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Tran, V., et al. (2013) On the Underlying Assumptions of Threshold Boolean Networks as a Model for Genetic Regulatory Network Behavior Frontiers in Genetics. Bioinformatics and Computational Biology, 4, Article 263.

has been cited by the following article:

  • TITLE: Role of Self-Loop in Cell-Cycle Network of Budding Yeast

    AUTHORS: Shu-ichi Kinoshita, Hiroaki Yamada

    KEYWORDS: Gene Regulatory Network, Attractors, Budding Yeast, Degenerate Self-Loop

    JOURNAL NAME: Open Journal of Biophysics, Vol.9 No.1, December 17, 2018

    ABSTRACT: Study of network dynamics is very active area in biological and social sciences. However, the relationship between the network structure and the attractors of the dynamics has not been fully understood yet. In this study, we numerically investigated the role of degenerate self-loops on the attractors and its basin size using the budding yeast cell-cycle network model. In the network, all self-loops negatively suppress the node (self-inhibition loops) and the attractors are only fixed points, i.e. point attractors. It is found that there is a simple division rule of the state space by removing the self-loops when the attractors consist only of point attractors. The point attractor with largest basin size is robust against the change of the self-inhibition loop. Furthermore, some limit cycles of period 2 appear as new attractor when a self-activation loop is added to the original network. It is also shown that even in that case, the point attractor with largest basin size is robust.