Simon Roux
@simrouxvirus.bsky.social
Virus-obsessed bioinformatician, DOE JGI Scientist, Enjoy exploring the viral world with #metagenomics and other cool #omics toys. He/him. Opinions my own.
Reposted by Simon Roux
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
🔗https://tinyurl.com/f6vjyjvr
November 10, 2025 at 3:25 PM
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
🔗https://tinyurl.com/f6vjyjvr
Reposted by Simon Roux
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 🧪🦠
@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
November 10, 2025 at 4:30 PM
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 🧪🦠
@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 🧪🦠
Reposted by Simon Roux
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.
November 10, 2025 at 9:57 PM
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.
Reposted by Simon Roux
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...
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...
November 10, 2025 at 4:56 PM
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...
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...
Reposted by Simon Roux
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?
November 10, 2025 at 10:34 AM
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
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)
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)
November 10, 2025 at 9:32 AM
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)
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
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
October 31, 2025 at 9:40 PM
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… 🧶🧬
Reposted by Simon Roux
Strain displacement in microbiomes via ecological competition
#microbes #ecology #microSky
www.nature.com/articles/s41...
#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
November 8, 2025 at 1:25 AM
Strain displacement in microbiomes via ecological competition
#microbes #ecology #microSky
www.nature.com/articles/s41...
#microbes #ecology #microSky
www.nature.com/articles/s41...
Reposted by Simon Roux
🚨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 👇
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
November 7, 2025 at 4:36 PM
🚨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 👇
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 👇
Reposted by Simon Roux
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
November 7, 2025 at 4:46 PM
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.
Reposted by Simon Roux
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...
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
November 6, 2025 at 3:43 PM
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...
blog.genesmindsmachines.com/p/llms-excel...
Reposted by Simon Roux
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.
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
November 6, 2025 at 11:25 PM
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.
genzplyr is dplyr, but bussin fr fr no cap.
Reposted by Simon Roux
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👇
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👇
November 6, 2025 at 10:39 AM
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👇
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 Simon Roux
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
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Simon Roux
November 6, 2025 at 6:58 PM
Reposted by Simon Roux
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.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
November 6, 2025 at 5:26 PM
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.jgi.doe.gov (8/8)
Reposted by Simon Roux
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)
November 6, 2025 at 5:26 PM
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
🚨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...
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...
November 6, 2025 at 5:26 PM
🚨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...
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
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
November 5, 2025 at 7:27 PM
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...
Reposted by Simon Roux
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
November 3, 2025 at 6:32 PM
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!
Reposted by Simon Roux
#OverlyHonestMethods 🤣 with Steph Martinez
November 4, 2025 at 11:10 PM
#OverlyHonestMethods 🤣 with Steph Martinez
Reposted by Simon Roux
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...
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
November 4, 2025 at 3:04 PM
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...
www.jle.com/fr/revues/vi...
Reposted by Simon Roux
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
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
November 4, 2025 at 3:10 PM
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
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
Reposted by Simon Roux
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
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
November 4, 2025 at 3:06 PM
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
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Reposted by Simon Roux
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
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
November 3, 2025 at 11:36 PM
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
Let us know if you'd like to host the world's leading conference on viruses of microbes!
isvm.org
#phagesky #virus