AND-NOT logic framework for steady state analysis of Boolean network models

DOI10.12785/AMIS/070401zbMATH Open1269.92008arXiv1211.5633OpenAlexW2963919759MaRDI QIDQ2842909FDOQ2842909

Authors: Alan Veliz-Cuba, Kristina Buschur, Rose Hamershock, Ariel Kniss, Esther Wolff, Reinhard Laubenbacher 

Publication date: 8 August 2013

Published in: Applied Mathematics \& Information Sciences (Search for Journal in Brave)

Abstract: Finite dynamical systems (e.g. Boolean networks and logical models) have been used in modeling biological systems to focus attention on the qualitative features of the system, such as the wiring diagram. Since the analysis of such systems is hard, it is necessary to focus on subclasses that have the properties of being general enough for modeling and simple enough for theoretical analysis. In this paper we propose the class of AND-NOT networks for modeling biological systems and show that it provides several advantages. Some of the advantages include: Any finite dynamical system can be written as an AND-NOT network with similar dynamical properties. There is a one-to-one correspondence between AND-NOT networks, their wiring diagrams, and their dynamics. Results about AND-NOT networks can be stated at the wiring diagram level without losing any information. Results about AND-NOT networks are applicable to any Boolean network. We apply our results to a Boolean model of Th-cell differentiation.

Full work available at URL: https://arxiv.org/abs/1211.5633

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zbMATH Keywords

Boolean modelsteady statesAND-NOT logicNAND gate

Mathematics Subject Classification ID

Neural networks for/in biological studies, artificial life and related topics (92B20) Classical propositional logic (03B05) Other applications of logic (03B80)

Cited In (5)

• Dimension reduction of large sparse AND-NOT network models
• Stability structures of conjunctive Boolean networks
• Learning Boolean logic models of signaling networks with ASP
• Boolean nested canalizing functions: a comprehensive analysis
• Algebraic Models and Their Use in Systems Biology

Uses Software

• Ginsim

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