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    Machine learning approaches on high throughput NGS data to unveil mechanisms of function in biology and disease

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    Authors
    Pezoulas, V. C.
    Hazapis, O.
    Lagopati, N.
    Exarchos, T. P.
    Goules, A. V.
    Tzioufas, A. G.
    Fotiadis, D. I.
    Stratis, I. G.
    Yannacopoulos, A. N.
    Gorgoulis, Vassilis G
    Affiliation
    Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, Ioannina, Greece
    Issue Date
    2021
    
    Metadata
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    Abstract
    In this review, the fundamental basis of machine learning (ML) and data mining (DM) are summarized together with the techniques for distilling knowledge from state-of-the-art omics experiments. This includes an introduction to the basic mathematical principles of unsupervised/supervised learning methods, dimensionality reduction techniques, deep neural networks architectures and the applications of these in bioinformatics. Several case studies under evaluation mainly involve next generation sequencing (NGS) experiments, like deciphering gene expression from total and single cell (scRNA-seq) analysis; for the latter, a description of all recent artificial intelligence (AI) methods for the investigation of cell sub-types, biomarkers and imputation techniques are described. Other areas of interest where various ML schemes have been investigated are for providing information regarding transcription factors (TF) binding sites, chromatin organization patterns and RNA binding proteins (RBPs), while analyses on RNA sequence and structure as well as 3D dimensional protein structure predictions with the use of ML are described. Furthermore, we summarize the recent methods of using ML in clinical oncology, when taking into consideration the current omics data with pharmacogenomics to determine personalized treatments. With this review we wish to provide the scientific community with a thorough investigation of main novel ML applications which take into consideration the latest achievements in genomics, thus, unraveling the fundamental mechanisms of biology towards the understanding and cure of diseases.
    Citation
    PEZOULAS VC, HAZAPIS O, LAGOPATI N, EXARCHOS TP, GOULES AV, TZIOUFAS AG, et al. Machine Learning Approaches on High Throughput NGS Data to Unveil Mechanisms of Function in Biology and Disease. Cancer Genomics Proteomics. 2021;18(5):605–26.
    Journal
    Cancer Genomics Proteomics
    URI
    http://hdl.handle.net/10541/624648
    DOI
    10.21873/cgp.20284
    PubMed ID
    34479914
    Additional Links
    https://dx.doi.org/10.21873/cgp.20284
    Type
    Article
    Language
    en
    ae974a485f413a2113503eed53cd6c53
    10.21873/cgp.20284
    Scopus Count
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    All Paterson Institute for Cancer Research

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