Sean is generally interested in developing models of infectious disease and using them to project incidence and the impact of interventions. He is currently working on modelling the public health impact of substandard and falsified medicines.
He/him/his
Thailand
Aluvaala J, Tuti T, Ogola M, Lim C, Cavany S, English M, . (2025). Situational analysis of antibiotic prescriptions in Kenyan neonatal units for antimicrobial stewardship: a retrospective longitudinal study. EClinicalMedicine, (82)
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)
Moore S, Cavany S, Perkins TA, España GFC. (2024). Projecting the future impact of emerging SARS-CoV-2 variants under uncertainty: Modeling the initial Omicron outbreak. Epidemics, (47)
Cavany SM, España G, Lloyd AL, Vazquez-Prokopec GM, Astete H, Waller LA, Kitron U, Scott TW, Morrison AC, Reiner RC Jr., Perkins TA. (2023). Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns. PLoS computational biology, 19(4)
Shea K, Borchering RK, Probert WJM, Howerton E, Bogich TL, Li SL, van Panhuis WG, Viboud C, Aguás R, Belov AA, Bhargava SH, Cavany SM, Chang JC, Chen C, Chen J, Chen S, Chen Y, Childs LM, Chow CC, Crooker I, Del Valle SY, España G, Fairchild G, Gerkin RC, Germann TC, Gu Q, Guan X, Guo L, Hart GR, Hladish TJ, Hupert N, Janies D, Kerr CC, Klein DJ, Klein EY, Lin G, Manore C, Meyers LA, Mittler JE, Mu K, Núñez RC, Oidtman RJ, Pasco R, Pastore Y Piontti A, Paul R, Pearson CAB, Perdomo DR, Perkins TA, Pierce K, Pillai AN, Rael RC, Rosenfeld K, Ross CW, Spencer JA, Stoltzfus AB, Toh KB, Vattikuti S, Vespignani A, Wang L, White LJ, Xu P, Yang Y, Yogurtcu ON, Zhang W, Zhao Y, Zou D, Ferrari MJ, Pannell D, Tildesley MJ, Seifarth J, Johnson E, Biggerstaff M, Johansson MA, Slayton RB, Levander JD, Stazer J, Kerr J, Runge MC. (2023). Multiple models for outbreak decision support in the face of uncertainty. Proceedings of the National Academy of Sciences of the United States of America, 120(18)
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
Cavany S, Nanyonga S, Hauk C, Lim C, Tarning J, Sartorius B, Dolecek C, Caillet C, Newton PN, Cooper BS. (2023). The uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance. Nature communications, 14(1)
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
Cavany S, Huber JH, Wieler A, Tran QM, Alkuzweny M, Elliott M, España G, Moore SM, Perkins TA. (2023). Does ignoring transmission dynamics lead to underestimation of the impact of interventions against mosquito-borne disease?. BMJ global health, 8(8)
Cavany SM, Barbera C, Carpenter M, Rodgers C, Sherman T, Stenglein M, Mayo C, Perkins TA. (2022). Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges. Virus evolution, 8(2)
Borchering RK, Mullany LC, Howerton E, Chinazzi M, Smith CP, Qin M, Reich NG, Contamin L, Levander J, Kerr J, Espino J, Hochheiser H, Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Hulse JD, Kaminsky J, Lee EC, Hill AL, Davis JT, Mu K, Xiong X, Pastore Y Piontti A, Vespignani A, 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, Chen S, Paul R, Janies D, Thill JC, Galanti M, Yamana T, Pei S, Shaman J, España G, Cavany S, Moore S, Perkins A, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Shea K, Truelove SA, Runge MC, Viboud C, Lessler J. (2023). Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: A multi-model study. Lancet regional health. Americas, (17)
Perkins TA, Stephens M, Alvarez Barrios W, Cavany S, Rulli L, Pfrender ME. (2022). Performance of Three Tests for SARS-CoV-2 on a University Campus Estimated Jointly with Bayesian Latent Class Modeling. Microbiology spectrum
España G, Cucunubá ZM, Diaz H, Cavany S, Castañeda N, Rodriguez L. (2022). Designing school reopening in the COVID-19 pre-vaccination period in Bogotá, Colombia: A modeling study. PLOS global public health, 2(6)
Kopanke J, Carpenter M, Lee J, Reed K, Rodgers C, Burton M, Lovett K, Westrich JA, McNulty E, McDermott E, Barbera C, Cavany S, Rohr JR, Perkins TA, Mathiason CK, Stenglein M, Mayo C. (2022). Bluetongue Research at a Crossroads: Modern Genomics Tools Can Pave the Way to New Insights. Annual review of animal biosciences, (10)
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)
Cavany S, Bivins A, Wu Z, North D, Bibby K, Perkins TA. (2022). Inferring SARS-CoV-2 RNA shedding into wastewater relative to the time of infection. Epidemiology and infection, (150)
Cavany S, Bivins A, Wu Z, North D, Bibby K, Perkins TA. (2022). Inferring SARS-CoV-2 RNA shedding into wastewater relative to the time of infection - CORRIGENDUM. Epidemiology and infection, (150)
Poterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Alex Perkins T, Cavany SM. (2022). Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence. Royal Society open science, 9(10)
España G, Cavany S, Oidtman R, Barbera C, Costello A, Lerch A, Poterek M, Tran Q, Wieler A, Moore S, Perkins TA. (2021). Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA. Epidemics, (37)
Cavany SM, España G, Vazquez-Prokopec GM, Scott TW, Perkins TA. (2021). Pandemic-associated mobility restrictions could cause increases in dengue virus transmission. PLoS neglected tropical diseases, 15(8)
Perkins TA, Cavany SM, Moore SM, Oidtman RJ, Lerch A, Poterek M. (2020). Estimating unobserved SARS-CoV-2 infections in the United States. Proceedings of the National Academy of Sciences of the United States of America
Cavany SM, España G, Lloyd AL, Waller LA, Kitron U, Astete H, Elson WH, Vazquez-Prokopec GM, Scott TW, Morrison AC, Reiner RC Jr., Perkins TA. (2020). Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response. PLoS computational biology, 16(4)
Shea K, Borchering RK, Probert WJM, Howerton E, Bogich TL, Li S, van Panhuis WG, Viboud C, Aguás R, Belov A, Bhargava SH, Cavany S, Chang JC, Chen C, Chen J, Chen S, Chen Y, Childs LM, Chow CC, Crooker I, Valle SYD, España G, Fairchild G, Gerkin RC, Germann TC, Gu Q, Guan X, Guo L, Hart GR, Hladish TJ, Hupert N, Janies D, Kerr CC, Klein DJ, Klein E, Lin G, Manore C, Meyers LA, Mittler J, Mu K, Núñez RC, Oidtman R, Pasco R, Piontti APY, Paul R, Pearson CAB, Perdomo DR, Perkins TA, Pierce K, Pillai AN, Rael RC, Rosenfeld K, Ross CW, Spencer JA, Stoltzfus AB, Toh KB, Vattikuti S, Vespignani A, Wang L, White L, Xu P, Yang Y, Yogurtcu ON, Zhang W, Zhao Y, Zou D, Ferrari M, Pannell D, Tildesley M, Seifarth J, Johnson E, Biggerstaff M, Johansson M, Slayton RB, Levander J, Stazer J, Salerno J, Runge MC. (2020). COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support. medRxiv : the preprint server for health sciences
Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. (2018). Arbovirus Coinfection and Co-Transmission: A Neglected Public Health Concern?. PLoS biology, 17(1)
Cavany SM, Vynnycky E, Anderson CS, Maguire H, Sandmann F, Thomas HL, White RG, Sumner T. (2019). Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London. Thorax, 74(2)
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