publications-epi

Publications on computational epidemiology

S. L. Chang, C. J. E. Suster, R. J. Rockett, A. J. Svahn, O. M. Cliff, Alicia Arnott, Q. Wang, R. Kim, B. Suliman, M. Gall, T. C. Sorrell, V. Sintchenko, M. Prokopenko, Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens, Physical Biology, 20, 046006, 2023.
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.