Papers

Pre-2025.9

Nguyen-Tran, H.^§, Park, S.W.^§, Vogt, M.R.^§, Permaul, P.^§, Spaulding, A.B., Hernandez, M.L., Bohl, J.A., Godbole, S., Ruckwardt, T.J., Krug, P.W., Moss, D.L., Derrien-Colemyn, A., Chowdhury, A., Dziubla, G., Wang, L., Castro, M., Narpala, S.R., Longtine, E.R., Henry, A.R., Ngo, T.-T.B., Dzantiev, L., Sigal, G.B., Metcalf, C.J.E., Kimberlin, D.W., Dominguez, S.R., Mittelman, A., McDermott, A.B., Serebryannyy, L.A., Grenfell, B., Messacar, K., and Douek, D.C., 2025. Dynamics of endemic virus re-emergence in children in the USA following the COVID-19 pandemic (2022–23): a prospective, multicentre, longitudinal, immunoepidemiological surveillance study. Lancet Infectious Diseases.
^§Contributed equally.

Howerton, E., Williams, T.C., Casalegno, J.-S., Dominguez, S., Gunson, R., Messacar, K., Metcalf, C.J.E., Park, S.W., Viboud, C., and Grenfell, B.T., 2025. Using COVID-19 pandemic perturbation to model RSV-hMPV interactions and potential implications under RSV interventions. Nature Communications 16(1), 7261

Park, S.W., Noble, B., Howerton, E., Nielsen, B.F., Lentz, S., Ambroggio, L., Dominguez, S., Messacar, K., and Grenfell, B.T., 2024. Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States. Epidemics 49, 100808.

Charniga, K., Park, S.W., Akhmetzhanov, A.R., Cori, A., Dushoff, J., Funk, S., Gostic, K.M., Linton, N.M., Lison, A., Overton, C.E., Pulliam, J.R.C., Ward, T., Cauchemez, S., and Abbott, S., 2024. Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data. PLoS Computational Biology, 20 (10) e1012520.

Park, S.W., Lawal, T., Marin, M., Marlow, M.A., Grenfell, B.T., Masters, N.B., 2024. Modeling the population-level impact of a third dose of MMR vaccine on a mumps outbreak at the University of Iowa. PNAS, 121 (43) e2403808121.

Park, S.W., Cobey, S., Metcalf, C.J.E., Levine, J.M., and Grenfell, B.T., 2024. Predicting pathogen mutual invasibility and co-circulation. Science, 386(6718), 175-179.

Yang, Q., Park, S.W., Saad-Roy, C.M., Ahmad, I., Viboud, C., Arinaminpathy, N., and Grenfell, B.T., 2024. Assessing population-level target product profiles of universal human influenza A vaccines. Epidemics, 48, 100776.

Earn, D.J., Park, S.W., amd Bolker, B.M., 2024. Fitting Epidemic Models to Data: A Tutorial in Memory of Fred Brauer. Bulletin of Mathematical Biology, 86(9), 1-32.

Holmdahl, I., Bents, S.J., Baker, R.E., Casalegno, J.S., Trovão, N.S., Park, S.W., Metcalf, C.J.E., and Grenfell, B.T., 2024. Differential impact of COVID-19 non-pharmaceutical interventions on the epidemiological dynamics of respiratory syncytial virus subtypes A and B. Scientific Reports, 14(1), 14527.

Park, S.W., Messacar, K., Douek, D.C., Spaulding, A.B., Metcalf, C.J.E., and Grenfell, B. T., 2024. Predicting the impact of COVID-19 non-pharmaceutical intervention on short-and medium-term dynamics of enterovirus D68 in the US. Epidemics, 46, 100736.

Yang, Q., Wang, B., Lemey, P., Dong, L., Mu, T., Wiebe, R. A., Guo, F., Sequeira Trovao, N., Park, S.W., Lweis, N., Tsui, J.L.-H., Bajaj, S., Cheng, Y., Yang, L., Haba, Y., Li, B., Zhang, G., Pybus, O.G., Tian, H., and Grenfell, B.T., 2024. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nature Communications, 15(1), 1126.

Park, S.W., Daskalaki, I., Izzo, R., Aranovich, I., te Velthuis, A., Notterman, D., Metcalf, C.J.E., and Grenfell, B.T., 2023. Relative role of community transmission and campus contagion in driving the spread of SARS-CoV-2: lessons from Princeton University. PNAS Nexus, 2(7): pgad201.

Park, S.W., Sun, K., Abbott, S., Sender, R., Bar-On, Y.M., Weitz, J.S., Funk, S., Grenfell, B.T., Backer, J.A., Wallinga, J., Viboud, C., and Dushoff, J., 2023. Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2. PNAS, 120(22), e2221887120.

Park, S.W., Dushoff, J., Grenfell, B.T., and Weitz, J.S., 2023. Intermediate levels of asymptomatic transmission can lead to the highest levels of epidemic fatalities. PNAS Nexus, 2(4): pgad106.

Harris, J.D.^§, Park, S.W.^§, Dushoff, J., and Weitz, J.S., 2022. How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics. Epidemics, 100664.
^§Contributed equally.

Lee, W.E., Park, S.W., Weinberger, D.M., Olson, D., Simonsen, L., Grenfell, B.T., and Viboud, C., 2023. Direct and indirect mortality impacts of the COVID-19 pandemic in the United States, March 1, 2020 to January 1, 2022. eLife, 12:e77562.

Baker, R.E., Saad Roy, C.M., Park, S.W., Farrar, J., Metcalf, C.J.E., and Grenfell, B.T., 2022. Long-term benefits of nonpharmaceutical interventions for endemic infections are shaped by respiratory pathogen dynamics. PNAS, 119(49), e2208895119.

Messacar, K., Baker, R.E., Park, S.W., Nguyen-Tran, H., Cataldi, J.R., and Grenfell, B.T., 2022. Preparing for uncertainty: endemic paediatric viral illnesses after COVID-19 pandemic disruption. The Lancet, 400(10364): 1663-1665.

Lizewski, R.A.^§, Sealfon, R.S.G.^§, Park, S.W.^§, Smith, G.R.^§, Porter, C.K.^§, Gonzalez-Reiche, A.S.^§, Ge, Y.^§, Miller, C.M.^§, Goforth, C.W., Pincas, H., Termini, M.S., Ramos, I., Nair, V.D., Lizewski, S.E., Alshammary, H., Cer, R.Z., Chen, H.W., George, M.-C., Arnold, C.E., Glang, L.A., Long, K.A., Malagon, F., Marayag, J.J., Nunez, E., Rice, G.K., Santa Ana, E., Schilling, M.A., Smith, D.R., Sugiharto, V.A., Sun, P., van de Guchte, A., Khan, Z., Dutta, J., Vangeti, S., Voegtly, L.J., Weir, D.L., Metcalf, C.J.E., Troyanskaya, O.G., Bishop-Lilly, K.A., Grenfell, B.T., van Bakel, H., Letizia, A.G.^§, and Sealfon, S.C.^§, 2022. SARS-CoV-2 outbreak dynamics in an isolated US military recruit training center with rigorous prevention measures. Epidemiology, 33(6): 797-807.
^§Contributed equally.

Sender, R., Bar-On, Y., Park, S.W., Noor, E., Dushoff, J., and Milo, R., 2022. The unmitigated profile of COVID-19 infectiousness. eLife, 11:e79134.

Park, S.W., Bolker, B.M., Funk, S., Metcalf, C.J.E., Weitz, J.S., Grenfell, B.T., and Dushoff, J., 2022. The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants. Journal of The Royal Society Interface, 19: 20220173-20220173

Nguyen-Tran, H., Park, S.W., Messacar, K., Dominguez, S.R., Vogt, M.R., Permar, S., Permaul, P., Hernandez, M., Douek, D.C., McDermott, A.B., Metcalf, C.J.E., Grenfell, B.T., and Spaulding, A.B., 2022. Enterovirus D68: a test case for the use of immunological surveillance to develop tools to mitigate the pandemic potential of emerging pathogens. The Lancet Microbe, 3(2): e83-e85.

Baker, R.E., Park, S.W., Wagner, C.E., and Metcalf, C.J.E., 2021. The limits of SARS-CoV-2 predictability. Nature Ecology & Evolution, 5(8): 1052-1054.

Dushoff, J., and Park, S.W., 2021. Speed and strength of an epidemic intervention. Proceedings of the Royal Society B: Biological Sciences, 288(1947): 20201556.

Park, S.W., Pons-Salort, M., Messacar, K., Cook, C., Meyers, L., Farrar, J., Grenfell, B.T., 2021. Epidemiological dynamics of enterovirus D68 in the United States and implications for acute flaccid myelitis. Science Translational Medicine, 13(584): eabd2400.

Park, S.W., Sun, K., Champredon, D., Li, M., Bolker, B.M., Earn, D.J.D., Weitz, J.S., Grenfell, B.T. and Dushoff, J., 2020. Forward-looking serial intervals correctly link epidemic growth to reproduction numbers. PNAS, 118(2): e2011548118.

Weitz, J.S., Park, S.W., Eksin, C. and Dushoff, J., 2020. Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations. PNAS, 117(51): 32764-32771.

Baker, R.E., Park, S.W., Yang, W., Vecchi, G.A., Metcalf, C.J.E. and Grenfell, B.T., 2020. The impact of COVID-19 nonpharmaceutical interventions on the future dynamics of endemic infections. PNAS, 117(48): 30547-30553.

Park, S.W., Sun, K., Viboud, C., Grenfell, B.T., and Dushoff, J., 2020. Potential Role of Social Distancing in Mitigating Spread of Coronavirus Disease, South Korea. Emerging Infectious Diseases, 26(11): 2697–2700.

Metcalf, C.J.E., Morris, D.H., and Park, S.W., 2020. Mathematical models to guide pandemic response. Science, 369(6502): 368-369.

Park, S.W., Bolker, B.M., Champredon, D., Earn, D.J.D., Li, M., Weitz, J.S., Grenfell, B.T. and Dushoff, J., 2020. Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak. Journal of the Royal Society Interface, 17: 20200144.

Park, S.W., Champredon, D., and Dushoff, J., 2020. Inferring generation-interval distributions from contact-tracing data. Journal of the Royal Society Interface, 17(167): 20190719.

Weitz, J.S., Beckett, S.J., Coenen, A.R., Demory, D., Dominguez-Mirazo, M., Dushoff, J., Leung, C.-Y., Li, G., Măgălie, A., Park, S.W., Rodriguez-Gonzalez, R., Shivam, S., and Zhao, C.Y., 2020. Modeling shield immunity to reduce COVID-19 epidemic spread. Nature medicine, 26(6): 849-854.

Park, S.W., Cornforth, D.M., Dushoff J., and Weitz J.S., 2020. The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak. Epidemics, 31: 100392.

Park, S.W., and Bolker, B.M., 2020. A note on observation processes in epidemic models. Bulletin of Mathematical Biology, 82(3): 1-8.

Park, S.W., Champredon, D., Weitz, J.S., and Dushoff, J., 2019. A practical generation-interval-based approach to inferring the strength of epidemics from their speed. Epidemics, 27: 12-18.

Park, S.W., Dushoff, J., Earn, D.J.D., Poinar, H., and Bolker, B.M., 2018. Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models. PNAS, 115(34): E7892-E7893.

Park, S.W., and Bolker, B.M., 2017. Effects of contact structure on the transient evolution of HIV virulence. PLoS Computational Biology, 13(3): e1005453.

Rekart, M.L., Ndifon, W., Brunham, R.C., Dushoff, J., Park, S.W., Rawart, S., and Cameron, C.E., 2017. A double-edged sword: does highly active antiretroviral therapy contribute to syphilis incidence by impairing immunity to Treponema pallidum?. Sexually Transmitted Infections, 93(5): 374-378.