Taylor, MK, Williams, EP, Xue, Y, Jenjaroenpun, P, Wongsurawat, T, Smith, AP, Smith, AM, [14 coauthors], Jonsson, CB. (2022). Dissecting phenotype from genotype with clinical isolates of SARS-CoV-2 first wave variants. Viruses 15(3):611.


Smith, AP, Lane, LC, Ramirez-Zuniga, I, Moquin, DJ, Vogel, P, Smith, AM*. (2022). Increased virus dissemination leads to enhanced lung injury but not inflammation during influenza-associated secondary bacterial infection. FEMS Microbes 3:1-9. doi: 10.1093/femsmc/xtac022.

Gaur, AH*, Panetta, JC, Smith, AM, Dallas, RH, Freeman, BB, Stewart, TB, Tang, L, John, E, Branum, KC, Patel, ND, Ost, S, Heine, RN, Richardson, JL, Hammill, JT, Bebrevska, L, Gusovsky, F, Maki, N, Yanagi, T, Flynn, PM, McCarthy, JS, Chalon, S, Guy, RK*. (2022). Combining the oral, Plasmodium falciparum ATP4 inhibitor SJ733 with the pharmacokinetic enhancer cobicistat: a novel approach in antimalarial drug development. eBioMedicine 80:104065. doi: 10.1016/j.ebiom.2022.104065.

Smith AP, Williams EP, Plunket TR, Selvaraj M, Lane LC, Zalduondo L, Xue Y, Vogel P, Channappanavar R, Jonsson CB*, Smith AM* (2022). Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infections During SARS-CoV-2. Frontiers Immunol 13:894534. doi: 10.3389/fimmu.2022.894534.


Cresta, D, Warren, DC, Quirouette, C, Smith, AP, Lane, LC, Smith, AM, Beauchemin, CAA* (2021). Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample’s infection concentration. PLoS Comput Biol 17(10): e1009480. doi: 10.1371/journal.pcbi.1009480

Pinky, L, Burke, CW, Russell, CJ, Smith, AM* (2021). Quantifying Dose-, Strain-, and Tissue-Specific Kinetics of Parainfluenza Virus Infection. PLoS Comput Biol 17(8): e1009299. doi: 10.1371/journal.pcbi.1009299

Jenner, AL, Aogo, RA, Alfonso, S, Crowe, V, Smith, AP, Morel, PA, Davis, CL, Smith, AM*, Craig, M*. (2021). COVID-19 virtual patient cohort reveals immune mechanisms driving disease outcomes. PLoS Pathog 17(7):e1009753. doi: 10.1371/journal.ppat.1009753

Myers, MA, Smith, AP, Lane, LC, Moquin, DJ, Woolard, S, Thomas, PG, Vogel, P, and Smith, AM* (2021). Dynamically Linking Influenza Virus Infection Kinetics, Lung Injury, Inflammation, and Disease Severity. eLife 10:e68864 doi: 10.7554/eLife.68864

Predictions validated within

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* (2021). Dynamic Pneumococcal Genetic Adaptations Support Bacterial Growth and Inflammation During Coinfection with Influenza. Infect Immun 89:e00023-21. doi: 10.1128/IAI.00023-21


Kumar, A, Kodidela, S, Tadrous, E, Cory, TJ, Walker, CMM, Smith, AM, Mukherjee, A and Kumar, S (2020). Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention. Viruses 12(8), 887. doi: 10.3390/v12080887

Penkert, RR, Smith, AP, Hrinicius, ER, McCullers, JA, Vogel, P, Smith, AM, and Hurwitz, JL (2020). Effect of Vitamin A Deficiency in Dysregulating Immune Responses to Influenza Virus and Increasing Mortality Rates After Bacterial Coinfections. J Infect Dis,jiaa597, doi: 10.1093/infdis/jiaa597

Jenner, AL, Aogo, RA, Davis, CL, Smith, AM, and Craig, M  (2020). Leveraging Computational Modeling to Understand Infectious Diseases. Curr Pathobiol Rep. doi: 10.1007/s40139-020-00213-x

Wang, Y, An, G, Becker, A, Cockrell, C, Collier, N, Craig, M, Davis, C, Faeder, J, Ford Versypt, AN, Gianlupi1, JF, Glazier, JA, Heiland, R, Hillen, T, Islam, MA, Jenner, A, Liu, B, Morel, PA, Narayanan, A, Ozik, J, Rangamani, P, Shoemaker, JE, Smith, AM, Macklin, P (2020). Rapid Community-Driven Development of a SARS-CoV-2 Tissue Simulator. Preprint

Ward, CE, Kimura D, Saini, A, Smith, AM, West, AN, Goedecke, PJ, Tolley, EA, Cormier, SA, DeVincenzo, JP. (2019) Longitudinal Viral Kinetics and Hypoxemic Respiratory Failure Severity in Respiratory Syncytial Virus-Infected Children. (submitted)

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 (2020). 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 20(8), 964-975 doi: 10.1016/S1473-3099(19)30611-5

Kwambana-Adams, B.A., Mulholland, E.K., Satzke, and ISPPD Group. State-of-the-art in the pneumococcal field: Proceedings of the 11th International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-11). Pneumonia 12, 2 (2020). doi: 10.1186/s41479-019-0064-y


Chung, M, Binois, M, Gramacy, RB, Moquin, DJ, Smith, AP and Smith, AM* (2019). Parameter and Uncertainty Estimation for Dynamical Systems Using Surrogate Stochastic Processes. SIAM J Sci Computing 41(4), A2212–A2238. doi: 10.1137/18M1213403

Rodriguez, A, McCullers, JA, Smith, AM, Kanneganti, T, Lupfer, CR* (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


Smith, AM* (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

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

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

Smith, AM*, Ribeiro, RM, and Perelson, AS* (2018). Population Dynamics of Host and Pathogens. Systems Immunology: An Introduction to Modeling Methods for Scientists.


Smith, AM* and Huber, VC*(2017). The Unexpected Impact of Vaccines on Secondary Bacterial Infections Following Influenza. Viral Immunology doi:10.1089/vim.2017.0138


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

Predictions validated within

Smith, AM* (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


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


Smith, AM*, Adler, FR, Ribeiro, RM, Gutenkunst, RN, McAuley, JL, McCullers, JA and Perelson, AS (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)

Smith, AM* and McCullers, JA (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


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

Smith, AM*, Adler, FR, McAuley, JL, Gutenkunst, RN, Ribeiro, RM, McCullers, JA and Perelson, AS* (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

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


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

Smith, AM*, Adler, FR and Perelson, AS (2010). An Accurate Two-Phase Approximate Solution to an Acute Viral Infection Model. J Math Biol, 60(5):711-726.


McAuley, JL, Hornung, F, Boyd, KL, Smith, AM, McKeon, R, Bennink, J, Yewdell, JW, and McCullers, JA* (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