The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
A comprehensive overview and evaluation of circular RNA detection tools
Open accessAbstract
Circular RNA (circRNA) is mainly generated by the splice donor of a downstream exon joining to an upstream splice acceptor, a phenomenon known as backsplicing. It has been reported that circRNA can function as microRNA (miRNA) sponges, transcriptional regulators, or potential biomarkers. The availability of massive non-polyadenylated transcriptomes data has facilitated the genome-wide identification of thousands of circRNAs. Several circRNA detection tools or pipelines have recently been developed, and it is essential to provide useful guidelines on these pipelines for users, including a comprehensive and unbiased comparison. Here, we provide an improved and easy-to-use circRNA read simulator that can produce mimicking backsplicing reads supporting circRNAs deposited in CircBase. Moreover, we compared the performance of 11 circRNA detection tools on both simulated and real datasets. We assessed their performance regarding metrics such as precision, sensitivity, F1 score, and Area under Curve. It is concluded that no single method dominated on all of these metrics. Among all of the state-of-the-art tools, CIRI, CIRCexplorer, and KNIFE, which achieved better balanced performance between their precision and sensitivity, compared favorably to the other methods.
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Cites
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RA-UNet: A Hybrid Deep Attention-Aware Network to Extract Liver and Tumor in CT Scans
Jin, Q., Meng, Z., Sun, C., Cui, H., & Su, R. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.605132 · Cited by 468
Machine Learning for Drug-Target Interaction Prediction
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Role of circular RNAs in brain development and CNS diseases
Mehta, S. L., Dempsey, R. J., & Vemuganti, R. (2020) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2020.101746 · Cited by 281
Circular RNAs: biogenesis, function, and a role as possible cancer biomarkers
Bolha, L., Ravnik-Glavač, M., & Glavač, D. (2017) · International Journal of Genomics · doi:10.1155/2017/6218353 · Cited by 166
“In general, these circRNA detection tools can be divided into two categories, based on the different strategies used for circRNA identification, according to the dependency on genome annotation [63].”
MethodClosing the circle: current state and perspectives of circular RNA databases
Vromman, M., Vandesompele, J., & Volders, P.-J. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbz175 · Cited by 111
Metadata
- Authors
- Zeng, X., Lin, W., Guo, M., & Zou, Q.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2017-06-08
- Volume
- 13
- Issue
- 6
- Pages
- e1005420
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2622004629
- Cited by
- 346
- References
- 55
- FWCI
- 17.86
- Type
- journal article
- Language
- en
- Open access
- gold
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