Publications

2025

Rasmussen D.A., Bursell, M.G., & Burkhart, F. Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes, Genetics, 2025;, iyaf244, https://doi.org/10.1093/genetics/iyaf244

Koelle, K., & Rasmussen, D.A. Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference. Philosophical Transactions B, 380(1919), 20230314. https://doi.org/10.1098/rstb.2023.0314

Coomber, A., Rasmussen, D.A., & Ristaino, J.B. Experimental Evolution of Phytophthora infestans on Tomato Reveals Rapid Genotypic and Phenotypic Adaptation and Dynamic RXLR Genome Variation. Phytopathology®, 115(8), 998-1007. https://doi.org/10.1094/PHYTO-12-24-0401-R

2024

Wang, X.M., Muller, J., McDowell, M., & Rasmussen, D.A. Quantifying the strength of viral fitness trade-offs between hosts: a meta-analysis of pleiotropic fitness effects. Evolution Letters, 8(6), 851-865. https://doi.org/10.1093/evlett/qrae038

Cen, S., & Rasmussen, D.A. Exploring the accuracy and limits of algorithms for localizing recombination breakpoints. Molecular Biology and Evolution, 41(7), msae133. https://doi.org/10.1093/molbev/msae133

Kepler, L. M., Jara, M., Mahmud, B., Dantas, G., Dubberke, E. R., Lanzas, C., & Rasmussen, D. A. Quantifying the genomic determinants of fitness in E. coli ST131 using phylodynamics. bioRxiv, 2024-06. https://doi.org/10.1101/2024.06.10.598183

Shymanovich, T., Saville, A. C., Mohammad, N., Wei, Q., Rasmussen, D.A., Lahre, K. A., … & Ristaino, J. B. Disease progress and detection of a California resistance-breaking strain of tomato spotted wilt virus in tomato with LAMP and CRISPR-Cas12a assays. PhytoFrontiers™, 4(1), 50-60. https://doi.org/10.1094/PHYTOFR-05-23-0058-FI

2023

Rasmussen, D. A., & Guo, F. Espalier: efficient tree reconciliation and ancestral recombination graphs reconstruction using maximum agreement forests. Systematic Biology, 72(5), 1154-1170. https://doi.org/10.1093/sysbio/syad040

Hasegawa, N., Techer, M. A., Adjlane, N., Al-Hissnawi, M. S., Antúnez, K., Beaurepaire, A., … & Rasmussen, D.A., Mikheyev, A. S. (2023). Evolutionarily diverse origins of deformed wing viruses in western honey bees. Proceedings of the National Academy of Sciences, 120(26), e2301258120. https://doi.org/10.1073/pnas.2301258120

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

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.