ArticleNucleic acids research2015
A framework for improving microRNA prediction in non-human genomes.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Comprehensive analysis of plasma exosomal and non-exosomal microRNA profiles identifies potential early indicators of carcass traits in Japanese Black cattle.BMC genomics · 2026Article
- Sequence-Based Protein-Protein Interaction Prediction and Its Applications in Drug Discovery.Cells · 2025Review
- Species-specific microRNA discovery and target prediction in the soybean cyst nematode.Scientific reports · 2023Article
- P-TarPmiR accurately predicts plant-specific miRNA targets.Scientific reports · 2023Article
- Infrared Plasmonic Biosensor with Tetrahedral DNA Nanostructure as Carriers for Label-Free and Ultrasensitive Detection of miR-155.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Hybrid Deep Neural Network for Handling Data Imbalance in Precursor MicroRNA.Frontiers in public health · 2021Article
- Two-Level Protein Methylation Prediction using structure model-based features.Scientific reports · 2020Article
- A Brief Survey for MicroRNA Precursor Identification Using Machine Learning Methods.Current genomics · 2020Review
- Article
- Selecting Essential MicroRNAs Using a Novel Voting Method.Molecular therapy. Nucleic acids · 2019Article
- A semi-supervised machine learning framework for microRNA classification.Human genomics · 2019Article
- Multi-view Co-training for microRNA Prediction.Scientific reports · 2019Article
- Development of species specific putative miRNA and its target prediction tool in wheat (Triticum aestivum L.).Scientific reports · 2019Article
- miPIE: NGS-based Prediction of miRNA Using Integrated Evidence.Scientific reports · 2019Article
- Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome.Genome biology and evolution · 2018Article
- Comparing miRNA structure of mirtrons and non-mirtrons.BMC genomics · 2018Article
- A novel method to identify pre-microRNA in various species knowledge base on various species.Journal of biomedical semantics · 2017Article
- BP Neural Network Could Help Improve Pre-miRNA Identification in Various Species.BioMed research international · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently. However, the majority of studies have focused on the human genome. Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they have failed to report the dramatic drop in specificity (the ability to correctly reject non-miRNA sequences) in non-human genomes. Considering the ratio of true miRNA sequences to pseudo-miRNA sequences is on the order of 1:1000, such low specificity prevents the application of most existing tools to non-human genomes, as the number of false positives overwhelms the true predictions. We here introduce a framework (SMIRP) for creating species-specific miRNA prediction systems, leveraging sequence conservation and phylogenetic distance information. Substantial improvements in specificity and precision are obtained for four non-human test species when our framework is applied to three different prediction systems representing two types of classifiers (support vector machine and Random Forest), based on three different feature sets, with both human-specific and taxon-wide training data. The SMIRP framework is potentially applicable to all miRNA prediction systems and we expect substantial improvement in precision and specificity, while sustaining sensitivity, independent of the machine learning technique chosen.
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