{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T21:22:29Z","timestamp":1791148949705,"version":"4.1.0"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T00:00:00Z","timestamp":1680652800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100001384","name":"Samuel Waxman Cancer Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001384","id-type":"DOI","asserted-by":"publisher"}]},{"name":"\u2018Shanghai Municipal Education Commission\u2014Gaofeng Clinical Medicine Grant Support","award":["20152504"],"award-info":[{"award-number":["20152504"]}]},{"name":"Shanghai Guangci Translational Medical Research Development Foundation","award":["82200157"],"award-info":[{"award-number":["82200157"]}]},{"name":"Shanghai Guangci Translational Medical Research Development Foundation","award":["82100153"],"award-info":[{"award-number":["82100153"]}]},{"name":"Shanghai Guangci Translational Medical Research Development Foundation","award":["82104582"],"award-info":[{"award-number":["82104582"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81770142"],"award-info":[{"award-number":["81770142"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81970132"],"award-info":[{"award-number":["81970132"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Shanghai Science and Technology Committee","doi-asserted-by":"publisher","award":["20JC1410600"],"award-info":[{"award-number":["20JC1410600"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA alternative splicing, a post-transcriptional stage in eukaryotes, is crucial in cellular homeostasis and disease processes. Due to the rapid development of the next-generation sequencing (NGS) technology and the flood of NGS data, the detection of differential splicing from RNA-seq data has become mainstream. A range of bioinformatic tools has been developed. However, until now, an independent and comprehensive comparison of available algorithms\/tools at the event level is still lacking. Here, 21 different tools are subjected to systematic evaluation, based on simulated RNA-seq data where exact differential splicing events are introduced. We observe immense discrepancies among these tools. SUPPA, DARTS, rMATS and LeafCutter outperforme other event-based tools. We also examine the abilities of the tools to identify novel splicing events, which shows that most event-based tools are unsuitable for discovering novel splice sites. To improve the overall performance, we present two methodological approaches i.e. low-expression transcript filtering and tool-pair combination. Finally, a new protocol of selecting tools to perform differential splicing analysis for different analytical tasks (e.g. precision and recall rate) is proposed. Under this protocol, we analyze the distinct splicing landscape in the DUX4\/IGH subgroup of B-cell acute lymphoblastic leukemia and uncover the differential splicing of TCF12. All codes needed to reproduce the results are available at https:\/\/github.com\/mhjiang97\/Benchmarking_DS.<\/jats:p>","DOI":"10.1093\/bib\/bbad121","type":"journal-article","created":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T04:31:09Z","timestamp":1680755469000},"source":"Crossref","is-referenced-by-count":44,"title":["A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level"],"prefix":"10.1093","volume":"24","author":[{"given":"Minghao","family":"Jiang","sequence":"first","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 197 Ruijin Er Road, Shanghai 200025 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 197 Ruijin Er Road, Shanghai 200025 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongxin","family":"Yin","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 197 Ruijin Er Road, Shanghai 200025 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyi","family":"Zhuo","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 197 Ruijin Er Road, Shanghai 200025 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoyu","family":"Meng","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 197 Ruijin Er Road, Shanghai 200025 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,5]]},"reference":[{"key":"2023052022112393400_ref1","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/s41392-021-00486-7","article-title":"Alternative splicing and cancer: a systematic review","volume":"6","author":"Zhang","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2023052022112393400_ref2","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1016\/0092-8674(94)90130-9","article-title":"Split genes and RNA splicing","volume":"77","author":"Sharp","year":"1994","journal-title":"Cell"},{"key":"2023052022112393400_ref3","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/286776a0","article-title":"RNA splicing generates a variant light chain from an aberrantly rearranged kappa gene","volume":"286","author":"Choi","year":"1980","journal-title":"Nature"},{"key":"2023052022112393400_ref4","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1038\/306602a0","article-title":"Alternative RNA splicing in expression of the H-2K gene","volume":"306","author":"Kress","year":"1983","journal-title":"Nature"},{"key":"2023052022112393400_ref5","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"2023052022112393400_ref6","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1007\/s00438-017-1350-0","article-title":"The determinants of alternative RNA splicing in human cells","volume":"292","author":"Ramanouskaya","year":"2017","journal-title":"Mol Genet Genomics"},{"key":"2023052022112393400_ref7","doi-asserted-by":"crossref","first-page":"2413","DOI":"10.1038\/onc.2015.318","article-title":"Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes","volume":"35","author":"Sveen","year":"2016","journal-title":"Oncogene"},{"key":"2023052022112393400_ref8","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/ng0102-13","article-title":"A genomic view of alternative splicing","volume":"30","author":"Modrek","year":"2002","journal-title":"Nat Genet"},{"key":"2023052022112393400_ref9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/onc.2013.570","article-title":"Alternative splicing in cancer: implications for biology and therapy","volume":"34","author":"Chen","year":"2015","journal-title":"Oncogene"},{"key":"2023052022112393400_ref10","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1172\/JCI24886","article-title":"Ikaros transcription factors: flying between stress and inflammation","volume":"115","author":"Chrousos","year":"2005","journal-title":"J Clin Invest"},{"key":"2023052022112393400_ref11","doi-asserted-by":"crossref","first-page":"3091","DOI":"10.4049\/jimmunol.170.6.3091","article-title":"Ikaros isoform x is selectively expressed in myeloid differentiation","volume":"170","author":"Payne","year":"2003","journal-title":"J Immunol"},{"key":"2023052022112393400_ref12","doi-asserted-by":"crossref","DOI":"10.1016\/j.drup.2020.100728","article-title":"The role of alternative splicing in cancer: from oncogenesis to drug resistance","volume":"53","author":"Sciarrillo","year":"2020","journal-title":"Drug Resist Updat"},{"key":"2023052022112393400_ref13","doi-asserted-by":"crossref","first-page":"e1476","DOI":"10.1002\/wrna.1476","article-title":"Alternative-splicing defects in cancer: splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics","volume":"9","author":"Urbanski","year":"2018","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2023052022112393400_ref14","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.semcdb.2014.03.016","article-title":"The alternative splicing side of cancer","volume":"32","author":"Biamonti","year":"2014","journal-title":"Semin Cell Dev Biol"},{"key":"2023052022112393400_ref15","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s13045-020-00927-w","article-title":"RNA-binding proteins in tumor progression","volume":"13","author":"Qin","year":"2020","journal-title":"J Hematol Oncol"},{"key":"2023052022112393400_ref16","doi-asserted-by":"crossref","first-page":"2385","DOI":"10.1093\/bioinformatics\/bts452","article-title":"SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts","volume":"28","author":"Ryan","year":"2012","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref17","doi-asserted-by":"crossref","first-page":"D909","DOI":"10.1093\/nar\/gky954","article-title":"CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer","volume":"47","author":"Tian","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023052022112393400_ref18","doi-asserted-by":"crossref","first-page":"1840","DOI":"10.1093\/bioinformatics\/btw076","article-title":"SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data","volume":"32","author":"Kahles","year":"2016","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref19","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.ccell.2018.07.001","article-title":"Comprehensive analysis of alternative splicing across tumors from 8,705 patients","volume":"34","author":"Kahles","year":"2018","journal-title":"Cancer Cell"},{"key":"2023052022112393400_ref20","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref21","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/j.celrep.2018.01.088","article-title":"Somatic mutational landscape of splicing factor genes and their functional consequences across 33 cancer types","volume":"23","author":"Seiler","year":"2018","journal-title":"Cell Rep"},{"key":"2023052022112393400_ref22","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13059-018-1417-1","article-title":"SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions","volume":"19","author":"Trincado","year":"2018","journal-title":"Genome Biol"},{"key":"2023052022112393400_ref23","doi-asserted-by":"crossref","first-page":"2215","DOI":"10.1016\/j.celrep.2017.08.012","article-title":"The functional impact of alternative splicing in cancer","volume":"20","author":"Climente-Gonzalez","year":"2017","journal-title":"Cell Rep"},{"key":"2023052022112393400_ref24","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.11752","article-title":"A new view of transcriptome complexity and regulation through the lens of local splicing variations","volume":"5","author":"Vaquero-Garcia","year":"2016","journal-title":"Elife"},{"key":"2023052022112393400_ref25","first-page":"11357","article-title":"Aberrant splicing in B-cell acute lymphoblastic leukemia","volume":"46","author":"Black","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023052022112393400_ref26","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023052022112393400_ref27","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nmeth.1528","article-title":"Analysis and design of RNA sequencing experiments for identifying isoform regulation","volume":"7","author":"Katz","year":"2010","journal-title":"Nat Methods"},{"key":"2023052022112393400_ref28","doi-asserted-by":"crossref","first-page":"3597","DOI":"10.1158\/1078-0432.CCR-20-0184","article-title":"RNA splicing alterations induce a cellular stress response associated with poor prognosis in acute myeloid leukemia","volume":"26","author":"Anande","year":"2020","journal-title":"Clin Cancer Res"},{"key":"2023052022112393400_ref29","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1016\/j.ccell.2016.10.005","article-title":"Transcriptomic characterization of SF3B1 mutation reveals its pleiotropic effects in chronic lymphocytic leukemia","volume":"30","author":"Wang","year":"2016","journal-title":"Cancer Cell"},{"key":"2023052022112393400_ref30","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1101\/gr.108662.110","article-title":"Conservation of an RNA regulatory map between drosophila and mammals","volume":"21","author":"Brooks","year":"2011","journal-title":"Genome Res"},{"key":"2023052022112393400_ref31","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2023.997383","article-title":"RNA-seq data science: from raw data to effective interpretation","volume-title":"Front Genet","author":"Deshpande","year":"2023"},{"key":"2023052022112393400_ref32","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1093\/bib\/bbz126","article-title":"Systematic evaluation of differential splicing tools for RNA-seq studies","volume":"21","author":"Mehmood","year":"2020","journal-title":"Brief Bioinform"},{"key":"2023052022112393400_ref33","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-015-0862-3","article-title":"Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage","volume":"17","author":"Soneson","year":"2016","journal-title":"Genome Biol"},{"key":"2023052022112393400_ref34","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1093\/bib\/bbx122","article-title":"A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies","volume":"20","author":"Merino","year":"2019","journal-title":"Brief Bioinform"},{"key":"2023052022112393400_ref35","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1186\/s12859-014-0364-4","article-title":"Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems","volume":"15","author":"Liu","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023052022112393400_ref36","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/s13059-019-1738-8","article-title":"Essential guidelines for computational method benchmarking","volume":"20","author":"Weber","year":"2019","journal-title":"Genome Biol"},{"key":"2023052022112393400_ref37","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1038\/s41467-019-09406-4","article-title":"Systematic benchmarking of omics computational tools","volume":"10","author":"Mangul","year":"2019","journal-title":"Nat Commun"},{"key":"2023052022112393400_ref38","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/s41588-017-0004-9","article-title":"Annotation-free quantification of RNA splicing using LeafCutter","volume":"50","author":"Li","year":"2018","journal-title":"Nat Genet"},{"key":"2023052022112393400_ref39","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1093\/bioinformatics\/btx690","article-title":"DIEGO: detection of differential alternative splicing using Aitchison's geometry","volume":"34","author":"Doose","year":"2018","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref40","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbi.2020.103378","article-title":"Differential splicing analysis based on isoforms expression with NBSplice","volume":"103","author":"Merino","year":"2020","journal-title":"J Biomed Inform"},{"key":"2023052022112393400_ref41","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13059-020-01967-8","article-title":"BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty","volume":"21","author":"Tiberi","year":"2020","journal-title":"Genome Biol"},{"key":"2023052022112393400_ref42","doi-asserted-by":"crossref","first-page":"213","DOI":"10.12688\/f1000research.17916.1","article-title":"Relative abundance of transcripts (RATs): identifying differential isoform abundance from RNA-seq","volume":"8","author":"Froussios","year":"2019","journal-title":"F1000Res"},{"key":"2023052022112393400_ref43","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1109\/TNB.2015.2388593","article-title":"A generalized dSpliceType framework to detect differential splicing and differential expression events using RNA-Seq","volume":"14","author":"Zhu","year":"2015","journal-title":"IEEE Trans Nanobioscience"},{"key":"2023052022112393400_ref44","doi-asserted-by":"crossref","first-page":"4469","DOI":"10.1093\/bioinformatics\/btz247","article-title":"IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences","volume":"35","author":"Vitting-Seerup","year":"2019","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref45","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.molcel.2017.01.011","article-title":"Multilayered control of alternative splicing regulatory networks by transcription factors","volume":"65","author":"Han","year":"2017","journal-title":"Mol Cell"},{"key":"2023052022112393400_ref46","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1101\/gr.177790.114","article-title":"Widespread intron retention in mammals functionally tunes transcriptomes","volume":"24","author":"Braunschweig","year":"2014","journal-title":"Genome Res"},{"key":"2023052022112393400_ref47","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1016\/j.cell.2014.11.035","article-title":"A highly conserved program of neuronal microexons is misregulated in autistic brains","volume":"159","author":"Irimia","year":"2014","journal-title":"Cell"},{"key":"2023052022112393400_ref48","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s13059-019-1720-5","article-title":"Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing","volume":"20","author":"Kosugi","year":"2019","journal-title":"Genome Biol"},{"key":"2023052022112393400_ref49","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2105-14-91","article-title":"A comparison of methods for differential expression analysis of RNA-seq data","volume":"14","author":"Soneson","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023052022112393400_ref50","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s13059-020-02001-7","article-title":"Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing","volume":"21","author":"Huang","year":"2020","journal-title":"Genome Biol"},{"key":"2023052022112393400_ref51","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky888","article-title":"Psichomics: graphical application for alternative splicing quantification and analysis","volume":"47","author":"Saraiva-Agostinho","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023052022112393400_ref52","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/bib\/bbx034","article-title":"CASH: a constructing comprehensive splice site method for detecting alternative splicing events","volume":"19","author":"Wu","year":"2018","journal-title":"Brief Bioinform"},{"key":"2023052022112393400_ref53","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/s41592-019-0351-9","article-title":"Deep-learning augmented RNA-seq analysis of transcript splicing","volume":"16","author":"Zhang","year":"2019","journal-title":"Nat Methods"},{"key":"2023052022112393400_ref54","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.molcel.2018.08.018","article-title":"Efficient and accurate quantitative profiling of alternative splicing patterns of any complexity on a laptop","volume":"72","author":"Sterne-Weiler","year":"2018","journal-title":"Mol Cell"},{"key":"2023052022112393400_ref55","doi-asserted-by":"crossref","first-page":"5048","DOI":"10.1093\/bioinformatics\/btz438","article-title":"PSI-sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis","volume":"35","author":"Lin","year":"2019","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref56","article-title":"ASpli: integrative analysis of splicing landscapes through RNA-Seq assays","volume":"37","author":"Estefania","year":"2021","journal-title":"Bioinformatics"},{"key":"2023052022112393400_ref57","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"key":"2023052022112393400_ref58","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1038\/s41467-020-15171-6","article-title":"Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns","volume":"11","author":"Tang","year":"2020","journal-title":"Nat Commun"},{"key":"2023052022112393400_ref59","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13073-015-0168-9","article-title":"Widespread intron retention diversifies most cancer transcriptomes","volume":"7","author":"Dvinge","year":"2015","journal-title":"Genome Med"},{"key":"2023052022112393400_ref60","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1038\/ng.3414","article-title":"Intron retention is a widespread mechanism of tumor-suppressor inactivation","volume":"47","author":"Jung","year":"2015","journal-title":"Nat Genet"},{"key":"2023052022112393400_ref61","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.ccell.2017.09.005","article-title":"Exploiting the hidden treasure of detained introns","volume":"32","author":"Fu","year":"2017","journal-title":"Cancer Cell"},{"key":"2023052022112393400_ref62","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/j.ccell.2017.08.018","article-title":"Coordinated splicing of regulatory detained introns within oncogenic transcripts creates an exploitable vulnerability in malignant glioma","volume":"32","author":"Braun","year":"2017","journal-title":"Cancer Cell"},{"key":"2023052022112393400_ref63","first-page":"D896","article-title":"ExonSkipDB: functional annotation of exon skipping event in human","volume":"48","author":"Kim","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023052022112393400_ref64","doi-asserted-by":"crossref","first-page":"D1340","DOI":"10.1093\/nar\/gkab851","article-title":"OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers","volume":"50","author":"Zhang","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023052022112393400_ref65","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaa179","article-title":"LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers","volume":"22","author":"Deng","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023052022112393400_ref66","doi-asserted-by":"crossref","first-page":"D1196","DOI":"10.1093\/nar\/gkac955","article-title":"ASCancer atlas: a comprehensive knowledgebase of alternative splicing in human cancers","volume":"51","author":"Wu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023052022112393400_ref67","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.molp.2019.11.003","article-title":"Global co-transcriptional splicing in Arabidopsis and the correlation with splicing regulation in mature RNAs","volume":"13","author":"Li","year":"2020","journal-title":"Mol Plant"},{"key":"2023052022112393400_ref68","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev-biochem-060614-034316","article-title":"Mechanisms and regulation of alternative pre-mRNA splicing","volume":"84","author":"Lee","year":"2015","journal-title":"Annu Rev Biochem"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/3\/bbad121\/50411099\/bbad121.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/3\/bbad121\/50411099\/bbad121.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T22:12:00Z","timestamp":1684620720000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad121\/7108868"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,5]]},"references-count":68,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,5,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad121","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,5]]},"published":{"date-parts":[[2023,4,5]]},"article-number":"bbad121"}}