ArticleGenomics, proteomics & bioinformatics2019
CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs.
Article in Genomics, proteomics & bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs.Genomics, proteomics & bioinformatics · 2026Article
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- Accurate Reconstruction of Circular RNAs from Complex Rolling Circular Long Reads with CircPlex.bioRxiv : the preprint server for biology · 2025Article
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- CircAI: a comprehensive database of CircRNA associated with A-to-I RNA editing.Database : the journal of biological databases and curation · 2025Article
- Comprehensive circular RNA profiling in various sheep tissues.Scientific reports · 2024Article
- Accurate assembly of circular RNAs with TERRACE.Genome research · 2024Article
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Systematic identification and characterization of exon-intron circRNAs.Genome research · 2024Article
- Importance of pre-mRNA splicing and its study tools in plants.Advanced biotechnology · 2024Review
- FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing.Nucleic acids research · 2024Article
- Circular RNA expression in turkey skeletal muscle satellite cells is significantly altered by thermal challenge.Frontiers in physiology · 2024Article
- Article
- New insight into circRNAs: characterization, strategies, and biomedical applications.Experimental hematology & oncology · 2023Review
- Dysregulation of circular RNAs in inflammation and cancers.Fundamental research · 2023Review
- Computational approaches for circRNAs prediction and in silico characterization.Briefings in bioinformatics · 2023Review
- CYCLeR-a novel tool for the full isoform assembly and quantification of circRNAs.Nucleic acids research · 2023Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- A Review and In Silico Analysis of Tissue and Exosomal Circular RNAs: Opportunities and Challenges in Thyroid Cancer.Cancers · 2022Review
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms at the same locus. However, the challenges of reconstruction and quantification of alternatively spliced full-length circRNAs remain unresolved. On the basis of the internal structural characteristics of circRNAs, we developed CircAST, a tool to assemble alternatively spliced circRNA transcripts and estimate their expression by using multiple splice graphs. Simulation studies showed that CircAST correctly assembled the full sequences of circRNAs with a sensitivity of 85.63%-94.32% and a precision of 81.96%-87.55%. By assigning reads to specific isoforms, CircAST quantified the expression of circRNA isoforms with correlation coefficients of 0.85-0.99 between theoretical and estimated values. We evaluated CircAST on an in-house mouse testis RNA-seq dataset with RNase R treatment for enriching circRNAs and identified 380 circRNAs with full-length sequences different from those of their corresponding cognate linear RNAs. RT-PCR and Sanger sequencing analyses validated 32 out of 37 randomly selected isoforms, thus further indicating the good performance of CircAST, especially for isoforms with low abundance. We also applied CircAST to published experimental data and observed substantial diversity in circular transcripts across samples, thus suggesting that circRNA expression is highly regulated. CircAST can be accessed freely at https://github.com/xiaofengsong/CircAST.
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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.