New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social
except my tokens keep running out
wow what a backdrop!
Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org !
Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these.
www.ebi.ac.uk/about/news/u...
Congratulations! (and also happy to know these cryptic messages are so universal. Do I mean happy really? Well it made me feel better about them at leasy)
And we think contributes to the 'why prokaryotes have pangenomes' debate on neutrality vs adaptation, hopefully bringing a lot more population genomes to bear on the issue!
Proud of this work and Sam for sticking with some very challenging modelling!
Core trees, core-accessory distance plots, and model fits for four bacterial species (A) Mycobacterium tuberculosis, (B) Streptococcus pneumoniae, (C) Escherichia coli and (D) Listeria monocytogenes.)
This started as an opportunistic reuse of poppunk/sketchlib core-accessory distances, which we noticed differed between species in their shape (e.g. accessory distance at same core; faster/slower accumulation of accessory changes with core)
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria
Person standing outside next to a building wearing a red jacket
Meet Leonie Johanna Lorenz 🇩🇪, a Predoctoral Fellow at EMBL-EBI who is bringing mathematical modelling to microbes.
Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵
www.ebi.ac.uk/about/news/p...
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Fine, Le Guin from now on
Wow
🎉 New year, NEW PREPRINT!
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement (also a German word for cat)
Thank you for asking, yes Stubentiger does indeed stand for STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement
There's also an R package: github.com/bacpop/Stube...
So others can more easily apply/reuse/adapt this important model
Our new preprint which reimplements "the NFDS model" (of Corander et al) to forecast populations after vaccination as a compartmental model, and uses new bioinformatic tools to create and process the pangenome data
We look at which surveillance strategies are best to correctly forecast changes
good god haha
At least nothing else is getting worse
It’s behind cloudflare captcha now (although I’m now wondering if that’s just the genome campus IPs) — so paperpile at least can’t auto download the pdf
Looks very promising!!
One thing I didn't quite follow, when you mention 'a novel parameter for trait simulation that accounts for uncertainty in deep ancestral branches of a phylogeny' -- is that referring to the time to first event parameter?
RIP automated downloads of PDFs from biorxiv it seems, I suppose we have AI to thank for that
Some blogging from over the holiday, something for everyone I'm sure:
Cooking johnlees.me/posts/xmas-d...
Video games johnlees.me/posts/review...
DIY johnlees.me/posts/towel-...
(back to preprints tomorrow)
We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!
Nice to see some of our tools getting used in public health
(in this case PopPIPE, which is downstream subclustering/transmission tool to be run on PopPUNK data)
The data was collected by the CABBAGE project, which has just been preprinted too: www.biorxiv.org/content/10.1...
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
A PhD project on historical genomics in the declining red squirrel in Britain is available in my group, through the @aries-dtp.bsky.social. Use historical genomes to track the effects of decline and genetic rescue in this charismatic species. aries-dtp.ac.uk/studentships...
Congratulations to Zam!
Just a quick plug: I've made a few updates to ExpEvoAnalyzer (variant functional annotation in experimental evolution studies) to use bwa as well as ska2, and to use existing or de novo annotations. It just might help streamline your pesky bioinformatics analysis! github.com/samhorsfield...
