{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T18:06:26Z","timestamp":1775325986556,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,7,3]],"date-time":"2019-07-03T00:00:00Z","timestamp":1562112000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"KBRIN Investigator Development Award"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20GM103436"],"award-info":[{"award-number":["P20GM103436"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","award":["R15GM126446"],"award-info":[{"award-number":["R15GM126446"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Over the past two decades, a circular form of RNA (circular RNA), produced through alternative splicing, has become the focus of scientific studies due to its major role as a microRNA (miRNA) activity modulator and its association with various diseases including cancer. Therefore, the detection of circular RNAs is vital to understanding their biogenesis and purpose. Prediction of circular RNA can be achieved in three steps: distinguishing non-coding RNAs from protein coding gene transcripts, separating short and long non-coding RNAs and predicting circular RNAs from other long non-coding RNAs (lncRNAs). However, the available tools are less than 80 percent accurate for distinguishing circular RNAs from other lncRNAs due to difficulty of classification. Therefore, the availability of a more accurate and fast machine learning method for the identification of circular RNAs, which considers the specific features of circular RNA, is essential to the development of systematic annotation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present an End-to-End deep learning framework, circDeep, to classify circular RNA from other lncRNA. circDeep fuses an RCM descriptor, ACNN-BLSTM sequence descriptor and a conservation descriptor into high level abstraction descriptors, where the shared representations across different modalities are integrated. The experiments show that circDeep is not only faster than existing tools but also performs at an unprecedented level of accuracy by achieving a 12 percent increase in accuracy over the other tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/UofLBioinformatics\/circDeep.<\/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\/btz537","type":"journal-article","created":{"date-parts":[[2019,7,2]],"date-time":"2019-07-02T03:09:55Z","timestamp":1562036995000},"page":"73-80","source":"Crossref","is-referenced-by-count":71,"title":["circDeep: deep learning approach for circular RNA classification from other long non-coding RNA"],"prefix":"10.1093","volume":"36","author":[{"given":"Mohamed","family":"Chaabane","sequence":"first","affiliation":[{"name":"Department of Computer Engineering and Computer Science , Louisville, KY 40208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert M","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering and Computer Science , Louisville, KY 40208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Austin T","family":"Stephens","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering and Computer Science , Louisville, KY 40208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4610-6893","authenticated-orcid":false,"given":"Juw Won","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering and Computer Science , Louisville, KY 40208, USA"},{"name":"KBRIN Bioinformatics Core, University of Louisville , Louisville, KY 40208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,7,3]]},"reference":[{"key":"2023013109502882100_btz537-B1","doi-asserted-by":"crossref","first-page":"e0141287.","DOI":"10.1371\/journal.pone.0141287","article-title":"Continuous distributed representation of biological sequences for deep proteomics and genomics","volume":"10","author":"Asgari","year":"2015","journal-title":"PLoS One"},{"key":"2023013109502882100_btz537-B2","doi-asserted-by":"crossref","first-page":"8057","DOI":"10.1038\/srep08057","article-title":"Correlation of circular RNA abundance with proliferation\u2013exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues","volume":"5","author":"Bachmayr-Heyda","year":"2015","journal-title":"Sci Rep"},{"key":"2023013109502882100_btz537-B3","doi-asserted-by":"crossref","first-page":"e1001233","DOI":"10.1371\/journal.pgen.1001233","article-title":"Expression of linear and novel circular forms of an INK4\/ARF-associated non-coding RNA correlates with atherosclerosis risk","volume":"6","author":"Burd","year":"2010","journal-title":"PLoS Genet"},{"key":"2023013109502882100_btz537-B4","doi-asserted-by":"crossref","first-page":"D983","DOI":"10.1093\/nar\/gks1099","article-title":"LncRNADisease: a database for long-non-coding RNA-associated diseases","volume":"41","author":"Chen","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023013109502882100_btz537-B5","doi-asserted-by":"crossref","first-page":"312","DOI":"10.2174\/1389202916666150707161554","article-title":"Circular RNAs in eukaryotic cells","volume":"16","author":"Chen","year":"2015","journal-title":"Curr. 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