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Reposted by Célia Souque

Louise Roer @louiseroer.bsky.social · 22d

✨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

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Reposted by Célia Souque

Sofya Garushyants @garushyants.bsky.social · 25d

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!

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Reposted by Célia Souque

Didier Mazel @amazeld.bsky.social · Jun 23

chng.it/jNJSnj2hjQ

Avez-vous une minute pour aider cette campagne?

Sauvons BIOASTER : Un Appel Urgent pour la Recherche en Microbiologie !

chng.it

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Reposted by Célia Souque

esgmap.bsky.social @esgmap.bsky.social · Jun 19

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.

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Reposted by Célia Souque

Siân Owen @sianowen.bsky.social · Jun 3

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 🙏

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Reposted by Célia Souque

Liana Merk @bacteriyay.bsky.social · May 24

(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...

Prevalence of Group II Introns in Phage Genomes

Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...

www.biorxiv.org

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Reposted by Célia Souque

Craig MacLean @craigmaclean.bsky.social · May 8

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...

Job Details

my.corehr.com

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Reposted by Célia Souque

Jose A Escudero @jaescudero.bsky.social · May 8

🧪
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/...

Mobile integrons encode phage defense systems

Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

www.science.org

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Célia Souque @celiasouque.bsky.social · Apr 25

The link is not working for me 😔

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Reposted by Célia Souque

Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · Mar 24

Cool preprint! The smallest Darwinian entity is a little smarter than we thought...

www.biorxiv.org/content/10.1...

RNA-guided nucleases enable a gene drive of insertion sequences in plasmids

Mobile genetic elements (MGEs) and the interactions between them are a major source of evolutionary innovation. Insertion sequences, the simplest MGEs usually encoding only the necessary genes for tra...

www.biorxiv.org

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Célia Souque @celiasouque.bsky.social · Mar 3

Any idea when the abstract submission portal opens for IMMEM XIV? 😊 @esgem-sg.bsky.social

Reposted by Célia Souque

Randall Munroe @xkcd.com · Feb 26

RNA xkcd.com/3056

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Célia Souque @celiasouque.bsky.social · Feb 21

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!)

Fernando Rossine @fernpizza.bsky.social · Feb 21

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics!
(1/n) www.biorxiv.org/content/earl...

Intracellular competition shapes plasmid population dynamics

Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-r...

www.biorxiv.org

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Célia Souque @celiasouque.bsky.social · Feb 6

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!

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Reposted by Célia Souque

Michael Baym @baym.lol · Jan 17

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

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jan 17

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

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Reposted by Célia Souque

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jan 17

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

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Reposted by Célia Souque

Alexandre Almeida @alexmsalmeida.bsky.social · Jan 10

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

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology

Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

www.nature.com

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Reposted by Célia Souque

Anna Dewar @annadewar.bsky.social · Jan 8

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

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

rdcu.be

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Reposted by Célia Souque

Rachel M. Wheatley @rachelmwheatley.bsky.social · Dec 30

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 ⬇️

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Reposted by Célia Souque

Michael Brockhurst @brockhurstlab.bsky.social · Dec 4

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

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance - Nature Reviews Microbiology

In this Review, Shepherd, Brockhurst and colleagues explore the clinical evidence in support of four major ecological and evolutionary mechanisms of within-patient antimicrobial resistance emergence i...

www.nature.com

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Célia Souque @celiasouque.bsky.social · Dec 3

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 😅

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Reposted by Célia Souque

Anita Williams @catanita.bsky.social · Dec 2

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:...

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Reposted by Célia Souque

Craig MacLean @craigmaclean.bsky.social · Nov 27

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

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Célia Souque @celiasouque.bsky.social · Dec 1

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

BRIG

beatsonlab.com

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Célia Souque @celiasouque.bsky.social · Nov 27

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!

Qagggy! @qagggy.bsky.social · Nov 26

Cities aren’t crowded. They’re just full of cars.

Same spot photographed by me in 2022 after pedestrianization was completed.

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