Publications on computational epidemiology
- S. L. Chang, Q. D. Nguyen, A. Martiniuk, V. Sintchenko, T. C. Sorrell, M. Prokopenko, Persistence of the Omicron variant of SARS-CoV-2 in Australia: The impact of fluctuating social distancing, PLOS Global Public Health, 3(4): e0001427, 2023.
- A. J. Svahn, C. J. E. Suster, S. L. Chang, R. J. Rockett, E. M. Sim, O. M. Cliff, Q. Wang, A. Arnott, M. Ramsperger, T. C. Sorrell, V. Sintchenko, M. Prokopenko, Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB, Microbiology Spectrum, 11(2): e02791-22, 2023.
- Q. D. Nguyen, M. Prokopenko, A general framework for optimising cost-effectiveness of pandemic response under partial intervention measures, Scientific Reports, 12: 19482, 2022.
- J. Thompson, R. McClure, N. Scott, M. Hellard, R. Abeysuriya, R. Vidinaarachichi, J. Thwaites, J. Lazarus, S. Michie, C. Bullen, M. Prokopenko, S. Chang, O. Cliff, C. Zachreson, T. Blakely, T. Wilson, D. Ait Oakrim, V. Sundararajan, A framework for communicating the utility of models when facing tough decisions in public health, Health Research Policy and Systems, 20, 107, 2022.
- C. Zachreson, S. L. Chang, N. Harding, M. Prokopenko, The effects of local homogeneity assumptions in metapopulation models of infectious disease, Royal Society Open Science, 9, 211919, 2022.
- S. L. Chang, O. M. Cliff, C. Zachreson, M. Prokopenko, Simulating Transmission Scenarios of the Delta Variant of SARS-CoV-2 in Australia, Frontiers in Public Health, 10, 10.3389/fpubh.2022.823043, 2022.
- A. J. Svahn, S. L. Chang, R. J. Rockett, O. M. Cliff, Q. Wang, A. Arnott, M. Ramsperger, T. C. Sorrell, V. Sintchenko, M. Prokopenko, Genome-wide networks reveal emergence of epidemic strains of Salmonella Enteritidis, International Journal of Infectious Diseases, 117: P65-73, 2022.
- C. Zachreson, S. L. Chang, O. M. Cliff, M. Prokopenko, How will mass-vaccination change COVID-19 lockdown requirements in Australia?, The Lancet Regional Health – Western Pacific, 14: 100224, 2021.
- J. Bell, G. Bianconi, D. Butler, J. Crowcroft, P. C. W. Davies, C. Hicks, H. Kim, I. Kiss, F. Di Lauro, C. Maple, A. Paul, M. Prokopenko, P. Tee, S. I. Walker, Beyond COVID-19: Network science and sustainable exit strategies, Journal of Physics: Complexity, 2(2): 021001, 2021.
- S. L. Chang, N. Harding, C. Zachreson, O. M. Cliff, M. Prokopenko, Modelling transmission and control of the COVID-19 pandemic in Australia, Nature Communications, 11, 5710, 2020.
- O. M. Cliff, N. McLean, V. Sintchenko, K. M. Fair, T. C. Sorrell, S. Kauffman, M. Prokopenko, Inferring evolutionary pathways and directed genotype networks of foodborne pathogens, PLoS Computational Biology, 16(10): e1008401, 2020.
- R. J. Rockett, A. Arnott, C. Lam, R. Sadsad, V. Timms, K.-A. Gray, J.-S. Eden, S. L. Chang, M. Gall, J. Draper, E. Sim, N. L. Bachmann, I. Carter, K. Basile, R. Byun, M. V. O. Sullivan, S. C. A. Chen, S. Maddocks, T. C. Sorrell, D. E. Dwyer, E. C. Holmes, J. Kok, M. Prokopenko, V. Sintchenko, Revealing COVID-19 transmission by SARS-CoV-2 genome sequencing and agent based modelling, Nature Medicine, 26: 1398–1404, 2020.
- S. L. Chang, M. Piraveenan, M. Prokopenko, Impact of network assortativity on epidemic and vaccination behaviour, Chaos, Solitons & Fractals, 140: 110143, 2020.
- M. Lenzen, M. Li, A. Malik, F. Pomponi, Y.-Y. Sun, T. Wiedmann, F. Faturay, J. Fry, B. Gallego, A. Geschke, J. Gómez-Paredes, K. Kanemoto, S. Kenway, K. Nansai, M. Prokopenko, T. Wakiyama, Y. Wang, M. Yousefzadeh, Global socio-economic losses and environmental gains from the Coronavirus pandemic, PLoS ONE, 15(7): e0235654, 2020.
- N. Harding, R. E. Spinney, M. Prokopenko, Population mobility induced phase separation in SIS epidemic and social dynamics, Scientific Reports, 10: 7646, 2020.
- C. Zachreson, K. M. Fair, N. Harding, M. Prokopenko, Interfering with influenza: nonlinear coupling of reactive and static mitigation strategies, Journal of Royal Society Interface, 17(165): 20190728, 2020.
- N. Harding, R. E. Spinney, M. Prokopenko, Phase transitions in spatial connectivity during influenza pandemics, Entropy, 22(2), 133, 2020.
- S. Chang, M. Piraveenan, P. Pattison, M. Prokopenko, Game theoretic modelling of infectious disease dynamics and intervention methods: a review, Journal of Biological Dynamics, 14(1): 57-89, 2020.
- K. M. Fair, C. Zachreson, M. Prokopenko, Creating a surrogate commuter network from Australian Bureau of Statistics census data, Scientific Data, 6, 150, 2019.
- S. L. Chang, M. Piraveenan, M. Prokopenko, The Effects of Imitation Dynamics on Vaccination Behaviours in SIR-Network Model, International Journal of Environmental Research and Public Health, 16(14), 2477, 2019.
- O. M. Cliff, V. Sintchenko, T. C. Sorrell, K. Vadlamudi, N. McLean, M. Prokopenko, Network properties of Salmonella epidemics, Scientific Reports, 9, 6159, 2019; see also: Supplementary Information.
- C. Zachreson, K. Fair, N. Harding, O. M. Cliff, M. Prokopenko, Large-scale Agent-based simulations of pandemic influenza in Australia: framework, historical trends, interventions, Conference on Complex Systems (CCS), Singapore, 30 Sept - 4 Oct 2019.
- S. L. Chang, M. Piraveenan, M. Prokopenko, Imitation dynamics in a SIR-network model with paediatric vaccination, Conference on Complex Systems (CCS), Singapore, 30 Sept - 4 Oct 2019.
- S. L. Chang, M. Piraveenan, M. Prokopenko, Impact of committed vaccine recipients on vaccination behaviours in a SIR-network model, Conference on Complex Systems (CCS), Singapore, 30 Sept - 4 Oct 2019.
- C. Zachreson, K. M. Fair, O. M. Cliff, N. Harding, M. Piraveenan, M. Prokopenko, Urbanization affects peak timing, prevalence, and bimodality of influenza pandemics in Australia: Results of a census-calibrated model, Science Advances, 4(12), eaau5294, 2018.
- N. Harding, R. Nigmatullin, M. Prokopenko, Thermodynamic efficiency of contagions: a statistical mechanical analysis of the SIS epidemic model, Interface Focus, 8 20180036, 2018.
- O. M. Cliff, N. Harding, M. Piraveenan, E. Y. Erten, M. Gambhir, M. Prokopenko, Investigating Spatiotemporal Dynamics and Synchrony of Influenza Epidemics in Australia: An Agent-Based Modelling Approach, Simulation Modelling Practice and Theory, 87, 412-431, 2018 (also on arXiv).
- E. Y. Erten, J. T. Lizier, M. Piraveenan, M. Prokopenko, Criticality and Information dynamics in epidemiological models, Entropy, 19 (5), 194, 2017.
- M. Piraveenan, M. Prokopenko, L. Hossein, Percolation Centrality: Quantifying Graph-Theoretic Impact of Nodes during Percolation in Networks, PLoS ONE, 8(1): e53095, 2013.