research-article

Evolution of discrete gene regulatory models

Authors:

Afshin Esmaeili,

Christian JacobAuthors Info & Claims

GECCO '08: Proceedings of the 10th annual conference on Genetic and evolutionary computation

Pages 307 - 314

https://doi.org/10.1145/1389095.1389150

Published: 12 July 2008 Publication History

Abstract

Gene regulatory networks (GRNs) are complex control systems that govern the interaction of genes, which ultimately control cellular processes at the protein level. GRNs can be represented using abstract models such as random Boolean networks (RBNs), where gene activities and their interactions are captured as nodes with associated Boolean functions, which receive activation or repressor signals from other nodes. We have developed an evolutionary model of gene regulatory networks using RBNs to study the dynamic behavior of these control systems. We explore a range of different network parameters such as excess graph, sensitivity, basin entropy, number of attractors and maximum length of attractors in RBNs. We investigate the effects of mutations and crossover on the fitness of RBNs, and we show that over the course of evolution, networks with a low level of damage spreading and a high tolerance to random perturbations can be produced. We also demonstrate that these networks are able to adapt to a range of different perturbations obtaining a high level of stability.

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Cited By

Villani MMagrì SRoli ASerra R(2020)Evolving Always-Critical NetworksLife10.3390/life1003002210:3(22)Online publication date: 4-Mar-2020
https://doi.org/10.3390/life10030022
Benedettini SVillani MRoli ASerra RManfroni MGagliardi APinciroli CBirattari M(2018)Dynamical regimes and learning properties of evolved Boolean networksNeurocomputing10.1016/j.neucom.2012.05.02399(111-123)Online publication date: 31-Dec-2018
https://dl.acm.org/doi/10.1016/j.neucom.2012.05.023
Roli AManfroni MPinciroli CBirattari M(2011)On the design of Boolean network robotsProceedings of the 2011 international conference on Applications of evolutionary computation - Volume Part I10.5555/2008402.2008408(43-52)Online publication date: 27-Apr-2011
https://dl.acm.org/doi/10.5555/2008402.2008408
Show More Cited By

Index Terms

Evolution of discrete gene regulatory models
1. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis

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cover image ACM Conferences

GECCO '08: Proceedings of the 10th annual conference on Genetic and evolutionary computation

July 2008

1814 pages

ISBN:9781605581309

DOI:10.1145/1389095

Conference Chair:
Conor Ryan
University of Limerick, Ireland
,
Editor:
Maarten Keijzer
Chordiant Software International B.V., The Netherlands

Copyright © 2008 ACM.

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Published: 12 July 2008

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GECCO08: Genetic and Evolutionary Computation Conference

July 12 - 16, 2008

GA, Atlanta, USA

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Overall Acceptance Rate 1,669 of 4,410 submissions, 38%

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Cited By

Villani MMagrì SRoli ASerra R(2020)Evolving Always-Critical NetworksLife10.3390/life1003002210:3(22)Online publication date: 4-Mar-2020
https://doi.org/10.3390/life10030022
Benedettini SVillani MRoli ASerra RManfroni MGagliardi APinciroli CBirattari M(2018)Dynamical regimes and learning properties of evolved Boolean networksNeurocomputing10.1016/j.neucom.2012.05.02399(111-123)Online publication date: 31-Dec-2018
https://dl.acm.org/doi/10.1016/j.neucom.2012.05.023
Roli AManfroni MPinciroli CBirattari M(2011)On the design of Boolean network robotsProceedings of the 2011 international conference on Applications of evolutionary computation - Volume Part I10.5555/2008402.2008408(43-52)Online publication date: 27-Apr-2011
https://dl.acm.org/doi/10.5555/2008402.2008408
Benedettini SRoli ASerra RVillani M(2011)Stochastic local search to automatically design Boolean networks with maximally distant attractorsProceedings of the 2011 international conference on Applications of evolutionary computation - Volume Part I10.5555/2008402.2008406(22-31)Online publication date: 27-Apr-2011
https://dl.acm.org/doi/10.5555/2008402.2008406
Roli AManfroni MPinciroli CBirattari M(2011)On the Design of Boolean Network RobotsApplications of Evolutionary Computation10.1007/978-3-642-20525-5_5(43-52)Online publication date: 2011
https://doi.org/10.1007/978-3-642-20525-5_5
Benedettini SRoli ASerra RVillani M(2011)Stochastic Local Search to Automatically Design Boolean Networks with Maximally Distant AttractorsApplications of Evolutionary Computation10.1007/978-3-642-20525-5_3(22-31)Online publication date: 2011
https://doi.org/10.1007/978-3-642-20525-5_3
He CRen Q(2009)Robustness during Network Evolution2009 International Conference on Complex, Intelligent and Software Intensive Systems10.1109/CISIS.2009.135(1240-1244)Online publication date: Mar-2009
https://doi.org/10.1109/CISIS.2009.135

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