Evan Qu
PhD candidate in the MIT Microbiology Program (co2020). @Lieberman Lab @contaminatedsci.bsky.social. I study the ecology and evolution of skin microbes, like this one -> 🤏
- Excited to share my preprint describing a new microbiome analysis method, PHLAME, for detecting strain-level associations in difficult sample types. 🧵 www.biorxiv.org/content/10.1... This work was done with my great coauthors and my amazing advisor @contaminatedsci.bsky.social
- Many health or environmental associations may be driven by intraspecies variants. The most straightforward approach for strain associations, direct inference of genotypes from metagenomics, is difficult in environments where many strains of the same species coexist.
- Standard practice for complex metagenomic samples is to use reference databases to detect strains. Because reference databases are never comprehensive, many of these methods will represent novel strains (i.e., not in the database) as a nearby representative genome in the database.
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View full threadPHLAME is available to try out on GitHub: github.com/quevan/phlame
