Smith, AP, Lane, LC, Moquin, DJ, van Opijnen, T, Woolard, S, Carter, R, Iverson, A, Burnham, C, Vogel, P, Roeber, D, Hochu, G, Johnson, MDL, McCullers, JA, Rosch, JR*, Smith, AM* (2019). Dynamic Pneumococcal Genetic Adaptations Support Bacterial Growth and Inflammation During Coinfection with Influenza. (submitted) Preprint

M.A Myers, A.P. Smith, L.C. Lane, D.J. Moquin, J.R. Michael, P. Vogel, S. Woolard, and A.M. Smith* (2019). The Nonlinear Relations that Predict Influenza Viral Dynamics, CD8+ T cell-Mediated Clearance, Lung Pathology, and Disease Severity. (submitted) Preprint

Gaur, AH, McCarthy, JS, Panetta JC, Dallas, R., Woodford, J, Tang, Li, Smith, AM, Stewart, TB, Branum, KC, Freeman III, BB, Patel, ND, John, E, Chalon, S, Ost, S, Heine, RN, Richardson, JL, Christensen, R, Flynn, PM, Van Gessel, Y, Mitasev, B, Möhrle, JJ, Gusovsky, F, Bebrevska, L, Guy, RK (2019). Safety, Tolerability, Pharmacokinetics, and Antimalarial Efficacy of a Novel Plasmodium falciparum ATP4 Inhibitor (SJ733): A First-in-Human and Induced Blood Stage Malaria Phase 1a/ 1b Study. Lancet Infectious Diseases (in press)

M. Chung, M. Binois, R.B. Gramacy, D.J. Moquin, A.P. Smith and A.M. Smith* (2019). Parameter and Uncertainty Estimation for Dynamical Systems Using Surrogate Stochastic Processes. SIAM J Sci Computing 41(4), A2212–A2238.

A. Rodriguez, J.A. McCullers, A.M. Smith, T. Kanneganti, C.R. Lupfer* (2019). Enhanced IL-1β production is mediated by a TLR2-MYD88-NLRP3 signaling axis during coinfection with influenza A virus and Streptococcus pneumoniae. PLoS One 14(2): e0212236. doi: 10.1371/journal.pone.0212236


A.M. Smith* (2018). Validated Models of Immune Response to Virus Infection. Current Opinion in Systems Biology 12:46-52. doi: 10.1016/j.coisb.2018.10.005

A.M. Smith* (2018). Host-Pathogen Kinetics During Influenza Infection and Coinfection: Insights From Predictive Modeling. Immunological Reviews 285:97–112. doi: 10.1111/imr.12692

A.P. Smith, D.J. Moquin, V. Bernhauerova, and A.M. Smith* (2018). Influenza Virus Infection Model with Density Dependence Supports Biphasic Viral Decay. Frontiers in Microbiology. 9:1554. doi: 10.3389/fmicb.2018.01554

A.M. Smith*, R.M. Ribeiro, and A.S. Perelson* (2018). Population Dynamics of Host and Pathogens. Systems Immunology: An Introduction to Modeling Methods for Scientists.


A.M. Smith* and V.C. Huber*(2017). The Unexpected Impact of Vaccines on Secondary Bacterial Infections Following Influenza. Viral Immunology doi:10.1089/vim.2017.0138


A.M. Smith* and A.P. Smith (2016). A Critical, Nonlinear Threshold Dictates Bacterial Invasion and Initial Kinetics During Influenza. Sci Rep, 6, 38703, doi:10.1038/srep38703

Prediction validated within

A.M. Smith* (2016). Quantifying the Therapeutic Requirements and Potential for Combination Therapy to Prevent Bacterial Coinfection During Influenza. J Pharmacokinet Pharm doi:10.1007/s10928-016-9494-9


A.M. Smith* and J.A. McCullers (2014). Secondary Bacterial Infections in Influenza Virus Infection Pathogenesis. Curr Top Microbiol. doi:10.1007/82_2014_394


A.M. Smith*, F.R. Adler, R.M. Ribeiro, R.N. Gutenkunst, J.L. McAuley, J.A. McCullers, and A.S. Perelson (2013). Kinetics of Coinfection With Influenza A Virus and Streptococcus pneumoniae. PLoS Pathog 9(3): e1003238. doi:10.1371/journal.ppat.1003238.

One prediction validated in vivo by Ghoneim et al. (2013)
One prediction validated in vitro (S. aureus) by Warnking et al. (2015)

A.M. Smith* and J.A. McCullers (2013). Molecular Signatures of Virulence in the PB1-F2 Proteins of H5N1 Influenza Viruses. Virus Res. 178 (1):146-150. doi:10.1016/j.virusres.2013.02.012


A.M. Smith*, J.A. McCullers, and F.R. Adler (2011). Mathematical Model of a Three-Stage Innate Immune Response to a Pneumococcal Lung Infection. J Theor Biol 276(1):106-116.

A.M. Smith*, F.R. Adler, J.L. McAuley, R.N. Gutenkunst, R.M. Ribeiro, J.A. McCullers and A.S. Perelson* (2011). Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics. PLoS Comput Biol7(2): e1001081. doi:10.1371/journal.pcbi.1001081

Faculty of 1000 Evaluation

A.M. Smith and A.S. Perelson* (2011). Influenza A Virus Infection Kinetics: Quantitative Data and Models. WIREs Syst Biol Med, DOI: 10.1002/wsbm.129


A.M. Smith and R.M. Ribeiro* (2010). Modeling the Viral Dynamics of Influenza A Virus Infection. Crit Rev Immunol, 30(3):291-298.

A.M. Smith*, F.R. Adler and A.S. Perelson (2010). An Accurate Two-Phase Approximate Solution to an Acute Viral Infection Model. J Math Biol, 60(5):711-726.


J.L. McAuley, F. Hornung, K.L. Boyd, A.M. Smith, R. McKeon, J. Bennink, J.W. Yewdell, and J.A. McCullers* (2007). Expression of the 1918 Influenza A Virus PB1-F2 Enhances the Pathogenesis of Viral and Secondary Bacterial Pneumonia. Cell Host & Microbe, 2(4):240-249.

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*corresponding/senior author