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

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. (submitted) Preprint

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