{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T08:56:31Z","timestamp":1782982591156,"version":"3.54.5"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP210102385"],"award-info":[{"award-number":["DP210102385"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP220101352"],"award-info":[{"award-number":["DP220101352"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1175388"],"award-info":[{"award-number":["GNT1175388"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["2018833"],"award-info":[{"award-number":["2018833"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Talo Computational Biology Accelerator Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool\u2019s capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>R2Dtool is freely available under the MIT license at github.com\/comprna\/R2Dtool.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae495","type":"journal-article","created":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T01:42:51Z","timestamp":1722822171000},"source":"Crossref","is-referenced-by-count":10,"title":["R2Dtool: integration and visualization of isoform-resolved RNA features"],"prefix":"10.1093","volume":"40","author":[{"given":"Aditya J","family":"Sethi","sequence":"first","affiliation":[{"name":"Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University , Canberra, Acton ACT 2601, Australia"},{"name":"Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University , Canberra, Acton ACT 2601, Australia"},{"name":"EMBL Australia Partner Laboratory Network at the Australian National University , Canberra, Acton ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Acera Mateos","sequence":"additional","affiliation":[{"name":"Children\u2019s Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney , Kensington NSW 2033, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rippei","family":"Hayashi","sequence":"additional","affiliation":[{"name":"Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University , Canberra, Acton ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolay E","family":"Shirokikh","sequence":"additional","affiliation":[{"name":"Shine-Dalgarno Centre 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