The dynamics of canalizing Boolean networks

DOI10.1155/2020/3687961zbMATH Open1432.92039arXiv1902.00056OpenAlexW3001795499WikidataQ126329426 ScholiaQ126329426MaRDI QIDQ2296155FDOQ2296155

Authors: Elijah Paul, William Qin, Reinhard Laubenbacher, Gleb Pogudin 

Publication date: 17 February 2020

Published in: Complexity (Search for Journal in Brave)

Abstract: Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by regulatory rules driving the dynamics that have certain so-called canalizing properties. In this paper, we investigate the dynamics of a random Boolean network with such properties using analytical methods and simulations. From our simulations, we observe that Boolean networks with higher canalizing depth have generally fewer attractors, the attractors are smaller, and the basins are larger, with implications for the stability and robustness of the models. These properties are relevant to many biological applications. Moreover, our results show that, from the standpoint of the attractor structure, high canalizing depth, compared to relatively small positive canalizing depth, has a very modest impact on dynamics. Motivated by these observations, we conduct mathematical study of the attractor structure of a random Boolean network of canalizing depth one (i.e., the smallest positive depth). For every positive integer $ell$, we give an explicit formula for the limit of the expected number of attractors of length $ell$ in an $n$-state random Boolean network as $n$ goes to infinity.

Full work available at URL: https://arxiv.org/abs/1902.00056

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Mathematics Subject Classification ID

Systems biology, networks (92C42)

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Cited In (12)

• Variable-depth simulation of most permissive Boolean networks
• Boolean networks: beyond generalized asynchronicity
• Combinatorics of Boolean automata circuits dynamics
• The influence of canalization on the robustness of Boolean networks
• Bifurcations in Boolean Networks
• Stratification and enumeration of Boolean functions by canalizing depth
• Ordered dynamics in biased and cooperative Boolean networks
• Dynamics of complex Boolean networks: canalization, stability, and criticality
• Canalization and symmetry in Boolean models for genetic regulatory networks
• Collectively canalizing Boolean functions
• Boolean nested canalizing functions: a comprehensive analysis
• Nested canalyzing depth and network stability

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