Staph Research
Publication update
This research led to my co-authored paper, “Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome”, published in mSystems on June 27, 2024.
Research
For the past couple of months I have been research the staph genome. I am using Staphopia as a tool which has thousands of public staph genomes.
Currently looking at how staph genes accessory(not all staph have these genes) staph genes can relate to core genome(genes all staph samples have)
I will be uploading a new github repository with my machine learning model for sequence type, if I can make sure it makes sense.
New plot
This is a graph showing a bunch of sequence types of staph. Sequence type, is a way which bacteria are typed into groups. Here I show how all the sequence types are related in 2D space, even though each point has over 260 variables. I reduced a 260 variable plot to a dimension plot using t-SNE. Pretty cool right!
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