Model checking the evolution of gene regulatory networks

DOI10.1007/S00236-016-0278-XMaRDI QIDQ1683930zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Mirco Giacobbe, Călin C. Guet, Ashutosh Gupta, Thomas A. Henzinger, Tiago Paixão, Tatjana Petrov

Publication date 1 December 2017

Published in Acta Informatica (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/1410.7704

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Problems related to evolution (92D15) Systems biology, networks (92C42) Specification and verification (program logics, model checking, etc.) (68Q60)

Abstract: The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs -an important problem of interest in evolutionary biology- more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.

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Cites work

• scientific article; zbMATH DE number 1405493 (Why is no real title available?)
• scientific article; zbMATH DE number 5585443 (Why is no real title available?)
• Formal molecular biology
• Model Checking Gene Regulatory Networks

Cited in

(8)

• Model Checking Gene Regulatory Networks
• Model Checking Liveness Properties of Genetic Regulatory Networks
• Symbolic coloured SCC decomposition
• Modeling evolutionary growth of a microRNA-mediated regulation system
• Aeon 2021: bifurcation decision trees in Boolean networks
• A genetically modified Hoare logic
• Synthesis of biological models from mutation experiments
• Model Checking Genetic Regulatory Networks with Parameter Uncertainty

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