miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure

miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure

In microRNA (miRNA) target prediction, typically two levels of information need to be modeled: the number of potential miRNA binding sites present in a target mRNA and the genomic context of each individual site. Single model structures insufficiently cope with this complex training data structure, consisting of feature vectors of unequal length as a consequence of the varying number of miRNA b...

Chapter 3 miRNA Target Prediction through Mining of miRNA Relationships Based on

miRTour: Plant miRNA and target prediction tool

UNLABELLED MicroRNAs (miRNAs) are important negative regulators of gene expression in plant and animals, which are endogenously produced from their own genes. Computational comparative approach based on evolutionary conservation of mature miRNAs has revealed a number of orthologs of known miRNAs in different plant species. The homology-based plant miRNA discovery, followed by target prediction,...

SVM-based miRNA: MiRNA∗ duplex prediction

We address the problem of predicting the miRNA:miRNA* duplex stemming from a microRNA (miRNA) hairpin precursor and we present a SVM-based methodology to address it. Predicting the miRNA:miRNA* duplex is a first step towards identifying the mature miRNA, suggesting possible miRNA targets and ultimately, reducing experimentation effort, time, and cost. We measure the error in terms of the absolu...

Using network context as a filter for miRNA target prediction

Recent discoveries in genetics show that gene expression in igher eukaryotes is regulated in part by small non-coding RNA olecules named microRNAs (miRNAs) (Ambros, 2004; Bartel, 004; Lim et al., 2003). In plants, miRNAs regulate protein xpression by binding to the coding region of the corresponding essenger RNA (mRNA). Plant miRNAs exhibit near-perfect comlementarity with the target sites. In ...