Alex Perkins Associate Professor

Research Interests:

Our research applies mathematical, computational, and statistical approaches to answer basic and applied research questions about the ecology and epidemiology of infectious diseases. This work is rooted primarily in mosquito-borne diseases of humans, although our portfolio has expanded in recent years to also include other vector-borne diseases of humans and animals, emerging diseases, and respiratory diseases. Across this range of systems, the goal of our research is to attain a predictive understanding of where and when these diseases occur, what the impact of interventions will be in curtailing their burden, and how the distribution of these diseases and their response to interventions will change over time as a result of changes in their underlying drivers. Through this research, we hope to elevate the rigor of the information on which decision makers act, both in terms of accuracy and quantification of uncertainty.

1. Infectious disease mapping

With relatively few exceptions, geographic mapping of infectious diseases relies on phenomenological descriptions of relationships between disease and its drivers and disregards a rich body of theory on transmission dynamics. The first theme of our research seeks to devise new approaches that leverage transmission dynamics theory to enhance the interpretability and utility of infectious disease mapping.

2. Infectious disease forecasting

As has been demonstrated repeatedly throughout the COVID-19 pandemic, dynamic models that account for biological, social, and epidemiological factors have much to offer to public health decision making. The second theme of our research seeks to improve the scientific basis for infectious disease forecasting with dynamic, mechanistic models of transmission and other relevant processes.

3. Interventions for infectious disease prevention

Mathematical modeling has a key role to play in designing and interpreting studies to assess intervention efficacy and to make projections of the impact of interventions when deployed at population scales. The third theme of our research seeks to advance these capabilities for prevention of mosquito-borne and other diseases.

Biography:

• Associate Professor, University of Notre Dame - Present
• Eck Family Assistant Professor, University of Notre Dame 2014-2020
• Concurrent Faculty in Applied and Computational Mathematics and Statistics, University of Notre Dame 2015-Present
• RAPIDD Postdoctoral Fellow, NIH Fogarty International Center and University of California, Davis 2011-2014
• Ph.D. Population Biology, University of California, Davis 2011
• B.A. Computational Ecology, University of Tennessee, Knoxville 2006

Selected Recent Papers:

• TA Perkins, JH Huber, QM Tran, RJ Oidtman, MK Walters, AS Siraj, SM Moore. 2021. Burden is in the eye of the beholder: Sensitivity of yellow fever disease burden estimates to modeling assumptions. Science Advances 7:eabg5033.
• RJ Oidtman, E Omodei, MUG Kraemer, CA Castaneda-Orjuela, E Cruz-Rivera, S Misnaza-Castrillon, MP Cifuentes, LE Rincon, V Canon, P de Alarcon, G España, J Huber, SC Hill, CM Barker, MA Johansson, CA Manore, RC Reiner, I Rodriguez-Barraquer, AS Siraj, E Frias-Martinez, M Garcia-Herranz, TA Perkins. 2021. Trade-offs between individual and ensemble forecasts of an emerging infectious disease. Nature Communications 12:5379.
• K Gaythorpe*, K Abbas*, J Huber*, A Karachaliou*, N Thakkar*, K Woodruff, X Li, S Echeverria-Londono, VIMC Working Group on COVID-19 Impact on Vaccine-Preventabe Disease, M Ferrari^, ML Jackson^, K McCarthy^, TA Perkins^, C Trotter^, M Jit^. 2021. Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries. eLife 10:e67023.
• AF Brito*, LC Machado LC*, MJL Siconelli*, RJ Oidtman*, JR Fauver*, RD Carvahlo, FZ Dezordi, MR Pereira, LA deCastro-Jorge, ECM Minto, LMR Passos, CC Kalinich, ME Petrone, E Allen, G España, AT Huang, DAT Cummings, G Baele, RFO Franca^, TA Perkins^, BAL da Fonseca^, GL Wallau^, ND Grubaugh^. 2021. Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil. Nature Communications 12:2619.
• SM Moore, RJ Oidtman, KJ Soda, AS Siraj, RC Reiner, CM Barker, TA Perkins. 2020. Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas. PLOS Neglected Tropical Diseases 14:e0008640.
• QA ten Bosch, JM Wagman, F Castro-Llanos, NL Achee, JP Grieco, TA Perkins. 2020. Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes. PLOS Computational Biology 16:1008190.
• TA Perkins*, SM Cavany*, SM Moore*, RJ Oidtman, A Lerch, M Poterek. 2020. Estimating unobserved SARS-CoV-2 infections in the United States. Proceedings of the National Academy of Sciences 117:22597.
• SM Cavany, G España, AL Lloyd, LA Waller, U Kitron, H Astete, WH Elson, GM Vazquez-Prokopec, TW Scott, AC Morrison, RC Reiner, TA Perkins. 2020. Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response. PLOS Computational Biology 16:e1007743.
• G España, Y Yao, KB Anderson, MC Fitzpatrick, DL Smith, AC Morrison, A Wilder-Smith, TW Scott, TA Perkins. 2019. Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure. PLOS Neglected Tropical Diseases 13:e0007482.
• RJ Oidtman, S Lai, Z Huang, J Yang, AS Siraj, RC Reiner, AJ Tatem,
  TA Perkins, H Yu. 2019. Inter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China. Nature Communications 10:1148.
• CBF Vogels*, C Ruckert*, SM Cavany*, TA Perkins, GD Ebel, ND Grubaugh. 2019. Arbovirus coinfection and co-transmission: a neglected public health concern? PLOS Biology 17:e3000130.
• SM Moore, QA ten Bosch, AS Siraj, KJ Soda, G España, A Campo, S Gomez, D Salas, B Raybaud, E Wenger, P Welkhoff, TA Perkins. 2018 Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity. BMC Medicine 16:152.
• QA ten Bosch, HE Clapham, L Lambrechts, V Duoung, P Buchy, BM Althouse, AL Lloyd, LA Waller, AC Morrison, U Kitron, GM Vazquez-Prokopec, TW Scott, TA Perkins. 2018 Contributions from the silent majority dominate dengue virus transmission. PLOS Pathogens 14:e1006965.
• S Flasche*, M Jit*, I Rodriguez-Barraquer*, L Coudeville*, M Recker*, K Koelle*, G Milne*, T Hladish*, TA Perkins*, I Dorigatti, DAT Cummings, G España, J Kelso, I Longini, J Lourenco, C Pearson, RC Reiner, Jr., NM Ferguson. 2016 The long-term safety, public health impact, and cost-effectiveness of a routine vaccination with a recombinant, live-attenuated dengue vaccine (Dengvaxia): a model comparison study. PLOS Medicine 13:e1002181.
• TA Perkins, AS Siraj, C Warren Ruktonanchai, MUG Kraemer, AJ Tatem. 2016 Model-based projections of Zika virus infections in childbearing women in the Americas. Nature Microbiology 1:16216.