I always speak politely to AI as there is a non-zero chance that this will be a situation in the future:
@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?!
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-...
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).
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...
EMBL-EBI
We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify).
On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!
BossSaru
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
Alan McNally
Charlotte Houldcroft
Andrew Rambaut (🐏🎀)
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)
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
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...
John Lees
John Lees
John Lees
John Lees
Charles Wei
Having an under five in your household increases your risk as an adult of having diarrhoea and vomiting.
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...
I did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely.
Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o...
I tried to think of factors and their likelihood to explain why this is happening now
🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨!
www.biorxiv.org/content/10.6...
John Lees
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...
Johanna von Wachsmann
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...
