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simrouxvirus.bsky.social
Simon Roux
@simrouxvirus.bsky.social
3.8K followers 1.8K following 180 posts

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

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Environmental science 40%
Biology 33%
Posts Replies Media Videos

Reposted by Simon Roux

pengellab.bsky.social
Philipp Engel @pengellab.bsky.social · 18h
New preprint from our lab! www.biorxiv.org/content/10.1...
@aiswarya.bsky.social tested the role of priority effects in shaping the honeybee gut microbiota using an elegant combinatorial experimental design. A thread🧵....
| bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org

Reposted by Simon Roux

erinedoherty.bsky.social
Erin Doherty @erinedoherty.bsky.social · 18h
Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.

www.sciencedirect.com/science/arti...
Divergent viral phosphodiesterases for immune signaling evasion
Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to …
www.sciencedirect.com

Reposted by Simon Roux

asm.org
ASM @asm.org · 1d
Share your research to the Applied & Environmental Microbiology Meeting at ASM Microbe 2026.

Early Abstract Deadline: Dec. 2, 2 p.m. ET.

asm.social/2HP
You work powers global resilience

Reposted by Simon Roux

colincarlson.bsky.social
Colin Carlson @colincarlson.bsky.social · 1d
NEW! 🦠🦧 We revisited a perplexing paradox: do wildlife really pose less of a risk to human health as they become more endangered? Turns out, it's sampling bias all the way down: conservation risks correlate with disease surveillance blindspots. 🔓 esajournals.onlinelibrary.wiley.com/doi/full/10....
Viral diversity and zoonotic risk in endangered species
A growing body of evidence links zoonotic disease risk, including pandemic threats, to biodiversity loss and other upstream anthropogenic impacts on ecosystem health. However, there is little current...
esajournals.onlinelibrary.wiley.com

Reposted by Simon Roux

biorxiv-microbiol.bsky.social
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 1d
A geothermal amoeba sets a new upper temperature limit for eukaryotes https://www.biorxiv.org/content/10.1101/2025.11.24.690213v1

Reposted by Simon Roux

cmichaelrose.bsky.social
Christopher Rose @cmichaelrose.bsky.social · 1d
I am looking for a PostDoc to join my group at Genentech to drive the development of proteomics technologies to fuel target and therapeutic discovery and development. Check out the link below!

careers.gene.com/us/en/job/20...

Reposted by Simon Roux

gbouras13.bsky.social
George Bouras @gbouras13.bsky.social · 1d
Keeping the naming convention - PholdAPhage - great work Renee github.com/reneegreen81... #ABACBS2025

simrouxvirus.bsky.social
Simon Roux @simrouxvirus.bsky.social · 1d
Some fantastic sessions being planned for ASM Microbe 2026, including "Long-term Dynamics of Environmental Microbiomes", and "Eco-evolutionary Dynamics of Phages and Their Roles in Horizontal Gene Transfer". Get your abstract(s) ready, and join us June 4–7, 2026 in D.C. ! asm.org/events/asm-m...

Reposted by Simon Roux

widdowquinn.bsky.social
Leighton Pritchard @widdowquinn.bsky.social · 2d
Teaching experimental design again tomorrow and once more reminded of this awesome distillation of why we need to teach it.

www.youtube.com/watch?v=PbOD...
Biostatistics vs. Lab Research
YouTube video by JavaMama926
www.youtube.com

Reposted by Shannon Vallor, Simon Roux, Alistair Munro , and 2 more

awest.uk
Andrew West @awest.uk · 4d
The malwarebytes Google opting-your-emails-into-ai-training thing is not true. The post is based on one bad tweet.

I know anti-tech lamenting is a Bluesky core principle, but please use the same judgement you would for any other clickbait.

www.theverge.com/news/826902/...
Google denies ‘misleading’ reports of Gmail using your emails to train AI
Google says “we do not use your Gmail content for training our Gemini AI model.”
www.theverge.com

Reposted by Simon Roux

steventdennis.bsky.social
Steven T. Dennis @steventdennis.bsky.social · 4d
Tonight on #FridayNightZillow: A trio of cheap, fab Victorians in Wichita, recently named America's most affordable major city, starting at just $190K! Also showing a blank check mansion with its own race track (!) and a lot more, so stick around!🧵

Reposted by Simon Roux, David Stott

sansculottid.es
The French Republican Calendar @sansculottid.es · 4d
Today is Duodi the 2nd of Frimaire in the year 234.
Frimaire is the month of frost.
Today we celebrate cattle turnips.#JacobinDay

More information on cattle turnips
An old time-y illustration of a Cattle turnips.

Reposted by Simon Roux, Alistair Munro, Ben Barr , and 9 more

sashagusevposts.bsky.social
Sasha Gusev @sashagusevposts.bsky.social · 4d
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com

Reposted by Simon Roux

fronzeslab.bsky.social
Rémi Fronzes @fronzeslab.bsky.social · 4d
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.

www.science.org/doi/10.1126/...
A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system
Cryo-EM structure reveals how a ubiquitin-like protein orchestrates assembly of a bacterial weapon system.
www.science.org

Reposted by Simon Roux, Marc Strous, Maria Faticov

daanspeth.bsky.social
Daan Speth @daanspeth.bsky.social · 4d
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org

Reposted by Simon Roux

kepatitis-c.bsky.social
Everyone's least favorite lab mate @kepatitis-c.bsky.social · 5d
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...

Reposted by Simon Roux

karthik-a.bsky.social
Karthik Anantharaman @karthik-a.bsky.social · 5d
Excited to share our new review article on Viral Dark Matter led by PhD student @kosmopoulos.bsky.social. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology. pubs.acs.org/doi/10.1021/...
Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
pubs.acs.org

Reposted by Simon Roux, Mart Krupovìč, Mya Breitbart , and 2 more

aharms485.bsky.social
Alexander Harms @aharms485.bsky.social · 5d
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Reposted by Simon Roux

microbiomedata.org
National Microbiome Data Collaborative (NMDC) @microbiomedata.org · 5d
We're headed to ASMCUE in San Antonio, TX this weekend! Educators, stop by our workshop with KBase tomorrow and our Microbrew Talk on Sunday to learn more about leveraging the NMDC's resources for microbiome workforce development and undergraduate education🧪 @ASM.org @kbase.us

Reposted by Simon Roux

merenbey.bsky.social
A. Murat Eren (Meren) @merenbey.bsky.social · 5d
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!

Please find more information on the venue, program, and the application form here, and spread the word 😇

anvio.org/workshops/20...

Reposted by Simon Roux

lgamon.bsky.social
Luke Gamon @lgamon.bsky.social · 5d
Quick heads up - there will soon be a job posting for a Staff Scientist / Senior Staff Scientist in our lab in Copenhagen to support all our mass spec proteomics adventures!

Great colleagues, lots of cool projects… and you’ll get to work with me 😅

Please DM if you’re interested!

Reposted by Simon Roux

judithmank.bsky.social
Judith Mank @judithmank.bsky.social · 5d
Team fish - we need your help! We are trying to build a database of all the fish chromosome-scale genomes where sex chromosomes have been identified. Have you build one or some? Do you know someone who has? Can you post the link in the comments? Please spread the word and repost! Thank you!

Reposted by Simon Roux

asm.org
ASM @asm.org · 6d
Early abstract submissions for ASM Microbe 2026—now 3 fully integrated meetings within 1 microbial world—are officially open. Submit by Dec. 2, 2 p.m. ET to elevate your research, spark new collaborations and join the conversations defining what’s next. asm.org/events/asm-m...
Early abstract submission now open!

Reposted by Simon Roux

apragsdale.bsky.social
Aaron Ragsdale @apragsdale.bsky.social · 6d
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.

Apply by Dec 15th here: shorturl.at/4a4O6
Early Career Scientist Awards 2026
Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.
urldefense.com

Reposted by Jesse M. Shapiro, Simon Roux, José R. Penadés , and 1 more

ellinoralseth.bsky.social
Ellinor Alseth @ellinoralseth.bsky.social · 6d
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
journals.plos.org

Reposted by Simon Roux

sianowen.bsky.social
Siân Owen @sianowen.bsky.social · 7d
Faculty search at UAlbany targeting folks broadly applying AI/ML to infectious disease research!! Please RT 🙏
albany.interviewexchange.com/jobofferdeta...

Reposted by Simon Roux

jwbee.bsky.social
Jeff Baker @jwbee.bsky.social · 7d
New lunch spot in downtown Berkeley: Aburaya Japanese-style fried chicken, every weekday, inside Spats!

Reposted by Simon Roux

simrouxvirus.bsky.social
Simon Roux @simrouxvirus.bsky.social · 7d
For prok vs euk, I like to look at RBS (if you see mostly SD, I'd argue it's a good sign you have a genome adapted to a prok machinery). That's assuming that you have predicted cds of course.
Also don't dismiss a viral origin for anything that is "sort of bacterial like but no hit in any db" 😁

Reposted by Simon Roux

titus.idyll.org
Titus Brown @titus.idyll.org · 7d
OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?