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Author Aracena, J.; Goles, E.; Moreira, A.; Salinas, L.
Title On the robustness of update schedules in Boolean networks Type
Year 2009 Publication Biosystems Abbreviated Journal Biosystems
Volume 97 Issue 1 Pages 1-8
Keywords Boolean network; Update schedule; Robustness; Attractor; Dynamical cycle
Abstract Deterministic Boolean networks have been used as models of gene regulation and other biological networks. One key element in these models is the update schedule, which indicates the order in which states are to be updated. We study the robustness of the dynamical behavior of a Boolean network with respect to different update schedules (synchronous, block-sequential, sequential), which can provide modelers with a better understanding of the consequences of changes in this aspect of the model. For a given Boolean network, we define equivalence classes of update schedules with the same dynamical behavior, introducing a labeled graph which helps to understand the dependence of the dynamics with respect to the update, and to identify interactions whose timing may be crucial for the presence of a particular attractor of the system. Several other results on the robustness of update schedules and of dynamical cycles with respect to update schedules are presented. Finally, we prove that our equivalence classes generalize those found in sequential dynamical systems. (C) 2009 Elsevier Ireland Ltd. All rights reserved.
Address [Aracena, J.] Univ Concepcion, Dept Ingn Matemat, Concepcion, Chile, Email: jaracena@ing-mat.udec.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:000267528900001 Approved
Call Number UAI @ eduardo.moreno @ Serial 29
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Author Goles, E.; Montalva, M.; Ruz, G.A.
Title Deconstruction and Dynamical Robustness of Regulatory Networks: Application to the Yeast Cell Cycle Networks Type
Year 2013 Publication Bulletin Of Mathematical Biology Abbreviated Journal Bull. Math. Biol.
Volume 75 Issue 6 Pages 939-966
Keywords Boolean networks; Attractors; Update robustness; Alliances; Dynamics
Abstract Analyzing all the deterministic dynamics of a Boolean regulatory network is a difficult problem since it grows exponentially with the number of nodes. In this paper, we present mathematical and computational tools for analyzing the complete deterministic dynamics of Boolean regulatory networks. For this, the notion of alliance is introduced, which is a subconfiguration of states that remains fixed regardless of the values of the other nodes. Also, equivalent classes are considered, which are sets of updating schedules which have the same dynamics. Using these techniques, we analyze two yeast cell cycle models. Results show the effectiveness of the proposed tools for analyzing update robustness as well as the discovery of new information related to the attractors of the yeast cell cycle models considering all the possible deterministic dynamics, which previously have only been studied considering the parallel updating scheme.
Address [Goles, Eric; Montalva, Marco; Ruz, Gonzalo A.] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago, Chile, Email: eric.chacc@uai.cl;
Corporate Author Thesis
Publisher Springer Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0092-8240 ISBN Medium
Area Expedition Conference
Notes WOS:000321220400005 Approved
Call Number UAI @ eduardo.moreno @ Serial 288
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Author Ruz, G.A.; Goles, E.; Montalva, M.; Fogel, G.B.
Title Dynamical and topological robustness of the mammalian cell cycle network: A reverse engineering approach Type
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
Call Number UAI @ eduardo.moreno @ Serial 350
Permanent link to this record