The Fox lab carries out research related to understanding and forecasting infectious disease dynamics with the goal of improving public health outcomes and policies. We specialize in integrating population-level infectious disease data with epidemiological models through statistical and artificial intelligence approaches, and we primarily work on respiratory viruses like influenza and COVID-19 and arboviruses like malaria and Zika (though we dabble in other emerging infectious diseases as needed).
He/him/his
United States
Suez E, Fox SJ. (2026). Basic Baseline model design choices can substantially influence performance in collaborative forecast hubs. medRxiv : the preprint server for health sciences
Kim D, Pasco R, Johnson K, Fox SJ, Reich NG, Meyers LA. (2026). Local Influenza Forecasts Outperform State-Level Forecasts in the United States. medRxiv : the preprint server for health sciences
Winter AK, Fox SJ. (2025). Measles is resurging in the Americas and the world is watching. Nature reviews. Microbiology
Gibson GC, Fox SJ, Javan E, Ptak SE, Ibrahim OM, Lachmann M, Meyers LA. (2025). Improving outbreak forecasts through model augmentation. Proceedings of the National Academy of Sciences of the United States of America, 122(43)
Qian Y, Marty É, Basu A, O'Dea EB, Wang X, Fox S, Rohani P, Drake JM, Li H. (2025). Physics-informed deep learning for infectious disease forecasting. ArXiv
Bi K, Bandekar SR, Bouchnita A, Cramer A, Fox SJ, Borchering RK, Biggerstaff M, Meyers LA. (2025). Estimated impact of 2022-2023 influenza vaccines on annual hospital burden in the United States. Proceedings of the National Academy of Sciences of the United States of America, 122(46)
Lyu L, Veytsel G, Stott G, Fox S, Dailey C, Damodaran L, Fujimoto K, Brown P, Sealy R, Brown A, Alabady M, Bahl J. (2025). Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count statistic. Communications medicine, 5(1)
Loo SL, Jung SM, Contamin L, Howerton E, Bents SJ, Hochheiser H, Runge MC, Smith CP, Carcelén EC, Yan K, Lemaitre JC, Przykucki E, McKee CD, Sato K, Hill AL, Chinazzi M, Davis JT, Bay C, Vespignani A, Chen S, Paul R, Janies D, Thill JC, Moore SM, Perkins TA, Srivastava A, Al Aawar M, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Lewis B, Chen J, Marathe M, Ben-Nun M, Turtle J, Riley P, Shea K, Viboud C, Lessler J, Truelove S. (2025). Scenario Projections of COVID-19 Burden in the US, 2024-2025. JAMA network open, 8(9)
Qian Y, Zhang K, Marty E, Basu A, O'Dea EB, Wang X, Fox SJ, Rohani P, Drake JM, Li H. (2025). Physics-informed deep learning for infectious disease forecasting. Journal of the Royal Society, Interface, 22(232)
Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, Rosenfeld R, Shemetov D, Tibshirani RJ, McDonald DJ, Kandula S, Pei S, Yaari R, Yamana TK, Shaman J, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Zhao Z, Rodríguez A, Meiyappan A, Omar S, Baccam P, Gurung HL, Suchoski BT, Stage SA, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Loo SL, McKee CD, Sato K, Smith C, Truelove S, Jung SM, Lemaitre JC, Lessler J, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Gibson GC, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Pastore Y Piontti A, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Suez E, Cojocaru MG, Thommes EW, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Aawar MA, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Ramakrishnan N, Muralidhar N, Reed C, Biggerstaff M, Borchering RK. (2024). Title evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. Nature communications, 15(1)
Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins TA, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Aawar MA, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. (2024). Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub. PLoS medicine, 21(4)
Pasco R, Fox SJ, Lachmann M, Meyers LA. (2024). Effectiveness of interventions to reduce COVID-19 transmission in schools. Epidemics, (47)
Bouchnita A, Bi K, Fox SJ, Meyers LA. (2024). Projecting Omicron scenarios in the US while tracking population-level immunity. Epidemics, (46)
Fox SJ, Javan E, Pasco R, Gibson GC, Betke B, Herrera-Diestra JL, Woody S, Pierce K, Johnson KE, Johnson-León M, Lachmann M, Meyers LA. (2023). Disproportionate impacts of COVID-19 in a large US city. PLoS computational biology, 19(6)
Johnson KE, Pasco R, Woody S, Lachmann M, Johnson-León M, Bhavnani D, Klima J, Paltiel AD, Fox SJ, Meyers LA. (2023). Optimizing COVID-19 testing strategies on college campuses: Evaluation of the health and economic costs. PLoS computational biology, 19(12)
Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee CD, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Pastore Y Piontti A, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Ben Toh K, Longini I Jr., Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox SJ, Meyers LA, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. (2023). Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty. Nature communications, 14(1)
Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins A, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Al Aawar M, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. (2023). Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub. medRxiv : the preprint server for health sciences
Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, McDonald DJ, Rosenfeld R, Shemetov D, Tibshirani RJ, Kandula S, Pei S, Shaman J, Yaari R, Yamana TK, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Rodríguez A, Zhao Z, Meiyappan A, Omar S, Baccam P, Gurung HL, Stage SA, Suchoski BT, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Jung SM, Lemaitre JC, Lessler J, Loo SL, McKee CD, Sato K, Smith C, Truelove S, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Piontti APY, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Gibson GC, Suez E, Thommes EW, Cojocaru MG, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Al Aawar M, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Muralidhar N, Ramakrishnan N, Reed C, Biggerstaff M, Borchering RK. (2023). Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. medRxiv : the preprint server for health sciences
Gibson GC, Woody S, James E, Weldon M, Fox SJ, Meyers LA, Bhavnani D. (2023). Real time monitoring of COVID-19 intervention effectiveness through contact tracing data. Scientific reports, 13(1)
Javan EM, Fox SJ, Meyers LA. (2023). Estimating the undetected emergence of COVID-19 in the US. PloS one, 18(4)
Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee C, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Piontti APY, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, Espana G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Toh KB, Longini I Jr., Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox S, Meyers LA, , Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. (2023). Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub. medRxiv : the preprint server for health sciences
Du Z, Shao Z, Bai Y, Wang L, Herrera-Diestra JL, Fox SJ, Ertem Z, Lau EHY, Cowling BJ. (2022). Reproduction number of monkeypox in the early stage of the 2022 multi-country outbreak. Journal of travel medicine
Bi K, Herrera-Diestra JL, Bai Y, Du Z, Wang L, Gibson G, Johnson-Leon M, Fox SJ, Meyers LA. (2023). The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs). Epidemics, (42)
Wang X, Du Z, James E, Fox SJ, Lachmann M, Meyers LA, Bhavnani D. (2022). The effectiveness of COVID-19 testing and contact tracing in a US city. Proceedings of the National Academy of Sciences of the United States of America, 119(34)
Cramer EY, Ray EL, Lopez VK, Bracher J, Brennen A, Castro Rivadeneira AJ, Gerding A, Gneiting T, House KH, Huang Y, Jayawardena D, Kanji AH, Khandelwal A, Le K, Mühlemann A, Niemi J, Shah A, Stark A, Wang Y, Wattanachit N, Zorn MW, Gu Y, Jain S, Bannur N, Deva A, Kulkarni M, Merugu S, Raval A, Shingi S, Tiwari A, White J, Abernethy NF, Woody S, Dahan M, Fox S, Gaither K, Lachmann M, Meyers LA, Scott JG, Tec M, Srivastava A, George GE, Cegan JC, Dettwiller ID, England WP, Farthing MW, Hunter RH, Lafferty B, Linkov I, Mayo ML, Parno MD, Rowland MA, Trump BD, Zhang-James Y, Chen S, Faraone SV, Hess J, Morley CP, Salekin A, Wang D, Corsetti SM, Baer TM, Eisenberg MC, Falb K, Huang Y, Martin ET, McCauley E, Myers RL, Schwarz T, Sheldon D, Gibson GC, Yu R, Gao L, Ma Y, Wu D, Yan X, Jin X, Wang YX, Chen Y, Guo L, Zhao Y, Gu Q, Chen J, Wang L, Xu P, Zhang W, Zou D, Biegel H, Lega J, McConnell S, Nagraj VP, Guertin SL, Hulme-Lowe C, Turner SD, Shi Y, Ban X, Walraven R, Hong QJ, Kong S, van de Walle A, Turtle JA, Ben-Nun M, Riley S, Riley P, Koyluoglu U, DesRoches D, Forli P, Hamory B, Kyriakides C, Leis H, Milliken J, Moloney M, Morgan J, Nirgudkar N, Ozcan G, Piwonka N, Ravi M, Schrader C, Shakhnovich E, Siegel D, Spatz R, Stiefeling C, Wilkinson B, Wong A, Cavany S, España G, Moore S, Oidtman R, Perkins A, Kraus D, Kraus A, Gao Z, Bian J, Cao W, Lavista Ferres J, Li C, Liu TY, Xie X, Zhang S, Zheng S, Vespignani A, Chinazzi M, Davis JT, Mu K, Pastore Y Piontti A, Xiong X, Zheng A, Baek J, Farias V, Georgescu A, Levi R, Sinha D, Wilde J, Perakis G, Bennouna MA, Nze-Ndong D, Singhvi D, Spantidakis I, Thayaparan L, Tsiourvas A, Sarker A, Jadbabaie A, Shah D, Della Penna N, Celi LA, Sundar S, Wolfinger R, Osthus D, Castro L, Fairchild G, Michaud I, Karlen D, Kinsey M, Mullany LC, Rainwater-Lovett K, Shin L, Tallaksen K, Wilson S, Lee EC, Dent J, Grantz KH, Hill AL, Kaminsky J, Kaminsky K, Keegan LT, Lauer SA, Lemaitre JC, Lessler J, Meredith HR, Perez-Saez J, Shah S, Smith CP, Truelove SA, Wills J, Marshall M, Gardner L, Nixon K, Burant JC, Wang L, Gao L, Gu Z, Kim M, Li X, Wang G, Wang Y, Yu S, Reiner RC, Barber R, Gakidou E, Hay SI, Lim S, Murray C, Pigott D, Gurung HL, Baccam P, Stage SA, Suchoski BT, Prakash BA, Adhikari B, Cui J, Rodríguez A, Tabassum A, Xie J, Keskinocak P, Asplund J, Baxter A, Oruc BE, Serban N, Arik SO, Dusenberry M, Epshteyn A, Kanal E, Le LT, Li CL, Pfister T, Sava D, Sinha R, Tsai T, Yoder N, Yoon J, Zhang L, Abbott S, Bosse NI, Funk S, Hellewell J, Meakin SR, Sherratt K, Zhou M, Kalantari R, Yamana TK, Pei S, Shaman J, Li ML, Bertsimas D, Skali Lami O, Soni S, Tazi Bouardi H, Ayer T, Adee M, Chhatwal J, Dalgic OO, Ladd MA, Linas BP, Mueller P, Xiao J, Wang Y, Wang Q, Xie S, Zeng D, Green A, Bien J, Brooks L, Hu AJ, Jahja M, McDonald D, Narasimhan B, Politsch C, Rajanala S, Rumack A, Simon N, Tibshirani RJ, Tibshirani R, Ventura V, Wasserman L, O'Dea EB, Drake JM, Pagano R, Tran QT, Ho LST, Huynh H, Walker JW, Slayton RB, Johansson MA, Biggerstaff M, Reich NG. (2022). Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States. Proceedings of the National Academy of Sciences of the United States of America, 119(15)
Du Z, Fox SJ, Ingle T, Pignone MP, Meyers LA. (2022). Projecting the Combined Health Care Burden of Seasonal Influenza and COVID-19 in the 2020-2021 Season. MDM policy & practice, 7(1)
Audirac M, Tec M, Meyers LA, Fox S, Zigler C. (2022). How Timing of Stay-at-Home Orders and Mobility Reductions Impacted First-Wave COVID-19 Deaths in US Counties. American journal of epidemiology
Fox SJ, Lachmann M, Tec M, Pasco R, Woody S, Du Z, Wang X, Ingle TA, Javan E, Dahan M, Gaither K, Escott ME, Adler SI, Johnston SC, Scott JG, Meyers LA. (2022). Real-time pandemic surveillance using hospital admissions and mobility data. Proceedings of the National Academy of Sciences of the United States of America, 119(7)
Kelly Pierce, Ethan N. Ho, Xutong Wang, Remy Pasco, Zhanwei Du, Spencer Fox, Greg Zynda, Jawon Song, Gordon Wells, Lauren Meyers. (2021). Early COVID-19 Pandemic Modeling: Three Compartmental Model Case Studies From Texas, USA. Computing in Science & Engineering, 23(1)
Johnson KE, Lachmann M, Stoddard M, Pasco R, Fox SJ, Meyers LA, Chakravarty A. (2021). Detecting in-school transmission of SARS-CoV-2 from case ratios and documented clusters. medRxiv : the preprint server for health sciences
Yang H, Sürer Ö, Duque D, Morton DP, Singh B, Fox SJ, Pasco R, Pierce K, Rathouz P, Valencia V, Du Z, Pignone M, Escott ME, Adler SI, Johnston SC, Meyers LA. (2021). Design of COVID-19 staged alert systems to ensure healthcare capacity with minimal closures. Nature communications, 12(1)
Ingle TA, Morrison M, Wang X, Mercer T, Karman V, Fox S, Meyers LA. (2021). Projecting COVID-19 isolation bed requirements for people experiencing homelessness. PloS one, 16(5)
Pasco RF, Fox SJ, Johnston SC, Pignone M, Meyers LA. (2020). Estimated Association of Construction Work With Risks of COVID-19 Infection and Hospitalization in Texas. JAMA network open, 3(10)
Du Z, Xu X, Wang L, Fox SJ, Cowling BJ, Galvani AP, Meyers LA. (2020). Proactive social distancing mitigates COVID-19 outbreaks within a month across 58 mainland China cities. medRxiv : the preprint server for health sciences
Wang X, Du Z, Huang G, Pasco RF, Fox SJ, Galvani AP, Pignone M, Johnston SC, Meyers LA. (2020). Effects of Cocooning on Coronavirus Disease Rates after Relaxing Social Distancing. Emerging infectious diseases, 26(12)
Du Z, Xu X, Wang L, Fox SJ, Cowling BJ, Galvani AP, Meyers LA. (2020). Effects of Proactive Social Distancing on COVID-19 Outbreaks in 58 Cities, China. Emerging infectious diseases, 26(9)
Scarpino SV, Iamarino A, Wells C, Yamin D, Ndeffo-Mbah M, Wenzel NS, Fox SJ, Nyenswah T, Altice FL, Galvani AP, Meyers LA, Townsend JP. (2015). Epidemiological and viral genomic sequence analysis of the 2014 ebola outbreak reveals clustered transmission. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 60(7)
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