AI/ML in microbiome big data

[ctbus]

Hi all,

I work with the Penn-CHOP Microbiome Program as a software engineer helping to develop, upgrade, and maintain metagenomics packages and pipelines. We’re looking to add AI/ML capabilities, especially in virus detection.

If anyone knows of cool examples of genomic AI/ML work or want to know more about my work please let me know.

Thanks,
Charlie

[Katherine_Moss]

Charlie,

Yes, would you mind telling us about your work? Sounds fascinating.

regards,

Katherine Moss
https://www.linkedin.com/pub/katherine-moss/3/b49/228

[ctbus]

Hi Katherine,

Thanks for your interest! Most of my work can be found on GitHub (Ulthran (Ulthran) / Repositories · GitHub, PennChopMicrobiomeProgram · GitHub, Sunbeam Labs · GitHub) and my website (Charlie Bushman).

I’ve mostly focused on shotgun metagenomic analysis, meaning lots of short reads from samples with lots of bacterial species. Some of the cooler projects I work on:

• A pipeline for automating standard quality control and decontamination that is extensible to running many tools for downstream analysis, including mapping, assembly, classification, annotation, etc (GitHub - sunbeam-labs/sunbeam: A robust, extensible metagenomics pipeline).
• A statistical package for estimating bacterial growth rates based on the ratio of genetic material close to the replication origin vs far away (GitHub - Ulthran/DEMIC: DEMIC PTR analysis software in the form of an R package, GitHub - Ulthran/pycov3: A package for generating cov3 files used in DEMIC, GitHub - sunbeam-labs/sbx_demic: A sunbeam extension to run DEMIC, a peak-to-trough ratio generator for bacteria short-reads).
• Some sunbeam extensions for virus detection and analysis (GitHub - sunbeam-labs/sbx_virus_id, GitHub - Ulthran/sbx_seeker, GitHub - Ulthran/sbx_mgv, GitHub - Ulthran/sbx_marker_magu: Sunbeam extension for running Marker-MAGu software).

Most of the ML/AI I’ve interacted with so far has been in wrapping existing tools in a new framework but it’s a goal to add some new research and tools in the area.

[Katherine_Moss]

Thank you for the details. A “shotgun” approach sounds very interesting – I guess you never know what collections of critters you will gather. I am guessing this can apply to the GI tract, which seems to be in the news more and more. There is, for example, a connection (of some kind) between certain genera of bacteria in the GI tract and Parkinson’s.