🎉 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." 🧵:
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
✨Célia Souque just showcased the outcomes of the 12th Microbial Bioinformatics Hackathon at IMMEM XIV.
She brilliantly presented the first sneak-peek of PORT – Plasmid Outbreak Reporting Tool! 🧬
Looking forward to continuing this collaboration with PORT!
#IMMEM #Hackathon #Plasmids #ESGEM #ESGMAP
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
ESGMAP is now on LinkedIn and Bluesky!
We published our first newsletter (lnkd.in/dUe43t8y). It introduces us, our mission, activities, and ways to get involved. Fill out our members' survey, and associate your publications with the group.
Follow us for updates on the mobile elements and plasmids.
The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!
www.biorxiv.org/content/10.1...
New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...
🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
The link is not working for me 😔
Cool preprint! The smallest Darwinian entity is a little smarter than we thought...
www.biorxiv.org/content/10.1...
Any idea when the abstract submission portal opens for IMMEM XIV? 😊 @esgem-sg.bsky.social
RNA xkcd.com/3056
Ground-breaking work by one of the most amazing of scientists. A must read for all plasmids afficionado (and and any evolutionary biologist in general!)
It seems really good but apparently rough around the edges regarding the UI, so I am waiting a bit for them to patch it first!
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
Sharing three fully funded PhD opportunities to join my lab at Queen’s to work on topics spanning bacterial pathogens, antibiotic resistance, microbial interactions, & mobile genetic elements 🦠. Closing dates in January and February, and open to international candidates 🌍 Projects detailed below ⬇️
In case you missed it: @matthewjshepherd.bsky.social surveyed the clinical literature to reveal how #AMR evolves within patients, why eco/evo mechanisms vary among infections, & what we can do better to improve treatments www.nature.com/articles/s41... #MicroSky
Gosh parts of me hate the concept of ChatGPT with a passion, but I have to acknowledge it's supremacy when trying to debug a Snakemake pipeline, which I am not convinced are made to be understood by humans 😅
Volume 2 of the #AMR Starter Pack is here!
go.bsky.app/EUY2FUJ
Follow these amazing people along with those in Vol. 1
go.bsky.app/KkZfvrh
And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place
bsky.app/profile/did:...
Don't know how to do polls in Bluesky, but am very curious to know how what the #microsky thinks.
Genes that increase fitness in natural conditions are:
A. Over-represented on plasmids
B. Over-represented on the chromosome
C. Evenly distributed between plasmids and the chromosome
For circular plots, I have found that out of the box elderly BRIG beatsonlab.com/softwares/br... remains the best. Otherwise for more custom plots I usually go with circos-like packages (like pyCirclize in Python) but it is much more work
That's low-key one of my favorite thing about Oslo - the city center is very often car free, and the few cars are often electric, which makes them much less audible.
Going to back to a 'proper' big city (Stockholm) for a week felt weird!
Please sign up, it will be fun!
Open for all with an interest in AMR and genomics (in the UK and elsewhere).
www.targetamr.org.uk
(and please give @target-amr.bsky.social a follow!)
Signed up! 😊
