{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T15:37:12Z","timestamp":1774625832272,"version":"3.50.1"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Innovation Project of Guangxi Graduate Education","award":["YCSW2021025"],"award-info":[{"award-number":["YCSW2021025"]}]},{"name":"Natural Science Foundation of Guangxi","award":["2021GXNSFAA075041"],"award-info":[{"award-number":["2021GXNSFAA075041"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62072124"],"award-info":[{"award-number":["62072124"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Accumulating evidences demonstrate that circular RNA (circRNA) plays an important role in human diseases. Identification of circRNA-disease associations can help for the diagnosis of human diseases, while the traditional method based on biological experiments is time-consuming. In order to address the limitation, a series of computational methods have been proposed in recent years. However, few works have summarized these methods or compared the performance of them. In this paper, we divided the existing methods into three categories: information propagation, traditional machine learning and deep learning. Then, the baseline methods in each category are introduced in detail. Further, 5 different datasets are collected, and 14 representative methods of each category are selected and compared in the 5-fold, 10-fold cross-validation and the de novo experiment. In order to further evaluate the effectiveness of these methods, six common cancers are selected to compare the number of correctly identified circRNA-disease associations in the top-10, top-20, top-50, top-100 and top-200. In addition, according to the results, the observation about the robustness and the character of these methods are concluded. Finally, the future directions and challenges are discussed.<\/jats:p>","DOI":"10.1093\/bib\/bbac613","type":"journal-article","created":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:44:13Z","timestamp":1673153053000},"source":"Crossref","is-referenced-by-count":39,"title":["Benchmarking of computational methods for predicting circRNA-disease associations"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5839-7504","authenticated-orcid":false,"given":"Wei","family":"Lan","sequence":"first","affiliation":[{"name":"School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University , Nanning, Guangxi 530004 , China"}]},{"given":"Yi","family":"Dong","sequence":"additional","affiliation":[{"name":"School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University , Nanning, Guangxi 530004 , China"}]},{"given":"Hongyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University , Nanning, Guangxi 530004 , China"}]},{"given":"Chunling","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University , Nanning, Guangxi 530004 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5506-8913","authenticated-orcid":false,"given":"Qingfeng","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Computer, Electronic and Information and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University , Nanning, Guangxi 530004 , China"}]},{"given":"Jin","family":"Liu","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1516-0480","authenticated-orcid":false,"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4122-3767","authenticated-orcid":false,"given":"Yi-Ping Phoebe","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Technology, La Trobe University , Melbourne, Victoria 3086 , Australia"}]}],"member":"286","published-online":{"date-parts":[[2023,1,5]]},"reference":[{"issue":"9","key":"2023011917101504700_ref1","doi-asserted-by":"crossref","first-page":"e1003777","DOI":"10.1371\/journal.pgen.1003777","article-title":"Cell-type specific features of circular RNA expression","volume":"9","author":"Salzman","year":"2013","journal-title":"PLoS Genet"},{"issue":"7","key":"2023011917101504700_ref2","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1093\/nar\/gkr1009","article-title":"Transcriptome-wide discovery of circular RNAs in archaea","volume":"40","author":"Danan","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2023011917101504700_ref3","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nbt.2890","article-title":"Detecting and characterizing circular RNAs","volume":"32","author":"Jeck","year":"2014","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2023011917101504700_ref4","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nrm.2015.32","article-title":"The biogenesis and emerging roles of circular RNAs","volume":"17","author":"Chen","year":"2016","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"9","key":"2023011917101504700_ref5","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1182\/blood-2015-06-649434","article-title":"Circular RNA enrichment in platelets is a signature of transcriptome degradation","volume":"127","author":"Alhasan","year":"2016","journal-title":"Blood"},{"issue":"10","key":"2023011917101504700_ref6","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1016\/j.bbagrm.2016.07.009","article-title":"The complexity of the translation ability of circRNAs","volume":"1859","author":"Granados-Riveron","year":"2016","journal-title":"Biochim Biophys Acta Gene Regul Mech"},{"issue":"7441","key":"2023011917101504700_ref7","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nature11993","article-title":"Natural RNA circles function as efficient microRNA sponges","volume":"495","author":"Hansen","year":"2013","journal-title":"Nature"},{"issue":"2019","key":"2023011917101504700_ref8","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.ebiom.2019.06.030","article-title":"The RNA-binding protein RBM3 promotes cell proliferation in hepatocellular carcinoma by regulating circular RNA SCD-circRNA 2 production","volume":"45","author":"Dong","year":"2019","journal-title":"EBioMedicine"},{"issue":"8","key":"2023011917101504700_ref9","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1093\/carcin\/bgy061","article-title":"RNA-binding protein trinucleotide repeat-containing 6A regulates the formation of circular RNA circ0006916, with important functions in lung cancer cells","volume":"39","author":"Dai","year":"2018","journal-title":"Carcinogenesis"},{"issue":"1","key":"2023011917101504700_ref10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12943-018-0934-6","article-title":"The novel roles of circRNAs in human cancer","volume":"18","author":"Shang","year":"2019","journal-title":"Mol Cancer"},{"issue":"1","key":"2023011917101504700_ref11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12282-017-0793-9","article-title":"CircRNA: a novel type of biomarker for cancer","volume":"25","author":"Jiang","year":"2018","journal-title":"Breast Cancer"},{"issue":"1","key":"2023011917101504700_ref12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12943-019-1125-9","article-title":"Roles of circRNAs in the tumour microenvironment","volume":"19","author":"Zhang","year":"2020","journal-title":"Mol Cancer"},{"issue":"9","key":"2023011917101504700_ref13","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1007\/s00018-019-03345-5","article-title":"CircRNA: a rising star in gastric cancer","volume":"77","author":"Li","year":"2020","journal-title":"Cell Mol Life Sci"},{"issue":"4","key":"2023011917101504700_ref14","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1159\/000489208","article-title":"CircRNA-Cdr1as exerts anti-oncogenic functions in bladder cancer by sponging MicroRNA-135a","volume":"46","author":"Li","year":"2018","journal-title":"Cell Physiol Biochem"},{"issue":"2018","key":"2023011917101504700_ref15","first-page":"239","article-title":"Circular RNA and Alzheimer\u2019s disease","volume":"1087","author":"Akhter","year":"2018","journal-title":"Circular RNAs"},{"issue":"2013","key":"2023011917101504700_ref16","first-page":"307","article-title":"(circRNA) in Alzheimer's disease (AD)","volume":"4","author":"Lukiw","year":"2013","journal-title":"Front Genet"},{"issue":"2020","key":"2023011917101504700_ref17","doi-asserted-by":"crossref","first-page":"110251","DOI":"10.1016\/j.biopha.2020.110251","article-title":"CircRNAs: a new perspective of biomarkers in the nervous system","volume":"128","author":"Ma","year":"2020","journal-title":"Biomed Pharmacother"},{"issue":"2017","key":"2023011917101504700_ref18","doi-asserted-by":"crossref","first-page":"354","DOI":"10.3389\/fncel.2017.00354","article-title":"Circular RNAs: a novel player in development and disease of the central nervous system","volume":"11","author":"Xie","year":"2017","journal-title":"Front Cell Neurosci"},{"issue":"1","key":"2023011917101504700_ref19","first-page":"1","article-title":"Relationships of circular RNA with diabetes and depression","volume":"7","author":"Jiang","year":"2017","journal-title":"Sci Rep"},{"issue":"12","key":"2023011917101504700_ref20","doi-asserted-by":"crossref","first-page":"353","DOI":"10.3390\/genes8120353","article-title":"Circular RNAs (circRNAs) in health and disease","volume":"8","author":"Haque","year":"2017","journal-title":"Genes"},{"issue":"2018","key":"2023011917101504700_ref21","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.canlet.2018.03.035","article-title":"Circular RNAs (circRNAs) in cancer","volume":"425","author":"Zhou","year":"2018","journal-title":"Cancer Lett"},{"issue":"18","key":"2023011917101504700_ref22","doi-asserted-by":"crossref","first-page":"8211","DOI":"10.7150\/thno.44419","article-title":"Hypoxia induced exosomal circRNA promotes metastasis of colorectal cancer via targeting GEF-H1\/RhoA axis","volume":"10","author":"Yang","year":"2020","journal-title":"Theranostics"},{"issue":"14","key":"2023011917101504700_ref23","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.7150\/ijbs.28260","article-title":"Prediction of CircRNA-disease associations using KATZ model based on heterogeneous networks","volume":"14","author":"Fan","year":"2018","journal-title":"Int J Biol Sci"},{"issue":"1","key":"2023011917101504700_ref24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-45954-x","article-title":"Fusion of multiple heterogeneous networks for predicting circRNA-disease associations","volume":"9","author":"Deng","year":"2019","journal-title":"Sci Rep"},{"issue":"4","key":"2023011917101504700_ref25","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1109\/TNB.2019.2922214","article-title":"Integrating bipartite network projection and KATZ measure to identify novel CircRNA-disease associations","volume":"18","author":"Zhao","year":"2019","journal-title":"IEEE Trans Nanobioscience"},{"key":"2023011917101504700_ref26","first-page":"929","volume-title":"Proceedings of the 2019 IEEE\/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2019)","author":"Vural","year":"2019"},{"key":"2023011917101504700_ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2019\/5938035","article-title":"BRWSP: predicting circRNA-disease associations based on biased random walk to search paths on a multiple heterogeneous network","volume":"2019","author":"Lei","year":"2019","journal-title":"Complexity"},{"issue":"2019","key":"2023011917101504700_ref28","doi-asserted-by":"crossref","first-page":"83474","DOI":"10.1109\/ACCESS.2019.2920942","article-title":"Predicting CircRNA-disease associations through linear neighborhood label propagation method","volume":"7","author":"Zhang","year":"2019","journal-title":"IEEE Access"},{"issue":"2","key":"2023011917101504700_ref29","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1016\/j.ygeno.2019.08.001","article-title":"Predicting human disease-associated circRNAs based on locality-constrained linear coding","volume":"112","author":"Ge","year":"2020","journal-title":"Genomics"},{"key":"2023011917101504700_ref30","article-title":"DAP: a web server for lncRNA-disease association prediction","volume":"33","author":"","journal-title":"Bioinformatics"},{"issue":"3","key":"2023011917101504700_ref31","doi-asserted-by":"crossref","first-page":"bbaa104","DOI":"10.1093\/bib\/bbaa104","article-title":"MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs","volume":"22","author":"Wang","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023011917101504700_ref32","doi-asserted-by":"crossref","DOI":"10.1109\/TCBB.2020.3034910","article-title":"LDICDL: LncRNA-disease association identification based on collaborative deep learning","volume":"19","author":"Lan","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2023011917101504700_ref33","article-title":"GANLDA: graph attention network for lncRNA-disease associations prediction","volume":"469","author":"","journal-title":"Neurocomputing"},{"issue":"3","key":"2023011917101504700_ref34","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1109\/TCBB.2019.2936476","article-title":"ILDMSF: inferring associations between long non-coding RNA and disease based on multi-similarity fusion","volume":"18","author":"Chen","year":"2019","journal-title":"IEEE\/ACM TransComput Biol Bioinform"},{"issue":"8","key":"2023011917101504700_ref35","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1039\/C3MB70608G","article-title":"Inferring novel lncRNA\u2013disease associations based on a random walk model of a lncRNA functional similarity network","volume":"10","author":"Sun","year":"2014","journal-title":"Mol Biosyst"},{"issue":"5","key":"2023011917101504700_ref36","doi-asserted-by":"crossref","first-page":"e1007872","DOI":"10.1371\/journal.pcbi.1007872","article-title":"iCDA-CGR: identification of circRNA-disease associations based on chaos game representation","volume":"16","author":"Zheng","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"2023011917101504700_ref37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-020-59040-0","article-title":"Integrating random walk with restart and k-nearest neighbor to identify novel circRNA-disease association","volume":"10","author":"Lei","year":"2020","journal-title":"Sci Rep"},{"issue":"2020","key":"2023011917101504700_ref38","doi-asserted-by":"crossref","first-page":"107287","DOI":"10.1016\/j.compbiolchem.2020.107287","article-title":"Predicting novel CircRNA-disease associations based on random walk and logistic regression model","volume":"87","author":"Ding","year":"2020","journal-title":"Comput Biol Chem"},{"issue":"13","key":"2023011917101504700_ref39","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.7150\/ijbs.33806","article-title":"GBDTCDA: predicting circRNA-disease associations based on gradient boosting decision tree with multiple biological data fusion","volume":"15","author":"Lei","year":"2019","journal-title":"Int J Biol Sci"},{"issue":"4","key":"2023011917101504700_ref40","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1093\/bib\/bbz080","article-title":"Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods","volume":"21","author":"Zeng","year":"2020","journal-title":"Brief Bioinform"},{"issue":"8","key":"2023011917101504700_ref41","first-page":"1813","article-title":"Learning to recommend with collaborative matrix factorization for new users","volume":"54","author":"Yukai","year":"2017","journal-title":"J Comput Res Dev"},{"key":"2023011917101504700_ref42","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1145\/3038912.3052585","volume-title":"Proceedings of the 26th International Conference on World Wide Web","author":"Cheng","year":"2017"},{"issue":"2018","key":"2023011917101504700_ref43","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.jocs.2018.08.007","article-title":"A genetic algorithms-based hybrid recommender system of matrix factorization and neighborhood-based techniques","volume":"28","author":"Kilani","year":"2018","journal-title":"J Comput Sci"},{"issue":"2020","key":"2023011917101504700_ref44","doi-asserted-by":"crossref","first-page":"105243","DOI":"10.1016\/j.knosys.2019.105243","article-title":"A matrix factorization based dynamic granularity recommendation with three-way decisions","volume":"191","author":"Liu","year":"2020","journal-title":"Knowl Based Syst"},{"issue":"3","key":"2023011917101504700_ref45","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.ipm.2018.02.005","article-title":"A novel recommendation method based on social network using matrix factorization technique","volume":"54","author":"Xu","year":"2018","journal-title":"Inf Process Manag"},{"issue":"6","key":"2023011917101504700_ref46","doi-asserted-by":"crossref","first-page":"2661","DOI":"10.1109\/JBHI.2019.2891779","article-title":"Computational prediction of human disease-associated circRNAs based on manifold regularization learning framework","volume":"23","author":"Xiao","year":"2019","journal-title":"IEEE J Biomed Health Inform"},{"issue":"4","key":"2023011917101504700_ref47","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.1093\/bib\/bbz057","article-title":"iCircDA-MF: identification of circRNA-disease associations based on matrix factorization","volume":"21","author":"Wei","year":"2020","journal-title":"Brief Bioinform"},{"issue":"5","key":"2023011917101504700_ref48","first-page":"1","article-title":"Prediction of circRNA-disease associations based on inductive matrix completion","volume":"13","author":"Li","year":"2020","journal-title":"BMC Med Genomics"},{"key":"2023011917101504700_ref49","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac155","article-title":"RNMFLP: predicting circRNA\u2013disease associations based on robust nonnegative matrix factorization and label propagation","volume":"23","author":"Peng","year":"2022","journal-title":"Brief Bioinform"},{"issue":"19","key":"2023011917101504700_ref50","first-page":"73","article-title":"DWNN-RLS: regularized least squares method for predicting circRNA-disease associations","volume":"19","author":"Yan","year":"2018","journal-title":"BMC Bioinform"},{"key":"2023011917101504700_ref51","doi-asserted-by":"crossref","first-page":"106694","DOI":"10.1016\/j.knosys.2020.106694","article-title":"Prediction of disease-associated circRNAs via circRNA\u2013disease pair graph and weighted nuclear norm minimization","volume":"214","author":"Zhang","year":"2021","journal-title":"Knowl Based Syst"},{"issue":"5","key":"2023011917101504700_ref52","doi-asserted-by":"crossref","first-page":"bbaa409","DOI":"10.1093\/bib\/bbaa409","article-title":"Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment","volume":"22","author":"Wang","year":"2021","journal-title":"Brief Bioinform"},{"issue":"3","key":"2023011917101504700_ref53","first-page":"891","article-title":"Deep matrix factorization improves prediction of human circRNA-disease associations","volume":"25","author":"","year":"2020","journal-title":"IEEE J Biomed Health Inform"},{"issue":"13","key":"2023011917101504700_ref54","doi-asserted-by":"crossref","first-page":"4038","DOI":"10.1093\/bioinformatics\/btz825","article-title":"An efficient approach based on multi-sources information to predict circRNA\u2013disease associations using deep convolutional neural network","volume":"36","author":"Wang","year":"2020","journal-title":"Bioinformatics"},{"issue":"2020","key":"2023011917101504700_ref55","first-page":"1042","article-title":"Prioritizing CircRNA-disease associations with convolutional neural network based on multiple similarity feature fusion","volume":"11","author":"Fan","year":"2020","journal-title":"Front Genet"},{"issue":"24","key":"2023011917101504700_ref56","doi-asserted-by":"crossref","first-page":"5656","DOI":"10.1093\/bioinformatics\/btaa1077","article-title":"Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks","volume":"36","author":"Lu","year":"2020","journal-title":"Bioinformatics"},{"issue":"11","key":"2023011917101504700_ref57","doi-asserted-by":"crossref","first-page":"5522","DOI":"10.1109\/TCYB.2020.3022852","article-title":"IMS-CDA: prediction of CircRNA-disease associations from the integration of multisource similarity information with deep stacked autoencoder model","volume":"51","author":"Wang","year":"2020","journal-title":"IEEE Trans Cybern"},{"issue":"1","key":"2023011917101504700_ref58","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1007\/s40291-020-00499-y","article-title":"Inferring potential CircRNA\u2013disease associations via deep autoencoder-based classification","volume":"25","author":"Deepthi","year":"2021","journal-title":"Mol Diagn Ther"},{"issue":"2021","key":"2023011917101504700_ref59","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.ins.2021.04.073","article-title":"Predicting circRNA-disease associations based on autoencoder and graph embedding","volume":"571","author":"Yang","year":"2021","journal-title":"Inform Sci"},{"issue":"5","key":"2023011917101504700_ref60","doi-asserted-by":"crossref","first-page":"e1007568","DOI":"10.1371\/journal.pcbi.1007568","article-title":"GCNCDA: a new method for predicting circRNA-disease associations based on graph convolutional network algorithm","volume":"16","author":"Wang","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2023011917101504700_ref61","doi-asserted-by":"crossref","DOI":"10.1109\/TCBB.2021.3111607","article-title":"IGNSCDA: predicting CircRNA-disease associations based on improved graph convolutional network and negative sampling","volume":"19","author":"Lan","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"3","key":"2023011917101504700_ref62","doi-asserted-by":"crossref","first-page":"bbac083","DOI":"10.1093\/bib\/bbac083","article-title":"iGRLCDA: identifying circRNA\u2013disease association based on graph representation learning","volume":"23","author":"Zhang","year":"2022","journal-title":"Brief Bioinform"},{"issue":"11","key":"2023011917101504700_ref63","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.3390\/cancers13112595","article-title":"GATCDA: predicting circRNA-disease associations based on graph attention network","volume":"13","author":"Bian","year":"2021","journal-title":"Cancer"},{"issue":"16","key":"2023011917101504700_ref64","doi-asserted-by":"crossref","first-page":"8505","DOI":"10.3390\/ijms22168505","article-title":"GATNNCDA: a method based on graph attention network and multi-layer neural network for predicting circRNA-disease associations","volume":"22","author":"Ji","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2023011917101504700_ref65","doi-asserted-by":"crossref","first-page":"bbac289","DOI":"10.1093\/bib\/bbac289","article-title":"MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction","volume":"2022","author":"Wu","year":"2022","journal-title":"Brief Bioinform"},{"issue":"8","key":"2023011917101504700_ref66","doi-asserted-by":"crossref","first-page":"2246","DOI":"10.1093\/bioinformatics\/btac079","article-title":"GMNN2CD: identification of circRNA\u2013disease associations based on variational inference and graph Markov neural networks","volume":"38","author":"Niu","year":"2022","journal-title":"Bioinformatics"},{"issue":"4","key":"2023011917101504700_ref67","doi-asserted-by":"crossref","first-page":"bbaa350","DOI":"10.1093\/bib\/bbaa350","article-title":"A comprehensive survey on computational methods of non-coding RNA and disease association prediction","volume":"22","author":"Lei","year":"2021","journal-title":"Brief Bioinform"},{"issue":"6","key":"2023011917101504700_ref68","doi-asserted-by":"crossref","first-page":"bbab286","DOI":"10.1093\/bib\/bbab286","article-title":"Circular RNAs and complex diseases: from experimental results to computational models","volume":"22","author":"Wang","year":"2021","journal-title":"Brief Bioinform"},{"issue":"11","key":"2023011917101504700_ref69","doi-asserted-by":"crossref","first-page":"1666","DOI":"10.1261\/rna.043687.113","article-title":"circBase: a database for circular RNAs","volume":"20","author":"Gla\u017ear","year":"2014","journal-title":"RNA"},{"issue":"D1","key":"2023011917101504700_ref70","doi-asserted-by":"crossref","first-page":"D925","DOI":"10.1093\/nar\/gkx863","article-title":"CSCD: a database for cancer-specific circular RNAs","volume":"46","author":"Xia","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023011917101504700_ref71","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1109\/SENSORCOMM.2008.79","volume-title":"2008 Second International Conference on Sensor Technologies and Applications (Sensorcomm 2008)","author":"Chen","year":"2008"},{"issue":"1","key":"2023011917101504700_ref72","first-page":"1","article-title":"circRNADb: a comprehensive database for human circular RNAs with protein-coding annotations","volume":"6","author":"Chen","year":"2016","journal-title":"Sci Rep"},{"issue":"D1","key":"2023011917101504700_ref73","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein\u2013RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023011917101504700_ref74","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bay044","article-title":"CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases","volume":"2018","author":"Fan","year":"2018","journal-title":"Database"},{"issue":"5","key":"2023011917101504700_ref75","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41419-018-0503-3","article-title":"circRNA disease: a manually curated database of experimentally supported circRNA-disease associations","volume":"9","author":"Zhao","year":"2018","journal-title":"cell death & disease"},{"key":"2023011917101504700_ref76","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baz003","article-title":"CircFunBase: a database for functional circular RNAs","volume":"2019","author":"Meng","year":"2019","journal-title":"Database"},{"issue":"D1","key":"2023011917101504700_ref77","doi-asserted-by":"crossref","first-page":"D209","DOI":"10.1093\/nar\/gkv940","article-title":"CircNet: a database of circular RNAs derived from transcriptome sequencing data","volume":"44","author":"Liu","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"2020","key":"2023011917101504700_ref78","article-title":"CircR2Cancer: a manually curated database of associations between circRNAs and cancers","volume":"2020","author":"Lan","year":"2020","journal-title":"Database"},{"key":"2023011917101504700_ref79","doi-asserted-by":"crossref","first-page":"283","DOI":"10.3389\/fgene.2013.00283","article-title":"Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits","volume":"4","author":"Ghosal","year":"2013","journal-title":"Front Genet"},{"issue":"2020","key":"2023011917101504700_ref80","doi-asserted-by":"crossref","first-page":"baaa019","DOI":"10.1093\/database\/baaa019","article-title":"Circad: a comprehensive manually curated resource of circular RNA associated with diseases","volume":"2020","author":"Rophina","year":"2020","journal-title":"Database"},{"issue":"6","key":"2023011917101504700_ref81","first-page":"984","article-title":"Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes","volume":"18","author":"Xia","year":"2017","journal-title":"Brief Bioinform"},{"issue":"36","key":"2023011917101504700_ref82","doi-asserted-by":"crossref","first-page":"57919","DOI":"10.18632\/oncotarget.11141","article-title":"IRWRLDA: improved random walk with restart for lncRNA-disease association prediction","volume":"7","author":"Chen","year":"2016","journal-title":"Oncotarget"},{"key":"2023011917101504700_ref83","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab494","article-title":"KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network","volume":"23","author":"Lan","year":"2022","journal-title":"Brief Bioinform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/1\/bbac613\/48781859\/bbac613.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/1\/bbac613\/48781859\/bbac613.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,10]],"date-time":"2024-10-10T08:45:45Z","timestamp":1728549945000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac613\/6972300"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1]]},"references-count":83,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac613","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1]]},"published":{"date-parts":[[2023,1]]},"article-number":"bbac613"}}