Bruce N, Weaver JJA, Jeynes-Smith C, Beigmohammadi F, Hegarty-Cremer S, Smith AP, Craig M, Smith AM*. Multivariate host-pathogen interactions driving heterogeneous viral shedding and CD8+ T cell control of influenza virus infection. (submitted) Preprint: 10.1101/2025.10.24.25338576

Beigmohammadi F, Weaver JJA, Hegarty-Cremer S, Jeynes-Smith C, Smith AM, Craig M*. (2025) Trajectory-matching ABC-MCMC for simulating heterogeneous dynamics in mechanistic models. (submitted) Preprint: 10.1101/2025.09.26.678800

Schughart K*, Threlkeld SC, Sellers S, Fischer WA, Schreiber J, Lücke E, Heise M, Smith AM. (2025) Analysis of blood proteome in influenza-infected patients reveals new insights into the host response and novel signatures distinguishing mild and severe infections. Frontiers in Immunology (in press)

Nichols J, Smith AM, Jonsson CB. (2025) The intersection of SARS-CoV-2 and diabetes. Microorganisms 13(6), 1390

Chen J, Yu Y, O’Brien SF, Charlton CL, Drews SJ, Heffernan JM, Smith AM, Nakagama Y, Kido Y, Buckeridge DL, Russell WA. (2025) The impact of statistical adjustment for assay performance on inferences from SARS-CoV-2 serological surveillance studies. Am J Epidemiology Jul 22:kwaf157. doi: 10.1093/aje/kwaf157.

Gazeau S, Deng X, Brunet-Ratnasignham E, Kaufmann DE, Larochelle C, Morel PA, Heffernan JM, Davis CL, Smith AM, Jenner AL, Craig M*. (2025) Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients. PLOS Computational Biology 21(6): e1013170. doi: 10.1371/journal.pcbi.1013170

Ramirez-Zuniga I, MacLeod WB, Chikoti C, Kwenda G, Lapidot R, Gill CJ*, Smith AM*. (2025) Sequential RSV and bacterial infections in the nasopharynx of Zambian infants and mothers. The Pediatric Infectious Disease Journal doi: 10.1097/INF.0000000000004779

Smith AM* . Decoding immune kinetics: unveiling secrets using custom-built mathematical models. Nature Methods (2024). doi: 10.1038/s41592-024-02265-y.

Schughart K*, Smith AM , Tsalik EL, Threlkeld SC, Sellers S, Fischer WA, Schreiber J, Lücke E, Cornberg M, Debarry J, Woods CW, Mcclain MT, Heise M (2024). Host response to influenza infections in human blood: Association of influenza severity with host genetics and transcriptomic response . Frontiers in Immunology 15:1385362. doi: 10.3389/fimmu.2024.1385362.

Weaver JJA, Smith AM* (2024). Quantitatively mapping immune control during influenza. Current Opinion in Systems Biology 38: 100516. doi: 10.1016/j.coisb.2024.100516

Laubenbacher R*, [14 co-authors], Smith AM, Voigt I, Yankeelov TE, Ziemssen T (2024). Toward mechanistic digital twins: Some use cases in immunology. Frontiers in Digital Health 6:1349595. doi: 10.3389/fdgth.2024.1349595

Malik-Sheriff RS*, Asari H, Hermjakob H, Huber W, Quail T, Santos SDM, Smith AM, Uhlmann V (2024). BioModels Model of the Year 2023. Frontiers in Systems Biology doi: 10.3389/fsysb.2024.1363884

Laubenbacher R*, [14 co-authors], Smith AM, Voigt I, Yankeelov TE, Ziemssen T. (2023). Forum on immune digital twins: a meeting report. npj Systems Biology and Applications 10(19) doi: 10.1038/s41540-024-00345-5

Pinky L, DeAguero JR, Remien CH, Smith AM*. (2023). How interactions during viral-viral coinfection can shape infection kinetics. Viruses 15(6):1303. doi: 10.3390/v15061303

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. doi: 10.3390/v15030611

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

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, 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, 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, Gianlupi 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 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 BA, Mulholland EK, Satzke C, 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, 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, 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, Perelson AS* (2018). Population Dynamics of Host and Pathogens. Systems Immunology: An Introduction to Modeling Methods for Scientists.

Smith AM*, Huber VC*(2017). The unexpected impact of vaccines on secondary bacterial infections following influenza. Viral Immunology doi:10.1089/vim.2017.0138

Smith AM*, Smith AP (2016). A critical, nonlinear threshold dictates bacterial invasion and initial kinetics during influenza. Sci Rep, 6, 38703, doi:10.1038/srep38703

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*, 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, Perelson AS (2013). Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae. PLoS Pathog 9(3): e1003238. doi:10.1371/journal.ppat.1003238.

Smith AM*, 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, 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, Perelson AS* (2011). Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics. PLoS Comput Biol 7(2): e1001081. doi:10.1371/journal.pcbi.1001081

Smith AM, Perelson AS* (2011). Influenza A virus infection kinetics: Quantitative data and models. WIREs Syst Biol Med, doi: 10.1002/wsbm.129

Smith AM, Ribeiro RM* (2010). Modeling the viral dynamics of influenza A virus infection. Crit Rev Immunol, 30(3):291-298.

Smith AM*, Adler FR, 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, 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.