CELLoGeNe - An energy landscape framework for logical networks controlling cell decisions

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskriftPeer review

    Sammanfattning

    Experimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and reprogramming. One powerful computational method is to consider cell commitment and reprogramming as movements in an energy landscape. Here, we develop Computation of Energy Landscapes of Logical Gene Networks (CELLoGeNe), which maps Boolean implementation of gene regulatory networks (GRNs) into energy landscapes. CELLoGeNe removes inadvertent symmetries in the energy landscapes normally arising from standard Boolean operators. Furthermore, CELLoGeNe provides tools to visualize and stochastically analyze the shapes of multi-dimensional energy landscapes corresponding to epigenetic landscapes for development and reprogramming. We demonstrate CELLoGeNe on two GRNs governing different aspects of induced pluripotent stem cells, identifying experimentally validated attractors and revealing potential reprogramming roadblocks. CELLoGeNe is a general framework that can be applied to various biological systems offering a broad picture of intracellular dynamics otherwise inaccessible with existing methods.
    Originalspråkengelska
    Artikelnummer104743
    Antal sidor28
    TidskriftiScience
    Volym25
    Nummer8
    DOI
    StatusPublished - 2022

    Ämnesklassifikation (UKÄ)

    • Bioinformatik (beräkningsbiologi)
    • Cellbiologi

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