David Alan Rasmussen

Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference

Philosophical Transactions of the Royal Society B: Biological Sciences.

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.

Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints

Molecular Biology and Evolution, 41(7).

Phylodynamics beyond neutrality: The impact of incomplete purifying selection on viral phylogenies and inference

Quantifying the genomic determinants of fitness in<i>E. coli</i>ST131 using phylodynamics

Quantifying the strength of viral fitness trade-offs between hosts: a meta-analysis of pleiotropic fitness effects

Evolution Letters, 8(6), 851–865.

Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data

Rivarez, M. P. S., Faure, C., Svanella-Dumas, L., Pecman, A., Tusek-Znidaric, M., Schonegger, D., … Candresse, T. (2023, July 3). PHYTOPATHOLOGY, Vol. 7.

Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests

Systematic Biology, 72(5), 1154–1170.

Evolutionarily diverse origins of deformed wing viruses in western honey bees

Proceedings of the National Academy of Sciences, 120(26).

Exploring the accuracy and limits of algorithms for localizing recombination breakpoints

Cen, S., & Rasmussen, D. A. (2023, December 12).

Quantifying the strength of viral fitness tradeoffs between hosts: A meta-analysis of pleiotropic fitness effects

Muller, J., McDowell, M., & Rasmussen, D. A. (2023, December 16).

Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli

Mahmud, B., Wallace, M. A., Reske, K. A., Alvarado, K., Muenks, C. E., Rasmussen, D. A., … Dantas, G. (2022, August 22). (C. W. Marshall, Ed.). MSYSTEMS, Vol. 8.

Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli

MSystems, 7(5).

Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests

Rasmussen, D. A., & Guo, F. (2022, January 20).

Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts

Lapp, Z., Obala, A. A., Abel, L., Rasmussen, D. A., Sumner, K. M., Freedman, E., … Prudhomme-O'Meara, W. (2022, September 8). MBIO, Vol. 9.

Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts

MBio, 13(5).

Recombination-aware Phylogeographic Inference Using the Structured Coalescent with Ancestral Recombination

Guo, F., Carbone, I., & Rasmussen, D. A. (2022, February 10). (Vol. 2). Vol. 2.

Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination

PLOS Computational Biology, 18(8), e1010422.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Science, 378(6615), 42-+.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Science, 374(6566), 423–431.

Decomposing the sources of SARS-CoV-2 fitness variation in the United States

Virus Evolution, 7(2).

HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network

SCIENTIFIC REPORTS, 11(1).

Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen

Journal of The Royal Society Interface, 18(179), 20210041.

Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens

PHYTOPATHOLOGY, 111(1), 68–77.

Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus

Viruses, 12(7), 773.

Decomposing the sources of SARS-CoV-2 fitness variation in the United States

Kepler, L., Hamins-Puertolas, M., & Rasmussen, D. A. (2020, December 14).

Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips

Scientific Reports, 10(1).

Evolutionary dynamics ofTomato spotted wilt viruswithin and between alternate plant hosts and thrips

Ruark-Seward, C. L., Bonville, B., Kennedy, G., & Rasmussen, D. A. (2020, January 14).

Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States

Transboundary and Emerging Diseases, 68(2), 667–683.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

PLOS COMPUTATIONAL BIOLOGY, 15(4).

Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models

Rasmussen, D. A., & Stadler, T. (2019, January 26). (Vol. 1). Vol. 1.

Coupling adaptive molecular evolution to phylodynamics using fittness-dependent birth-death models

ELIFE, 8.

Entry of bunyaviruses into plants and vectors

Estimating Epidemic Incidence and Prevalence from Genomic Data

MOLECULAR BIOLOGY AND EVOLUTION, 36(8), 1804–1816.

MASCOT: parameter and state inference under the marginal structured coalescent approximation

BIOINFORMATICS, 34(22), 3843–3848.

Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa

VIRUS EVOLUTION, 4(2).

Phylodynamics on local sexual contact networks

PLOS Computational Biology, 13(3), e1005448.

Taming the BEAST—A Community Teaching Material Resource for BEAST 2

Systematic Biology, 67(1), 170–174.

The Structured Coalescent and Its Approximations

Molecular Biology and Evolution, 34(11), 2970–2981.

Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective

Infection, Genetics and Evolution, 46, 200–208.

Phylodynamics on local sexual contact networks

Rasmussen, D. A., Kouyos, R., Günthard, H. F., & Stadler, T. (2016, October 24).

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

Molecular Biology and Evolution, 34(1), 185–203.

The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

ELife, 4.

Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data

PLoS Currents, 10.

Phylodynamic Inference for Structured Epidemiological Models

PLoS Computational Biology, 10(4), e1003570.

Prediction is worth a shot

Nature, 507(7490), 47–48.

Reconciling Phylodynamics with Epidemiology: The Case of Dengue Virus in Southern Vietnam

Molecular Biology and Evolution, 31(2), 258–271.

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.

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

Genetics, 187(1), 271–287.

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

PLoS Computational Biology, 7(8), e1002136.

Rates of coalescence for common epidemiological models at equilibrium

Journal of The Royal Society Interface, 9(70), 997–1007.

Sunflower domestication alleles support single domestication center in eastern North America

Proceedings of the National Academy of Sciences, 108(34), 14360–14365.

One size fits all? Molecular evidence for a commonly inherited petal identity program in Ranunculales

American Journal of Botany, 96(1), 96–109.

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.