John Burns, B.Sc., Ph.D.
School of Computing
Dublin City University
Ireland

The title of my Ph.D. thesis was Emergent Networks in Immune System Shape Space. The models developed in the thesis offer a viable theory to explain how primary, secondary and continuous reinfection by heterologous pathogens may affect effector T cell function. This was done, from the modelling perspective, by demonstrating how emergent network topology in immune system shape space affects immune function, especially when node loss or suppression is introduced. Furthermore, it was shown that minor topological alteration results in downward causation (the converse of the reductionist principle) in that the behaviour of the microscopic parts of the model are determined by the behaviour of the whole and thus determination moves downwards instead of upwards. It was demonstrated that individual immune system may develop minor topological variations in network topology which effect the clearance rates and therefore the duration and pathology of similar pathogen strain.

Recent Publications

2006

Ruskin, H., Burns, J.: Weighted networks in immune system shape space. Physica A, 365(2):549-555, 2006

2005

Ruskin, H., Burns, J.: Network Emergence in Immune System Shape. ERCIM News 64, January 2006

Ruskin, H., Burns, J.: Network Emergence in Immune System Shape Space. Gervasi O., et al. (eds.): Lecture Notes in Computer Science, Vol. 3481. Springer-Verlag, Berlin Heidelberg New York (2005) 1254-1263

2004

Burns, J., Ruskin, H.: A Stochastic Model of the Effector T Cell Lifecycle. In: Sloot P.M.A., Chopard, B. and Hoekstra A.G., (eds.): Cellular Automata, Lecture Notes in Computer Science, Vol. 3305. Springer-Verlag, Berlin Heidelberg (2004) 454-463

Burns, J., Ruskin, H.: Network Topology in Immune System Shape Space. In: Bubak, M.; Albada, G.D.v.; Sloot, P.M.A.; Dongarra, J. (eds.): Lecture Notes in Computer Science, Vol. 3038. Springer-Verlag, Berlin Heidelberg New York (2004) 1094-1101

Burns, J., Ruskin, H.: Diversity Emergence and Dynamics During Primary Immune Response: A Shape Space, Physical Space Model. Theor. in Biosci. 123(2):183-194, 2004.

2003

Burns, J., Ruskin, H.: Viral Strain Diversity and Immune Response - a Computational Model. In: M.A. Hamza (ed.): Proceedings of the International Conference on Biomedical Engineering. ACTA Press (2003) 60-65

Burns, J., Ruskin, H.: A Model of Immune Suppression and Repertoire Evolution. In: Sloot, P.M.A., Gorbachev, Y.E., (eds.): Lecture Notes in Computer Science, Vol. 2660. Springer-Verlag, Berlin Heidelberg New York (2003) 75-85

2002

Burns, J., Ruskin, H.: A Monte Carlo Model of Immune System T-Cell Receptor Cross-Reactivity During Primary Response. In: P.L. Garrido (ed): 7th Granada Conference in Computational and Statistical Physics. Vol. 661 (1). American Institute of Physics (2002), 255-256

Burns, J. (2002): Modelling the Human Immune Response using the Shape Space Paradigm. Working Paper, CA-0402, Dublin City University,

Presentations and Posters

Presentation entitled "Scientific Writing using Latex, Bibtex, MetaPost and R" given to the MSC group, DCU, April 20th, 2004

Presentation entitled "Network topology in immune system shape space" given to the MSC group, DCU, Decemeber 18th, 2003, is available in .ps format here

Poster entitled "A Monte Carlo model of immune system T-Cell receptor cross-reactivity during primary response", presented at the 7th Granada Conference Computational and Statistical Physics, 12-7 September in Granada, Spain.

"Time is a great teacher, but unfortunately it kills all its pupils" - Hector Berlioz