ArticlePloS one2012
Integrated sequence-structure motifs suffice to identify microRNA precursors.
Article in PloS one, 2012. 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.
- Species-specific microRNA discovery and target prediction in the soybean cyst nematode.Scientific reports · 2023Article
- In silico analysis suggests the RNAi-enhancing antibiotic enoxacin as a potential inhibitor of SARS-CoV-2 infection.Scientific reports · 2021Article
- RNA-Seq reveals novel genes and pathways involved in bovine mammary involution during the dry period and under environmental heat stress.Scientific reports · 2018Article
- Inhibition of MiR-92a May Protect Endothelial Cells After Acute Myocardial Infarction in Rats: Role of KLF2/4.Medical science monitor : international medical journal of experimental and clinical research · 2016Article
- Automatic learning of pre-miRNAs from different species.BMC bioinformatics · 2016Article
- N-acetylcysteine Ameliorates Prostatitis via miR-141 Regulating Keap1/Nrf2 Signaling.Inflammation · 2016Article
- iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions.Scientific reports · 2016Article
- A framework for improving microRNA prediction in non-human genomes.Nucleic acids research · 2015Article
- MatPred: Computational Identification of Mature MicroRNAs within Novel Pre-MicroRNAs.BioMed research international · 2015Article
- MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori.BMC genomics · 2014Article
- The discriminant power of RNA features for pre-miRNA recognition.BMC bioinformatics · 2014Article
- Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.BMC research notes · 2014Article
- Evolutionary relationships between miRNA genes and their activity.BMC genomics · 2012Article
- Prediction of conserved precursors of miRNAs and their mature forms by integrating position-specific structural features.PloS one · 2012Article
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5 authors.
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Abstract
backgroundUpwards of 1200 miRNA loci have hitherto been annotated in the human genome. The specific features defining a miRNA precursor and deciding its recognition and subsequent processing are not yet exhaustively described and miRNA loci can thus not be computationally identified with sufficient confidence.
resultsWe rendered pre-miRNA and non-pre-miRNA hairpins as strings of integrated sequence-structure information, and used the software Teiresias to identify sequence-structure motifs (ss-motifs) of variable length in these data sets. Using only ss-motifs as features in a Support Vector Machine (SVM) algorithm for pre-miRNA identification achieved 99.2% specificity and 97.6% sensitivity on a human test data set, which is comparable to previously published algorithms employing combinations of sequence-structure and additional features. Further analysis of the ss-motif information contents revealed strongly significant deviations from those of the respective training sets, revealing important potential clues as to how the sequence and structural information of RNA hairpins are utilized by the miRNA processing apparatus.
conclusionIntegrated sequence-structure motifs of variable length apparently capture nearly all information required to distinguish miRNA precursors from other stem-loop structures.
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