ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2024
CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3.Nature biotechnology · 2026Article
- Circular RNAs in osteosarcoma: mechanistic insights, autophagy regulation, and potential therapeutic strategies.Cancer cell international · 2026Review
- CircRNAs: Novel biomarkers and therapeutic targets for diseases of the central nervous system.Biochemistry and biophysics reports · 2026Review
- Review
- Diagnostic and therapeutic potential of exosomal circRNAs in cancer: decoding the circular code toward precision medicine.Cancer cell international · 2025Review
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Past, present, and future strategies for detecting and quantifying circular RNA variants.The FEBS journal · 2025Review
- Mitigating Cellular Dysfunction Through Contaminant Reduction in Synthetic circRNA for High-Efficiency mRNA-Based Cell Reprogramming.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genome-wide profiling and functional characterization of circular RNAs in neural development and injury: insights from a rat model research.Cellular and molecular life sciences : CMLS · 2025Article
- Global dysregulation of circular RNAs in frontal cortex and whole blood from DM1 and DM2.Human genetics · 2025Article
- From immune suppression to immunotherapy sensitization: the dual roles of circRNAs in cancer progression.Frontiers in immunology · 2025Review
- Circular RNA-Encoded Proteins in Disease Pathogenesis.International journal of biological sciences · 2025Review
- Review
- 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
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patterns. Despite the advances in single-cell and spatial transcriptomics, these technologies face difficulties in effectively profiling circRNAs due to inherent limitations in circRNA sequencing efficiency. To address this gap, a deep learning model, CIRI-deep, is presented for comprehensive prediction of circRNA regulation on diverse types of RNA-seq data. CIRI-deep is trained on an extensive dataset of 25 million high-confidence circRNA regulation events and achieved high performances on both test and leave-out data, ensuring its accuracy in inferring differential events from RNA-seq data. It is demonstrated that CIRI-deep and its adapted version enable various circRNA analyses, including cluster- or region-specific circRNA detection, BSJ ratio map visualization, and trans and cis feature importance evaluation. Collectively, CIRI-deep's adaptability extends to all major types of RNA-seq datasets including single-cell and spatial transcriptomic data, which will undoubtedly broaden the horizons of circRNA research.
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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.