Computer Engineering / Bilgisayar Mühendisliği

Permanent URI for this collectionhttps://hdl.handle.net/11147/10

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Author: search.filters.author.Işık, ZerrinPublication Index: search.filters.publicationIndex.WoS

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  • Article
    Citation - WoS: 4
    Citation - Scopus: 4
    Integrative Biological Network Analysis To Identify Shared Genes in Metabolic Disorders
    (Institute of Electrical and Electronics Engineers, 2022) Tenekeci, Samet; Işık, Zerrin
    Identification of common molecular mechanisms in interrelated diseases is essential for better prognoses and targeted therapies. However, complexity of metabolic pathways makes it difficult to discover common disease genes underlying metabolic disorders; and it requires more sophisticated bioinformatics models that combine different types of biological data and computational methods. Accordingly, we built an integrative network analysis model to identify shared disease genes in metabolic syndrome (MS), type 2 diabetes (T2D), and coronary artery disease (CAD). We constructed weighted gene co-expression networks by combining gene expression, protein-protein interaction, and gene ontology data from multiple sources. For 90 different configurations of disease networks, we detected the significant modules by using MCL, SPICi, and Linkcomm graph clustering algorithms. We also performed a comparative evaluation on disease modules to determine the best method providing the highest biological validity. By overlapping the disease modules, we identified 22 shared genes for MS-CAD and T2D-CAD. Moreover, 19 out of these genes were directly or indirectly associated with relevant diseases in the previous medical studies. This study does not only demonstrate the performance of different biological data sources and computational methods in disease-gene discovery, but also offers potential insights into common genetic mechanisms of the metabolic disorders.
  • Article
    Citation - WoS: 8
    Citation - Scopus: 9
    Dementia diagnosis by ensemble deep neural networks using FDG-PET scans
    (Springer, 2022) Yiğit, Altuğ; Baştanlar, Yalın; Işık, Zerrin
    Dementia is a type of brain disease that affects the mental abilities. Various studies utilize PET features or some two-dimensional brain perspectives to diagnose dementia. In this study, we have proposed an ensemble approach, which employs volumetric and axial perspective features for the diagnosis of Alzheimer’s disease and the patients with mild cognitive impairment. We have employed deep learning models and constructed two disparate networks. The first network evaluates volumetric features, and the second network assesses grid-based brain scan features. Decisions of these networks were combined by an adaptive majority voting algorithm to create an ensemble learner. In the evaluations, we compared ensemble networks with single ones as well as feature fusion networks to identify possible improvement; as a result, the ensemble method turned out to be promising for making a diagnostic decision. The proposed ensemble network achieved an average accuracy of 91.83% for the diagnosis of Alzheimer’s disease; to the best of our knowledge, it is the highest diagnosis performance in the literature.