ArticlePloS one2013
miReader: Discovering Novel miRNAs in Species without Sequenced Genome.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 44 citations in OpenAlex.
- miRNAs in Heart Development and Disease.International journal of molecular sciences · 2024Review
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.GigaScience · 2022Article
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry.International journal of molecular sciences · 2021Review
- Newly identified miRNAs may contribute to aerenchyma formation in sugarcane roots.Plant direct · 2020Article
- Trends in the development of miRNA bioinformatics tools.Briefings in bioinformatics · 2019Review
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.Nucleic acids research · 2017Article
- Automatic learning of pre-miRNAs from different species.BMC bioinformatics · 2016Article
- Bioinformatic tools for microRNA dissection.Nucleic acids research · 2016Review
- MicroRNAs in the Host Response to Viral Infections of Veterinary Importance.Frontiers in veterinary science · 2016Review
- MicroRNA from Moringa oleifera: Identification by High Throughput Sequencing and Their Potential Contribution to Plant Medicinal Value.PloS one · 2016Article
- Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Along with computational approaches, NGS led technologies have caused a major impact upon the discoveries made in the area of miRNA biology, including novel miRNAs identification. However, to this date all microRNA discovery tools compulsorily depend upon the availability of reference or genomic sequences. Here, for the first time a novel approach, miReader, has been introduced which could discover novel miRNAs without any dependence upon genomic/reference sequences. The approach used NGS read data to build highly accurate miRNA models, molded through a Multi-boosting algorithm with Best-First Tree as its base classifier. It was comprehensively tested over large amount of experimental data from wide range of species including human, plants, nematode, zebrafish and fruit fly, performing consistently with >90% accuracy. Using the same tool over Illumina read data for Miscanthus, a plant whose genome is not sequenced; the study reported 21 novel mature miRNA duplex candidates. Considering the fact that miRNA discovery requires handling of high throughput data, the entire approach has been implemented in a standalone parallel architecture. This work is expected to cause a positive impact over the area of miRNA discovery in majority of species, where genomic sequence availability would not be a compulsion any more.
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Registered trials
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