Mapping biology onto computation

Research students: Nic Geard, Ben Skellett, James Watson, Kai Willadsen

Network computation and evolutionary computation provide analytic tools to explore the fundamental computational properties of biological systems, abstracting away from the myriad details of real biology. The value of such computational modelling depends on matching the level of abstraction to the research aims of the project. Network analysis tools have been widely used to model genetic regulatory networks at a variety of levels from biologically detailed to abstract Boolean models. In this project we are investigating how models of genetic regulatory networks can be derived from artificial genomes represented as nucleotide sequences. We report simulations mapping an artificial genome to a network, and the application of such genetic networks to the ontogeny of organisms.

Complex and Intelligent Systems Group faculty working on related systems biology projects

Lindsay Hood

Research students

Nic Geard

Ben Skellett

Brad Tonkes(graduated)

James Watson

Kai Willadsen

Research Assistants

Daniel Bradley

Links

Complex and Intelligent Systems (CIS) Group, School of ITEE, UQ

Festival of Doubt

School of Psychology

ARC Centre for Complex Systems

ARC Centre for Bioinformatics

Institute for Molecular Bioscience

Advanced Computational Modelling Centre

Selected artificial GRN papers

Geard, N. & Wiles, J., (2003). A Gene Regulatory Network for Cell Differentiation in Caenorhabditis elegans. In H. Abbass and J. Wiles (editors) Proceedings of the First Australian Conference on Artificial Life (ACAL2003), pp. 86-100. [abstract] [PDF]

Geard, N. & Wiles, J., (2003). Structure and dynamics of a gene network model incorporating small RNAs. In R. Sarker, R. Reynolds, H. Abbass, K.-C. Tan, R. McKay, D. Essam and T. Gedeon (editors) Proceedings of the 2003 Congress on Evolutionary Computation (CEC2003), pp. 199-206, Piscataway, NJ: IEEE Press. [abstract] [PDF]

Hallinan, J. (Accepted). Tunable asynchrony in an artificial genome. International Conference on Complex Systems (ICCS 2004). Boston, May 16 - 22, 2004. [abstract]

Hallinan, J. & Wiles, J. (Accepted). Asynchronous dynamics of an artificial genetic regulatory network. Ninth International Conference on the Simulation and Synthesis of Living Systems (ALife9) Boston, September 12 - 15, 2004.

Hallinan, J. & Wiles, J. (2004). Evolving genetic regulatory networks using an artificial genome. In Chen, Y.-P. (ed.) 2nd Asia-Pacific Bioinformatics Conference (APBC2004), Dunedin, New Zealand. Conferences in Research and Practice in Information Technology, Australian Computer Society, Inc. Vol. 29:291 - 296.

Hallinan, J. (In press). Gene duplication and hierarchical modularity in intracellular interaction networks. BioSystems.

Watson, J., Wiles, J., & Hanan, J. (2003). Towards more relevant evolutionary models: Integrating an artificial genome with a developmental phenotype. In proceedings of The Australian Conference on Artificial Life (ACAL 2003), pp. 288-298. [Abstract] [PDF]

Watson, J., Geard, N. & Wiles, J. (2003). Towards more biological mutation operators in gene regulation studies. Presented at the 5th International Workshop on Information Processing in Cells and Tissues (IPCAT 2003). [Abstract] [PDF]

Wiles, J. (accepted) Mapping biology onto computation: modelling and analysis of artificial genetic regulatory networks. International Conference on Complex Systems (ICCS 2004). Boston, May 16 - 22, 2004. [Abstract]