David Alan Rasmussen
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Works (22)
Updated: November 18th, 2024 11:06
2024 journal article
Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints
MOLECULAR BIOLOGY AND EVOLUTION, 41(7).
author keywords: recombination detection; ancestral recombination graph; breakpoint localization; informative sites; phylogeny reconstruction
open access via academic.oup.com (publisher PDF)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 22, 2024
2024 article
Quantifying the strength of viral fitness trade-offs between hosts: a meta-analysis of pleiotropic fitness effects
Wang, X. 'M., Muller, J., McDowell, M., & Rasmussen, D. A. (2024, July 29). EVOLUTION LETTERS.
author keywords: mutation; pleiotropy; distribution of fitness effects; fitness trade-offs; host range; viral evolution
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Source: Web Of Science
Added: August 19, 2024
2023 article
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.
author keywords: histopathology; Ilarvirus; phylogenetics; pollen; Serratus; Solanaceae; symptomatology; virion morphology; virus diversity; virus transmission
TL;DR:
Modern and classical virological tools were combined to accelerate the characterization of SnIV1 and it was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: November 27, 2023
2023 journal article
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests
SYSTEMATIC BIOLOGY, 72(5), 1154–1170.
author keywords: Ancestral recombination graph; maximum agreement forest; phylogenetic discordance; recombination; reconciliation
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: Web Of Science
Added: April 1, 2024
2023 journal article
Evolutionarily diverse origins of deformed wing viruses in western honey bees
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 120(26).
author keywords: varroa; single-stranded RNA viruses; apis; phylogeography
TL;DR:
It is shown that two closely related honey bee deformed wing virus strains, transmitted by ectoparasitic varroa mites, show different patterns of spread, illustrating the dynamic nature of viral adaptation and competition, as well as the risks posed by globalization.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: October 10, 2023
2022 article
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.
Ed(s): C. Marshall
author keywords: Escherichia coli; beta-lactamases; plasmid-mediated resistance
MeSH headings : Humans; Escherichia coli / genetics; Escherichia coli Infections / epidemiology; beta-Lactamases / genetics; Plasmids / genetics; Hospitals
TL;DR:
This work provides a detailed picture of plasmid-mediated spread of ESBLs, demonstrating the extensive sequence diversity within identified lineages, while highlighting the genetic elements that underlie the persistence of these plasmids within the clinical E. coli population.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 24, 2022
2022 article
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.
author keywords: malaria; Plasmodium falciparum; transmission; comparative genomics; genetic diversity
MeSH headings : Animals; Humans; Culicidae / parasitology; Genetic Variation; Longitudinal Studies; Malaria, Falciparum / parasitology; Plasmodium falciparum / genetics
TL;DR:
The overall and sample-level parasite populations were more diverse in mosquitoes than in humans, and haplotype prevalences were more even in the P. falciparum human population than in the mosquito population, consistent with balancing selection occurring at these loci in humans.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: September 26, 2022
2022 journal article
Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination
PLOS COMPUTATIONAL BIOLOGY, 18(8).
MeSH headings : Genetics, Population; Genome; Humans; Models, Genetic; Phylogeography; Population Density; Recombination, Genetic / genetics
TL;DR:
The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: March 6, 2023
2022 journal article
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
SCIENCE, 378(6615), 42-+.
MeSH headings : Africa / epidemiology; COVID-19 / epidemiology; COVID-19 / virology; Epidemiological Monitoring; Genomics; Humans; Pandemics; SARS-CoV-2 / genetics
TL;DR:
Findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: February 13, 2023
2021 journal article
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
SCIENCE, 374(6566), 423-+.
MeSH headings : Africa / epidemiology; COVID-19 / epidemiology; COVID-19 / transmission; COVID-19 / virology; Epidemiological Monitoring; Genetic Variation; Genomics; Humans; Pandemics; SARS-CoV-2 / genetics; SARS-CoV-2 / isolation & purification
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: November 15, 2021
2021 journal article
Decomposing the sources of SARS-CoV-2 fitness variation in the United States
VIRUS EVOLUTION, 7(2).
author keywords: SARS-CoV-2; transmission fitness; phylodynamics; birth-death model
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 7, 2022
2021 journal article
HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network
SCIENTIFIC REPORTS, 11(1).
MeSH headings : Adolescent; Adult; Brazil / epidemiology; Female; Genotype; HIV Infections / blood; HIV Infections / epidemiology; HIV Infections / virology; HIV Seropositivity; HIV-1 / classification; HIV-1 / genetics; Humans; Longitudinal Studies; Male; Middle Aged; Phylogeny; Young Adult
TL;DR:
The results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks, which suggests a greater penetrance of non-B subtypes in MSM transmission chains.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 30, 2021
2021 journal article
Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 18(179).
author keywords: environmental transmission; disease transmission modelling; phylodynamics; whole-genome sequencing
MeSH headings : Epidemics; Phylogeny; Probability
TL;DR:
It is concluded that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 9, 2021
2020 review
Aphid Transmission ofPotyvirus: The Largest Plant-Infecting RNA Virus Genus
[Review of ]. VIRUSES-BASEL, 12(7).
author keywords: potyviruses; vector-virus interactions; aphid transmission; plant viruses; insect vectors
MeSH headings : Agriculture; Animals; Aphids / physiology; Aphids / virology; Genetic Variation; Genomics; Host Microbial Interactions; Insect Vectors / virology; Plant Diseases / virology; Potyvirus / genetics; Potyvirus / physiology; Proteomics
TL;DR:
How the fundamental understanding of these multi-partite interactions through multi-omics approaches is already contributing to, and can have future implications for, devising effective and sustainable management strategies against aphid-transmitted potyviruses to global agriculture is examined.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
13. Climate Action
(Web of Science)
Source: Web Of Science
Added: August 24, 2020
2020 journal article
Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips
Scientific Reports, 10(1).
MeSH headings : Animals; Biodiversity; Biological Evolution; Datura stramonium / virology; Flowers / virology; Host Specificity / genetics; Insect Vectors / virology; Plant Diseases / genetics; Plant Diseases / virology; Thysanoptera / virology; Tospovirus / genetics; Tospovirus / isolation & purification
TL;DR:
It is suggested that high levels of genetic diversity together with the positive pleiotropic effects of mutations have allowed TSWV to rapidly adapt to new hosts and expand its host range.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, Crossref
Added: November 2, 2020
2020 journal article
Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens
PHYTOPATHOLOGY, 111(1), 68–77.
author keywords: coalescent theory; evolution; genomics; population biology; population genetics; phylogenetics; techniques
MeSH headings : Models, Genetic; Phylogeny; Phylogeography; Plant Diseases
TL;DR:
The theory, methods, and approaches underpinning phylogeographic inference are reviewed and applications providing novel insights into the emergence and spread of select pathogens are highlighted.
(via Semantic Scholar)
Source: Web Of Science
Added: March 15, 2021
2019 journal article
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
PLOS COMPUTATIONAL BIOLOGY, 15(4).
MeSH headings : Animals; Bayes Theorem; Biological Evolution; Computational Biology; Computer Simulation; Evolution, Molecular; Humans; Markov Chains; Models, Genetic; Monte Carlo Method; Phylogeny; Software
TL;DR:
The full range of new tools and models available on the BEAST 2.5 platform are described, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: May 28, 2019
2019 journal article
Coupling adaptive molecular evolution to phylodynamics using fittness-dependent birth-death models
ELIFE, 8.
MeSH headings : Adaptation, Biological; Ebolavirus / genetics; Ebolavirus / physiology; Evolution, Molecular; Genetic Fitness; Genotype; Models, Genetic; Orthomyxoviridae / genetics; Orthomyxoviridae / physiology
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: September 23, 2019
2019 article
Entry of bunyaviruses into plants and vectors
VIRUS ENTRY, Vol. 104, pp. 65–96.
MeSH headings : Animals; Arthropod Vectors / virology; Bunyaviridae / physiology; Feeding Behavior; Plants / parasitology; Plants / virology; Virus Internalization
TL;DR:
This review highlights the transmission and entry strategies of three genera of plant-infecting bunyaviruses: orthotospoviruses, tenuivirus, and emaravIRuses.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
12. Responsible Consumption and Production
(OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 21, 2019
2019 journal article
Estimating Epidemic Incidence and Prevalence from Genomic Data
MOLECULAR BIOLOGY AND EVOLUTION, 36(8), 1804–1816.
author keywords: phylodynamics; particle filter; epidemiology; Bayesian phylogenetics
MeSH headings : Bayes Theorem; Genomics / methods; Hemorrhagic Fever, Ebola / epidemiology; Humans; Incidence; Molecular Epidemiology / methods; Prevalence; Sierra Leone / epidemiology
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: November 18, 2019
2018 journal article
MASCOT: parameter and state inference under the marginal structured coalescent approximation
BIOINFORMATICS, 34(22), 3843–3848.
MeSH headings : Algorithms; Influenza A Virus, H3N2 Subtype; Phylogeny; Probability; Software
TL;DR:
This work provides a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree and shows that this algorithm is able to increase the probability attributed to the true node states.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: December 3, 2018
2018 journal article
Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa
VIRUS EVOLUTION, 4(2).
author keywords: HIV; molecular epidemiology; phylodynamics; migration
TL;DR:
A phylodynamic model is used to reconstruct epidemic dynamics and estimate the relative contribution of local transmission versus external introductions to overall incidence in KwaZulu-Natal from HIV-1 phylogenies, showing that it can reliably estimate incidence from viral phylogenies once viral movement in and out of the local population is accounted for.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: February 11, 2019
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