Modelling the effects of biological intervention in a dynamical gene network.

Nicolas Champagnat; Rodolphe Loubaton; Laurent Vallat; Pierre Vallois

doi:10.1007/s00285-026-02458-3

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Modelling the effects of biological intervention in a dynamical gene network.

Nicolas Champagnat·Rodolphe Loubaton·Laurent Vallat·Pierre Vallois

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Abstract

Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (1) non-quantitative (or data-based) models which do not describe the probability distribution of gene expressions; (2) quantitative models which fully describe the probability distribution of all genes co-expression; and (3) mechanistic models which allow for a causal interpretation of gene interactions. We propose two rigorous frameworks to model gene alteration in a dynamical GRN, depending on whether the network model is quantitative or mechanistic. We explain how these models can be used for design of experiment, or, if additional alteration data are available, for validation purposes or to improve the parameter estimation of the original model. We apply these methods to the Gaussian graphical model, which is quantitative but non-mechanistic, and to mechanistic models of Bayesian networks and penalized linear regression.

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Gene Regulatory Networks Models, Genetic Bayes Theorem Mathematical Concepts Animals Linear Models Computer Simulation Normal Distribution Bayesian network Dynamical gene regulatory networks Gaussian graphical model Gene knockdown experiments Inference Penalized linear regression Journal Article

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Nicolas Champagnat, Rodolphe Loubaton, Laurent Vallat, Pierre Vallois. 2026-09-01. Modelling the effects of biological intervention in a dynamical gene network.. https://doi.org/10.1007/s00285-026-02458-3

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Journal Article resource Animals subject Bayes Theorem subject Computer Simulation subject Gene Regulatory Networks subject Journal Article subject Models, Genetic subject

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