Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increas...

Decoding the patterns of miRNA regulation in diseases are important to properly realize its potential in diagnostic, prog- nostic, and therapeutic applications. Only a handful of studies computationally predict possible miRNA-miRNA interactions; hence, such interactions require a thorough investigation to understand their role in disease progression. In this paper, we design a novel computation...

objective(s): vascular calcification is one the major characteristics in patients with various types of chronic inflammatory disorders. mirnas have been shown to be involved in many normal biological functions as well as diseases; however, their role in vascular calcification has not received much attention. materials and methods: in the current study, we built a vascular calcification rat mode...

micrornas (mirnas) are short, endogenous non-coding rnas that function as guide molecules to regulate transcription of their target messenger rnas. several methods including low-density qpcr arrays are being increasingly used to profile the expression of these molecules in a variety of different biological conditions. reliable analysis of expression profiles demands removal of technical variati...

MicroRNAs (miRNAs) have emerged as a novel class of endogenous, small, noncoding RNAs that negatively regulate gene expression via degradation or translational inhibition of their target mRNAs. Over 700 miRNAs have been identified and sequenced in humans, and the number of miRNA genes is estimated at more than 1000. Individual miRNA is functionally important as a transcription factor because it...

INTRODUCTION An increasing number of studies have investigated microRNAs (miRNAs) as potential markers of diagnosis, treatment and prognosis. So far, agreement between studies has been minimal, which may in part be explained by intratumoral heterogeneity of miRNA expression. The aim of the present study was to assess the heterogeneity of a panel of selected miRNAs in rectal cancer, using two di...

Over the past several years, several microRNA (miRNA) expression profiling studies have been carried out on bronchopulmonary dysplasia (BPD) in mammalian lung tissues. The most effective way to identify these important miRNAs is to systematically search for similar signatures identified in multiple independent studies. Accordingly, a meta-analysis was conducted to review published miRNA express...

INTRODUCTION In the last decade microRNAs (miRNAs) have been widely investigated in prostate cancer (PCa) and have shown to be promising biomarkers in diagnostic, prognostic and predictive settings. However, tumor heterogeneity may influence miRNA expression. The aims of this study were to assess the impact of tumor heterogeneity, as demonstrated by a panel of selected miRNAs in PCa, and to cor...

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...

Despite a library full of literature on miRNA biology, core issues relating to miRNA target detection, biological effect, and mode of action remain controversial. This essay proposes that the predominant mechanism of direct miRNA action is translational inhibition, whereas the bulk of miRNA effects are mRNA based. It explores several issues confounding miRNA target detection, and discusses thei...