Publications
2023
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2022
Guo, F., Carbone, I., & Rasmussen, D.A. Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1010422
Lapp, Z., Obala, A. A., Abel, L., Rasmussen, D.A., Sumner, K.M., Freedman, E., … & Prudhomme-O’Meara, W. Plasmodium falciparum genetic diversity in coincident human and mosquito hosts. bioRxiv. https://doi.org/10.1101/2022.05.05.490756
Mahmud, B., Wallace, M., Reske, K., Alvarado, K., Muenks, C., Rasmussen, D.A., Burnham, C., Lanzas, C., Dubberke, E., & Dantas, G. Epidemiology of plasmid lineages mediating the spread of extended spectrum beta-lactamases among clinical Escherichia coli. mSystems. DOI:10.1128/msystems.00519-22
Rasmussen, D.A., & Guo, F. Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests. bioRxiv. https://doi.org/10.1101/2022.01.17.476639
2021
Wilkinson, E., Giovanetti, M., Tegally, H., San, J. E., Lessells, R., Cuadros, D., Rasmussen, D.A. … Oliveira, T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science, 374(6566) 423-431. https://doi.org/10.1126/science.abj4336
Kepler, L., Hamins-Puertolas, M., & Rasmussen, D.A. Decomposing the sources of SARS-CoV-2 fitness variation in the United States. Virus Evolution, 7(2). https://doi.org/10.1093/ve/veab073
Dawson, D., Rasmussen, D.A., Peng, X., & Lanzas, C. Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen. Journal Roy. Soc. Interface, 18(179). https://doi.org/10.1098/rsif.2021.0041
Graf, T., Bello, G., Andrade, P., Arantes, I., Pereira, J. M., Silva, A. B., … Rasmussen, D.A., Tanuri, A. HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network. Scientific Reports, 11(1) 1-9. https://doi.org/10.1038/s41598-021-94542-5
Rasmussen D.A. & Grünwald, N. 2021. Phylogeographic approaches to characterize the emergence and spread of plant pathogens. Phytopathology, 111(1) 68-77. https://doi.org/10.1094/PHYTO-07-20-0319-FI
2020
Ruark-Seward, C., Bonville, B., Kennedy, G., & Rasmussen D.A. Evolutionary dynamics of Tomato spotted wilt virus with and between alternate plant hosts and thrips. Scientific Reports 10(1), 1-16. 2020. https://doi.org/10.1038/s41598-020-72691-3
Jara, M., Rasmussen, D.A., Corzo, C.A., Machado, G. On reproductive and respiratory syndrome virus dissemination across pig production systems in the United States. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.13728
Gadhave, K.R., Gautam, S. Rasmussen, D.A., Srinivasan, R. Aphid Transmission of Potyviruses: The Largest Plant-Infecting RNA Virus Genus. Viruses 12(7), 773. doi.org/10.3390/v12070773
2019
Rasmussen, D.A. & Stadler, T. Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models. eLife 8, e45562. https://doi.org/10.7554/eLife.45562
Chen, Y., Dessau, M., Rotenberg, D., Rasmussen, D.A. & Whitfield, A. Entry of bunyaviruses into plants and vectors. Advances in Virus Research: Virus Entry 104: 65-96. doi.org/10.1016/bs.aivir.2019.07.001
Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duchene, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kuhnert, D., de Maio N., Rasmussen D.A… & Drummond, A.J. BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology, 15(4):e1006650. doi.org/10.1371/journal.pcbi.1006650
Vaughan, T.G., Leventhal, G.E., Rasmussen, D.A., Drummond, A.J., Welch, D. & Stadler, T. Estimating epidemic incidence and prevalence from genomic data. Molecular Biology and Evolution. 38(8), 1804-1816. doi.org/10.1093/molbev/msz106
2018
Rasmussen, D.A., Wilkinson, E., Vandormael, A., Tanser, F., Pillay, D., Stadler, T., & de Oliveira, T. Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa. Virus Evolution, 4(2). doi.org/10.1093/ve/vey037
Müller, N.F., Rasmussen, D.A., & Stadler, T. MASCOT: Parameter and state inference under the marginal structured coalescent approximation. Bioinformatics, 34 (22), 3843-3848. doi.org/10.1093/bioinformatics/bty406
Please see David Rasmussen’s Google Scholar Profile for a complete list of work published before 2018.