ArticleFrontiers in genetics2019
CircSLNN: Identifying RBP-Binding Sites on circRNAs
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 57 citations in OpenAlex.
- The circular RNA landscape: Biogenesis, functions, identification pipelines, and biomedical applications.Non-coding RNA research · 2026Review
- Review
- EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events.Bioinformatics (Oxford, England) · 2024Article
- CRBPSA: CircRNA-RBP interaction sites identification using sequence structural attention model.BMC biology · 2024Article
- Predicting circRNA-RBP Binding Sites Using a Hybrid Deep Neural Network.Interdisciplinary sciences, computational life sciences · 2024Article
- iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites.PLoS computational biology · 2024Article
- Review
- CircSI-SSL: circRNA-binding site identification based on self-supervised learning.Bioinformatics (Oxford, England) · 2024Article
- CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization.BMC bioinformatics · 2023Article
- Nucleotide-level prediction of CircRNA-protein binding based on fully convolutional neural network.Frontiers in genetics · 2023Article
- Supervised promoter recognition: a benchmark framework.BMC bioinformatics · 2022Article
- Artificial intelligence methods enhance the discovery of RNA interactions.Frontiers in molecular biosciences · 2022Review
- Pan-Cancer Bioinformatics Analysis of Gene UBE2C.Frontiers in genetics · 2022Article
- CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.PLoS computational biology · 2022Article
- Emerging Role of Circular RNA-Protein Interactions.Non-coding RNA · 2021Review
- ncRNAs regulate bovine adipose tissue deposition.Molecular and cellular biochemistry · 2021Review
- Roles of circRNAs on tumor autophagy.Molecular therapy. Nucleic acids · 2021Article
- Representation learning applications in biological sequence analysis.Computational and structural biotechnology journal · 2021Review
- The Emerging Role and Promise of Circular RNAs in Obesity and Related Metabolic Disorders.Cells · 2020Review
- Matrix factorization with neural network for predicting circRNA-RBP interactions.BMC bioinformatics · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The interactions between RNAs and RNA binding proteins (RBPs) are crucial for understanding post-transcriptional regulation mechanisms. A lot of computational tools have been developed to automatically predict the binding relationship between RNAs and RBPs. However, most of the methods can only predict the presence or absence of binding sites for a sequence fragment, without providing specific information on the position or length of the binding sites. Besides, the existing tools focus on the interaction between RBPs and linear RNAs, while the binding sites on circular RNAs (circRNAs) have been rarely studied. In this study, we model the prediction of binding sites on RNAs as a sequence labeling problem, and propose a new model called circSLNN to identify the specific location of RBP-binding sites on circRNAs. CircSLNN is driven by pretrained RNA embedding vectors and a composite labeling model. On our constructed circRNA datasets, our model has an average
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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.