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.
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.
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.