Infectious Diseases Modelling Group

Description of Group
We are a group of scientists from diverse backgrounds such as physics, biochemistry, mathematics, biostatistics, computer science, and neuroscience. We work with clinicians, epidemiologists, behavioural scientists, policy makers, pharmaceutical companies, molecular biologists and microbiologists and we develop models to understand infectious disease dynamics; this includes epidemiological transmission dynamics, forecasting epidemic trajectories under various interventions in order to design health policy tools, and obtaining insight into kinetic virological and immunological interactions of various diseases with the immune system and host cells. We are a group in the Biostatistics & Databases Program of NCHECR. The main infections we investigate are HIV, Chlamydia, and HPV. Recently we have designed innovative Sampling and Sensitivity Analysis Tools (SaSAT) as a free downloadable software package for analysing computational models and their broad parameter spaces. We have also recently completed a report on understanding the key drivers of the increase in HIV in Australia (downloadable below).

Who we are

	A/Prof David Wilson Interests include: Understanding cellular and intracellular dynamics and pathology of Chlamydia and HIV, developing HIV transmission models to influence public health policy development for epidemic control in Southeast Asia and sub-Saharan Africa. Dwilson@nchecr.unsw.edu.au +61 2 9385 0968		Dr David Regan Interests include: The development and analysis of mathematical models of infectious disease transmission with a focus on sexually transmissible infections (e.g., HPV, Chlamydia, HIV) and the evaluation of interventions for control and prevention. Dregan@nchecr.unsw.edu.au +61 2 9385 0860
	Dr Richard Gray Interests include: The dynamics of infectious diseases, modelling of HIV and STI transmission, impact of interventions on disease propagation, application of quantitative medicine to public health, complex networks and brain dynamics. Rgray@nchecr.unsw.edu.au +61 2 9385 0969		Alex Hoare (PhD Student) Interests include: Modelling the HIV epidemic in SE Asia, specifically at the emergence of ARV drug resistance. Also interested in developing software for analysing models. Ahoare@nchecr.unsw.edu.au +61 2 9385 0927
	A/Prof John Murray Interests include: Epidemiological modelling and linking data with models to gain insight into viral kinetics for HIV and HBV, and other viral infections. Website j.murray@unsw.edu.au +61 2 9385 7042		Amy Kwon (PhD Student) Interests include: Applying mathematics to HIV/AIDS in Southeast Asia, with special focus on transmission among injecting drug users, and forecasting epidemic trajectories. Akwon@nchecr.unsw.edu.au +61 2 9385 0927
	Kel Heymer (PhD Student) Interests include: Developing mathematical models of HIV transmission that are applied, in settings of SE Asian populations. Kheymer@nchecr.unsw.edu.au +61 2 9385 0934 �		Charisse Farr (Masters student) Interests include: Understanding key drivers of the HIV epidemic in the Philippines and informing policy to ensure HIV levels remain low.

Software

Sampling and Sensitivity Analyses Tools (SaSAT) Software for Computational Models

Download SaSAT version 1.01 (32-bit version, with MCR installer)
Download SaSAT Version 1.01 (64-bit version, with MCR installer)
Download SaSAT version 1.01 (32-bit version, without MCR installer)
What is MCR Installer
Download User Guide and installation instructions (1Mb)
Download scientific manuscript accompanying software (2Mb)

Contact us if you would like us to send you a CD with the software and for the free password to unzip the downloaded program
Troubleshooting

Publications

Report: Wilson, Hoare, Regan, Wand, Law (2008) Mathematical models to investigate recent trends in HIV notifications among men who have sex with men in Australia.

HIV Epidemiology Publications

Blower SM, Wilson DP, Coplan PM, Wainberg MA. (2008). Response to ‘Predicting the unpredictable real world impact of ARV-based microbicides’. PNAS, In Press.
Wilson DP, Law MG, Grulich AE, Cooper DA, Kaldor JM. (2008). Relation between HIV viral load and infectiousness? A model-based analysis. The Lancet, 372:314-20.
Wilson DP, Coplan PM, Wainberg MA, Blower SM. (2008). The paradoxical effects of using antiretroviral-based microbicides to control HIV epidemics. PNAS, 105 (28):9835-40.
(Editor’s Choice in the field of Virology. (2008). Modeling microbicides. Science, 321 (5888):466 & Publicised in Nature and Nature Medicine).
Wilson DP, Coplan PM. (2008). Mathematical models and health economic aspects of microbicides. Current Opinion in HIV and AIDS, 3: 587-592.
Hoare A, Wilson DP, Regan DG, Kaldor J, Law MG (2008) Mathematical models to investigate recent trends in HIV notifications among men who have sex with men in Australia. Sexual Health, 5:169-187.
Londish, G.J., and J.M. Murray, Significant reduction in HIV prevalence according to male circumcision intervention in sub-Saharan Africa, International Journal of Epidemiology 2008; 1-8, doi:10.1093/ije/dyn038.
Health Outcomes International Pty Ltd, National Centre in HIV Epidemiology and Clinical Research (Law M). (2007) Report: The impact of HIV/AIDS in NSW – Mortality, Morbidity and Economic Impact. New South Wales Department of Health.
Wilson DP, Blower SM. (2007). How far will we need to go to reach HIV-infected people in rural South Africa? BMC Medicine, 5:16-. (BMC status of ‘Highly accessed’ article)
Wilson DP, Kahn JO, Blower SM. (2006). Predicting the epidemiological impact of antiretroviral allocation strategies in KwaZulu-Natal: The effect of the urban-rural divide. PNAS, 103(38):14228-14233. (Editor’s Choice in the field of Biomedicine. (2006). To Have or Have Not. Science, 313 (5795):1855).
Wilson DP, Blower SM. (2006). Rational choices for allocating antiretrovirals in Africa: treatment equity, epidemiological efficiency and feasibility. PLoS Medicine, 3(3):410-411.
Kaldor J, Worth H, Henderson K, Law M, McKay M, Warner B, Razali K. Impacts of HIV/AIDS 2005-2025 in Papua New Guinea, Indonesia and East Timor. Final Report of the HIV Epidemiological Modelling and Impact Study. Canberra: Australian Government. AusAID; February 2006.
Wilson DP, Blower SM. (2005). Allocating Antiretrovirals in South Africa: Using Modeling to Determine Treatment Equity. PLoS Medicine, 2(6):563-564.
Wilson DP, Blower SM. (2005). Designing Equitable Antiretroviral Allocation Strategies in Resource-Constrained Countries. PLoS Medicine, 2(2):132-141.
Wilson DP, Bodine EN, Smith RJ, Blower SM. (2005). Response to Foss et al., 'Care should be taken when promoting microbicide use among sex workers who are able to use condoms consistently'. AIDS, 19(17):2044-2046.
Smith RJ, Bodine EN, Wilson DP, Blower SM. (2005). Evaluating the potential impact of vaginal microbicides to reduce the risk of acquiring HIV in female sex workers. AIDS, 19:413-421.
Wilson DP, Blower SM. (2004) Microbicides: Anti-HIV Efficacy and Ethics. Science, 206 (5703):1890.
Clements MS, Prestage G, Grulich A, Van de Ven P, Kippax S, Law MG. (2004). Modeling trends in HIV incidence among homosexual men in Australia 1995-2006. J Acquir Immune Defic Syndr, 35:401-406.
Murray JM, Law MG, Gao Z, Kaldor JM. (2003). The impact of behavioural changes on the prevalence of human immunodeficiency virus and hepatitis C among injecting drug users. Int J Epidemiol, 32:708-714.
Law MG, Prestage G, Grulich A, Van de Ven P, Kippax S. (2002). Modelling HIV incidence in gay men: increased treatment, unsafe sex and sexually transmissible infections. AIDS. 16:499-501.
Law MG, Prestage G, Grulich A, Van de Ven P, Kippax S. (2001). Modelling the effect of combination antiretroviral treatments on HIV incidence. AIDS. 15:1287-1294.

HIV Virology & Immunology Publications

Lewin SR, Murray JM, Solomon A, Wightman F, Cameron PU, Purcell DJ, Zaunders JJ, Grey P, Bloch M, Smith D, Cooper DA, Kelleher AD. (2008). Virologic Determinants of Success After Structured Treatment Interruptions of Antiretrovirals in Acute HIV-1 Infection. J Acquir Immune Defic Syndr, 47:140-147.
Murray JM, Emery S, Kelleher AD, Law M, Chen J, Hazuda DJ, Nguyen BYT, Teppler H, Cooper DA. (2007). Antiretroviral therapy with the integrase inhibitor raltegravir alters decay kinetics of HIV, significantly reducing the second phase. AIDS, 21:2315-2321.
Wilson DP, Mattapallil JJ, Lay M, Zhang L, Roederer M, Davenport MP. (2007). Estimating the infectivity of CCR5-tropic SIVmac251 in the gut. Journal of Virology, 81 (15): 8025-8029.
Davenport MP, Ribeiro RM, Zhang L, Wilson DP, Perelson AS. (2007). Understanding the mechanisms and limitations of immune control of HIV. Immunological Reviews, 216:164-175.
Wilson DP, Zhang L, Ribeiro RM, Perelson AS, Davenport MP. (2005). Explaining mechanisms behind the virus-specific CD8+ T lymphocyte response to a viral infection. Tissue Antigens, 66 (5):590-591.
Murray JM, Perelson AS. (2005). Human immunodeficiency virus: quasi-species and drug resistance. Multiscale Modeling and Simulation, 3(4):300-311.
Macpherson JL, Boyd MP, Arndt AJ, Todd AV, Fanning GC, Ely JA, Elliott F, Knop A, Raponi M, Murray J, Gerlach W, Sun LQ, Penny R, Symonds GP, Carr A, Cooper DA. (2005). Long-term survival and concomitant gene expression of ribozyme-transduced CD4+ T-lymphocytes in HIV-infected patients. J Gene Med, 7(5) :552-564.
Wilson DP, McElwain DLS. (2002). A Mathematical Model of Continuous HIV Mutations Eluding Immune Defence. Journal of Theoretical Medicine. 4(4): 241-249.

Within-host Chlamydia Publications

Hoare A, Timms P, Bavoil PM, Wilson DP. (2008). Spatial constraints within the chlamydial host cell inclusion predict interrupted development and persistence. BMC Microbiology, 8:5-.
Peters J, Wilson DP, Myers G, Timms P, Bavoil PM. (2007). Type III Secretion � la Chlamydia. Trends in Microbiology, 15 (6):241-251.
Wilson DP, Timms P, McElwain DLS, Bavoil PM. (2006). Type Three Secretion, contact-dependent model for the intracellular development of Chlamydia. Bulletin of Mathematical Biology, 68:161-178.
Wilson DP. (2004). Mathematical Modelling of Chlamydia. Proceedings of Computational Techniques and Applications, ANZIAM Journal, 45:C201-C214.
Wilson DP, Mathews S, Wan C, Pettitt AN, McElwain DLS. (2004). Use of a Quantitative Gene Expression Assay based on Micro-array Techniques and a Mathematical Model for the Investigation of Chlamydial Generation Time. Bulletin of Mathematical Biology, 66:523-537.
Wilson DP, McElwain DLS. (2004). A model of neutralization of Chlamydia trachomatis based on antibody and host cell aggregation on the elementary body surface. Journal of Theoretical Biology. 226(3):321-330.
Wilson DP, Timms P, McElwain DLS. (2003). A mathematical model for the investigation of the Th1 immune response to Chlamydia trachomatis. Mathematical Biosciences. 182(1) :27-44.
Mallet D, Heymer K, Wilson DP. (2007). A novel cellular automata-partial differential equation model for understanding chlamydial infection and ascension of the female genital tract. Proc. Appl. Math. Mech., 7:2120001-2120002.

Chlamydia Epidemiology Publications

Regan DG, Wilson DP, Hocking JS (2008) Coverage is the key for effective screening of Chlamydia trachomatis in Australia. Journal of Infectious Diseases under review. Journal of Infectious Diseases, 198:349-58.
Hocking, JS, Walker J, Regan DG, Chen M, Fairley CK (2008) Chlamydia screening- Australia should strive to achieve what others have not. Medical Journal of Australia 188:106-108.

HPV Publications

Regan DG, Philp DJ, Hocking JS, Law MG (2007) Modelling the population-level impact of vaccination on the transmission of human papillomavirus type 16 in Australia. Sexual Health 4:147-163.
Kulasingam S, Connelly L, Conway E, Hocking JS, Myers E, Regan DG, Roder D, Ross J, Wain G (2007) A cost-effectiveness analysis of adding a human papillomavirus vaccine to the Australian National Cervical Screening Program. Sexual Health 4:165-175.

HCV Publications

Razali K, Thein H-H, Bell J, Cooper-Stanbury M, Dolan K, Dore G, George J, Kaldor J, Karvelas M, Li J, Maher L, McGregor S, Hellard M, Poeder F, Quaine J, Stewart K, Tyrrell H, Weltman M, Westcott O, Wodak A, Law M. (2007) Modelling the Hepatitis C virus epidemic in Australia. Drug and Alcohol Dependence 91:228-235.
Hepatitis C Virus Projections Working Group. Estimates and projections of the hepatitis C virus epidemic in Australia 2006. National Centre in HIV Epidemiology and Clinical Research, UNSW, Sydney, October 2006.
Law MG, Dore GJ, Bath N, Thompson S, Crofts N, Dolan K, Giles W, Gow P, Kaldor J, Loveday S, Powell E, Spencer J, Wodak A. (2003) Modelling hepatitis C virus incidence, prevalence and long-term sequelae in Australia, 2001. International Journal of Epidemiology 32:717-724.
Law MG on behalf of the Hepatitis C Virus Projections Working Group. (1999) Modelling the hepatitis C virus epidemic in Australia. Journal of Gastroenterology and Hepatology 14: 1100-1107.
Hepatitis C Virus Projections Working Group. Estimates and projections of the hepatitis C virus epidemic in Australia 2002. National Centre in HIV Epidemiology and Clinical Research, UNSW, Sydney, August 2002. Available at: www.health.gov.au/pubhlth/publicat/hac.htm.
Hepatitis C Virus Projections Working Group. Estimates and projections of the hepatitis C virus epidemic in Australia. National Centre in HIV Epidemiology and Clinical Research, UNSW, Sydney, August 1998.

HBV Publications

Dandri, M, J.M. Murray, M. Lutgehetmann, T. Volz, A.W. Lohse, J. Petersen, Virion half-life in chronic hepatitis B infection is strongly correlated with levels of viremia, Hepatology, 2008. 48.
Volz, T., M. Lutgehetmann, P. Wachtler, A. Jacob, A. Quaas, J.M. Murray, M. Dandri, and J. Petersen, Impaired Intrahepatic Hepatitis B Virus Productivity Contributes to Low Viremia in Most HBeAg-Negative Patients. Gastroenterology, 2007. 133(3): p. 843-852
Murray, J.M., R.H. Purcell, and S.F. Wieland, The half-life of hepatitis B virions. Hepatology, 2006. 44(5): p. 1117-21.
Murray, J.M., S.F. Wieland, R.H. Purcell, and F.V. Chisari, Dynamics of hepatitis B virus clearance in chimpanzees. Proc Natl Acad Sci U S A, 2005. 102(49): p. 17780-5.
Whalley, S.A., J.M. Murray, D. Brown, G.J. Webster, V.C. Emery, G.M. Dusheiko, and A.S. Perelson, Kinetics of acute hepatitis B virus infection in humans. Journal of Experimental Medicine, 2001. 193(7): p. 847-54.

Methodology Publications

Regan, DG, Wilson DP (2008) Modelling sexually transmitted infections: less is usually more for informing public health policy. Transactions of the Royal Society of Tropical Medicine and Hygiene, 102:207-208.
Hoare A, Regan DG, Wilson DP (2008) Sampling and Sensitivity Analyses Tools (SaSAT) for Computational Modelling. Theoretical Biology and Medical Modelling, 5:4-.

Innate Immunity Publications

Orr Y, Wilson DP, Taylor JM, Bannon PG, Geczy C, Davenport MP, Kritharides L. (2007). A kinetic model of bone marrow neutrophil production which characterizes late phenotypic maturation. Am J Physiol Regul Integr Comp Physiol., 292 (4):R1707-1716.

Other Relevant Publications

Wilson DP. Epidemiological Modeling for the Real World. Book chapter for Mathematical Biology Research Advances, Nova Publishers, In Press 2008.
Wilson DP. Mathematics is applied by everyone except applied mathematicians. Appled Mathematics Letters, In press.
Wilson DP. (2007). Australian migration policy of HIV-infected individuals requires renewed discussions. Australian and New Zealand Journal of Public Health, 31 (4):385-386.
Wilson DP. (2007). Analysis and Approximation for Solving Highly Coupled Master Differential Equations of Receptor Interactions. World Applied Sciences Journal, 2 (2):81-89.
Wilson DP. (2005). Report: Probability-based predictions of the development of microbicide products in the clinical trial pipeline. Consultancy performed for International Partnership for Microbicides.
Wilson DP, Blower SM. (2005). Report: Mathematical Modeling of Vaginal Microbicides and Resistance to HIV Antiretrovirals Amongst Heterosexual Populations. Consultancy performed for International Partnership for Microbicides.
Wilson DP, Blower SM. (2005). Report: Mathematical Modeling of Vaginal Microbicides: NNRTIs versus NRTIs. Consultancy performed for International Partnership for Microbicides.
Wilson DP, McElwain DLS. (2005). Diffusion theory can be applied to antibodies attaching to ligand sites. ANZIAM Journal, 46:495-505.
Wilson DP. (2003). Concentration of cell receptors is more important in effecting binding reactions than cell receptor affinity. Australian Mathematical Society Gazette. 30(2) :82-85.
Wilson D. (2001). Book Review of "Virus dynamics: Mathematical Principles of Immunology and Virology" by Martin A. Nowak and Robert M. May. Australian Mathematical Society Gazette. 28(4):219-220.

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