ArticleScientific reports2017
Predicting siRNA efficacy based on multiple selective siRNA representations and their combination at score level.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- A smart nanocomposite bioactive ink for controlled siRNA delivery in calvarial mesenchymal stromal cells as a minimally invasive treatment for craniosynostosis.Regenerative biomaterials · 2026Article
- Design, pharmacology, and toxicology of a novel chemically modified siRNA targeting hepatic angiotensinogen.Molecular therapy. Nucleic acids · 2025Article
- Small interfering RNA: From designing to therapeutic in cancer.Journal, genetic engineering & biotechnology · 2025Review
- siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.Briefings in bioinformatics · 2024Article
- Novel Golden Lipid Nanoparticles with Small Interference Ribonucleic Acid for Substrate Reduction Therapy in Fabry Disease.Pharmaceutics · 2023Article
- A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks.International journal of molecular sciences · 2022Article
- Cheminformatics Modeling of Gene Silencing for Both Natural and Chemically Modified siRNAs.Molecules (Basel, Switzerland) · 2022Article
- Constructing the boundary between potent and ineffective siRNAs by MG-algorithm with C-features.BMC bioinformatics · 2022Article
- Systematics for types and effects of RNA variations.RNA biology · 2021Article
- Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03).Virology journal · 2020Article
- Functional features defining the efficacy of cholesterol-conjugated, self-deliverable, chemically modified siRNAs.Nucleic acids research · 2018Article
- SiRNA silencing efficacy prediction based on a deep architecture.BMC genomics · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small interfering RNAs (siRNAs) may induce to targeted gene knockdown, and the gene silencing effectiveness relies on the efficacy of the siRNA. Therefore, the task of this paper is to construct an effective siRNA prediction method. In our work, we try to describe siRNA from both quantitative and qualitative aspects. For quantitative analyses, we form four groups of effective features, including nucleotide frequencies, thermodynamic stability profile, thermodynamic of siRNA-mRNA interaction, and mRNA related features, as a new mixed representation, in which thermodynamic of siRNA-mRNA interaction is introduced to siRNA efficacy prediction for the first time to our best knowledge. And then an F-score based feature selection is employed to investigate the contribution of each feature and remove the weak relevant features. Meanwhile, we encode the siRNA sequence and existed empirical design rules as a qualitative siRNA representation. These two kinds of siRNA representations are combined to predict siRNA efficacy by supported Vector Regression (SVR) at score level. The experimental results indicate that our method may select the features with powerful discriminative ability and make the two kinds of siRNA representations work at full capacity. The prediction results also demonstrate that our method can outperform other popular siRNA efficacy prediction algorithms.
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