Introduction to gene regulatory networks

Sylvain Cussat-Blanc (1, 2) , Wolfgang Banzhaf (3)

1 IRIT-REVA - Real Expression Artificial Life
2 UT Capitole - Université Toulouse Capitole
3 MUN - Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada]

Gene regulatory networks are a central mechanism in the regulation of gene expression in all living organisms? cells. Their functioning is nowadays very well understood: they are based on the production of proteins enhanced or inhibited by other proteins inside and outside the cells. This produces a complex dynamics with which, with the exact same DNA, cells from the same organism can form very different types (through cell differentiation) and very different behaviors according to their types and positions. This tutorial will first review the biology of these networks, from the genetic aspect to the dynamics of gene regulation. Then, a biologically plausible model will be presented to highlight the complexity of dynamics gene regulatory networks can produce. Using that model, we will show how a computational model can be designed so that a genetic algorithm can optimize the network efficiently. We will present a set of applications in which artificial gene regulatory networks are plugged into diverse virtual agents (artificial cells in an artificial embryogenesis context, direct connection to the sensors and effectors or high-level behavior regulation in others). Demos, showing the results obtained with this system, will be presented all along the tutorial.

Domaines: Informatique [cs]

Sylvain Cussat-Blanc, Wolfgang Banzhaf. Introduction to gene regulatory networks. Genetic and Evolutionary Computation Conference (GECCO 2015), ACM-SIGEVO : Special Interest Group on Genetic and Evolutionary Computation, Jul 2015, Madrid, Spain. pp.589-601, ⟨10.1145/2739482.2756586⟩. ⟨hal-03198241⟩