Works (20)

Updated: April 6th, 2024 05:02

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.

By: M. Rivarez*, C. Faure*, L. Svanella-Dumas*, A. Pecman*, M. Tusek-Znidaric*, D. Schonegger*, K. De Jonghe, A. Blouin* ...

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
15. Life on Land (OpenAlex)
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.

By: D. Rasmussen n & F. Guo n

author keywords: Ancestral recombination graph; maximum agreement forest; phylogenetic discordance; recombination; reconciliation
UN Sustainable Development Goal Categories
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
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.

By: B. Mahmud, M. Wallace*, K. Reske*, K. Alvarado*, C. Muenks*, D. Rasmussen n, C. Burnham*, C. Lanzas n, E. Dubberke*, G. Dantas*

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
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.

By: Z. Lapp*, A. Obala*, L. Abel*, D. Rasmussen n, K. Sumner*, E. Freedman*, S. Taylor*, W. Prudhomme-O'Meara*

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)
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).

By: F. Guo n, I. Carbone n & D. Rasmussen n

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
10. Reduced Inequalities (OpenAlex)
Sources: Web Of Science, ORCID
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-+.

By: H. Tegally*, J. San*, M. Cotten*, M. Moir*, B. Tegomoh*, G. Mboowa*, D. Martin*, C. Baxter* ...

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)
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-+.

By: E. Wilkinson*, M. Giovanetti*, H. Tegally*, J. San*, R. Lessells*, D. Cuadros*, D. Martin*, D. Rasmussen n ...

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
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).

By: L. Kepler n, M. Hamins-Puertolas n & D. Rasmussen n

author keywords: SARS-CoV-2; transmission fitness; phylodynamics; birth-death model
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).

By: T. Graf*, G. Bello*, P. Andrade*, I. Arantes*, J. Pereira*, A. Silva*, R. Veiga*, D. Mariani* ...

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)
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).

By: D. Dawson n, D. Rasmussen n, X. Peng n & C. Lanzas n

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
Added: June 9, 2021

2021 journal article

Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens

PHYTOPATHOLOGY, 111(1), 68–77.

By: D. Rasmussen n & N. Grunwald*

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

2020 review

Aphid Transmission ofPotyvirus: The Largest Plant-Infecting RNA Virus Genus

[Review of ]. VIRUSES-BASEL, 12(7).

By: K. Gadhave n, S. Gautam*, D. Rasmussen n & R. Srinivasan*

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).

By: C. Ruark-Seward n, B. Bonville n, G. Kennedy n & D. Rasmussen n

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
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, Crossref
Added: November 2, 2020

2019 journal article

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

PLOS COMPUTATIONAL BIOLOGY, 15(4).

By: R. Bouckaert*, T. Vaughan*, J. Barido-Sottani*, S. Duchene*, M. Fourment*, A. Gavryushkina*, J. Heled, G. Jones* ...

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)
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.

By: D. Rasmussen n & T. Stadler*

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.

By: Y. Chen n, M. Dessau*, D. Rotenberg n, D. Rasmussen n & A. Whitfield n

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, ORCID
Added: October 21, 2019

2019 journal article

Estimating Epidemic Incidence and Prevalence from Genomic Data

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

By: T. Vaughan*, G. Leventhal*, D. Rasmussen n, A. Drummond*, D. Welch* & T. Stadler*

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.

By: N. Mueller, D. Rasmussen n & T. Stadler*

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).

By: D. Rasmussen n, E. Wilkinson*, A. Vandormael*, F. Tanser*, D. Pillay*, T. Stadler*, T. Oliveira*

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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