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  1. Article ; Online: Top Trends in Multiomics Research: Evaluation of 52 Published Studies and New Ways of Thinking Terminology and Visual Displays.

    Kolenc, Živa / Pirih, Nina / Gretic, Petra / Kunej, Tanja

    Omics : a journal of integrative biology

    2021  Volume 25, Issue 11, Page(s) 681–692

    Abstract: Multiomics study designs have significantly increased understanding of complex biological systems. The multiomics literature is rapidly expanding and so is their heterogeneity. However, the intricacy and fragmentation of omics data are impeding further ... ...

    Abstract Multiomics study designs have significantly increased understanding of complex biological systems. The multiomics literature is rapidly expanding and so is their heterogeneity. However, the intricacy and fragmentation of omics data are impeding further research. To examine current trends in multiomics field, we reviewed 52 articles from PubMed and Web of Science, which used an integrated omics approach, published between March 2006 and January 2021. From studies, data regarding investigated loci, species, omics type, and phenotype were extracted, curated, and streamlined according to standardized terminology, and summarized in a previously developed graphical summary. Evaluated studies included 21 omics types or applications of omics technology such as genomics, transcriptomics, metabolomics, epigenomics, environmental omics, and pharmacogenomics, species of various phyla including human, mouse,
    MeSH term(s) Animals ; COVID-19 ; Computational Biology/trends ; Computer Graphics ; Epigenomics/trends ; Gene Expression Profiling/trends ; Genomics/trends ; Humans ; Metabolomics/trends ; Pharmacogenetics/trends ; Proteomics/trends ; Publications ; SARS-CoV-2 ; Terminology as Topic
    Language English
    Publishing date 2021-10-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2021.0160
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Syndromic male subfertility: A network view of genome-phenome associations.

    Mikec, Špela / Kolenc, Živa / Peterlin, Borut / Horvat, Simon / Pogorevc, Neža / Kunej, Tanja

    Andrology

    2022  Volume 10, Issue 4, Page(s) 720–732

    Abstract: Background: Male infertility is a disorder of the reproductive system with a highly complex genetic landscape. In most cases, the reason for male infertility remains unknown; however, the importance of genetic abnormalities in the diagnosis of ... ...

    Abstract Background: Male infertility is a disorder of the reproductive system with a highly complex genetic landscape. In most cases, the reason for male infertility remains unknown; however, the importance of genetic abnormalities in the diagnosis of subfertility/infertility is becoming increasingly recognized. Several syndromes include impaired male fertility in the clinical picture, although a comprehensive analysis of genetic causes of the syndromology perspective of male reproduction is not yet available.
    Objectives: (1) To develop a catalog of syndromes and corresponding genes associated with impaired male fertility and (2) to visualize an up-to-date genome-phenome network of syndromic male subfertility.
    Materials and methods: Published literature was retrieved from the Online Mendelian Inheritance in Man, Orphanet, Human Phenotype Ontology and PubMed databases using keywords "male infertility," "syndrome," "gene," and "case report"; time period from 1980 to September, 2021. Retrieved data were organized as a catalog and complemented with identification numbers of syndromes (MIM ID) and genes (Gene ID). The genome-phenome network and the phenome network were visualized using Cytoscape and Gephi software platforms. Protein-protein interaction analysis was performed using STRING tool.
    Results: Retrieved syndromes were presented as (1) a catalog containing 63 syndromes and 93 associated genes, (2) a genome-phenome network including CHD7 and WT1 genes and Noonan and Kartagener syndromes, and (3) a phenome network including 63 syndromes, and 25 categories of clinical features.
    Discussion: The developed catalog will contribute to the advances and translational impact toward understanding the factors of syndromic male infertility. Visualized networks provide simple, flexible tools for clinicians and researchers to quickly generate hypotheses and gain a deeper understanding of underlying mechanisms affecting male reproduction.
    Conclusion: Recognition of the significance of genome-phenome visualization as part of network medicine can help expedite efforts toward unravelling molecular mechanisms and enable advances personal/precision medicine of male reproduction and other complex traits.
    MeSH term(s) Genome ; Genome-Wide Association Study ; Humans ; Infertility, Male/genetics ; Male ; Phenotype ; Syndrome
    Language English
    Publishing date 2022-03-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2696108-8
    ISSN 2047-2927 ; 2047-2919
    ISSN (online) 2047-2927
    ISSN 2047-2919
    DOI 10.1111/andr.13167
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6983: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Molecular Mechanisms of Syndromic Cryptorchidism: Data Synthesis of 50 Studies and Visualization of Gene-Disease Network.

    Urh, Kristian / Kolenc, Živa / Hrovat, Maj / Svet, Luka / Dovč, Peter / Kunej, Tanja

    Frontiers in endocrinology

    2018  Volume 9, Page(s) 425

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2018-07-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2592084-4
    ISSN 1664-2392
    ISSN 1664-2392
    DOI 10.3389/fendo.2018.00425
    Database MEDical Literature Analysis and Retrieval System OnLINE

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