ArticleBioinformatics (Oxford, England)2020
circDeep: deep learning approach for circular RNA classification from other long non-coding RNA.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 94 citations in OpenAlex.
- Non-coding RNAs and Mitochondrial Dysfunction in Alzheimer's Disease: A Systematic Review.Molecular neurobiology · 2026Pooled it
- The circular RNA landscape: Biogenesis, functions, identification pipelines, and biomedical applications.Non-coding RNA research · 2026Review
- Circular RNAs in metabolic health: bridging the gap between molecular biology and therapy.Cell death & disease · 2026Review
- Circular RNAs in human biology: from splicing noise to master regulators.Molecular biology reports · 2026Review
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- BPA: a BERT-based priority annotation strategy for assessing the rationality of aquatic algal protein sequences.Briefings in bioinformatics · 2025Article
- Article
- Review
- lncRNAs'p potential roles in the pathogenesis of cancer via interacting with signaling pathways; special focus on lncRNA-mediated signaling dysregulation in lung cancer.Medical oncology (Northwood, London, England) · 2024Review
- MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm.PLoS computational biology · 2024Article
- Predicting circRNA-RBP Binding Sites Using a Hybrid Deep Neural Network.Interdisciplinary sciences, computational life sciences · 2024Article
- CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs.Scientific reports · 2024Article
- Big data and deep learning for RNA biology.Experimental & molecular medicine · 2024Review
- Molecular insights into regulatory RNAs in the cellular machinery.Experimental & molecular medicine · 2024Review
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- CircRNA identification and feature interpretability analysis.BMC biology · 2024Article
- BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.RNA biology · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationOver the past two decades, a circular form of RNA (circular RNA), produced through alternative splicing, has become the focus of scientific studies due to its major role as a microRNA (miRNA) activity modulator and its association with various diseases including cancer. Therefore, the detection of circular RNAs is vital to understanding their biogenesis and purpose. Prediction of circular RNA can be achieved in three steps: distinguishing non-coding RNAs from protein coding gene transcripts, separating short and long non-coding RNAs and predicting circular RNAs from other long non-coding RNAs (lncRNAs). However, the available tools are less than 80 percent accurate for distinguishing circular RNAs from other lncRNAs due to difficulty of classification. Therefore, the availability of a more accurate and fast machine learning method for the identification of circular RNAs, which considers the specific features of circular RNA, is essential to the development of systematic annotation.
resultsHere we present an End-to-End deep learning framework, circDeep, to classify circular RNA from other lncRNA. circDeep fuses an RCM descriptor, ACNN-BLSTM sequence descriptor and a conservation descriptor into high level abstraction descriptors, where the shared representations across different modalities are integrated. The experiments show that circDeep is not only faster than existing tools but also performs at an unprecedented level of accuracy by achieving a 12 percent increase in accuracy over the other tools. AVAILABILITY AND IMPLEMENTATION: https://github.com/UofLBioinformatics/circDeep. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.