Staff Profile

Professor of Systems Biology

Don Kulasiri

BSc (Hons) (Eng) MS PhD (Virginia Tech)

Don Kulasiri

Contact Details

Faculty of Agriculture and Life Sciences

Location RFH 066
Phone +64 3 423 0631
Extension 30631
Email Don.Kulasiri@lincoln.ac.nz
 

Currently Teaching

  • COMP308 Computer Modelling and Simulation
  • QMET610 Computational Molecular Systems Biology; Stochastic Processes
  • BICH326 Protein Biochemistry
  • BICH634 Plant Cell Physiology
  • BICH638 Bioinformatics
 

Academic and Professional Background

Founding member and Head of Centre for Advanced Computational Solutions (C-fACS); Visiting Professor, Integrated Systems Biology Cente/Centre for Mathematical Biology, University of Oxford, UK (Jan - June, 2008, Nov 2010, June 2013) Visiting Fellow, Princeton University, New Jersey (Jan-June, 2004; July 2006) Visiting Professor to Institute of Scientific Computing, Technical University of Braunschweig, Germany (since 2001); Visiting Scholar, Stanford University (Jan-June, 1998); A visiting member of the Centre for Mathematical Biology, Oxford University; a member of Modelling and Simulation Society of Australia and New Zealand, and Sigma Xi honour society; A Panel member of Mathematics, Information Science and Technology (MIST) panel for the PBRF 2012 quality evaluations, Govt  of New Zealand.

 

Current Research and Publications / Selected Publications

  • Molecular Systems Biology
  • Stochastic modelling of biological and environmental systems
  • Bio-Engineering (biotechnology)


Research Monographs

Kulasiri, Don. 2013. Non-Fickian Solute Transport in Porous Media: A Mechanistic and Stochastic Theory (Advances in Geophysical and Environmental Mechanics and Mathematics Series) Springer-Verlag Berlin Heidelberg, 227 pages.

Kulasiri, Don, and Verwoerd, Wynand. 2002. Stochastic Dynamics: Modeling solute transport in porous media.  North Holland Applied Mathematics and Mechanics Series . Elsevier Science, Amsterdam. Volume 44. 256 pages.

 

Proceedings

Les Oxley and Don Kulasiri (editors) Proceedings of the International Congress of Modelling and Simulation, Modelling and Simulation Society of Australia and New Zealand (MSSANZ), December, Christchurch, 2007. 3104 pages.

 

Book Chapters

Don Kulasiri. 2010. Computing Molecular Fluctuations in Biochemical Reaction Systems Based on a Mechanistic, Statistical Theory of Irreversible Processes. In Michael Johnson editor: Methods in Enzymology, Vol. 487,Burlington: Academic Press, pp. 253-278

Wannige, T., Kulasiri, D. and Samarasinghe, S. 2013. Modelling Stochasticity in Multi-stable and Oscillatory Biological Networks far from Equilibrium, IN: Biological Networks, Nova Science Publishers, New York (Editor: Prof. W.J. Zhang) 163-193 pages

 

Invited Review Articles

Kulasiri, D., Nguyen, L., Samarasinghe, S. and Xie, Z. A review of systems biology perspective on genetic regulatory networks with examples.  Current Bioinformatics. (2008) 3. pp. 197-225. (Invited review)

Rains, G., Kulasiri, D., Zhou, Z., Samarasinghe, S. Tomberlin, J.K. and Olson, D.M. 2009.  Synthesizing Neurophysiology, Genetics, Behaviour and Learning to Produce Whole-Insect Programmable Sensors to Detect Volatile Chemicals. Biotechnology and Genetic Engineering Reviews. Vol. 26. 191-216

Chaiboonchoe, A., Samarasinghe, S. and Kulasiri, D. 2010. Machine learning for childhood acute lymphoblastic leukaemia gene expression data analysis: A review. Current Bioinformatics (5): 118-133

 

Refereed Journal Papers

C. T. Wannige, D. Kulasiri, S. Samarasinghe. 2014. A nutrient dependent switch explains mutually exclusive existence of meiosis and mitosis initiation in budding yeast. Journal of Theoretical Biology, 314: 88-101

Hong Ling, Sandhya Samarasinghe and Don Kulasiri. 2013. Novel recurrent neural network for modelling biological networks: Oscillatory p53 interaction dynamics. BioSystems, 114: 191-205

Ling, H., Samarasinghe, S. and Kulasiri, D. 2013.  Computational experiments reveal the efficacy of targeting CDK2 and CKIs for significantly lowering cellular senescence bar for potential cancer treatment.  BioSystems 111: 71– 82 

Z. Zhou, G. C. Rains, D. Kulasiri. 2012. Development of a behaviour parameter in classically conditioned parasitic wasps that detect changes in odor intensity. Biological Engineering Transactions, 5(1):19-31.

Don Kulasiri, Hong Ling and Sandhya Samarasinghe. 2012. A generalised stochastic solute transport model for Multiscale dispersion in porous media. Journal of Porous Media. 15(2):153-170.

D. Kulasiri, Y. He, S. Samarasinghe. 2011. Robustness of circadian rhythms in the presence of molecular fluctuations: An investigation based on a mechanistic, statistical theory and a simulation algorithm. BioSystems, Volume 106, 57-66.

Lan K. Nguyen and Don Kulasiri. 2011. Distinct Noise-controlling Roles of Multiple Negative Feedback Mechanisms in a Prokaryotic Operon System, IET Systems Biology , Vol. 5, Iss. 2, pp. 145–156.

Ling, H. , Kulasiri, D. and Samarasinghe S. 2010. Robustness of G1/S checkpoint pathway in cell cycle regulation based on the probability of DNA-damaged cells passing as healthy cells.  BioSystems . 101: 213–221

Xie Z, Kulasiri G D, Samarasinghe S, Qian J. 2010. An unbiased sensitivity analysis reveals important parameters controlling periodicity of circadian clock. Biotechnology and Bioengineering, 105: (2) : February: 250-259.

Xie Z, Kulasiri G D. 2010. On exploring effects of molecular noise in a simple viral infection model.  International Journal of Biomathematics.  Vol. 3, No. 1 : 1–19.

Sarmah, C., Samarasinghe, S. and Kulasiri, D. and Catchpoole, D. 2010. A simple Affymetrix Ratio-Transformation Method yields comparable expression levels quantifications with cDNA data. International Journal of Medicine and Medical Sciences, Volume 1(3):157 – 162. 2010.

Ling, H., Samarasinghe, S. and Kulasiri, D.  2009 Modelling variability in full-field displacement profiles and Poisson ratios of wood in compression using stochastic neural networks. Silva Fennica. 43(5): 871–887. 

Lan K. Nguyen, Don Kulasiri. 2009. On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems. BMC Systems Biology  3 (51) May pp: 1-30.

Kulasiri, D. and Z. Xie. Modelling circadian rhythms in Drosophila and investigation of VRI and PDP1 feedback loops using a new mathematical model.Math. Model. Nat. Phenom. Vol. 3, No. 2, 2008, pp. 1-26. (Invited article for the special issue on gene regulation).

Nguyen, L. and Kulasiri, D. On multiple regulatory mechanisms in the Tryptophan operon system. In Silico Biology. (2008) 8: 485-510.

Kulasiri, D. and Richards, S. Investigation of a stochastic model for multiscale dispersion in porous media. Journal of Porous Media. (2008) 6:275-292.

Rains, G., Tomberlin, J.K. and  Kulasiri, D. Using insect sniffing devices for detection. Trends in Biotechnology, Vol 26, Issue 6, (2008) pp. 288-294 (invited article).

Connell, R.J., Kulasiri, D. Lennon, J. and Hill, D.F. 2007. Computational modelling of turbulent velocity structures for an open channel flow using Karhunen-Loeve expansion. International Journal of Computational Methods, vol. 4, No. 3, pp. 493-519.

Z. Xie, Kulasiri. D. 2007. Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops. Journal of Theoretical Biology, 245 (2007) 290-304.

Xie, Z, Kulasiri, G D, Samarasinghe, S & Rajanayaka, C N. The estimation of parameters for stochastic differential equations using neural networks. Inverse Problems in Science and Engineering 15: (6): (2007) 629-641.

 

Page last updated on: 06/03/2012