Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

Dimitrios A. Kleftogiannis, Aigli Korfiati, Konstantinos A. Theofilatos, Spiridon D. Likothanassis, Athanasios K. Tsakalidis, Seferina P. Mavroudi

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.
Original languageEnglish (US)
Pages (from-to)563-573
Number of pages11
JournalJournal of Biomedical Informatics
Issue number3
StatePublished - Jun 2013

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: This research has been co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus II. Investing in knowledge society through the European Social Fund.

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications


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