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Phylodynamics for cell biologists
Science, 2021Ancestry and evolution in cell biology Advances in experimental approaches for single-cell analysis allow in situ sequencing, genomic barcoding, and mapping of cell lineages within tissues and organisms. Large amounts of data have thus accumulated and present an analytical challenge.
T. Stadler, O. G. Pybus, M. P. H. Stumpf
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Development of Phylodynamic Methods for Bacterial Pathogens
Trends in Microbiology, 2021Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data ...
Danielle J. Ingle +2 more
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Inferring the Global Phylodynamics of Influenza A/H3N2 Viruses in Taiwan
Journal of the Formosan Medical Association, 2019 Background/Purpose: Influenza A/H3N2 viruses are characterized by highly mutated RNA genomes. In this study, we focused on tracing the phylodynamics of Taiwanese strains over the past four decades. Methods: All Taiwanese H3N2 HA1 sequences and references
Guang-Wu Chen +2 more
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High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE
Methods in Molecular Biology, 2019 In this chapter, we focus on the computational challenges associated with statistical phylogenomics and how use of the broad-platform evolutionary analysis general likelihood evaluator (BEAGLE), a high-performance library for likelihood computation, can ...
Marc A. Suchard +2 more
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Characterizing enterovirus C96 genome and phylodynamics analysis
Journal of Medical Virology, 2023AbstractEnterovirus C96 (EV‐C96) is a recently discovered serotype belonging to enterovirus C species. It had been isolated from patients with acute flaccid paralysis, hand, foot, and mouth disease, diarrhea, healthy people, or environmental specimens. Despite increasing reports of the virus, the small number of full‐length genomes available for EV‐C96
Tingting Yang +14 more
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Maximum Likelihood Phylodynamic Analysis
2018Die Anzahl der verfügbaren Genomsequenzen für verschiedene Pathogene hat in den letzten Jahren ausserordentlich zugenommen. Bestehende tradi- tionelle Methoden für die phylodynamische Analyse sind nicht effizient für eine große Anzahl von Sequenzen. Um mit den heute verfügbaren Daten- sätzen umzugehen, sind effiziente Heuristiken notwendig.
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Phylodynamics of Human Coxsackievirus B5
Future Virology, 2014ABSTRACT: Aim: Coxsackievirus B5 is recognized as an important pathogen in aseptic meningitis and hand, foot and mouth disease of children. A new distinctive sublineage of Coxsackievirus B5 associated with outbreak of neurological hand, foot and mouth disease in China was recently reported. Materials & methods: We employed a molecular evolution method
Congjun Hao +4 more
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Phylodynamics of Influenza A Viruses
2015Human populations are constantly exposed to emerging pathogens such as influenza A viruses that result from cross-species transmissions. Generally these sporadic events are evolutionary dead-ends, but occasionally, viruses establish themselves in a new host that offers a novel genomic context to which the virus must adjust to avoid attenuation. However,
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