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With the wider diffusion of pangenomes, integrating genetic variability with transcriptome diversity is becoming a natural extension that demands specific methods for its exploration. In this work, we extend the notion of spliced pangenomes to that of <jats:italic>annotated spliced pangenomes<\/jats:italic>; this allows us to introduce a formal definition of Alternative Splicing (AS) events on a graph structure. To investigate the usage of graph pangenomes for the quantification of AS events across conditions, we developed <jats:monospace specific-use=\"no-wrap\">pantas<\/jats:monospace>, the first pangenomic method for the detection and differential analysis of AS events from short RNA-Seq reads. A comparison with state-of-the-art linear reference-based approaches proves that <jats:monospace specific-use=\"no-wrap\">pantas<\/jats:monospace> achieves competitive accuracy, making spliced pangenomes effective for conducting AS events quantification and opening future directions for the analysis of population-based transcriptomes.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012665","type":"journal-article","created":{"date-parts":[[2024,12,9]],"date-time":"2024-12-09T18:36:13Z","timestamp":1733769373000},"page":"e1012665","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Differential quantification of alternative splicing events on spliced pangenome graphs"],"prefix":"10.1371","volume":"20","author":[{"given":"Simone","family":"Ciccolella","sequence":"first","affiliation":[]},{"given":"Davide","family":"Cozzi","sequence":"additional","affiliation":[]},{"given":"Gianluca","family":"Della Vedova","sequence":"additional","affiliation":[]},{"given":"Stephen Njuguna","family":"Kuria","sequence":"additional","affiliation":[]},{"given":"Paola","family":"Bonizzoni","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8786-2276","authenticated-orcid":true,"given":"Luca","family":"Denti","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2024,12,9]]},"reference":[{"issue":"7960","key":"pcbi.1012665.ref001","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","article-title":"A draft human pangenome reference","volume":"617","author":"WW Liao","year":"2023","journal-title":"Nature"},{"key":"pcbi.1012665.ref002","first-page":"1","article-title":"Haplotype-aware pantranscriptome analyses using spliced pangenome graphs","author":"JA Sibbesen","year":"2023","journal-title":"Nature Methods"},{"key":"pcbi.1012665.ref003","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1007\/s40520-019-01360-x","article-title":"Alternative splicing in Alzheimer\u2019s disease","volume":"33","author":"G Biamonti","year":"2021","journal-title":"Aging clinical and experimental research"},{"issue":"19","key":"pcbi.1012665.ref004","doi-asserted-by":"crossref","first-page":"2413","DOI":"10.1038\/onc.2015.318","article-title":"Aberrant RNA splicing in cancer; 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