Forthcoming and preprints

Tuschhoff BM, Kennedy DA. Detecting and quantifying heterogeneity in susceptibility using contact tracing data. bioRXiv. Link to preprint.

Ortigas-Vasquez A, Pandey U, Renner DW, Bown CD, Baigent S, Dunn J, Cheng H, Yao Y, Read AF, Nair V, Kennedy DA, Szpara ML. Deep whole-genome resequencing of Marek’s disease virus strains reveals intrastrain variation. bioRXiv. Link to preprint.

Published

Bhattacharya A, Aluquin AA, Kennedy DA. 2024. Exceptions to the rule: when does resistance evolution not undermine antibiotic therapy in human bacterial infections? Evolution Letters. qrae005. Link.

Kennedy DA. 2023. Death is overrated: the potential role of detection in driving virulence evolution. Proceedings of the Royal Society of London Series B. 290: 20230117. Link.

Day T, Kennedy DA, Read AF, Gandon S. 2022. The evolutionary epidemiology of pathogens during vaccination campaigns. PLoS Biology, 20: e3001804. Link.

Shaw CL, Kennedy DA. 2022. Developing an empirical model for spillover and emergence: Orsay virus host range in Caenorhabditis. Proceedings of the Royal Society of London Series B. 289: 20221165. Link.

Day T, Kennedy DA, Read AF, McAdams. 2021. The economics of evolution management. PLoS Biology, 19: e3001409. Link.

Shaw CL, Kennedy DA. 2021. What the reproductive number R0 can and cannot tell us about COVID-19 dynamics. Theoretical Population Biology, 137: 2-9. Link.

Kennedy DA, Read AF. 2020. Monitor for COVID-19 vaccine resistance evolution during clinical trials. PLoS Biology, 18: e3001000. Link.

Bell AS, Kennedy DA, Jones MJ, Cairns CL, Pandey U, Dunn PA, Szpara ML, Read AF. 2019. Molecular epidemiology of Marek’s disease virus in central Pennsylvania, USA. Virus Evolution, 5: vey042. Link.

Kennedy DA, Read AF. 2018. Why the evolution of vaccine resistance is less of a concern than the evolution of drug resistance. Proceedings of the National Academy of Science USA, 115: 12878-12886.  Link.

Kennedy DA, Dwyer G. 2018. Effects of multiple sources of genetic drift on pathogen variation within hosts. PLoS Biology, 16: e2004444.  Link.

Kennedy DA, Dunn PA, Read AF. 2018. Modeling Marek’s disease virus transmission: a framework for evaluating the impact of farming practices and evolution. Epidemics, 23: 85–95. Link.

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. Avian Diseases, 61: 153–164. Link.

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. Link.
— Proc R Soc B most read article: Oct 2017, Feb 2018

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. Link.

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. Link.

Read AF, Baigent SJ, Powers C, Kgosana LB, Blackwell L, Smith LP, Kennedy DA, Walkden-Brown SW, Nair VK. 2015. Imperfect vaccination can enhance the transmission of highly virulent pathogens. PLoS Biology, 13: e1002198. Link.

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. Link.

Kennedy DA, Dukic V, Dwyer G. 2015. Combining principal component analysis with parameter line-searches to improve the efficacy of Metropolis-Hastings MCMC. Environmental and Ecological Statistics, 22: 1–28. Link.

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. Link.

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. Link.

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. 2014. Using quantitative disease dynamics as a tool for guiding response to avian influenza in USA poultry. Preventive Veterinary Medicine, 113: 376–397. Link.

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. Link.

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 USA, 105: 7478–7483. Link.

Howard KJ, Kennedy D. 2007. Alternative mating behaviors of the queen polymorphic ant Temnothorax longispinosus. Naturwissenschaften, 94: 945–950. Link.

Parker MA, Kennedy D. 2006. Diversity and relationships of bradyrhizobia from legumes native to eastern North America. Canadian Journal of Microbiology, 52: 1148–1157. Link.