Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
TLDR
Probabilistic Boolean Networks (PBN) are introduced that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty.Abstract:
Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i) incorporates rule-based dependencies between genes; (ii) allows the systematic study of global network dynamics; (iii) is able to cope with uncertainty, both in the data and the model selection; and (iv) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes. Results: We introduce Probabilistic Boolean Networks (PBN) that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty. We show how the dynamics of these networks can be studied in the probabilistic context of Markov chains, with standard Boolean networks being special cases. Then, we discuss the relationship between PBNs and Bayesian networks—a family of graphical models that explicitly represent probabilistic relationships between variables. We show how probabilistic dependencies between a gene and its parent genes, constituting the basic building blocks of Bayesian networks, can be obtained from PBNs. Finally, we present methods for quantifying the influence of genes on other genes, within the context of PBNs. Examples illustrating the above concepts are presented throughout the paper.read more
Citations
More filters
Journal ArticleDOI
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information.
TL;DR: This work demonstrates that MI3 outperforms the frequently used control methods, and provides a powerful method for inferring mechanistic relationships underlying biological and other complex systems.
Journal ArticleDOI
Biochemical and Statistical Network Models for Systems Biology
Nathan D. Price,Ilya Shmulevich +1 more
TL;DR: A number of modeling approaches are discussed in the context of the assumptions that they entail, the types of data required for their inference, and the range of their applicability.
Journal ArticleDOI
Digital clocks: simple Boolean models can quantitatively describe circadian systems
TL;DR: An approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable and demonstrating that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data is developed.
Journal ArticleDOI
Mathematical and Computational Modeling in Complex Biological Systems
TL;DR: This review studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations, providing an update of important solutions using computational modeling approaches in systems biology.
Journal ArticleDOI
Optimal control policy for probabilistic Boolean networks with hard constraints
TL;DR: A formulation for the optimal finite-horizon control problem with hard constraints introduced by the authors is presented, which is state independent and the objective function is only dependent on the distance between the desirable states and the terminal states.
References
More filters
Book
The Origins of Order: Self-Organization and Selection in Evolution
TL;DR: The structure of rugged fitness landscapes and the structure of adaptive landscapes underlying protein evolution, and the architecture of genetic regulatory circuits and its evolution.
Journal ArticleDOI
Metabolic stability and epigenesis in randomly constructed genetic nets
TL;DR: The hypothesis that contemporary organisms are also randomly constructed molecular automata is examined by modeling the gene as a binary (on-off) device and studying the behavior of large, randomly constructed nets of these binary “genes”.
Journal ArticleDOI
Using Bayesian networks to analyze expression data
TL;DR: A new framework for discovering interactions between genes based on multiple expression measurements is proposed and a method for recovering gene interactions from microarray data is described using tools for learning Bayesian networks.
Book
An introduction to Bayesian networks
TL;DR: The principal ideas of probabilistic reasoning - known as Bayesian networks - are outlined and their practical implications illustrated and are intended for MSc students in knowledge-based systems, artificial intelligence and statistics, and for professionals in decision support systems applications and research.