A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics

2006 ◽  
Vol 13 (9) ◽  
pp. 1630-1639 ◽  
Author(s):  
Andre Ribeiro ◽  
Rui Zhu ◽  
Stuart A. Kauffman
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Stochastic Dynamics ◽  
Gene Regulatory ◽  
Modeling Strategy

Modeling Gene Regulatory Networks with Delayed Stochastic Dynamics

2010 ◽  
pp. 198-218
Author(s):  
Andre S. Ribeiro ◽  
John J. Grefenstette ◽  
Stuart A. Kauffman
Keyword(s):  
Gene Expression ◽  
Stochastic Simulation ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Stochastic Dynamics ◽  
Single Gene ◽  
Stochastic Simulation Algorithm ◽  
Simulation Algorithm ◽  
Gene Regulatory ◽  
Modeling Strategy

We present a recently developed modeling strategy of gene regulatory networks (GRN) that uses the delayed stochastic simulation algorithm to drive its dynamics. First, we present experimental evidence that led us to use this strategy. Next, we describe the stochastic simulation algorithm (SSA), and the delayed SSA, able to simulate time-delayed events. We then present a model of single gene expression. From this, we present the general modeling strategy of GRN. Specific applications of the approach are presented, beginning with the model of single gene expression which mimics a recent experimental measurement of gene expression at single-protein level, to validate our modeling strategy. We also model a toggle switch with realistic noise and delays, used in cells as differentiation pathway switches. We show that its dynamics differs from previous modeling strategies predictions. As a final example, we model the P53-Mdm2 feedback loop, whose malfunction is associated to 50% of cancers, and can induce cells apoptosis. In the end, we briefly discuss some issues in modeling the evolution of GRNs, and outline some directions for further research.

scholarly journals Stochastic resonances in a distributed genetic broadcasting system: the NF κ B/I κ B paradigm

2018 ◽  
Vol 15 (138) ◽  
pp. 20170809 ◽  
Author(s):  
Zhipeng Wang ◽  
Davit A. Potoyan ◽  
Peter G. Wolynes
Keyword(s):  
Gene Regulatory Networks ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Stochastic Dynamics ◽  
Extracellular Signals ◽  
Broadcasting System ◽  
Gene Regulatory ◽  
And Performance ◽  
The Impact ◽  
Kinetic Regulation

Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of information not to one but to many genes carrying out distinct functions whose dynamical binding and unbinding characteristics are widely distributed. In such broadcasting networks, the intended target sites are also often dwarfed in number by the even more numerous non-functional binding sites. Taking the genetic regulatory network of NF κ B as an exemplary system we explore the impact of having numerous distributed sites on the stochastic dynamics of oscillatory broadcasting genetic networks pointing out how resonances in binding cycles control the network's specificity and performance. We also show that active kinetic regulation of binding and unbinding through molecular stripping of DNA bound transcription factors can lead to a higher coherence of gene-co-expression and synchronous clearance.

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