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Author (up) Ruz, G.A.; Goles, E.; Montalva, M.; Fogel, G.B. pdf  doi
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  Title Dynamical and topological robustness of the mammalian cell cycle network: A reverse engineering approach Type Journal Article
  Year 2014 Publication Biosystems Abbreviated Journal Biosystems  
  Volume 115 Issue Pages 23-32  
  Keywords Gene regulatory networks; Boolean networks; Threshold networks; Update robustness; Topology robustness; Bees algorithm  
  Abstract A common gene regulatory network model is the threshold Boolean network, used for example to model the Arabidopsis thaliana floral morphogenesis network or the fission yeast cell cycle network. In this paper, we analyze a logical model of the mammalian cell cycle network and its threshold Boolean network equivalent. Firstly, the robustness of the network was explored with respect to update perturbations, in particular, what happened to the attractors for all the deterministic updating schemes. Results on the number of different limit cycles, limit cycle lengths, basin of attraction size, for all the deterministic updating schemes were obtained through mathematical and computational tools. Secondly, we analyzed the topology robustness of the network, by reconstructing synthetic networks that contained exactly the same attractors as the original model by means of a swarm intelligence approach. Our results indicate that networks may not be very robust given the great variety of limit cycles that a network can obtain depending on the updating scheme. In addition, we identified an omnipresent network with interactions that match with the original model as well as the discovery of new interactions. The techniques presented in this paper are general, and can be used to analyze other logical or threshold Boolean network models of gene regulatory networks. (C) 2013 Elsevier Ireland Ltd. All rights reserved.  
  Address [Ruz, Gonzalo A.; Goles, Eric; Montalva, Marco] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago, Chile, Email: gonzalo.ruz@uai.cl  
  Corporate Author Thesis  
  Publisher Elsevier Sci Ltd Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0303-2647 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000330500100004 Approved no  
  Call Number UAI @ eduardo.moreno @ Serial 350  
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