Publications

2020

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. (submitted)

Penkert, RR, Smith, AP, Hrinicius, ER, McCullers, JA, Vogel, P, Smith, AM, and Hurwitz, JL (2020). Vitamin A deficiency dysregulates immune responses toward influenza virus and increases mortality after bacterial coinfections. (submitted)

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)

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

Myers, MA, Smith, AP, Lane, LC, Moquin, DJ, Vogel, P, Woolard, S, and Smith, AM* (2019). Dynamically Linking Influenza Virus Infection with Lung Injury to Predict 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 (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 (in press)

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

2019

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

2018

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.

2017

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

2016

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

Prediction 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

2014

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

2013

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

2011

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

2010

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.

2007

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