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Evolving genetic regulatory networks using an artificial genome

Lookup NU author(s): Dr Jennifer Hallinan


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Boolean models of genetic regulatory networks (GRNs) have been shown to exhibit many of the characteristic dynamics of real GRNs, with gene expression patterns settling to point attractors or limit cycles, or displaying chaotic behaviour, depending upon the connectivity of the network and the relative proportions of excitatory and inhibitory interactions. This range of behaviours is only apparent, however, when the nodes of the GRN are updated synchronously, a biologically implausible state of affairs. In this paper we demonstrate that evolution can produce GRNs with interesting dynamics under an asynchronous update scheme. We use an Artificial Genome to generate networks which exhibit limit cycle dynamics when updated synchronously, but collapse to a point attractor when updated asynchronously. Using a hill climbing algorithm the networks are then evolved using a fitness function which rewards patterns of gene expression which revisit as many previously seen states as possible. The final networks exhibit “fuzzy limit cycle” dynamics when updated asynchronously.

Publication metadata

Author(s): Hallinan J, Wiles J

Editor(s): Chen, Y.-P. P.

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Bioinformatics: Second Asia-Pacific Bioinformatics Conference (APBC)

Year of Conference: 2004

Pages: 291-296

Publisher: Australian Computer Society Inc.