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  1. Article ; Online: Exploratory adaptation in large random networks

    Hallel I. Schreier / Yoav Soen / Naama Brenner

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 9

    Abstract: Recent works suggest that cellular networks may respond to novel challenges on the time-scale of cellular lifetimes through large-scale perturbation of gene expression and convergence to a new state. Here, the authors demonstrate the theoretical ... ...

    Abstract Recent works suggest that cellular networks may respond to novel challenges on the time-scale of cellular lifetimes through large-scale perturbation of gene expression and convergence to a new state. Here, the authors demonstrate the theoretical feasibility of exploratory adaptation in cellular networks by showing that convergence to new states depends on known features of these networks.
    Keywords Science ; Q
    Language English
    Publishing date 2017-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Exploratory adaptation in large random networks.

    Schreier, Hallel I / Soen, Yoav / Brenner, Naama

    Nature communications

    2017  Volume 8, Page(s) 14826

    Abstract: The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader ... ...

    Abstract The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader array of conditions. However, the process of adaptation by exploratory dynamics within the lifetime of a cell is not well understood. Here we demonstrate the feasibility of exploratory adaptation in a high-dimensional network model of gene regulation. Exploration is initiated by failure to comply with a constraint and is implemented by random sampling of network configurations. It ceases if and when the network reaches a stable state satisfying the constraint. We find that successful convergence (adaptation) in high dimensions requires outgoing network hubs and is enhanced by their auto-regulation. The ability of these empirically validated features of gene regulatory networks to support exploratory adaptation without fine-tuning, makes it plausible for biological implementation.
    MeSH term(s) Adaptation, Physiological/genetics ; Gene Regulatory Networks ; Models, Genetic
    Language English
    Publishing date 2017-04-21
    Publishing country England
    Document type Journal Article
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms14826
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Exploratory Adaptation in Large Random Networks

    Schreier, Hallel I. / Soen, Yoav / Brenner, Naama

    2016  

    Abstract: The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader ... ...

    Abstract The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader array of conditions. However, the process of adaptation by exploratory dynamics within the lifetime of a cell is not well understood. Here we demonstrate the feasibility of exploratory adaptation in a high-dimensional network model of gene regulation. Exploration is initiated by failure to comply with a constraint and is implemented by random sampling of network configurations. It ceases if and when the network reaches a stable state satisfying the constraint. We find that successful convergence (adaptation) in high dimensions requires outgoing network hubs and is enhanced by their auto-regulation. The ability of these empirically-validated features of gene regulatory networks to support exploratory adaptation without fine-tuning, makes it plausible for biological implementation.

    Comment: Article includes 16 pages, 7 figures; Supplementary includes 18 pages 17 figures
    Keywords Quantitative Biology - Molecular Networks
    Subject code 612
    Publishing date 2016-05-31
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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