ReviewPLoS computational biology2017
A comprehensive overview and evaluation of circular RNA detection tools.
Review in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 203 papers, 1 of them a synthesis that pooled it.
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Who cites it
203 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Korean Society for Genetic Diagnostics Guidelines for Validation of Next-Generation Sequencing-Based Somatic Variant Detection in Hematologic Malignancies.Annals of laboratory medicine · 2019Guideline
- Circular and Long Non-Coding RNAs in Cancer Metabolism: Dual Perspective of Biomarkers and Therapeutic Targets.Non-coding RNA · 2026Review
- Landscape of circular RNAs in acute myeloid leukemia and their clinical significance.NPJ precision oncology · 2026Article
- Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.GigaScience · 2026Article
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- Identification and characterization of tissue- and stress-specific circular RNAs (circRNAs) of tea to generate the largest tea circRNAs data repository.Scientific reports · 2025Article
- Functional regulatory mechanisms of circRNAs in bovine adipogenesis.Cytotechnology · 2025Review
- The potential of circular RNAs as biomarkers and therapeutic targets for gastric cancer: A comprehensive review.Journal of advanced research · 2025Review
- Mining, validating, and quantifying circular RNA transcriptome from total RNA as a biomarker or target.Scientific reports · 2025Article
- Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity.Nucleic acids research · 2025Article
- Circular RNAs increase during vascular cell differentiation and are biomarkers for vascular disease.Cardiovascular research · 2025Article
- Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism.The plant genome · 2025Article
- Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data.Nature protocols · 2025Review
- Circular RNAs: Biogenesis and Functions : Circular RNA detection and bioinformatic analysis.Advances in experimental medicine and biology · 2025Review
- Challenges and Future Prospectives in Circular RNA Investigation.Advances in experimental medicine and biology · 2025Review
- Circular RNAs in Archaea.Advances in experimental medicine and biology · 2025Review
- Comprehensive circular RNA profiling in various sheep tissues.Scientific reports · 2024Article
- Article
- Long-range alternative splicing contributes to neoantigen specificity in glioblastoma.Briefings in bioinformatics · 2024Article
- iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites.PLoS computational biology · 2024Article
143 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.