ArticleBioinformatics (Oxford, England)2016
TarPmiR: a new approach for microRNA target site prediction.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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Who cites it
98 citing papers in PubMed.
- Time-Restricted Eating Regimen Differentially Affects Circulatory miRNA Expression in Older Overweight Adults.Nutrients · 2022Trial
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- miRNA Target Prediction: An Overview of the Past and Current Tools.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Molecular Insights into the Regulatory Mechanisms Mediated by Hypoxia-Conditioned Skeletal Muscle Exosomal miRNAs.Biomarker insights · 2026Article
- Profiling fear-extinction learning induced small ncRNAs landscape and identifying miR-29b-3p as a promising biomarker for PTSD.Journal of translational medicine · 2025Article
- New characteristics of MiRNA and IsomiR interactions with mRNA.Scientific reports · 2025Article
- Characterization of Genetic and Chemical Drivers in the Pathogenesis of DRESS Syndrome: In Silico Study.Health science reports · 2025Article
- Paradoxical mTORC1-Dependent microRNA-mediated Translation Repression in the Nucleus Accumbens of Male Mice Consuming Alcohol Attenuates Glycolysis.Nature communications · 2025Article
- The power of microRNA regulation-insights into immunity and metabolism.FEBS letters · 2025Review
- Identification of a circRNA-miRNA-mRNA interactome associated with Parkinson's disease progression.Journal of Parkinson's disease · 2025Article
- Modeling ncRNA Synergistic Regulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2025Review
- MicroRNAs and rs1803274 SNP-based BuChe downregulation are associated with metabolic syndrome through ghrelin hydrolysis and expression quantitative trait loci regulation in PD patients.Frontiers in molecular neuroscience · 2025Article
- Comparative analysis of miRNA-mRNA interaction prediction tools based on experimental head and neck cancer data.Einstein (Sao Paulo, Brazil) · 2025Article
- Advanced computational predictive models of miRNA-mRNA interaction efficiency.Computational and structural biotechnology journal · 2024Article
- Differential expression of ion channel coding genes in the endometrium of women experiencing recurrent implantation failures.Scientific reports · 2024Article
- Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions.PLoS computational biology · 2024Article
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- Empowering prediction of miRNA-mRNA interactions in species with limited training data through transfer learning.Heliyon · 2024Article
- Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases.Molecular therapy. Nucleic acids · 2024Review
- LncRNA LUESCC promotes esophageal squamous cell carcinoma by targeting the miR-6785-5p/NRSN2 axis.Cellular and molecular life sciences : CMLS · 2024Article
38 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
motivationThe identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods.
resultsApplying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. AVAILABILITY AND IMPLEMENTATION: The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ CONTACTS: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.