C.V.
Assistant Professor (starting Jan 2019), Department of Biology, Penn State University
Research Associate (2015-2018), Department of Biology, Penn State University
RAPIDD Postdoctoral Fellow (2012-2015), Department of Biology, Penn State University
Ph.D. in Ecology and Evolution (2012), University of Chicago with Greg Dwyer
B.S. in Biology (2005), State University of New York at Binghamton
Assistant Professor (starting Jan 2019), Department of Biology, Penn State University
Research Associate (2015-2018), Department of Biology, Penn State University
RAPIDD Postdoctoral Fellow (2012-2015), Department of Biology, Penn State University
Ph.D. in Ecology and Evolution (2012), University of Chicago with Greg Dwyer
B.S. in Biology (2005), State University of New York at Binghamton
Research interests
I study the effects of disease ecology on pathogen evolution. Pathogen evolution can have important consequences in a variety of settings, including public health, food production, and wildlife conservation. Moreover, infectious diseases offer great opportunities to study evolution in biological systems, because both the ecological and evolutionary dynamics of disease occur on short timescales. In my research, I use variation in host-pathogen systems to address fundamental questions about infectious disease dynamics. This leads me to ask: Why does pathogen resistance evolve more readily against one public health intervention than another? Why does one pathogen strain cause more harm to hosts than another? Why is a pathogen population diverse in one host, and clonal in another? My approach to studying these questions is to combine data collection with mathematical modeling using high-performance computing. By adopting a quantitative approach, my goal is to develop a deeper understanding of how host-pathogen ecology affects pathogen evolution, with the aim of improving pathogen management.
I study the effects of disease ecology on pathogen evolution. Pathogen evolution can have important consequences in a variety of settings, including public health, food production, and wildlife conservation. Moreover, infectious diseases offer great opportunities to study evolution in biological systems, because both the ecological and evolutionary dynamics of disease occur on short timescales. In my research, I use variation in host-pathogen systems to address fundamental questions about infectious disease dynamics. This leads me to ask: Why does pathogen resistance evolve more readily against one public health intervention than another? Why does one pathogen strain cause more harm to hosts than another? Why is a pathogen population diverse in one host, and clonal in another? My approach to studying these questions is to combine data collection with mathematical modeling using high-performance computing. By adopting a quantitative approach, my goal is to develop a deeper understanding of how host-pathogen ecology affects pathogen evolution, with the aim of improving pathogen management.
Publications
Kennedy DA, Read AF (In press) Why the evolution of vaccine resistance is less of a concern than the evolution of drug resistance. Proceedings of the National Academy of Science.
Bell AS, Kennedy DA, Jones MJ, Cairns CL, Pandey U, Dunn PA, Szpara ML, Read AF (In press) Molecular epidemiology of Marek’s disease virus in central Pennsylvania, USA. Virus Evolution.
Kennedy DA, Dwyer G. (2018) Effects of multiple sources of genetic drift on pathogen variation within hosts. PLoS Biology, 16: e2004444, doi: 10.1101/190918.
Kennedy DA, Dunn PA, Read AF. (2018) Modeling Marek's disease virus transmission: a framework for evaluating the impact of farming practices and evolution on disease. Epidemics, 23: 85-95, doi: 10.1101/185785.
Kennedy DA, Cairns C, Jones MJ, Bell AS, Salathe RM, Baigent SJ, Nair VK, Dunn PA, Read AF. (2017) Industry-wide surveillance of Marek’s disease virus on commercial poultry farms: underlying potential for virulence evolution and vaccine escape. Avian Diseases, 61: 153-164, doi: 10.1101/07592.
Kennedy DA, Read AF. (2017) Why does drug resistance readily evolve but vaccine resistance does not? Proceedings of the Royal Society of London Series B, 284: 20162562.
Pandey U, Bell AS, Renner DW, Kennedy DA, Shreve JT, Cairns C, Jones M, Dunn PA, Read AF, Szpara ML (2016) DNA from dust: comparative genomics of large DNA viruses in field surveillance samples. mSphere, 1: e00132-16.
Kennedy DA, Kurath G, Brito IL, Purcell MK, Read AF, Winton JR, Wargo AR (2016) Potential drivers of virulence evolution in aquaculture. Evolutionary Applications, 9: 344-354.
Read AF, Baigent SJ, Powers C, Kgosana LB, Blackwell L, Smith LP, Kennedy DA, Walken-Brown SW, Nair VK (2015) Imperfect vaccination can enhance the transmission of highly virulent pathogens. PLoS Biology, e1002198.
Kennedy DA, Dunn JR, Dunn PA, Read AF (2015) An observational study of the temporal and spatial patterns of Marek's-disease-associated leukosis condemnation of young chickens in the United States of America. Preventive Veterinary Medicine, 120: 328-335.
Kennedy DA, Dukic V, Dwyer G (2014) Pathogen growth in insect hosts: Inferring the importance of different mechanisms using stochastic models and response time data. The American Naturalist, 184: 407-423.
Kennedy DA, Dukic V, Dwyer G (2014) Combining principal component analysis with parameter line-searches to improve the efficacy of Metropolis-Hastings MCMC. Environmental and Ecological Statistics, 22: 247-274.
Barclay V, Kennedy DA, Weaver VC, Sim D, Lloyd-Smith JO, Read AF (2014) The effect of immunodeficiency on the evolution of virulence: an experimental test with the rodent malaria Plasmodium chabaudi. The American Naturalist, 184: S47-S57.
Pepin KM, Spackman E, Brown JD, Pabilonia KL, Garber LP, Weaver JT, Kennedy DA, Patyk KA, Huyvaert KP, Miller RS, Franklin AB, Pedersen K, Bogich TL, Rohani P, Shriner SA, Webb CT, Riley S (2014) Using quantitative disease dynamics as a tool for guiding response to avian influenza in poultry in the United States of America. Preventive Veterinary Medicine, 113: 376-397.
Mideo N, Kennedy DA, Carlton JM, Bailey JA, Juliano JJ, Read AF (2013) Ahead of the curve: next generation estimators of drug resistance in malaria infections. Trends in Parasitology. 29: 321-328.
Dai HZ, Chen Y, Chen SD, Mao QY, Kennedy D, Landback P, Eyre-Walker A, Du W, Long MY (2008) The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proceedings of the National Academy of Science. 105: 7478-7483.
Howard KJ, Kennedy D (2007) Alternative mating behaviors of the queen polymorphic ant Temnothorax longispinosis. Naturwissenschaften. 94: 945-950.
Parker MA, Kennedy D (2006) Diversity and relationships of bradyrhizobia from legumes native to eastern North America. Canadian Journal of Microbiology. 52: 1148-1157.
Kennedy DA, Read AF (In press) Why the evolution of vaccine resistance is less of a concern than the evolution of drug resistance. Proceedings of the National Academy of Science.
Bell AS, Kennedy DA, Jones MJ, Cairns CL, Pandey U, Dunn PA, Szpara ML, Read AF (In press) Molecular epidemiology of Marek’s disease virus in central Pennsylvania, USA. Virus Evolution.
Kennedy DA, Dwyer G. (2018) Effects of multiple sources of genetic drift on pathogen variation within hosts. PLoS Biology, 16: e2004444, doi: 10.1101/190918.
Kennedy DA, Dunn PA, Read AF. (2018) Modeling Marek's disease virus transmission: a framework for evaluating the impact of farming practices and evolution on disease. Epidemics, 23: 85-95, doi: 10.1101/185785.
Kennedy DA, Cairns C, Jones MJ, Bell AS, Salathe RM, Baigent SJ, Nair VK, Dunn PA, Read AF. (2017) Industry-wide surveillance of Marek’s disease virus on commercial poultry farms: underlying potential for virulence evolution and vaccine escape. Avian Diseases, 61: 153-164, doi: 10.1101/07592.
Kennedy DA, Read AF. (2017) Why does drug resistance readily evolve but vaccine resistance does not? Proceedings of the Royal Society of London Series B, 284: 20162562.
Pandey U, Bell AS, Renner DW, Kennedy DA, Shreve JT, Cairns C, Jones M, Dunn PA, Read AF, Szpara ML (2016) DNA from dust: comparative genomics of large DNA viruses in field surveillance samples. mSphere, 1: e00132-16.
Kennedy DA, Kurath G, Brito IL, Purcell MK, Read AF, Winton JR, Wargo AR (2016) Potential drivers of virulence evolution in aquaculture. Evolutionary Applications, 9: 344-354.
Read AF, Baigent SJ, Powers C, Kgosana LB, Blackwell L, Smith LP, Kennedy DA, Walken-Brown SW, Nair VK (2015) Imperfect vaccination can enhance the transmission of highly virulent pathogens. PLoS Biology, e1002198.
Kennedy DA, Dunn JR, Dunn PA, Read AF (2015) An observational study of the temporal and spatial patterns of Marek's-disease-associated leukosis condemnation of young chickens in the United States of America. Preventive Veterinary Medicine, 120: 328-335.
Kennedy DA, Dukic V, Dwyer G (2014) Pathogen growth in insect hosts: Inferring the importance of different mechanisms using stochastic models and response time data. The American Naturalist, 184: 407-423.
Kennedy DA, Dukic V, Dwyer G (2014) Combining principal component analysis with parameter line-searches to improve the efficacy of Metropolis-Hastings MCMC. Environmental and Ecological Statistics, 22: 247-274.
Barclay V, Kennedy DA, Weaver VC, Sim D, Lloyd-Smith JO, Read AF (2014) The effect of immunodeficiency on the evolution of virulence: an experimental test with the rodent malaria Plasmodium chabaudi. The American Naturalist, 184: S47-S57.
Pepin KM, Spackman E, Brown JD, Pabilonia KL, Garber LP, Weaver JT, Kennedy DA, Patyk KA, Huyvaert KP, Miller RS, Franklin AB, Pedersen K, Bogich TL, Rohani P, Shriner SA, Webb CT, Riley S (2014) Using quantitative disease dynamics as a tool for guiding response to avian influenza in poultry in the United States of America. Preventive Veterinary Medicine, 113: 376-397.
Mideo N, Kennedy DA, Carlton JM, Bailey JA, Juliano JJ, Read AF (2013) Ahead of the curve: next generation estimators of drug resistance in malaria infections. Trends in Parasitology. 29: 321-328.
Dai HZ, Chen Y, Chen SD, Mao QY, Kennedy D, Landback P, Eyre-Walker A, Du W, Long MY (2008) The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proceedings of the National Academy of Science. 105: 7478-7483.
Howard KJ, Kennedy D (2007) Alternative mating behaviors of the queen polymorphic ant Temnothorax longispinosis. Naturwissenschaften. 94: 945-950.
Parker MA, Kennedy D (2006) Diversity and relationships of bradyrhizobia from legumes native to eastern North America. Canadian Journal of Microbiology. 52: 1148-1157.
Miscellaneous