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simrouxvirus.bsky.social
Simon Roux
@simrouxvirus.bsky.social
3.8K followers 1.8K following 200 posts

Virus-obsessed bioinformatician, DOE JGI Scientist, Enjoy exploring the viral world with #metagenomics and other cool #omics toys. He/him. Opinions my own.

Videos
Environmental science 40%
Biology 33%
Posts Replies Media Videos

Reposted by Simon Roux

rhystwhite.bsky.social
Rhys White @rhystwhite.bsky.social · 12h
Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics

📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing

www.doi.org/10.1099/mgen.0.001644

🖥️🧬💻
#AcademicSky
#MicroSky
#IDSky
🧪🧫🦠
Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem res...
www.doi.org

Reposted by George A. O’Toole, Simon Roux

asm.org
ASM @asm.org · 15h
The American Academy of Microbiology proudly announces the election of 63 fellows to the Class of 2026. Over the past 50 years, the Academy has elected +2,700 distinguished scientists. This year, the new fellows hail from 14 countries. Read press release: asm.social/2OC
Congratulations Fellows!

Reposted by Simon Roux

evbc.bsky.social
European Virus Bioinformatics Center @evbc.bsky.social · 15h
A new NAR Genomics and Bioinformatics resource introduces SquiDBase, a community repository of raw #nanopore #microbiome sequencing data, supporting open access and broader utility for bioinformatics and comparative analyses. #Genomics
📄 https://doi.org/10.1093/nargab/lqaf213
👤 EVBC: Daan Jansen
doi.org

Reposted by Simon Roux

ctrlalttim.com
Timothée Poisot @ctrlalttim.com · 15h
This past year, I have been fascinated by the way fields that are not biodiversity sciences / biogeography use and think about species distribution models. Most of my attention was on ML and paleo/anthropo, which, I think, are interesting end points. I believe there are important lessons for us. 🌎

Reposted by Simon Roux

tomstafford.mastodon.online.ap.brid.gy
Tom Stafford @tomstafford.mastodon.online.ap.brid.gy · 16h
# AcademicChatter
butterfly meme 8 hours writing achievement: deleted two lines in this progress?

Reposted by Simon Roux, Gilles Louppe

edogia.bsky.social
Edoardo Gianni @edogia.bsky.social · 20h
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
www.science.org

Reposted by Jens‐Christian Svenning, Simon Roux, Stephen D. Murphy , and 3 more

jotlovell.bsky.social
John Lovell @jotlovell.bsky.social · 1d
I'm super excited to share that this article was published today in Science! www.science.org/doi/10.1126/...

All made possible by the fantastic group of donors, volunteers and scientists at The American Chestnut Foundation (tacf.org), HudsonAlpha Institute for Biotechnology, and our collaborators.

Reposted by Jesse M. Shapiro, Simon Roux

nanditagarud.bsky.social
Nandita Garud @nanditagarud.bsky.social · 1d
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Reposted by Anna O. Law, Dorothy Bishop, Jesse M. Shapiro , and 18 more

lettersofnote.com
Letters of Note @lettersofnote.com · 1d
Happy birthday to one of my favourite haters, Charles Darwin

Reposted by Simon Roux

cmungall.bsky.social
Chris Mungall @cmungall.bsky.social · 1d
Over the last few months I've been helping organize various tutorials and workshops on agentic AI, aimed mostly at biocurators, ontology developers, and PIs of knowledge bases / data resources. Some of this might be generally useful to folks who don't identify as a 'technical' or an 'AI' person.🧵

Reposted by Simon Roux

silverja.bsky.social
Andrea Silverj @silverja.bsky.social · 3d
Yesterday’s #MVIF 46 Pacific premiere was a real blast!

I had the pleasure of chairing the keynote session, featuring a fantastic talk and Q&A with Dr. Simon Roux (@simrouxvirus.bsky.social).

Don’t miss the Atlantic replay today at 8:30 a.m. (New York time)!
www.microbiome-vif.org/en-US/-/futu...

Reposted by Jesse M. Shapiro, Simon Roux

jaytlennon.bsky.social
Jay T Lennon @jaytlennon.bsky.social · 4d
www.growkudos.com/publications...

New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org
The hidden energy cost of cellular dormancy
Many organisms survive harsh environments by switching into special survival modes. Some bacteria do this by forming spores—dormant, highly resilient cells that can persist for years or even centuries...
www.growkudos.com

Reposted by Simon Roux

raw937.bsky.social
raw9371 @raw937.bsky.social · 4d
The first automated computer vision–based software enabling the detection, enumeration, and sizing of virus-like particles from epifluorescence microscopy (EFM) images of environmental samples.

Published online in BMC methods today. #giantvirus #phagesky

Paper
link.springer.com/article/10.1...
Resolving and quantifying viral-like particles via blind deconvolution - BMC Methods
BMC Methods - Viruses represent the most numerous’biological entities’on Earth; but the direct quantification of viruses within ecosystems is a significant challenge. The classical...
link.springer.com

Reposted by Jonathan A. Eisen, Brian A. Nosek, Gavin L. Foster , and 23 more

theo.io
Theo Sanderson @theo.io · 5d
I made a map of 3.4 million Bluesky users - see if you can find yourself!

bluesky-map.theo.io

I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
bluesky-map.theo.io

Reposted by Graeme S. Cumming, Simon Roux

ron-kichurchak.bsky.social
ron-kichurchak.bsky.social @ron-kichurchak.bsky.social · 6d
McCoy's elf skink from northeastern Australia. Look at those stubby little arms, likely an adaptation to its burrowing lifestyle.

simrouxvirus.bsky.social
Simon Roux @simrouxvirus.bsky.social · 7d
In (real, not TV) France it can actually be both: some boarding schools are for the "elite", others are for ill behaved kids to "straighten them up". But it's true that the latter seems maybe more common.

Reposted by Simon Roux

kranzuschlab.bsky.social
Kranzusch Lab @kranzuschlab.bsky.social · 7d
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!

www.nature.com/articles/s41...
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
www.nature.com

Reposted by Simon Roux, Susan Strasser

tsch.uy
tschuy 🏳️‍🌈 @tsch.uy · 8d
California's great outdoors is more transit accessible than you think -- I've added trailheads all across the state to Hiking by Transit, ready for your outdoor adventure!

Check it out: hikingbytransit.com
map showing trailheads all across California by what kind of transit access they have

Reposted by Simon Roux

gmeric.bsky.social
Guillaume Méric @gmeric.bsky.social · 9d
More and more cool work looks at the role of human archaea in health outcomes. In this preprint, authors suggest protective role & show that colonisation of mice with M. smithii or M. stadtmanae thickens mucus, boosts reg. T cells & protects vs DSS colitis.
www.biorxiv.org/content/10.6...

Reposted by Simon Roux

up-8.bsky.social
Paul Houle @up-8.bsky.social · 9d
🧬 Golden Gate method enables fully-synthetic engineering of therapeutically relevant bacteriophages

phys.org/news/2026-01...

#molbio #virus #bacteriophage #bacteria #microbes #biotech #gmo
Golden Gate method enables fully-synthetic engineering of therapeutically relevant bacteriophages
Bacteriophages have been used therapeutically to treat infectious bacterial diseases for over a century. As antibiotic-resistant infections increasingly threaten public health, interest in bacteriopha...
phys.org

Reposted by Simon Roux

wcratcliff.bsky.social
Will Ratcliff @wcratcliff.bsky.social · 10d
27/28 More broadly, this framework may apply to other apparent "evolutionary singularities." Eukaryogenesis. The origin of life itself. The evolution of animals. Events that happened once might not be improbable: they might simply have created priority effects that prevented repeats.

Reposted by Simon Roux

wcratcliff.bsky.social
Will Ratcliff @wcratcliff.bsky.social · 10d
New paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects.

www.nature.com/articles/s44...
Priority effects inhibit the repeated evolution of phototrophy - npj Complexity
npj Complexity - Priority effects inhibit the repeated evolution of phototrophy
www.nature.com

Reposted by Simon Roux, Marc Strous

emilruff.bsky.social
Emil Ruff @emilruff.bsky.social · 10d
Come work with us on #darkoxygen as part of the NASA Postdoctoral Fellowship Program. It is an amazing opportunity to get up to 3 years of funding. Deadlines are March 1. and November 1. Happy to discuss your ideas! Details here: zintellect.com/Opportunity/...

@mblscience.bsky.social #astrobiology
Zintellect - National Aeronautics and Space Administration (NASA) - ICAR - OxyMoRon: Understanding dioxygen production and consumption in apparently anoxic environments - 0042-NPP-MAR26-ABProg-Astrobi...
About the NASA Postdoctoral Program The NASA Postdoctoral Program (NPP) offers unique research opportunities to highly-talented scientists to engage in ong
zintellect.com

Reposted by Simon Roux

surtlab.bsky.social
Dave Baltrus 🦦 @surtlab.bsky.social · 10d
Result 1) you can see from complete genomes that there’s been multiple independent expansions of IS5 and we don’t quite know why

Result 2) ~50% of the (>100 copies) of IS5 elements differ in location between nearly identical genomes

Result 3) IS5 from can hotwire gene expression

Reposted by Jesse M. Shapiro, Simon Roux, Alan McNally

surtlab.bsky.social
Dave Baltrus 🦦 @surtlab.bsky.social · 10d
Hey y’all,

New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae

www.microbiologyresearch.org/content/jour...
Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae
Insertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strain...
www.microbiologyresearch.org

Reposted by Simon Roux

jcamthrash.bsky.social
Cameron Thrash @jcamthrash.bsky.social · 10d
Phage-microbe interactions may contribute to the population structure and dynamics of hydrothermal vent symbionts academic.oup.com/ismecommun/a... #jcampubs

Reposted by Simon Roux

sansculottid.es
The French Republican Calendar @sansculottid.es · 11d
Today is Quintidi the 15th of Pluviôse in the year 234.
Pluviôse is the month of rain.
Today we celebrate cows.#JacobinDay

More information on cows
An old time-y illustration of a Cows.

Reposted by Simon Roux, Jay T. Lennon

spearmicrobe.bsky.social
John Spear @spearmicrobe.bsky.social · 11d
Want to ride the front of the wave of all-things-microbiology; field work, cultivation, microscopy, molecular, bioinformatics and AI tools? Me too!
Please join us @mblscience.bsky.social for the 2026 Summer Microbial Diversity Course!
Applications due soon.
www.mbl.edu/education/ad...
Microbial Diversity | Marine Biological Laboratory
The goal of the course is to teach professors, postdocs and advanced graduate students how to discover, cultivate, and isolate diverse microorganisms catalyzing a breadth of chemical transformations, ...
www.mbl.edu

Reposted by Simon Roux

axelvisel.bsky.social
Axel Visel @axelvisel.bsky.social · 11d
Myth of Fact?

🌿Plant pangenomes show massive presence-absence variation affecting protein-coding gene content 🧬

@jgi.doe.gov's @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social and Avinash Sreedasyam searched for answers

academic.oup.com/nargab/artic...
Four-panel “expanding brain” meme. Panel 1 shows a small glowing brain with the text “PAV reflects evolution.” Panel 2 shows a brighter brain with the text “PAV reflects genome quality.” Panel 3 shows an even brighter brain with the text “PAV reflects annotation method.” Panel 4 shows a fully illuminated brain with rays of light and the text “Re-annotate everything before interpreting biology.”

Reposted by Ben C. Sheldon, Simon Roux, Craig R. Primmer , and 3 more

jsmartin.bsky.social
Jordan S. Martin @jsmartin.bsky.social · 11d
I am looking for a PhD student to join my new Socio-Eco-Evo group, hosted in Katie Peichel's Evolutionary Ecology Division @ University of Bern. We're offering a fully funded 4-year position, studying social plasticity and behavioral adaptation among stickleback in Greenland. Please share around!