Simon Roux

@simrouxvirus.bsky.social

3.7K 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.

Videos

Environmental science 40%

Biology 33%

Posts Replies Media Videos

Reposted by Peter Thorne, Simon Roux, Trevor A. Branch , and 1 more Peter Thorne, Simon Roux, Trevor A. Branch, Stephen D. Murphy

Helen Czerski @helenczerski.bsky.social · 13h

Oh, I love this. A new species of sea anemone was discovered recently that parks itself on top of a hermit crab shell like a hat. It seems to feed partly off the crab's faeces, but it also excretes a hard shell that extends the crab's home. In return, it's carried around the seafloor like a king.

Pictures of a pink sea anemone sitting on top of a hermit crab shell.

Reposted by Simon Roux, Delphine K. Farmer

Linsey Marr @linseymarr.bsky.social · 18h

Thanks to Erica Hartmann for leading a newly published paper, "Ten questions concerning indoor dust."

What is it?
Where does it come from?
How does it mediate environmental exposures?
How does it affect chemicals indoors?

www.sciencedirect.com/science/arti...

Dust life cycle: sources, elimination, exposure

Reposted by Simon Roux

Maria Dzunkova @dzunkovam.bsky.social · 18h

Our Springer Nature book is just published! Big thanks to the co-editor Chris Rinke
@chrisrinke.bsky.social and to all book contributors, coming from @i2sysbio.es, @jgi.doe.gov and many other institutes I couldn't find on BlueSky
link.springer.com/book/10.1007...
#microsky #singlecell #genomics 🧪🦠

Single-Cell Omics in Microbiome Research

This volume introduces single-cell microbial (gen)omics as an innovative approach to study microbial diversity and symbiosis

link.springer.com

Reposted by Richard E. Lenski, Simon Roux

MSU MGI @msumgi.bsky.social · 19h

The Long-Term Evolution Experiment has returned home. Led by Professors Richard Lenski (@relenski.bsky.social) and Jeffrey Barrick, this groundbreaking work continues to reveal how bacteria evolve in real time. 12 flasks. 1 legacy.

🔗https://tinyurl.com/f6vjyjvr

Rich Lenski adds information to the Long-Term Evolution Experiment lab notebook after restarting the experiment at MSU. Jeff Barrick and Devin Lake stand behind him.

Reposted by Simon Roux

Dominik Lücking @dominikluecking.bsky.social · 1d

I'm looking for a specific figure I saw on bsky recently on here: It was a heatmap-like plot showing the effectiveness of vaccines. X axis was time, Y axis was different viruses / diseases and you could easily see how each of them disappeared after a vaccine was developed. Any ideas?

Reposted by Simon Roux, Dustin J. Marshall

Lars Gamfeldt @gamfeldt.bsky.social · 1d

Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)

Reposted by Simon Roux

Brian D. Wade @astrobrian.bsky.social · 3d

Strain displacement in microbiomes via ecological competition
#microbes #ecology #microSky

www.nature.com/articles/s41...

Strain displacement in microbiomes via ecological competition - Nature Microbiology

Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

www.nature.com

Reposted by Simon Roux

Quanta Magazine @quantamagazine.bsky.social · 3d

Every cubic meter of air contains anywhere from 10 to 10 million microbes, depending on the altitude, location, season and time of day. At an observatory Watop Puy de Dôme, a 4,800-foot inactive volcano in France, microbiologists sample the aeromicrobiome.

Microbes Also Change the Climate. Could That Help Us? | Quanta Magazine

A collection of short dispatches from the field of climate microbiology conveys the contributions that single-celled life forms make to our climate system, and how we can work with them to address…

www.quantamagazine.org

Reposted by Simon Roux

Sullivan Lab at OSU @sullivan-lab.bsky.social · 3d

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

Scalable and systematic hierarchical virus taxonomy with vConTACT3

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

doi.org

Reposted by Simon Roux, Jacob Montgomery, Jesse D. Berman , and 3 more Simon Roux, Jacob Montgomery, Jesse D. Berman, Masatoshi Katabuchi, Connor Morozumi, Jason J. Mercer

Hadley Wickham @hadley.nz · 4d

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap

dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

github.com

Reposted by Simon Roux

Sarah Whorley, Ph.D. @dralgaegirl.bsky.social · 4d

#PhD opportunity in Spain from my fellow lab alumni #PFAS #Bisphenols #Neuro

Reposted by Simon Roux

Antonio Camargo @apcamargo.bsky.social · 4d

To facilitate adoption by the community, we provide online tools to allow users to explore UHGV in the browser. If you don't mind using the command line, we also provide all of the data for download :)
🌐 uhgv.jgi.doe.gov (8/8)

UHGV

A comprehensive resource of viruses from the human gut microbiome that includes thoroughly annotated genomes, protein structures, and a novel hierarchical classification system that systematically org...

uhgv.jgi.doe.gov

Reposted by Simon Roux

Antonio Camargo @apcamargo.bsky.social · 4d

Another key challenge in virome research is that most viruses lack taxonomic classification, leading to ad hoc approaches that hinder cross-study comparisons. To address this, we developed a taxonomy-like framework and a tool for assigning user's genomes to UHGV clusters. (4/8)

Reposted by Simon Roux, Alan McNally

Antonio Camargo @apcamargo.bsky.social · 4d

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

Reposted by Simon Roux

Claus Wilke @clauswilke.com · 4d

I think I understand how it can be that LLMs are both exceptionally good and quite terrible at programming. It's because there are two entirely different skillsets that we both call "good at programming." LLMs have only one of them.
blog.genesmindsmachines.com/p/llms-excel...

LLMs excel at programming—how can they be so bad at it?

My explanation for the mystery of why LLMs can be both exceptionally good and quite terrible at programming.

blog.genesmindsmachines.com

Reposted by Simon Roux

Patrick Pausch @patrick-pausch.bsky.social · 4d

After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...

An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology

An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

www.nature.com

Reposted by Simon Roux, Mart Krupovìč, José R. Penadés

Sorek Lab @soreklab.bsky.social · 5d

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides

tinyurl.com/ch3damp

We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity

Revealed by the amazing Ilya Osterman. See his thread below👇

Reposted by Scott C. Doney, Brian J. Enquist, Jesse M. Shapiro , and 4 more Scott C. Doney, Brian J. Enquist, Jesse M. Shapiro, Simon Roux, Elena Litchman, Joshua S. Weitz, James E. Wood

Tami Lieberman @contaminatedsci.bsky.social · 5d

If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...

Faculty Position in the Department of Civil and Environmental Engineering and the Schwarzman College of Computing - cee.mit.edu

The Department of Civil and Environmental Engineering (CEE), together with the Schwarzman College of Computing (SCC) at the Massachusetts Institute of Technology (MIT) in Cambridge MA, seeks candidate...

cee.mit.edu

Reposted by Simon Roux

Carolyn Rasmussen @carolynplants.bsky.social · 6d

#OverlyHonestMethods 🤣 with Steph Martinez

I’m sitting on top of a blue car to get a mediocre picture of a maize plant with a black tablecloth underneath. With grad student Steph Martinez

Reposted by Simon Roux

Ingrida Olendraite @ingrida.bsky.social · 6d

RNA Virus Journal Club – Upcoming Talk - this thursday (Nov 6th !)

With @rdrpsummit.bsky.social - excited to announce talk and discussion with Dr Sanguu Kim about HF nanopore sequencing strategy for virology :)

calendar.app.google/oyRVP6v5Tvjg...
CET: 14:00–15:00,
Format: 30 min + 30 min

CLAE: A High‐Fidelity Nanopore Sequencing Strategy for Read‐Level Viral Variant Detection and Environmental RNA Virus Discovery

High-fidelity Nanopore sequencing offers a cost-effective, portable path to uncovering viral dark matter in complex environments—but suffers from severe read-length bias, low throughput, and limited ...

doi.org

Reposted by Simon Roux

Aude Bernheim @audeber.bsky.social · 6d

Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).

Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky

Labs in bacterial immunity

docs.google.com

Reposted by Simon Roux

Clara Torres-Barceló @clara-inrae.bsky.social · 6d

L’Europe autorise son premier additif phagique 🧫🐔 ! Une avancée pour limiter les antibiotiques… mais vigilance : l’histoire pourrait se répéter. #phages #OneHealth @phimresearch.bsky.social @inrae-dpt-spe.bsky.social @sfp-france.bsky.social
www.jle.com/fr/revues/vi...

JLE - Virologie - Commercialisation en Europe d’un nouvel additif alimentaire à base de bactériophages dans le contexte « une seule santé » : qu’en disent les autorités réglementaires ?

www.jle.com

Reposted by Simon Roux

Rob Edwards @linsalrob.bsky.social · 7d

Expressions of interest are now open to host the @isvm-society.bsky.social #VOM28 conference.

Let us know if you'd like to host the world's leading conference on viruses of microbes!

isvm.org

#phagesky #virus

ISVM – International Society for Viruses of Microorganisms

isvm.org

Reposted by Simon Roux

Sarah Bagby @scbagby.bsky.social · 7d

Microbial eukaryote folks, you've got two more weeks to apply for this TT job: apply.interfolio.com/174456. We're a supportive department with a great breadth of interests, with really sharp students, in a very livable city with the nation's best park system. Come join us!

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

apply.interfolio.com

Reposted by Simon Roux

PCE3 @pce3-sci.bsky.social · 7d

Looking for a PostDoc in Origins? The Wisconsin Center for Origins Research might be the right place for you!
Apply here:
wicor.wisc.edu/postdoc/

Reposted by Simon Roux

Max Renner @maxrenner.bsky.social · 7d

Our new preprint is out 🥳🥳🥳

Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?

👇

Reposted by Simon Roux

Emmanuele Severi @emmseveri.bsky.social · 8d

#phagesky #phage #microsky

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

Rolling out plaque-2-sequence: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques

Rapid, accurate, and scalable sequencing of bacteriophage genomes is critical to advance phage therapy, build phage biobanks and understand phage genomic diversity. Current methods are based on sequen...

www.biorxiv.org

Reposted by Simon Roux

Quadram Institute @quadraminstitute.bsky.social · 8d

"Should #phage therapy look like an antibiotic prescription, standardised and mass-produced, or more like personalised cancer treatment, tailored to the individual? The answer is: both."

💬 @deuskamya.bsky.social

Shades of Phage: The complexity of the biology of bacteriophages - Quadram Institute

PhD student Deus Dedit Kamya explains the nuances of biology bacteriophages and their potential for live-saving treatments

buff.ly

Reposted by Simon Roux

Kate Michie @kmichie.bsky.social · 10d

This is amazing work lead by Tom (@tlitfin.bsky.social) in my team. Always trying to get more for less and making computing efficient. So satisfying making science resources go further. Boltz2 is great for protein structure prediction and hopefully LMI4Boltz extends its use. Code on GitHub… 🧶🧬

LMI4Boltz: Optimizing VRAM utilization to predict large macromolecular complexes with consumer grade hardware

AlphaFold2 has revolutionized structural biology by enabling the prediction of protein structures approaching experimental quality. AlphaFold3 extends this framework to support modelling broad biomole...

www.biorxiv.org

Reposted by Simon Roux

DSMZ Digital Diversity @dsmzd3.bsky.social · 10d

📣 Open position:

We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.

Read and share!

👉 www.dsmz.de/dsmz/career/...

🧪🦠🌱🦋💽

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