ArticleScientific reports2016
Acfs: accurate circRNA identification and quantification from RNA-Seq data.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 95 citations in OpenAlex.
- Recent advances in the detection and functional analysis of circRNAs with short-read RNA sequencing-based methods.Molecular biology reports · 2026Review
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Mining, validating, and quantifying circular RNA transcriptome from total RNA as a biomarker or target.Scientific reports · 2025Article
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- Circular RNAs: Biogenesis and Functions : Circular RNA detection and bioinformatic analysis.Advances in experimental medicine and biology · 2025Review
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- An updated resource for the detection of protein-coding circRNA with CircProPlus.Scientific reports · 2024Article
- Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.ACS pharmacology & translational science · 2024Review
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- CircRNA identification and feature interpretability analysis.BMC biology · 2024Article
- Article
- New insight into circRNAs: characterization, strategies, and biomedical applications.Experimental hematology & oncology · 2023Review
- INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA.Bioinformatics (Oxford, England) · 2023Article
- Computational approaches for circRNAs prediction and in silico characterization.Briefings in bioinformatics · 2023Review
- Review
- Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion.Briefings in bioinformatics · 2023Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- Comprehensive identification and characterization of lncRNAs and circRNAs reveal potential brown planthopper-responsive ceRNA networks in rice.Frontiers in plant science · 2023Article
- StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy.BMC bioinformatics · 2022Article
- Emerging roles of circular RNAs in retinal diseases.Neural regeneration research · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form. They are splicing-generated, widely expressed in various tissues and have functional implications in development and diseases. To facilitate genome-wide characterization of circRNAs using RNA-Seq data, we present a freely available software package named acfs. Acfs allows de novo, accurate and fast identification and abundance quantification of circRNAs from single- and paired-ended RNA-Seq data. On simulated datasets, acfs achieved the highest F1 accuracy and lowest false discovery rate among current state-of-the-art tools. On real-world datasets, acfs efficiently identified more bona fide circRNAs. Furthermore, we demonstrated the power of circRNA analysis on two leukemia datasets. We identified a set of circRNAs that are differentially expressed between AML and APL samples, which might shed light on the potential molecular classification of complex diseases using circRNA profiles. Moreover, chromosomal translocation, as manifested in numerous diseases, could produce not only fusion transcripts but also fusion circRNAs of clinical relevance. Featured with high accuracy, low FDR and the ability to identify fusion circRNAs, we believe that acfs is well suited for a wide spectrum of applications in characterizing the landscape of circRNAs from non-model organisms to cancer biology.
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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.