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Viruses, 12(7), 773. https://doi.org/10.3390/v12070773 Kepler, L., Hamins-Puertolas, M., & Rasmussen, D. A. (2020, December 14). Decomposing the sources of SARS-CoV-2 fitness variation in the United States. https://doi.org/10.1101/2020.12.14.422739 Ruark-Seward, C. L., Bonville, B., Kennedy, G., & Rasmussen, D. A. (2020). Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-72691-3 Ruark-Seward, C. L., Bonville, B., Kennedy, G., & Rasmussen, D. A. (2020, January 14). Evolutionary dynamics ofTomato spotted wilt viruswithin and between alternate plant hosts and thrips. https://doi.org/10.1101/2020.01.13.904250 Rasmussen, D. A., & Grunwald, N. J. (2021). Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens. PHYTOPATHOLOGY, 111(1), 68–77. https://doi.org/10.1094/PHYTO-07-20-0319-FI Jara, M., Rasmussen, D. A., Corzo, C. A., & Machado, G. (2020). Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States. Transboundary and Emerging Diseases, 68(2), 667–683. https://doi.org/10.1111/tbed.13728 Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchene, S., Fourment, M., Gavryushkina, A., … Drummond, A. J. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS COMPUTATIONAL BIOLOGY, 15(4). https://doi.org/10.1371/journal.pcbi.1006650 Rasmussen, D. A., & Stadler, T. (2019, January 26). Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models (Vol. 1). Vol. 1. https://doi.org/10.1101/531525 Rasmussen, D. A., & Stadler, T. (2019). Coupling adaptive molecular evolution to phylodynamics using fittness-dependent birth-death models. ELIFE, 8. https://doi.org/10.7554/eLife.45562 Chen, Y., Dessau, M., Rotenberg, D., Rasmussen, D. A., & Whitfield, A. E. (2019). Entry of bunyaviruses into plants and vectors. https://doi.org/10.1016/bs.aivir.2019.07.001 Vaughan, T. G., Leventhal, G. E., Rasmussen, D. A., Drummond, A. J., Welch, D., & Stadler, T. (2019). Estimating Epidemic Incidence and Prevalence from Genomic Data. MOLECULAR BIOLOGY AND EVOLUTION, 36(8), 1804–1816. https://doi.org/10.1093/molbev/msz106 Mueller, N. F., Rasmussen, D., & Stadler, T. (2018). MASCOT: parameter and state inference under the marginal structured coalescent approximation. BIOINFORMATICS, 34(22), 3843–3848. https://doi.org/10.1093/bioinformatics/bty406 Rasmussen, D. A., Wilkinson, E., Vandormael, A., Tanser, F., Pillay, D., Stadler, T., & Oliveira, T. (2018). Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa. VIRUS EVOLUTION, 4(2). https://doi.org/10.1093/ve/vey037 Rasmussen, D. A., Kouyos, R., Günthard, H. F., & Stadler, T. (2017). Phylodynamics on local sexual contact networks. PLOS Computational Biology, 13(3), e1005448. https://doi.org/10.1371/journal.pcbi.1005448 Barido-Sottani, J., Bošková, V., Plessis, L. D., Kühnert, D., Magnus, C., Mitov, V., … Stadler, T. (2017). Taming the BEAST—A Community Teaching Material Resource for BEAST 2. Systematic Biology, 67(1), 170–174. https://doi.org/10.1093/sysbio/syx060 Müller, N. F., Rasmussen, D. A., & Stadler, T. (2017). The Structured Coalescent and Its Approximations. Molecular Biology and Evolution, 34(11), 2970–2981. https://doi.org/10.1093/molbev/msx186 Wilkinson, E., Rasmussen, D., Ratmann, O., Stadler, T., Engelbrecht, S., & de Oliveira, T. (2016). Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective. Infection, Genetics and Evolution, 46, 200–208. https://doi.org/10.1016/j.meegid.2016.07.008 Rasmussen, D. A., Kouyos, R., Günthard, H. F., & Stadler, T. (2016, October 24). Phylodynamics on local sexual contact networks. https://doi.org/10.1101/082966 Ratmann, O., Hodcroft, E. B., Pickles, M., Cori, A., Hall, M., Lycett, S., … Fraser, C. (2016). Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. Molecular Biology and Evolution, 34(1), 185–203. https://doi.org/10.1093/molbev/msw217 Koelle, K., & Rasmussen, D. A. (2015). The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans. ELife, 4. https://doi.org/10.7554/elife.07361 Stadler, T., Kühnert, D., Rasmussen, D. A., & du Plessis, L. (2014). Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data. PLoS Currents, 10. https://doi.org/10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f Rasmussen, D. A., Volz, E. M., & Koelle, K. (2014). Phylodynamic Inference for Structured Epidemiological Models. PLoS Computational Biology, 10(4), e1003570. https://doi.org/10.1371/journal.pcbi.1003570 Koelle, K., & Rasmussen, D. A. (2014). Prediction is worth a shot. Nature, 507(7490), 47–48. https://doi.org/10.1038/nature13054 Rasmussen, D. A., Boni, M. F., & Koelle, K. (2013). Reconciling Phylodynamics with Epidemiology: The Case of Dengue Virus in Southern Vietnam. Molecular Biology and Evolution, 31(2), 258–271. https://doi.org/10.1093/molbev/mst203 Koelle, K., Ratmann, O., Rasmussen, D. A., Pasour, V., & Mattingly, J. (2011). A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses. Proceedings of the Royal Society B: Biological Sciences, 278(1725), 3723–3730. https://doi.org/10.1098/rspb.2011.0435 Rasmussen, D. A., Ratmann, O., & Koelle, K. (2011). Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series. PLoS Computational Biology, 7(8), e1002136. https://doi.org/10.1371/journal.pcbi.1002136 Koelle, K., & Rasmussen, D. A. (2011). Rates of coalescence for common epidemiological models at equilibrium. Journal of The Royal Society Interface, 9(70), 997–1007. https://doi.org/10.1098/rsif.2011.0495 Blackman, B. K., Scascitelli, M., Kane, N. C., Luton, H. H., Rasmussen, D. A., Bye, R. A., … Rieseberg, L. H. (2011). Sunflower domestication alleles support single domestication center in eastern North America. Proceedings of the National Academy of Sciences, 108(34), 14360–14365. https://doi.org/10.1073/pnas.1104853108 Blackman, B. K., Rasmussen, D. A., Strasburg, J. L., Raduski, A. R., Burke, J. M., Knapp, S. J., … Rieseberg, L. H. (2011). Contributions of Flowering Time Genes to Sunflower Domestication and Improvement. Genetics, 187(1), 271–287. https://doi.org/10.1534/genetics.110.121327 Rasmussen, D. A., & Noor, M. A. F. (2009). What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics, 10(1), 382. https://doi.org/10.1186/1471-2164-10-382 Rasmussen, D. A., Kramer, E. M., & Zimmer, E. A. (2009). One size fits all? Molecular evidence for a commonly inherited petal identity program in Ranunculales. American Journal of Botany, 96(1), 96–109. https://doi.org/10.3732/ajb.0800038