{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T21:25:29Z","timestamp":1783113929614,"version":"3.54.6"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,1,27]],"date-time":"2024-01-27T00:00:00Z","timestamp":1706313600000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62231013"],"award-info":[{"award-number":["62231013"]}],"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":["62201129"],"award-info":[{"award-number":["62201129"]}],"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":["62303328"],"award-info":[{"award-number":["62303328"]}],"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":["62302341"],"award-info":[{"award-number":["62302341"]}],"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":["62271329"],"award-info":[{"award-number":["62271329"]}],"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":["62372332"],"award-info":[{"award-number":["62372332"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022ZD0117700"],"award-info":[{"award-number":["2022ZD0117700"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research fund of Shenzhen Polytechnic University","award":["6022331007K"],"award-info":[{"award-number":["6022331007K"]}]},{"name":"Research fund of Shenzhen Polytechnic University","award":["6022310036K"],"award-info":[{"award-number":["6022310036K"]}]},{"name":"Research fund of Shenzhen Polytechnic University","award":["6023310037K"],"award-info":[{"award-number":["6023310037K"]}]},{"name":"Key Field of Department of Education of Guangdong Province","award":["2022ZDZX2082"],"award-info":[{"award-number":["2022ZDZX2082"]}]},{"name":"Special Science Foundation of Quzhou","award":["2023D036"],"award-info":[{"award-number":["2023D036"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Virus-encoded circular RNA (circRNA) participates in the immune response to viral infection, affects the human immune system, and can be used as a target for precision therapy and tumor biomarker. The coronaviruses SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1\/2) that have emerged in recent years are highly contagious and have high mortality rates. In coronaviruses, little is known about the circRNA encoded by the SARS-CoV-1\/2. Therefore, this study explores whether SARS-CoV-1\/2 encodes circRNA and characteristics and functions of circRNA. Based on RNA-seq data of SARS-CoV-1 and SARS-CoV-2 infections, we used circRNA identification tools (circRNA_finder, find_circ and CIRI2) to identify circRNAs. The number of circRNAs encoded by SARS-CoV-1 and SARS-CoV-2 was identified as 151 and 470, respectively. It can be found that SARS-CoV-2 shows more prominent circRNA encoding ability than SARS-CoV-1. Expression analysis showed that only a few circRNAs encoded by SARS-CoV-1\/2 showed high expression levels, and the positive strand produced more abundant circRNAs. Then, based on the identified SARS-CoV-1\/2-encoded circRNAs, we performed circRNA identification and characterization using the previously developed CirRNAPL. Finally, target gene prediction and functional enrichment analysis were performed. It was found that viral circRNA is closely related to cancer and has a potential role in regulating host cell functions. This study studied the characteristics and functions of viral circRNA encoded by coronavirus SARS-CoV-1\/2, providing a valuable resource for further research on the function and molecular mechanism of coronavirus circRNA.<\/jats:p>","DOI":"10.1093\/bib\/bbad537","type":"journal-article","created":{"date-parts":[[2024,1,27]],"date-time":"2024-01-27T09:00:17Z","timestamp":1706346017000},"source":"Crossref","is-referenced-by-count":16,"title":["Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9175-4649","authenticated-orcid":false,"given":"Mengting","family":"Niu","sequence":"first","affiliation":[{"name":"School of Electronic and Communication Engineering, Shenzhen Polytechnic University , Shenzhen 518055 , China"},{"name":"School of Life Science and Technology, University of Electronic Science and Technology of China , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , Harbin, Heilongjiang 150000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaojia","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China , No.4 Block 2 North Jianshe Road, Chengdu 610054 , China"},{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China , Quzhou , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China , No.4 Block 2 North Jianshe Road, Chengdu 610054 , China"},{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China , Quzhou , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Electronic and Communication Engineering, Shenzhen Polytechnic University , Shenzhen 518055 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,1,26]]},"reference":[{"issue":"11","key":"2024012709000657200_ref1","doi-asserted-by":"crossref","first-page":"3852","DOI":"10.1073\/pnas.73.11.3852","article-title":"Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures","volume":"73","author":"Sanger","year":"1976","journal-title":"Proc Natl Acad Sci"},{"key":"2024012709000657200_ref2","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.virol.2019.01.014","article-title":"Identification of virus-encoded circular RNA","volume":"529","author":"Huang","year":"2019","journal-title":"Virology"},{"issue":"6","key":"2024012709000657200_ref3","doi-asserted-by":"crossref","first-page":"e01952","DOI":"10.1128\/JVI.01952-18","article-title":"Comparative analysis of gammaherpesvirus circular RNA repertoires: conserved and unique viral circular RNAs","volume":"93","author":"Ungerleider","year":"2019","journal-title":"J Virol"},{"issue":"15","key":"2024012709000657200_ref4","doi-asserted-by":"crossref","first-page":"4488","DOI":"10.1111\/febs.15639","article-title":"Viruses join the circular RNA world","volume":"288","author":"Tan","year":"2021","journal-title":"FEBS J"},{"issue":"37","key":"2024012709000657200_ref5","doi-asserted-by":"crossref","first-page":"E8737","DOI":"10.1073\/pnas.1811728115","article-title":"Circular DNA tumor viruses make circular RNAs","volume":"115","author":"Toptan","year":"2018","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"2024012709000657200_ref6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-020-03944-1","article-title":"PCirc: random forest-based plant circRNA identification software","volume":"22","author":"Yin","year":"2021","journal-title":"BMC Bioinform"},{"issue":"6","key":"2024012709000657200_ref7","doi-asserted-by":"crossref","DOI":"10.1099\/mgen.0.000848","article-title":"Identification and characterization of virus-encoded circular RNAs in host cells","volume":"8","author":"Chen","year":"2022","journal-title":"Microb Genomics"},{"issue":"4","key":"2024012709000657200_ref8","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1128\/JVI.02136-07","article-title":"Epstein-Barr virus latent membrane protein 1 induces cellular MicroRNA miR-146a, a modulator of lymphocyte signaling pathways","volume":"82","author":"Cameron","year":"2008","journal-title":"J Virol"},{"issue":"2","key":"2024012709000657200_ref9","doi-asserted-by":"crossref","first-page":"e00071","DOI":"10.1128\/mBio.00071-19","article-title":"Gammaherpesvirus RNAs come full circle","volume":"10","author":"Ungerleider","year":"2019","journal-title":"MBio"},{"issue":"5","key":"2024012709000657200_ref10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3892\/ijmm.2021.4921","article-title":"Role of circRNAs in viral infection and their significance for diagnosis and treatment","volume":"47","author":"Mo","year":"2021","journal-title":"Int J Mol Med"},{"issue":"2","key":"2024012709000657200_ref11","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.molcel.2017.05.023","article-title":"Coordinated circRNA biogenesis and function with NF90\/NF110 in viral infection","volume":"67","author":"Li","year":"2017","journal-title":"Mol Cell"},{"issue":"6","key":"2024012709000657200_ref12","doi-asserted-by":"crossref","first-page":"e03075","DOI":"10.1128\/mBio.03075-21","article-title":"The cellular and viral circRNAome induced by respiratory syncytial virus infection","volume":"12","author":"Yao","year":"2021","journal-title":"MBio"},{"issue":"12","key":"2024012709000657200_ref13","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1016\/j.tibs.2020.08.006","article-title":"Circular RNAs in immune response and viral infection","volume":"45","author":"Yan","year":"2020","journal-title":"Trends Biochem Sci"},{"key":"2024012709000657200_ref14","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.ijbiomac.2022.12.173","article-title":"BmNPV circular RNA-encoded peptide VSP39 promotes viral replication","volume":"228","author":"Zhang","year":"2023","journal-title":"Int J Biol Macromol"},{"issue":"6","key":"2024012709000657200_ref15","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2212864120","article-title":"A virus-induced circular RNA maintains latent infection of Kaposi\u2019s sarcoma herpesvirus","volume":"120","author":"Tagawa","year":"2023","journal-title":"Proc Natl Acad Sci"},{"key":"2024012709000657200_ref16","doi-asserted-by":"crossref","first-page":"110044","DOI":"10.1016\/j.knosys.2022.110044","article-title":"Sparse regularized joint projection model for identifying associations of non-coding RNAs and human diseases","volume":"258","author":"Li","year":"2022","journal-title":"Knowl-Based Syst"},{"issue":"5","key":"2024012709000657200_ref17","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41579-022-00713-0","article-title":"SARS-CoV-2 pathogenesis","volume":"20","author":"Lamers","year":"2022","journal-title":"Nat Rev Microbiol"},{"issue":"7830","key":"2024012709000657200_ref18","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/s41586-020-2798-3","article-title":"SARS-CoV-2 vaccines in development","volume":"586","author":"Krammer","year":"2020","journal-title":"Nature"},{"issue":"16","key":"2024012709000657200_ref19","doi-asserted-by":"crossref","first-page":"2207","DOI":"10.1093\/cid\/ciaa227","article-title":"Diagnosis and management of first case of COVID-19 in Canada: lessons applied from SARS-CoV-1","volume":"71","author":"Marchand-Sen\u00e9cal","year":"2020","journal-title":"Clin Infect Dis"},{"key":"2024012709000657200_ref20","doi-asserted-by":"crossref","DOI":"10.1080\/19420862.2021.1922134","article-title":"Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies","volume":"13","author":"Rouet","year":"2021","journal-title":"MAbs"},{"issue":"17","key":"2024012709000657200_ref21","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.2217\/fmb-2021-0019","article-title":"Drug repurposing against SARS-CoV-1, SARS-CoV-2 and MERS-CoV","volume":"16","author":"Aherfi","year":"2021","journal-title":"Future Microbiol"},{"issue":"9","key":"2024012709000657200_ref22","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1002\/prot.26143","article-title":"Comparative protein structure network analysis on 3CLpro from SARS-CoV-1 and SARS-CoV-2","volume":"89","author":"Lata","year":"2021","journal-title":"Proteins"},{"issue":"12","key":"2024012709000657200_ref23","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1107\/S1399004714023931","article-title":"\u03b2-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism","volume":"70","author":"Kim","year":"2014","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"6","key":"2024012709000657200_ref24","doi-asserted-by":"crossref","first-page":"e02984","DOI":"10.1128\/mBio.02984-21","article-title":"A previously undiscovered circular RNA, circTNFAIP3, and its role in coronavirus replication","volume":"12","author":"Du","year":"2021","journal-title":"MBio"},{"issue":"1","key":"2024012709000657200_ref25","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1039\/D2MD00350C","article-title":"Synthesis of bis-furyl-pyrrolo[3,4-b]pyridin-5-onesviaUgi\u2013Zhu reaction and in vitro activity assays against human SARS-CoV-2 and in silico studies on its main proteins","volume":"14","author":"Morales-Salazar","year":"2023","journal-title":"RSC Med Chem"},{"issue":"10","key":"2024012709000657200_ref26","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1016\/j.cell.2022.03.044","article-title":"Circular RNA vaccines against SARS-CoV-2 and emerging variants","volume":"185","author":"Qu","year":"2022","journal-title":"Cell"},{"key":"2024012709000657200_ref27","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.6267","article-title":"Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection","volume":"7","author":"Pang","year":"2019","journal-title":"PeerJ"},{"key":"2024012709000657200_ref28","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.virusres.2018.07.010","article-title":"To accelerate the Zika beat: candidate design for RNA interference-based therapy","volume":"255","author":"Giulietti","year":"2018","journal-title":"Virus Res"},{"issue":"1","key":"2024012709000657200_ref29","doi-asserted-by":"crossref","first-page":"2300","DOI":"10.1038\/s41467-019-10246-5","article-title":"Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus","volume":"10","author":"Zhao","year":"2019","journal-title":"Nat Commun"},{"key":"2024012709000657200_ref30","doi-asserted-by":"crossref","first-page":"8023","DOI":"10.2147\/CMAR.S218967","article-title":"Knockdown of EBV-encoded circRNA circRPMS1 suppresses nasopharyngeal carcinoma cell proliferation and metastasis through sponging multiple miRNAs","volume":"Volume 11","author":"Liu","year":"2019","journal-title":"Cancer Manag Res"},{"issue":"10","key":"2024012709000657200_ref31","doi-asserted-by":"crossref","first-page":"e49689","DOI":"10.15252\/embr.201949689","article-title":"Epstein\u2013Barr virus-derived circular RNA LMP 2A induces stemness in EBV-associated gastric cancer","volume":"21","author":"Lp","year":"2020","journal-title":"EMBO Rep"},{"key":"2024012709000657200_ref32","volume-title":"Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB","author":"Fu","year":"2014"},{"issue":"7441","key":"2024012709000657200_ref33","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature11928","article-title":"Circular RNAs are a large class of animal RNAs with regulatory potency","volume":"495","author":"Memczak","year":"2013","journal-title":"Nature"},{"issue":"5","key":"2024012709000657200_ref34","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/bib\/bbx014","article-title":"Circular RNA identification based on multiple seed matching","volume":"19","author":"Gao","year":"2018","journal-title":"Brief Bioinform"},{"key":"2024012709000657200_ref35","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1016\/j.csbj.2020.03.028","article-title":"CirRNAPL: a web server for the identification of circRNA based on extreme learning machine","volume":"18","author":"Niu","year":"2020","journal-title":"Comput Struct Biotechnol J"},{"issue":"20","key":"2024012709000657200_ref36","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkz740","article-title":"BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2024012709000657200_ref37","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.3390\/life13061361","article-title":"The intricate interplay between cancer stem cells and oncogenic miRNAs in breast cancer progression and metastasis","volume":"13","author":"Tsintarakis","year":"2023","journal-title":"Life"},{"issue":"1","key":"2024012709000657200_ref38","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3390\/ijms24010079","article-title":"Hepato-protective effects of delta-tocotrienol and alpha-tocopherol in patients with non-alcoholic fatty liver disease: regulation of circulating MicroRNA expression","volume":"24","author":"Pervez","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2024012709000657200_ref39","doi-asserted-by":"crossref","first-page":"4175","DOI":"10.1007\/s11033-019-04868-7","article-title":"Novel miRNAs as potential biomarkers in stage II colon cancer: microarray analysis","volume":"46","author":"Gungormez","year":"2019","journal-title":"Mol Biol Rep"},{"issue":"2","key":"2024012709000657200_ref40","doi-asserted-by":"crossref","first-page":"2182","DOI":"10.1093\/bib\/bbaa052","article-title":"VirusCircBase: a database of virus circular RNAs","volume":"22","author":"Cai","year":"2021","journal-title":"Brief Bioinform"},{"key":"2024012709000657200_ref41","article-title":"Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention","author":"Wyler"},{"issue":"1","key":"2024012709000657200_ref42","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1080\/22221751.2020.1738277","article-title":"Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation","volume":"9","author":"Zhang","year":"2020","journal-title":"Emerg Microbes Infect"},{"key":"2024012709000657200_ref43","first-page":"e27553v1","article-title":"PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets","volume":"7","author":"Cantu","year":"2019","journal-title":"PeerJ Preprints"},{"key":"2024012709000657200_ref44","doi-asserted-by":"crossref","first-page":"W6","DOI":"10.1093\/nar\/gkl164","article-title":"BLAST: improvements for better sequence analysis","volume":"34","author":"Ye","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2024012709000657200_ref45","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac166","article-title":"HAlign 3: fast multiple alignment of ultra-large numbers of similar DNA\/RNA sequences","volume":"39","author":"Tang","year":"2022","journal-title":"Mol Biol Evol"},{"issue":"15","key":"2024012709000657200_ref46","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1093\/bioinformatics\/btv177","article-title":"HAlign: fast multiple similar DNA\/RNA sequence alignment based on the centre star strategy","volume":"31","author":"Zou","year":"2015","journal-title":"Bioinformatics"},{"key":"2024012709000657200_ref47","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13015-017-0116-x","article-title":"HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing","volume":"12","author":"Wan","year":"2017","journal-title":"Algorithms Mol Biol"},{"key":"2024012709000657200_ref48","article-title":"SBSM-Pro: support bio-sequence machine for proteins","author":"Wang","year":"2023"},{"issue":"6","key":"2024012709000657200_ref49","doi-asserted-by":"crossref","first-page":"5265","DOI":"10.1016\/j.ygeno.2020.09.042","article-title":"Cell type-specific circular RNA expression in human glial cells","volume":"112","author":"Curry-Hyde","year":"2020","journal-title":"Genomics"},{"issue":"W1","key":"2024012709000657200_ref50","doi-asserted-by":"crossref","first-page":"W65","DOI":"10.1093\/nar\/gkv458","article-title":"Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences","volume":"43","author":"Liu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024012709000657200_ref51","article-title":"A unified approach to interpreting model predictions","volume":"30","author":"Lundberg","year":"2017","journal-title":"Adv Neural Inf Process Syst"},{"issue":"1","key":"2024012709000657200_ref52","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/s41746-023-00887-8","article-title":"A gender specific risk assessment of coronary heart disease based on physical examination data","volume":"6","author":"Yang","year":"2023","journal-title":"NPJ Digit Med"},{"issue":"1","key":"2024012709000657200_ref53","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s12915-023-01596-0","article-title":"m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation","volume":"21","author":"Ao","year":"2023","journal-title":"BMC Biol"},{"issue":"7","key":"2024012709000657200_ref54","doi-asserted-by":"crossref","first-page":"3017","DOI":"10.1093\/nar\/gkad055","article-title":"DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2024012709000657200_ref55","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-022-02780-1","article-title":"iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations","volume":"23","author":"Jin","year":"2022","journal-title":"Genome Biol"},{"issue":"18","key":"2024012709000657200_ref56","doi-asserted-by":"crossref","first-page":"2768","DOI":"10.1093\/bioinformatics\/btw318","article-title":"TarPmiR: a new approach for microRNA target site prediction","volume":"32","author":"Ding","year":"2016","journal-title":"Bioinformatics"},{"key":"2024012709000657200_ref57","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in Drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Biol"},{"key":"2024012709000657200_ref58","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2020.104060","article-title":"Web-based tools for miRNA studies analysis","volume":"127","author":"Shaker","year":"2020","journal-title":"Comput Biol Med"},{"issue":"D1","key":"2024012709000657200_ref59","doi-asserted-by":"crossref","first-page":"D127","DOI":"10.1093\/nar\/gkz757","article-title":"miRDB: an online database for prediction of functional microRNA targets","volume":"48","author":"Chen","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024012709000657200_ref60","first-page":"D148","article-title":"miRTarBase 2020: updates to the experimentally validated microRNA\u2013target interaction database","volume":"48","author":"Huang","year":"2020","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/2\/bbad537\/56428110\/bbad537.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/2\/bbad537\/56428110\/bbad537.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,27]],"date-time":"2024-01-27T09:01:00Z","timestamp":1706346060000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad537\/7590317"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,22]]},"references-count":60,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,1,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad537","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,1,22]]},"article-number":"bbad537"}}