Chapter 3 - Computational Challenges and -omics Approaches for the Identification of microRNAs and Targets

Abstract

From very early on, computational methods have been deemed as key players in microRNA (miRNA) research. Currently, there are numerous implemented approaches that can be used to support miRNA-related studies by identifying their coding and noncoding targets, their expression, their regulators, as well as by inferring their underlying regulatory networks. This chapter aims to provide an overview of the available state-of-the-art tools, web servers, and databases utilized in miRNA research. The selected tools cover an extensive scope ranging from miRNA annotation, promoter identification, and transcription to the identification of miRNA-controlled pathways. Significant attention has been paid to present and explain standard and novel -omics approaches that can be used to support, complement, or even substitute their in silico counterparts. Importantly, current open challenges, limitations, and good experimental practices followed in the field are comprehensively explored.