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Foto på Victor Olariu

Victor Olariu

Universitetslektor

Foto på Victor Olariu

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

Författare

  • Emil Andersson
  • Mattias Sjö
  • Keisuke Kaji
  • Victor Olariu

Summary, in English

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.

Avdelning/ar

  • Beräkningsbiologi och biologisk fysik - Genomgår omorganisation

Publiceringsår

2022

Språk

Engelska

Publikation/Tidskrift/Serie

iScience

Volym

25

Issue

8

Dokumenttyp

Artikel i tidskrift

Förlag

Elsevier

Ämne

  • Bioinformatics (Computational Biology)
  • Cell Biology

Status

Published

ISBN/ISSN/Övrigt

  • ISSN: 2589-0042