Group Leader at Wellcome Sanger Institute. Using omics to understand chronic lung infections and lung microbiomes in disease
Josie Bryant
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@oldenoughtosay.com I see that your house has recently been visited by the Bad Enterovirus Fairy, aka Hand, foot and mouth disease. I got so het up about baby germs that I wrote a 9.5k word review article on them (800 word version here theconversation.com/if-you-think...). Normal response, right?!
I always speak politely to AI as there is a non-zero chance that this will be a situation in the future:
You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium):
taxonium.org/atb
That's a big tree!
(unless you're used to SC2 trees)
The genomic diversity and spatial patterns of Mycobacterium bovis in Ireland revealed by whole genome sequencing rdcu.be/e50zT
Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years
www.sciencedirect.com/science/arti...
So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).
It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...
Welcome, @stephlo.bsky.social, our new Team Leader for Protein Function.
Find out how Stephanie’s experience in genomics shaped her approach to protein curation and AI integration.
#ProteinScience #AI
www.embl.org/news/people-...
Some more thoughts on why this outbreak (large, happening quickly, in one place) might be happening:
johnlees.me/posts/menb-o...
Perhaps strain + immunity + high transmission
New work on using transformers (using gene order) for tasks in genomic epidemiology:
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...
Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…
Posted some thoughts on the menB outbreak yesterday. Now nine more cases, total at 27.
A few more thoughts today, also after discussing with some others.
A local factor seems necessary. I think pathog...
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
