{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T07:54:27Z","timestamp":1772092467766,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,2,15]],"date-time":"2021-02-15T00:00:00Z","timestamp":1613347200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fulbright Fellowship Grant"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Despite the continuous discovery of new transcript isoforms, fueled by the recent increase in accessibility and accuracy of long-read RNA sequencing data, functional differences between isoforms originating from the same gene often remain obscure. To address this issue and enable researchers to assess potential functional consequences of transcript isoform variation on the proteome, we developed IsoTV. IsoTV is a versatile pipeline to process, predict and visualize the functional features of translated transcript isoforms. Attributes such as gene and isoform expression, transcript composition and functional features are summarized in an easy-to-interpret visualization. IsoTV is able to analyze a variety of data types from all eukaryotic organisms, including short- and long-read RNA-seq data. Using Oxford Nanopore long read data, we demonstrate that IsoTV facilitates the understanding of potential protein isoform function in different cancer cell types.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>IsoTV is available at https:\/\/github.molgen.mpg.de\/MayerGroup\/IsoTV, with the corresponding documentation at https:\/\/isotv.readthedocs.io\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab103","type":"journal-article","created":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T04:43:43Z","timestamp":1613105023000},"page":"3070-3072","source":"Crossref","is-referenced-by-count":10,"title":["IsoTV: processing and visualizing functional features of translated transcript isoforms"],"prefix":"10.1093","volume":"37","author":[{"given":"Siddharth","family":"Annaldasula","sequence":"first","affiliation":[{"name":"Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics , Berlin 14195, Germany"},{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin , Berlin 14195, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6731-3736","authenticated-orcid":false,"given":"Martyna","family":"Gajos","sequence":"additional","affiliation":[{"name":"Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics , Berlin 14195, Germany"},{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin , Berlin 14195, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4532-9382","authenticated-orcid":false,"given":"Andreas","family":"Mayer","sequence":"additional","affiliation":[{"name":"Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics , Berlin 14195, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,2,15]]},"reference":[{"key":"2023061310473997700_btab103-B1","doi-asserted-by":"crossref","first-page":"W362","DOI":"10.1093\/nar\/gkl124","article-title":"ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins","volume":"34","author":"de Castro","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023061310473997700_btab103-B2","doi-asserted-by":"crossref","first-page":"e167","DOI":"10.7717\/peerj.167","article-title":"Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology","volume":"1","author":"Cock","year":"2013","journal-title":"PeerJ"},{"key":"2023061310473997700_btab103-B3","doi-asserted-by":"crossref","first-page":"e99","DOI":"10.1002\/cpbi.99","article-title":"Analyzing protein disorder with IUPred2A","volume":"70","author":"Erd\u0151s","year":"2020","journal-title":"Curr. 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