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

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    Type
    Article
    Authors
    Kleftogiannis, Dimitrios A. cc
    Korfiati, Aigli
    Theofilatos, Konstantinos A.
    Likothanassis, Spiridon D.
    Tsakalidis, Athanasios K.
    Mavroudi, Seferina P.
    KAUST Department
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2013-06
    Permanent link to this record
    http://hdl.handle.net/10754/566055
    
    Metadata
    Show full item record
    Abstract
    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.
    Citation
    Kleftogiannis, D., Korfiati, A., Theofilatos, K., Likothanassis, S., Tsakalidis, A., & Mavroudi, S. (2013). Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. Journal of Biomedical Informatics, 46(3), 563–573. doi:10.1016/j.jbi.2013.02.002
    Sponsors
    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.
    Publisher
    Elsevier BV
    Journal
    Journal of Biomedical Informatics
    DOI
    10.1016/j.jbi.2013.02.002
    PubMed ID
    23501016
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.jbi.2013.02.002
    Scopus Count
    Collections
    Articles; Computer Science Program; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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