Abstract
Circular RNA (circRNA) is a covalently closed RNA molecule formed by back splicing. The role of circRNAs in posttranscriptional gene regulation provides new insights into several types of cancer and neurological diseases. CircRNAs are associated with multiple diseases and are emerging biomarkers in cancer diagnosis and treatment. The associations prediction is one of the current research hotspots in the field of bioinformatics. Although research on circRNAs has made great progress, the traditional biological method of verifying circRNA-disease associations is still a great challenge because it is a difficult task and requires much time. Fortunately, advances in computational methods have made considerable progress in circRNA research. This review comprehensively discussed the functions and databases related to circRNA, and then focused on summarizing the calculation model of related predictions, detailed the mainstream algorithm into 4 categories, and analyzed the advantages and limitations of the 4 categories. This not only helps researchers to have overall understanding of circRNA, but also helps researchers have a detailed understanding of the past algorithms, guide new research directions and research purposes to solve the shortcomings of previous research.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Sanger H L, Klotz G, Riesner D, Gross H J, Kleinschmidt A K. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proceedings of the National Academy of Sciences of the United States of America, 1976, 73(11): 3852–3856
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak S D, Gregersen L H, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, Le Noble F, Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 2013, 495(7441): 333–338
Qu S, Yang X, Li X, Wang J, Gao Y, Shang R, Sun W, Dou K, Li H. Circular RNA: a new star of noncoding RNAs. Cancer Letters, 2015, 365(2): 141–148
Ye C Y, Chen L, Liu C, Zhu Q H, Fan L. Widespread noncoding circular RNAs in plants. New Phytologist, 2015, 208(1): 88–95
Hsiao K Y, Sun H S, Tsai S J. Circular RNA–new member of noncoding RNA with novel functions. Experimental Biology and Medicine, 2017, 242(11): 1136–1141
Jeck W R, Sharpless N E. Detecting and characterizing circular RNAs. Nature Biotechnology, 2014, 32(5): 453–461
Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Li P, Wu M. CircRNA: functions and properties of a novel potential biomarker for cancer. Molecular Cancer, 2017, 16(1): 94
Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J, Chen D, Gu J, He X, Huang S. Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Research, 2015, 25(8): 981–984
Verduci L, Strano S, Yarden Y, Blandino G. The circRNA–microRNA code: emerging implications for cancer diagnosis and treatment. Molecular Oncology, 2019, 13(4): 669–680
Zheng Q, Bao C, Guo W, Li S, Chen J, Chen B, Luo Y, Lyu D, Li Y, Shi G, Liang L, Gu J, He X, Huang S. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nature Communications, 2016, 7(1): 11215
Verduci L, Tarcitano E, Strano S, Yarden Y, Blandino G. CircRNAs: role in human diseases and potential use as biomarkers. Cell Death & Disease, 2021, 12(5): 468
Wang Y, Zhang X, Ju Y, Liu Q, Zou Q, Zhang Y, Ding Y, Zhang Y. Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learning. Frontiers of Computer Science, 2024, 18(2): 182903
Wang C-C, Han C-D, Zhao Q, Chen X. Circular RNAs and complex diseases: from experimental results to computational models. Briefings in Bioinformatics, 2021, 22(6): bbab286
Lan W, Dong Y, Zhang H, Li C, Chen Q, Liu J, Wang J, Chen Y P P. Benchmarking of computational methods for predicting circRNA-disease associations. Briefings in Bioinformatics, 2023, 24(1): bbac613
Chen Y, Wang J, Wang C, Liu M, Zou Q. Deep learning models for disease-associated circRNA prediction: a review. Briefings in Bioinformatics, 2022, 23(6): bbac364
Xiao Q, Dai J, Luo J. A survey of circular RNAs in complex diseases: databases, tools and computational methods. Briefings in Bioinformatics, 2022, 23(1): bbab444
Belousova E A, Filipenko M L, Kushlinskii N E. Circular RNA: new regulatory molecules. Bulletin of Experimental Biology and Medicine, 2018, 164(6): 803–815
Gao J-L, Chen G, He H-Q, Wang J. CircRNA as a new field in human disease research. China Journal of Chinese Materia Medica, 2018, 43(3): 457–462
Lou J, Hao Y, Lin K, Lyu Y, Chen M, Wang H, Zou D, Jiang X, Wang R, Jin D, Lam E W F, Shao S, Liu Q, Yan J, Wang X, Chen P, Zhang B, Jin B. Circular RNA CDR1as disrupts the p53/MDM2 complex to inhibit Gliomagenesis. Molecular Cancer, 2020, 19(1): 138
Capel B, Swain A, Nicolis S, Hacker A, Walter M, Koopman P, Goodfellow P, Lovell-Badge R. Circular transcripts of the testisdetermining gene Sry in adult mouse testis. Cell, 1993, 73(5): 1019–1030
Pamudurti N R, Patop I L, Krishnamoorthy A, Bartok O, Maya R, Lerner N, Ashwall-Fluss R, Konakondla J V V, Beatus T, Kadener S. circMbl functions in cis and in trans to regulate gene expression and physiology in a tissue-specific fashion. Cell Reports, 2022, 39(4): 110740
Panda A C. Circular RNAs act as miRNA sponges. Circular RNAs: Biogenesis and Functions, 2018: 67–79
Su M, Xiao Y, Ma J, Tang Y, Tian B, Zhang Y, Li X, Wu Z, Yang D, Zhou Y, Wang H, Liao Q, Wang W. Circular RNAs in Cancer: emerging functions in hallmarks, stemness, resistance and roles as potential biomarkers. Molecular Cancer, 2019, 18(1): 90
Hansen T B, Jensen T I, Clausen B H, Bramsen J B, Finsen B, et al. Natural RNA circles function as efficient microRNA sponges. Nature, 2013, 495(7441): 384–388
Gupta S K, Garg A, Bär C, Chatterjee S, Foinquinos A, Milting H, Streckfuß-Bömeke K, Fiedler J, Thum T. Quaking inhibits doxorubicin-mediated cardiotoxicity through regulation of cardiac circular RNA expression. Circulation Research, 2018, 122(2): 246–254
Chen Y-J, Chen C-Y, Mai T-L, Chuang C-F, Chen Y-C, Gupta S K, Yen L, Wang Y D, Chuang T J. Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism. Genome Research, 2020, 30(3): 375–391
Zhang F, Zhang R, Zhang X, Wu Y, Li X, Zhang S, Hou W, Ding Y, Tian J, Sun L, Kong X. Comprehensive analysis of circRNA expression pattern and circRNA-miRNA-mRNA network in the pathogenesis of atherosclerosis in rabbits. Aging, 2018, 10(9): 2266–2283
Chia W, Liu J, Huang Y-G, Zhang C. A circular RNA derived from DAB1 promotes cell proliferation and osteogenic differentiation of BMSCs via RBPJ/DAB1 axis. Cell Death & Disease, 2020, 11(5): 372
Liu Y, Song J, Liu Y, Zhou Z, Wang X. Transcription activation of circ-STAT3 induced by Gli2 promotes the progression of hepatoblastoma via acting as a sponge for miR-29a/b/c-3p to upregulate STAT3/Gli2. Journal of Experimental & Clinical Cancer Research, 2020, 39(1): 101
Kong P, Yu Y, Wang L, Dou Y-Q, Zhang X-H, Cui Y, Wang H-Y, Yong Y-T, Liu Y-B, Hu H-J, Cui W, Sun S-G, Li B-H, Zhang F, Han M. circ-Sirt1 controls NF-κB activation via sequence-specific interaction and enhancement of SIRT1 expression by binding to miR-132/212 in vascular smooth muscle cells. Nucleic Acids Research, 2019, 47(7): 3580–3593
Liang W-C, Wong C-W, Liang P-P, Shi M, Cao Y, Rao S-T, Tsui S K W, Waye M M Y, Zhang Q, Fu W-M, Zhang J-F. Translation of the circular RNA circβ-catenin promotes liver cancer cell growth through activation of the Wnt pathway. Genome Biology, 2019, 20(1): 84
Bai N, Peng E, Qiu X, Lyu N, Zhang Z, Tao Y, Li X, Wang Z. circFBLIM1 act as a ceRNA to promote hepatocellular cancer progression by sponging miR-346. Journal of Experimental & Clinical Cancer Research, 2018, 37(1): 172
Zhou J, Zhang S, Chen Z, He Z, Xu Y, Li Z. CircRNA-ENO1 promoted glycolysis and tumor progression in lung adenocarcinoma through upregulating its host gene ENO1. Cell Death & Disease, 2019, 10(12): 885
He R, Liu P, Xie X, Zhou Y, Liao Q, Xiong W, Li X, Li G, Zeng Z, Tang H. circGFRA1 and GFRA1 act as ceRNAs in triple negative breast cancer by regulating miR-34a. Journal of Experimental & Clinical Cancer Research, 2017, 36(1): 145
Ou R, Lv J, Zhang Q, Lin F, Zhu L, Huang F, Li X, Li T, Zhao L, Ren Y, Xu Y. circAMOTL1 motivates AMOTL1 expression to facilitate cervical cancer growth. Molecular Therapy Nucleic Acids, 2020, 19: 50–60
Yang L, Zeng Z, Kang N, Yang J C, Wei X, Hai Y. Circ-VANGL1 promotes the progression of osteoporosis by absorbing miRNA-217 to regulate RUNX2 expression. European Review for Medical and Pharmacological Sciences, 2019, 23(3): 949–957
Wan L, Han Q, Zhu B, Kong Z, Feng E. Circ-TFF1 facilitates breast cancer development via regulation of miR-338-3p/FGFR1 Axis. Biochemical Genetics, 2022, 60(1): 315–335
Lu M. Circular RNA: functions, applications and prospects. ExRNA, 2020, 2(1): 1
Geng X, Lin X, Zhang Y, Li Q, Guo Y, Fang C, Wang H. Exosomal circular RNA sorting mechanisms and their function in promoting or inhibiting cancer. Oncology Letters, 2020, 19(5): 3369–3380
Aufiero S, Reckman Y J, Pinto Y M, Creemers E E. Circular RNAs open a new chapter in cardiovascular biology. Nature Reviews Cardiology, 2019, 16(8): 503–514
Xu Z, Song L, Liu S, Zhang W. DeepCRBP: improved predicting function of circRNA-RBP binding sites with deep feature learning. Frontiers of Computer Science, 2024, 18(2): 182907
Guo Y, Lei X, Liu L, Pan Y. circ2CBA: prediction of circRNA-RBP binding sites combining deep learning and attention mechanism. Frontiers of Computer Science, 2023, 17(5): 175904
Zhou R, Wu Y, Wang W, Su W, Liu Y, Wang Y, Fan C, Li X, Li G, Li Y, Xiong W, Zeng Z. Circular RNAs (circRNAs) in cancer. Cancer Letters, 2018, 425: 134–142
Peng L, Yuan X Q, Li G C. The emerging landscape of circular RNA ciRS-7 in cancer. Oncology Reports, 2015, 33(6): 2669–2674
Chen B, Huang S. Circular RNA: an emerging non-coding RNA as a regulator and biomarker in cancer. Cancer Letters, 2018, 418: 41–50
Hansen T B, Kjems J, Damgaard C K. Circular RNA and miR-7 in cancer. Cancer Research, 2013, 73(18): 5609–5612
Akhter R. Circular RNA and Alzheimer’s disease. In: Xiao J, ed. Circular RNAs: Biogenesis and Functions. Singapore: Springer, 2018, 239–243
Hong H, Zhu H, Zhao S, Wang K, Zhang N, Tian Y, Li Y, Wang Y, Lv X, Wei T, Liu Y, Fan S, Liu Y, Li Y, Cai A, Jin S, Qin Q, Li H. The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression. Cell Death & Disease, 2019, 10(12): 950
Ashwal-Fluss R, Meyer M, Pamudurti N R, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S. circRNA biogenesis competes with pre-mRNA splicing. Molecular Cell, 2014, 56(1): 55–66
Ji X, Shan L, Shen P, He M. Circular RNA circ_001621 promotes osteosarcoma cells proliferation and migration by sponging miR-578 and regulating VEGF expression. Cell Death & Disease, 2020, 11(1): 18
Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA, 2014, 20(11): 1666–1670
Li S, Li Y, Chen B, Zhao J, Yu S, Tang Y, Zheng Q, Li Y, Wang P, He X, Huang S. exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. Nucleic Acids Research, 2018, 46(D1): D106–D112
Dong R, Ma X-K, Li G-W, Yang L. CIRCpedia v2: an updated database for comprehensive circular RNA annotation and expression comparison. Genomics, Proteomics & Bioinformatics, 2018, 16(4): 226–233
Pan X, Xiong K, Anthon C, Hyttel P, Freude K K, Jensen L J, Gorodkin J. WebCircRNA: classifying the circular RNA potential of coding and noncoding RNA. Genes, 2018, 9(11): 536
Ruan H, Xiang Y, Ko J, Li S, Jing Y, Zhu X, Ye Y, Zhang Z, Mills T, Feng J, Liu C J, Jing J, Cao J, Zhou B, Wang L, Zhou Y, Lin C, Guo A Y, Chen X, Diao L, Li W, Chen Z, He X, Mills G B, Blackburn M R, Han L. Comprehensive characterization of circular RNAs in ∼ 1000 human cancer cell lines. Genome Medicine, 2019, 11(1): 55
Liu Q, Cai Y, Xiong H, Deng Y, Dai X. CCRDB: a cancer circRNAs-related database and its application in hepatocellular carcinoma-related circRNAs. Database, 2019, 2019: baz063
Zhao M, Liu Y, Qu H. circExp database: An online transcriptome platform for human circRNA expressions in cancers. Database, 2021, 2021: baab045
Meng X, Hu D, Zhang P, Chen Q, Chen M. CircFunBase: a database for functional circular RNAs. Database, 2019, 2019: baz003
Dudekula D B, Panda A C, Grammatikakis I, De S, Abdelmohsen K, Gorospe M. CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biology, 2016, 13(1): 34–42
Chen X, Han P, Zhou T, Guo X, Song X, Li Y. circRNADb: a comprehensive database for human circular RNAs with protein-coding annotations. Scientific Reports, 2016, 6(1): 34985
Hamosh A, Scott A F, Amberger J S, Bocchini C A, McKusick V A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research, 2005, 33(S1): D514–D517
Rappaport N, Nativ N, Stelzer G, Twik M, Guan-Golan Y, Stein T I, Bahir I, Belinky F, Morrey C P, Safran M, Lancet D. MalaCards: an integrated compendium for diseases and their annotation. Database, 2013, 2013: bat018
Canese K, Weis S. PubMed: the bibliographic database. 2002 Oct 9 [Updated 2013 Mar 20]. In: The NCBI Handbook[Internet]. 2nd edn. Bethesda (MD): National Center for Biotechnology Information (US). 2013, Available from the website of ncbi.nlm.nih.gov/books/NBK153385/
Zhu L, Ren T, Zhu Z, Cheng M, Mou Q, Mu M, Liu Y, Yao Y, Cheng Y, Zhang B, Cheng Z. Thymosin-β4 mediates hepatic stellate cell activation by interfering with CircRNA-0067835/miR-155/FoxO3 signaling pathway. Cellular Physiology and Biochemistry, 2018, 51(3): 1389–1398
Zhao Z, Wang K, Wu F, Wang W, Zhang K, Hu H, Liu Y, Jiang T. circRNA disease: a manually curated database of experimentally supported circRNA-disease associations. Cell Death & Disease, 2018, 9(5): 475
Yao D, Zhang L, Zheng M, Sun X, Lu Y, Liu P. Circ2Disease: a manually curated database of experimentally validated circRNAs in human disease. Scientific Reports, 2018, 8(1): 11018
Zhang W, Liu Y, Min Z, Liang G, Mo J, Ju Z, Zeng B, Guan W, Zhang Y, Chen J, Zhang Q, Li H, Zeng C, Wei Y, Chan G C F. circMine: a comprehensive database to integrate, analyze and visualize human disease–related circRNA transcriptome. Nucleic Acids Research, 2022, 50(D1): D83–D92
Rophina M, Sharma D, Poojary M, Scaria V. Circad: a comprehensive manually curated resource of circular RNA associated with diseases. Database, 2020, 2020: baaa019
Lan W, Zhu M, Chen Q, Chen B, Liu J, Li M, Chen Y P P. CircR2Cancer: a manually curated database of associations between circRNAs and cancers. Database, 2020, 2020: baaa085
Deng L, Zhang W, Shi Y, Tang Y. Fusion of multiple heterogeneous networks for predicting circRNA-disease associations. Scientific Reports, 2019, 9(1): 9605
Xiao Q, Yu H, Zhong J, Liang C, Li G, Ding P, Luo J. An in-silico method with graph-based multi-label learning for large-scale prediction of circRNA-disease associations. Genomics, 2020, 112(5): 3407–3415
Xiao Q, Fu Y, Yang Y, Dai J, Luo J. NSL2CD: identifying potential circRNA–disease associations based on network embedding and subspace learning. Briefings in Bioinformatics, 2021, 22(6): bbab177
Lei X, Fang Z, Chen L, Wu F-X. PWCDA: path weighted method for predicting circRNA-disease associations. International Journal of Molecular Sciences, 2018, 19(11): 3410
Li G, Yue Y, Liang C, Xiao Q, Ding P, Luo J. NCPCDA: network consistency projection for circRNA–disease association prediction. RSC Advances, 2019, 9(57): 33222–33228
Xiao Q, Zhong J, Tang X, Luo J. iCDA-CMG: identifying circRNA-disease associations by federating multi-similarity fusion and collective matrix completion. Molecular Genetics and Genomics, 2021, 296(1): 223–233
Shu L, Zhou C, Yuan X, Zhang J, Deng L. MSCFS: inferring circRNA functional similarity based on multiple data sources. BMC Bioinformatics, 2021, 22(10): 371
Lei X, Zhang W. BRWSP: predicting circRNA-disease associations based on biased random walk to search paths on a multiple heterogeneous network. Complexity, 2019, 2019: 5938035
Lei X, Fang Z, Guo L. Predicting circRNA–disease associations based on improved collaboration filtering recommendation system with multiple data. Frontiers in Genetics, 2019, 10: 897
Wei H, Xu Y, Liu B. iCircDA-LTR: identification of circRNA–disease associations based on Learning to Rank. Bioinformatics, 2021, 37(19): 3302–3310
Wei H, Liu B. iCircDA-MF: identification of circRNA-disease associations based on matrix factorization. Briefings in Bioinformatics, 2020, 21(4): 1356–1367
Peng L, Yang C, Huang L, Chen X, Fu X, Liu W. RNMFLP: predicting circRNA–disease associations based on robust nonnegative matrix factorization and label propagation. Briefings in Bioinformatics, 2022, 23(5): bbac155
Zheng K, You Z-H, Li J-Q, Wang L, Guo Z-H, Huang Y-A. iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation. PLoS Computational Biology, 2020, 16(5): e1007872
Wang L, You Z H, Li J Q, Huang Y A. IMS-CDA: prediction of CircRNA-disease associations from the integration of multisource similarity information with deep stacked autoencoder model. IEEE Transactions on Cybernetics, 2021, 51(11): 5522–5531
Shen S, Liu J, Zhou C, Qian Y, Deng L. XGBCDA: a multiple heterogeneous networks-based method for predicting circRNA-disease associations. BMC Medical Genomics, 2022, 13(1): 196
Wang L, You Z-H, Zhou X, Yan X, Li H-Y, Huang Y-A. NMFCDA: Combining randomization-based neural network with non-negative matrix factorization for predicting CircRNA-disease association. Applied Soft Computing, 2021, 110: 107629
Deng L, Liu D, Li Y, Wang R, Liu J, Zhang J, Liu H. MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network. BMC Bioinformatics, 2022, 23(3): 427
Yan C, Wang J, Wu F-X. DWNN-RLS: regularized least squares method for predicting circRNA-disease associations. BMC Bioinformatics, 2018, 19(19): 520
Lan W, Dong Y, Chen Q, Liu J, Wang J, Chen Y P P, Pan S. IGNSCDA: predicting CircRNA-disease associations based on improved graph convolutional network and negative sampling. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022, 19(6): 3530–3538
Wang L, Yan X, You Z-H, Zhou X, Li H-Y, Huang Y-A. SGANRDA: semi-supervised generative adversarial networks for predicting circRNA–disease associations. Briefings in Bioinformatics, 2021, 22(5): bbab028
Chen Y, Wang Y, Ding Y, Su X, Wang C. RGCNCDA: Relational graph convolutional network improves circRNA-disease association prediction by incorporating microRNAs. Computers in Biology and Medicine, 2022, 143: 105322
Yan X, Wang L, You Z-H, Li L-P, Zheng K. GANCDA: a novel method for predicting circRNA-disease associations based on deep generative adversarial network. International Journal of Data Mining and Bioinformatics, 2020, 23(3): 265–283
Wu Q, Deng Z, Pan X, Shen H-B, Choi K-S, Wang S, Wu J, Yu D J. MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction. Briefings in Bioinformatics, 2022, 23(5): bbac289
Wang L, You Z-H, Li Y-M, Zheng K, Huang Y-A. GCNCDA: a new method for predicting circRNA-disease associations based on graph convolutional network algorithm. PLoS Computational Biology, 2020, 16(5): e1007568
Bian C, Lei X-J, Wu F-X. GATCDA: predicting circRNA-disease associations based on graph attention network. Cancers, 2021, 13(11): 2595
Dai Q, Liu Z, Wang Z, Duan X, Guo M. GraphCDA: a hybrid graph representation learning framework based on GCN and GAT for predicting disease-associated circRNAs. Briefings in Bioinformatics, 2022, 23(5): bbac379
Lan W, Dong Y, Chen Q, Zheng R, Liu J, Pan Y, Chen Y P P. KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network. Briefings in Bioinformatics, 2022, 23(1): bbab494
Lan W, Zhang H, Dong Y, Chen Q, Cao J, Peng W, Liu J, Li M. DRGCNCDA: Predicting circRNA-disease interactions based on knowledge graph and disentangled relational graph convolutional network. Methods, 2022, 208: 35–41
Yuan L, Zhao J, Shen Z, Zhang Q, Geng Y, Zheng C-H, Huang D-S. iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction. PLoS Computational Biology, 2023, 19(8): e1011344
Lu C, Zhang L, Zeng M, Lan W, Wang J. Identifying disease-associated circRNAs based on edge-weighted graph attention and heterogeneous graph neural network. bioRxiv, 2022: 2022.05.04.490565
Niu M, Zou Q, Wang C. GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks. Bioinformatics, 2022, 38(8): 2246–2253
Wang Y, Zhai Y, Ding Y, Zou Q. SBSM-Pro: support bio-sequence machine for proteins. 2023, arXiv preprint arXiv: 2308.10275
Fan C, Lei X, Wu F-X. Prediction of CircRNA-disease associations using KATZ model based on heterogeneous networks. International Journal of Biological Sciences, 2018, 14(14): 1950–1959
Fan C, Lei X, Pan Y. Prioritizing CircRNA–disease associations with convolutional neural network based on multiple similarity feature fusion. Frontiers in Genetics, 2020, 11: 540751
Acknowledgements
The work was supported by the National Natural Science Foundation of China (Grant Nos. 62231013, 62201129, 62303328, 62302341, 62271329, 62372332), the National Key R&D Program of China (2022ZD0117700), the National funded postdoctoral researcher program of China (GZC20230382), the Shenzhen Polytechnic University Research Fund (6024310027K, 6022310036K, 6023310037K), the Key Field of Department of Education of Guangdong Province (2022ZDZX2082), and the Special Science Foundation of Quzhou (2023D036). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests The authors declare that they have no competing interests or financial conflicts to disclose.
Additional information
Mengting Niu is a postdoctoral fellow at University of Electronic Science and Technology of China and Shenzhen Polytechnic University, China. Her research interests include bioinformatics, data mining, and biomedicine.
Yaojia Chen is a PhD candidate at the Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, China. Her research interests include machine learning and bioinformatics.
Chunyu Wang is a professor at Faculty of Computing, Harbin Institute of Technology, China. His research fields include computational biology and machine learning, especially on the structure and function prediction of biomolecules, artificial intelligence-assisted drug discovery, high-throughput sequence data analysis etc.
Quan Zou received the BSc, MSc, and the PhD degrees in computer science from the Harbin Institute of Technology, China in 2004, 2007, and 2009, respectively. He is currently a professor with the Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China. His research is in the areas of bioinformatics, machine learning, and parallel computing. Several related works have been published by Science, Briefings in Bioinformatics, Bioinformatics, the IEEE/ACM Transactions on Computational Biology and Bioinformatitcs, etc. He is the editor-inchief of Current Bioinformatics, associate editor of IEEE Access, and an editorial board member of Computers in Biology and Medicine, Genes, Scientific Reports, etc.
Lei Xu is an associate professor at the School of Electronic and Communication Engineering, Shenzhen Polytechnic, China. She received her BSc and MSc from the School of Computer Science and Technology in Harbin Institute of Technology, China in 2006 and 2008, respectively. She got her PhD degree from the Department of Computing, The Hong Kong Polytechnic University, China in 2013. Her research interests are focused on bioinformatics, pattern recognition.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Niu, M., Chen, Y., Wang, C. et al. Computational approaches for circRNA-disease association prediction: a review. Front. Comput. Sci. 19, 194904 (2025). https://doi.org/10.1007/s11704-024-40060-2
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11704-024-40060-2