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Ghosh S, Heffernan JM.  2010.  “Influenza Pandemic waves under various mitigation strategies: A look at H1N1. PLoS One. published online in December 2010
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Heffernan JM, Wilson DJ.  2011.  The Undead: A Plague on Mankind or a Powerful New Tool for Epidemiological Research? Mathematical Modelling of Zombies.
Heffernan JM, Keeling MJ.  2008.  An in-host model of acute infection: measles as a case study.. Theoretical population biology. 73(1):134-47. Abstract
Heffernan JM, Keeling MJ.  2009.  Implications of vaccination and waning immunity.. Proceedings. Biological sciences / The Royal Society. 276(1664):2071-80. Abstract
Heffernan JM, Wahl LM.  2005.  Treatment Interruptions and Resistance: A Review.. Deterministic and Stochastic Models for AIDS Epidemics and HIV Infection with Interventions. :423-456.
Heffernan JM, Wahl LM.  2006.  Improving estimates of the basic reproductive ratio: using both the mean and the dispersal of transition times.. Theoretical population biology. 70(2):135-45. Abstract
Heffernan JM, Corless RM.  2006.  Solving some delay differential equations with computer algebra. The Mathematical Scientist. 31(1):22pages.
Heffernan JM.  2011.  Mathematical Immunology of Infectious Diseases. Mathematical Population Studies. 18(2):47-54.
Heffernan JM, Smith RJ, Wahl LM.  2005.  Perspectives on the basic reproductive ratio.. Journal of the Royal Society, Interface / the Royal Society. 2(4):281-93. Abstract
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Qesmi R, ElSaadany S, Heffernan JM, Wu J.  2011.  Model of Hepatitis B Virus with Age since Infection that Exhibits Backward Bifurcation. SIAM J. Appl. Math.. 71,1509-1530
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Wang Y, Zhou Y, Wu J, Heffernan JM.  2009.  Oscillatory viral dynamics in a delayed HIV pathogenesis model. Math Biosci. 219(2):104-112.