{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T02:50:17Z","timestamp":1779936617836,"version":"3.53.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,29]],"date-time":"2022-12-29T00:00:00Z","timestamp":1672272000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https:\/\/github.com\/yollct\/spycone and the documentation at https:\/\/spycone.readthedocs.io\/en\/latest\/.<\/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\/btac846","type":"journal-article","created":{"date-parts":[[2022,12,29]],"date-time":"2022-12-29T08:26:53Z","timestamp":1672302413000},"source":"Crossref","is-referenced-by-count":9,"title":["Systematic analysis of alternative splicing in time course data using Spycone"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2297-831X","authenticated-orcid":false,"given":"Chit Tong","family":"Lio","sequence":"first","affiliation":[{"name":"Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9 , Hamburg 22607, Germany"},{"name":"Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich , Freising 85354, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon","family":"Grabert","sequence":"additional","affiliation":[{"name":"Division Data Science in Biomedicine, Peter L. 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