation","volume":"39","author":"Zhong","year":"2006","journal-title":"Bone"},{"key":"10.1016\/j.celrep.2025.116839_bib34","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1091\/mbc.e12-07-0531","article-title":"Competitive binding of CUGBP1 and HuR to occludin mRNA controls its translation and modulates epithelial barrier function","volume":"24","author":"Yu","year":"2013","journal-title":"Mol. Biol. Cell"},{"key":"10.1016\/j.celrep.2025.116839_bib35","doi-asserted-by":"crossref","first-page":"8472","DOI":"10.1093\/nar\/gkr567","article-title":"Chk2-dependent HuR phosphorylation regulates occludin mRNA translation and epithelial barrier function","volume":"39","author":"Yu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib36","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkq1069","article-title":"RBPDB: a database of RNA-binding specificities","volume":"39","author":"Cook","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib37","doi-asserted-by":"crossref","first-page":"12787","DOI":"10.1073\/pnas.2133766100","article-title":"Alu elements and hominid phylogenetics","volume":"100","author":"Salem","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116839_bib38","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1016\/j.tig.2017.08.006","article-title":"The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution","volume":"33","author":"Yang","year":"2017","journal-title":"Trends Genet."},{"key":"10.1016\/j.celrep.2025.116839_bib39","doi-asserted-by":"crossref","first-page":"2084","DOI":"10.1093\/bioinformatics\/bty895","article-title":"Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences","volume":"35","author":"Zhu","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116839_bib40","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib41","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116839_bib42","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib43","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1093\/nar\/gkv1461","article-title":"MethylAction: detecting differentially methylated regions that distinguish biological subtypes","volume":"44","author":"Bhasin","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib44","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkz114","article-title":"The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads","volume":"47","author":"Liao","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib45","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: an R package for interfacing with genome browsers","volume":"25","author":"Lawrence","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116839_bib46","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116839_bib47","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib48","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ramirez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib49","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":"10.1016\/j.celrep.2025.116839_bib50","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116839_bib51","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.celrep.2025.116839_bib52","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":"10.1016\/j.celrep.2025.116839_bib53","doi-asserted-by":"crossref","first-page":"W361","DOI":"10.1093\/nar\/gku406","article-title":"RBPmap: a web server for mapping binding sites of RNA-binding proteins","volume":"42","author":"Paz","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib54","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib55","article-title":"Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data","volume":"4","author":"Svoboda","year":"2022","journal-title":"NAR Genom. Bioinform."},{"key":"10.1016\/j.celrep.2025.116839_bib56","doi-asserted-by":"crossref","first-page":"15377","DOI":"10.1073\/pnas.1307202110","article-title":"Drift and conservation of differential exon usage across tissues in primate species","volume":"110","author":"Reyes","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116839_bib57","doi-asserted-by":"crossref","first-page":"5701","DOI":"10.1093\/bioinformatics\/btaa1009","article-title":"glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data","volume":"36","author":"Ahlmann-Eltze","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116839_bib58","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib59","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giy083","article-title":"Clustering trees: a visualization for evaluating clusterings at multiple resolutions","volume":"7","author":"Zappia","year":"2018","journal-title":"GigaScience"},{"key":"10.1016\/j.celrep.2025.116839_bib60","doi-asserted-by":"crossref","first-page":"4050","DOI":"10.1038\/s41467-024-48254-9","article-title":"Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression","volume":"15","author":"Fansler","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116839_bib61","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib62","doi-asserted-by":"crossref","first-page":"R24","DOI":"10.1186\/gb-2007-8-2-r24","article-title":"Quantifying similarity between motifs","volume":"8","author":"Gupta","year":"2007","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116839_bib63","doi-asserted-by":"crossref","first-page":"W276","DOI":"10.1093\/nar\/gkac240","article-title":"Search and sequence analysis tools services from EMBL-EBI in 2022","volume":"50","author":"Madeira","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116839_bib64","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1101\/gr.097857.109","article-title":"Detection of nonneutral substitution rates on mammalian phylogenies","volume":"20","author":"Pollard","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116839_bib65","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"Siepel","year":"2005","journal-title":"Genome Res."}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725016110?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725016110?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:22:14Z","timestamp":1791260534000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124725016110"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":65,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["S2211124725016110"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116839","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Differentiation in the human urothelia is defined by distinct alternative polyadenylation","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116839","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"116839"}}