Sitemap
A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Posts
Skylines, Skyrides, and Skygrids
Published:
This blog post will focus on Skygrid, dabbling in Skyride and Skylines in general before talking about the specifics around Skygrid parameter selection.
ESS in Phylogenetics
Published:
This post will focus on ESS values in Phylogenetics. What are they and how do we improve them?
publications
Phylogeny and Metadata Network Database for Epidemiologic Surveillance
Published in BioRxiv, 2022
A preprint describing our work on developing a pipeline for the generation of a graph database for epidemiologic surveillance.
Recommended citation: Garrick Stott, Leke Lyu, Gabriella Veytsel, Jacky Kuo, Ryan Lewis, Armand Brown, Kayo Fujimoto, Justin Bahl. Phylogeny and Metadata Network Database for Epidemiologic Surveillance. bioRxiv 2022.04.19.488067
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Beyond scale-free networks: integrating multilayer social networks with molecular clusters in the local spread of COVID-19
Published in Scientific Reports, 2023
This paper uses our preprint, Phylogeny and Metadata Network Database for Epidemiologic Surveillance, to investigate the scale-free network assumption in the context of local molecular clusters.
Recommended citation: Fujimoto, K., Kuo, J., Stott, G. et al. Beyond scale-free networks: integrating multilayer social networks with molecular clusters in the local spread of COVID-19. Sci Rep 13, 21861 (2023).
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talks
Phylogeny and Metadata Database for Epidemiologic Surveillance
Published:
A poster with work in progress on a graph database which combines multiple data layers related to epidemiology.
Phylogenetic Analysis Subsampling Tool (PAST): A Novel Tool to Address Sequencing Bias in Phylodynamic Analysis
Published:
A poster demonstrating work in progress on a subsampling tool which helps make more informed choices in phylodynamic analysis.
Balanced and Well-spread Subsampling for Better Phylogenetic Inferences in Epidemiology
Published:
Presentation on my subsampling work. Investigating alternative downsampling methods and how subsampling strategies impact phylodynamic estimates. Link to slide deck…
Wrangling Reproducibility in your Research with Nextflow, Conda, and Docker
Published:
A brief introduction to Nextflow, Conda, and Docker for biostatisticians and epidemiologists at UGA. A case example taken from an REU mentee, Victoria, is included to demonstrate how Nextflow can be used in a research project. Link to slide deck…