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Alex Perkins

Associate Professor

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Papers

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

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)

España G, Perkins TA, Pollett SD, Smith ME, Moore SM, Kwon PO, Hall TL, Beagle MH Jr., Murray CK, Hakre S, Peel SA, Modjarrad K, Scott PT. (2022). Prioritizing interventions for preventing COVID-19 outbreaks in military basic training. PLoS computational biology, 18(10)

Gaythorpe KAM, Abbas K, Huber J, Karachaliou A, Thakkar N, Woodruff K, Li X, Echeverria-Londono S, , Ferrari M, Jackson M, McCarthy K, Perkins AT, Trotter C, Jit M. (2021). Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries. eLife, (10)

Schaber KL, Morrison AC, Elson WH, Astete-Vega H, Córdova-López JJ, Ríos López EJ, Flores WLQ, Santillan ASV, Scott TW, Waller LA, Kitron U, Barker CM, Perkins TA, Rothman AL, Vazquez-Prokopec GM, Elder JP, Paz-Soldan VA. (2021). The impact of dengue illness on social distancing and caregiving behavior. PLoS neglected tropical diseases, 15(7)

Schaber KL, Perkins TA, Lloyd AL, Waller LA, Kitron U, Paz-Soldan VA, Elder JP, Rothman AL, Civitello DJ, Elson WH, Morrison AC, Scott TW, Vazquez-Prokopec GM. (2021). Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics. PLoS computational biology, 17(1)

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)

Perkins TA, Huber JH, Tran QM, Oidtman RJ, Walters MK, Siraj AS, Moore SM. (2021). Burden is in the eye of the beholder: Sensitivity of yellow fever disease burden estimates to modeling assumptions. Science advances, 7(42)

Toor J, Echeverria-Londono S, Li X, Abbas K, Carter ED, Clapham HE, Clark A, de Villiers MJ, Eilertson K, Ferrari M, Gamkrelidze I, Hallett TB, Hinsley WR, Hogan D, Huber JH, Jackson ML, Jean K, Jit M, Karachaliou A, Klepac P, Kraay A, Lessler J, Li X, Lopman BA, Mengistu T, Metcalf CJE, Moore SM, Nayagam S, Papadopoulos T, Perkins TA, Portnoy A, Razavi H, Razavi-Shearer D, Resch S, Sanderson C, Sweet S, Tam Y, Tanvir H, Tran Minh Q, Trotter CL, Truelove SA, Vynnycky E, Walker N, Winter A, Woodruff K, Ferguson NM, Gaythorpe KA. (2021). Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world. eLife, (10)

Brito AF, Machado LC, Oidtman RJ, Siconelli MJL, Tran QM, Fauver JR, Carvalho RDO, Dezordi FZ, Pereira MR, de Castro-Jorge LA, Minto ECM, Passos LMR, Kalinich CC, Petrone ME, Allen E, España GC, Huang AT, Cummings DAT, Baele G, Franca RFO, da Fonseca BAL, Perkins TA, Wallau GL, Grubaugh ND. (2021). Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil. Nature communications, 12(1)

Bron GM, Strimbu K, Cecilia H, Lerch A, Moore SM, Tran Q, Perkins TA, Ten Bosch QA. (2021). Over 100 Years of Rift Valley Fever: A Patchwork of Data on Pathogen Spread and Spillover. Pathogens (Basel, Switzerland), 10(6)

Poterek ML, Kraemer MUG, Watts A, Khan K, Perkins TA. (2021). Air Passenger Travel and International Surveillance Data Predict Spatiotemporal Variation in Measles Importations to the United States. Pathogens (Basel, Switzerland), 10(2)

Oidtman RJ, España G, Perkins TA. (2021). Co-circulation and misdiagnosis led to underestimation of the 2015-2017 Zika epidemic in the Americas. PLoS neglected tropical diseases, 15(3)

Chaves LF, Huber JH, Rojas Salas O, Ramírez Rojas M, Romero LM, Gutiérrez Alvarado JM, Perkins TA, Prado M, Rodríguez RM. (2020). Malaria Elimination in Costa Rica: Changes in Treatment and Mass Drug Administration. Microorganisms, 8(7)

Moore SM, Oidtman RJ, Soda KJ, Siraj AS, Reiner RC Jr., Barker CM, Perkins TA. (2020). Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas. PLoS neglected tropical diseases, 14(9)

Ten Bosch QA, Wagman JM, Castro-Llanos F, Achee NL, Grieco JP, Perkins TA. (2020). Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes. PLoS computational biology, 16(9)

Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A. (2020). Aggregated mobility data could help fight COVID-19. Science (New York, N.Y.)

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)

Kraemer MUG, Sadilek A, Zhang Q, Marchal NA, Tuli G, Cohn EL, Hswen Y, Perkins TA, Smith DL, Reiner RC Jr., Brownstein JS. (2020). Mapping global variation in human mobility. Nature human behaviour

Bivins A, North D, Ahmad A, Ahmed W, Alm E, Been F, Bhattacharya P, Bijlsma L, Boehm AB, Brown J, Buttiglieri G, Calabro V, Carducci A, Castiglioni S, Cetecioglu Gurol Z, Chakraborty S, Costa F, Curcio S, de Los Reyes FL 3rd., Delgado Vela J, Farkas K, Fernandez-Casi X, Gerba C, Gerrity D, Girones R, Gonzalez R, Haramoto E, Harris A, Holden PA, Islam MT, Jones DL, Kasprzyk-Hordern B, Kitajima M, Kotlarz N, Kumar M, Kuroda K, La Rosa G, Malpei F, Mautus M, McLellan SL, Medema G, Meschke JS, Mueller J, Newton RJ, Nilsson D, Noble RT, van Nuijs A, Peccia J, Perkins TA, Pickering AJ, Rose J, Sanchez G, Smith A, Stadler L, Stauber C, Thomas K, van der Voorn T, Wigginton K, Zhu K, Bibby K. (2020). Wastewater-Based Epidemiology: Global Collaborative to Maximize Contributions in the Fight Against COVID-19. Environmental science & technology

Siraj AS, Sorichetta A, España G, Tatem AJ, Perkins TA. (2020). Modeling human migration across spatial scales in Colombia. PloS one, 15(5)

Perkins TA, España G. (2020). Optimal Control of the COVID-19 Pandemic with Non-pharmaceutical Interventions. Bulletin of mathematical biology, 82(9)

Walters M, Perkins TA. (2020). Hidden heterogeneity and its influence on dengue vaccination impact. Infectious Disease Modelling, (5)

Kraemer MUG, Reiner RC Jr., Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Weaver ND, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay SI, Golding N. (2019). Publisher Correction: Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nature microbiology, 4(5)

España G, Hogea C, Guignard A, Ten Bosch QA, Morrison AC, Smith DL, Scott TW, Schmidt A, Perkins TA. (2019). Biased efficacy estimates in phase-III dengue vaccine trials due to heterogeneous exposure and differential detectability of primary infections across trial arms. PLoS One, 14(1)

Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW 4th., Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH, , Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG. (2019). Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic. Cell, 178(5)

Perkins TA, Rodriguez-Barraquer I, Manore C, Siraj AS, España G, Barker CM, Johansson MA, Reiner RC Jr.. (2019). Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data. Epidemics, (29)

Lloyd AL, Kitron U, Perkins TA, Vazquez-Prokopec GM, Waller LA. (2019). The basic reproductive number for disease systems with multiple coupled heterogeneities. Mathematical biosciences, (321)

Kraemer MUG, Reiner RC Jr., Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Weaver ND, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay SI, Golding N. (2019). Publisher Correction: Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nature microbiology, 4(5)

Oidtman RJ, Lai S, Huang Z, Yang J, Siraj AS, Reiner RC Jr., Tatem AJ, Perkins TA, Yu H. (2019). Inter-annual Variation in Seasonal Dengue Epidemics Driven by Multiple Interacting Factors in Guangzhou, China. Nature communications, 10(1)

Kraemer MUG, Reiner RC Jr., Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Davis Weaver N, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay SI, Golding N. (2019). Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nature microbiology, 4(5)

España G, Yao Y, Anderson KB, Fitzpatrick MC, Smith DL, Morrison AC, Wilder-Smith A, Scott TW, Perkins TA. (2019). Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure. PLoS neglected tropical diseases, 13(7)

Fox SJ, Bellan SE, Perkins TA, Johansson MA, Meyers LA. (2019). Downgrading disease transmission risk estimates using terminal importations. PLoS neglected tropical diseases, 13(6)

Schaber KL, Paz-Soldan VA, Morrison AC, Elson WHD, Rothman AL, Mores CN, Astete-Vega H, Scott TW, Waller LA, Kitron U, Elder JP, Barker CM, Perkins TA, Vazquez-Prokopec GM. (2019). Dengue illness impacts daily human mobility patterns in Iquitos, Peru. PLoS neglected tropical diseases, 13(9)

Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. (2019). Arbovirus Coinfection and Co-Transmission: A Neglected Public Health Concern?. PLoS biology, 17(1)

Perkins TA, Reiner RC Jr., España G, Ten Bosch QA, Verma A, Liebman KA, Paz-Soldan VA, Elder JP, Morrison AC, Stoddard ST, Kitron U, Vazquez-Prokopec GM, Scott TW, Smith DL. (2019). An Agent-Based Model of Dengue Virus Transmission Shows How Uncertainty About Breakthrough Infections Influences Vaccination Impact Projections. PLoS computational biology, 15(3)

España G, Grefenstette J, Perkins A, Torres C, Campo Carey A, Diaz H, de la Hoz F, Burke DS, van Panhuis WG. (2018). Exploring scenarios of chikungunya mitigation with a data-driven agent-based model of the 2014-2016 outbreak in Colombia. Scientific reports, 8(1)

Perkins TA, Paz-Soldan VA, Stoddard ST, Morrison AC, Forshey BM, Long KC, Halsey ES, Kochel TJ, Elder JP, Kitron U, Scott TW, Vazquez-Prokopec GM. (2016). Calling in Sick: Impacts of Fever on Intra-Urban Human Mobility. Proceedings. Biological sciences, 283(1834)

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