Hasegawa, N.Techer M.A.Adjlane, N., Sabah al-Hissnawi, M.Antúnez, K., … Rasmussen, D.A., & Mikheyev, A.S. Evolutionary diverse origins of honey bee deformed wing viruses. bioRxiv, 2023-01.


Guo, F., Carbone, I., & Rasmussen, D.A. Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination. PLoS Computational Biology.

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.

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.


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.

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).

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).

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.

Rasmussen D.A. & Grünwald, N. 2021. Phylogeographic approaches to characterize the emergence and spread of plant pathogens. Phytopathology, 111(1) 68-77.


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.

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.

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.


Rasmussen, D.A. & Stadler, T. Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models. eLife 8, e45562.

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.

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.

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.


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).

Müller, N.F., Rasmussen, D.A., & Stadler, T. MASCOT: Parameter and state inference under the marginal structured coalescent approximation. Bioinformatics, 34 (22), 3843-3848.


Please see David Rasmussen’s Google Scholar Profile for a complete list of work published before 2018.