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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.

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Environmental science 40%
Biology 33%
Posts Replies Media Videos

Reposted by Simon Roux

prsecor.bsky.social
Patrick R. Secor @prsecor.bsky.social · 3h
Friends, please help spread the word about our microbiology REU program at Montana State University.
www.montana.edu/mbi/reu/

Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided.

Details in the attached pic--Feb 14 deadline
🧫🧪🦠#microsky
This Research Experiences for Undergraduates (REU) program is funded by the National Science Foundation to create "points of entry" for students interested in research. Students apply from across the country to spend 10 weeks in Bozeman, Montana this summer (May 26, 2026 - August 1, 2026). Admitted students are paired with a faculty mentor, who serves as an advisor for a student's summer project. Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Our program leverages MSU’s unique microbiology expertise, focusing specifically on microbes living with little or no oxygen (like those in the hot springs of nearby Yellowstone). Low oxygen microbes are essential to human and ecosystem health. They influence (or control) such processes as the breakdown of food in the GI tract, removal of toxins from our bodies and the environment, and production of greenhouse gases. They are also models for understanding the origins of life on this planet, and the potential for life on other planets. A key goal of our program is to recruit students from schools with limited research infrastructure. Being in Montana, a state with a vibrant Native American community, we are particularly interested in applications from students at tribal colleges. However, ANYONE with an interest in microbiology - or biology/science in general - can and should apply. If willing and able, please share/tweet/spread the word far and wide. Applications are due February 14, 2026. Full details can be found through our website http://www.montana.edu/mbi/reu/

Reposted by Rebecca Solnit, Mark A. Lemley, Simon Roux , and 5 more

usili.bsky.social
Mistress Usili (Sage) 🏳️‍⚧️ @usili.bsky.social · 21h
Bilbo looking at his phone top on bottom is ChatGPT After all, why not? Why shouldn't I keep it? You're absolutely right — you found it, it's been with you a long while, and it's only natural to feel fond of something that's served you so well, especially when someone like Gandalf suddenly seems to want it for himself.

Reposted by Simon Roux

axelvisel.bsky.social
Axel Visel @axelvisel.bsky.social · 1d
⏱️Deadline reminder: February 3rd, 2026

Register and submit your abstract for the upcoming @jgi.doe.gov -EMSL meeting in Seattle

Do it now, or do it like Kermit. Up to you.

jgi.doe.gov/work-with-us...

Reposted by Simon Roux

bffo.bsky.social
BF Francis Ouellette @bffo.bsky.social · 1d
From #NCBI Insight | Starting this spring, you will be able to complete all #GenBank submissions in the "Submission Portal GenBank". It will support data types that you currently submit through BankIt | 🧬 🖥️ 🧪 #Bioinformatics #Genomics #OpenScience
⬇️
ncbiinsights.ncbi.nlm.nih.gov/2026/01/27/b...
BankIt Submitters: Upcoming Changes to How You Submit to GenBank - NCBI Insights
Are you a GenBank submitter? Do you use BankIt or the GenBank app in the NCBI Submission Portal to submit your sequences? Or do you split your data between the two systems?    Starting this spring, yo...
ncbiinsights.ncbi.nlm.nih.gov

Reposted by Simon Roux

bffo.bsky.social
BF Francis Ouellette @bffo.bsky.social · 1d
As a reminder to future #Computational #Biology Quick Tips or Ten Simple Rules (or any #PLOSCB #Education paper #PLOSCBTSR #PLOSCBQT):

There are no publication charges for those papers. The attached text is from the last paragraph of our TSR on Quick Tips paper.

doi.org/10.1371/jour...

Reposted by Simon Roux

vscooper.micropopbio.org
Vaughn Cooper @vscooper.micropopbio.org · 1d
Phage therapy offers a powerful tool against AMR infections—but only if we move from isolated cases to coordinated systems. The first initiative of the ASM Health Unit, led by Colleen Kraft and Dev Mittar, will tackle this. Delighted by this scientific leadership, join us!

asm.org/about-asm/as...
Phage Therapy Coordination Network | ASM.org
ASM Health is unlocking bacteriophage therapies for antimicrobial resistance (AMR) through coordinated access and regulatory approvals.
asm.org

Reposted by Simon Roux, Dean Eckles, Julie Novkov , and 2 more

matthighton.bsky.social
Matthew Highton @matthighton.bsky.social · 1d
If Bilbo had Chat GPT

Reposted by Simon Roux, Samuele Ramellini

dianakwon.bsky.social
Diana Kwon @dianakwon.bsky.social · 2d
Looking for sources for a @nature.com story about how researchers are coping in the midst of current events: If you're a PhD or other academic who's struggling to focus with everything that's happening in the world and would like to be interviewed for this story, please get in touch ASAP!

Reposted by Simon Roux

asaflevylab.bsky.social
Asaf Levy @asaflevylab.bsky.social · 2d
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...

How bacteria evolved thousands of precision nanoinjectors?

Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems - Nature Communications
Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...
www.nature.com

Reposted by Simon Roux, Jason Stajich

microbiomeresearch.bsky.social
Microbiome Research Lab, ETH Zürich @microbiomeresearch.bsky.social · 5d
🚨We are hiring a Bioinformatician who will be embedded in our lab and work with members of the NCCR Microbiomes at ETH Zurich, as well as the Institute of Microbiology.🚨
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
Bioinformatician in Microbiome Research
jobs.ethz.ch

Reposted by George A. O’Toole, Simon Roux, Wolfgang Huber

buzzbaum.bsky.social
Buzz Baum @buzzbaum.bsky.social · 5d
A reminder to sign up for the 2026 EMBO archaeal meeting im Cambridge: meetings.embo.org/event/26-arc.... Registration is open. We are looking forward to hosting you!
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
meetings.embo.org

Reposted by Simon Roux

emmseveri.bsky.social
Emmanuele Severi @emmseveri.bsky.social · 5d
#microsky #phagesky #phage defence

www.nature.com/articles/s41...
A bacterial defense system targeting modified cytosine of phage genomic DNA - Nature Communications
In this study, the authors identify and structurally characterize a single-component anti-phage defense system named CMoRE (Cytosine Modification Restriction Endonuclease).
www.nature.com

Reposted by Simon Roux

hobbslabutah.bsky.social
Sam Hobbs @hobbslabutah.bsky.social · 6d
Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)

Reposted by Simon Roux

jcamthrash.bsky.social
Cameron Thrash @jcamthrash.bsky.social · 6d
Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology
Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...
www.nature.com

Reposted by Jesse M. Shapiro, Simon Roux

cibiocm.bsky.social
Segata Lab @cibiocm.bsky.social · 7d
🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10
Baby-to-baby strain transmission shapes the developing gut microbiome - Nature
A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...
doi.org

Reposted by Simon Roux

rachidtahzima.bsky.social
rachidtahzima.bsky.social @rachidtahzima.bsky.social · 7d
Investigating Viral Protein Dynamics remains very challenging in/with the current frameworks

pubs.acs.org/doi/10.1021/...
Evolutionary Constraints Guide AlphaFold2 in Predicting Alternative Conformations and Inform Rational Mutation Design
Investigating structural variability is essential for understanding protein biological functions. Although AlphaFold2 accurately predicts static structures, it fails to capture the full spectrum of f...
pubs.acs.org

Reposted by George A. O’Toole, Simon Roux, Jay T. Lennon

asm.org
ASM @asm.org · 8d
Final call to submit your science! General abstract submission for ASM Microbe 2026 closes Jan. 21 at 2 p.m. ET. This is your last chance to present your research at the meeting. Submit now: asm.social/2Mc
Last chance! Submit your science. Deadline: Jan. 21, 2 p.m. ET.

Reposted by Jonathan A. Eisen, Simon Roux, Alan McNally

relenski.bsky.social
Richard Lenski @relenski.bsky.social · 8d
Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework?

Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
relenski.bsky.social Richard Lenski @relenski.bsky.social · Aug 12
Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
STEPS To It
Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.
telliamedrevisited.wordpress.com

Reposted by Simon Roux

jhdcate.bsky.social
Jamie Cate @jhdcate.bsky.social · 8d
"Use it or lose it." This is great advice for exercise, but when cells need to slow down or go dormant, they need to store ribosomes to recover growth in the future. They use hibernation factors to do this. Here is our latest story on how archaea hibernate ribosomes (1/7):
doi.org/10.64898/202...
doi.org

Reposted by Simon Roux

jaytlennon.bsky.social
Jay T Lennon @jaytlennon.bsky.social · 8d
ALERT: Abstract submission deadline is tomorrow (21 January) for the ASM Applied & Environmental Microbiology Meeting within ASM Microbe 2026 in Washington, D.C. (4-7 June). @asm.org

asm.org/events/asm-m...

🧵 for more information including themes for Contributed Abstracts for In-Depth Sessions:
ASM Microbe | Abstracts
ASM Microbe showcases the best microbial sciences in the world and provides a one-of-a-kind forum to explore everything from basic microbiology to translation and application.
asm.org

Reposted by Jesse M. Shapiro, Simon Roux, Mart Krupovìč

merenbey.bsky.social
A. Murat Eren (Meren) @merenbey.bsky.social · 8d
We just released #anvio v9, "eunice" 🎉

This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.

Read the release notes:

github.com/merenlab/anv...

Visit our up-to-date web page:

anvio.org

Reposted by Simon Roux, Valentin Loux, Alan McNally

torstenseemann.bsky.social
Torsten Seemann @torstenseemann.bsky.social · 8d
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.

libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix

github.com/ebiggers/lib...
GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
github.com

Reposted by Simon Roux

ianhewson.bsky.social
Ian Hewson @ianhewson.bsky.social · 9d
We have a lot of interest in culturing the Dino Triops (Cerarium) furca, Protoperidinium, and a couple of others. Only problem is my knowledge of Dino culture is awful. Anyone have any experience or advice? Or want to collaborate :)?

Reposted by Simon Roux

cnyasm.bsky.social
CNY ASM @cnyasm.bsky.social · 9d
Excited to announce the re-establishment of the Central New York Branch of the American Society for Microbiology (CNY ASM)! Founded in 1921, revived in 2025 to support collaboration, inclusive programming, and microbiologists at all career stages! This is our official BlueSky account!

Reposted by Simon Roux

jamesgurney.bsky.social
James Gurney @jamesgurney.bsky.social · 9d
Phage folks who use the wizard DNA clean up kit to extract Phage DNA, I understand how the silica can hold onto DNA, how does the kit open up the phage in the first place? Mechanical stress from the 10µm silica beads in the resin? Or does the guanidinium thiocyanate do the job?

Reposted by Simon Roux

behavecolpapers.bsky.social
BehavEcolPapers @behavecolpapers.bsky.social · 9d
Temperate phage evolve to integrate host stress and quorum signals in lysis–lysogeny decisions @PLOSBiology.org
Temperate phage evolve to integrate host stress and quorum signals in lysis–lysogeny decisions
by John B. Bruce, Robyn Manley, Elvina Smith, Philippe Carmona, Sylvain Gandon, Edze R. Westra Temperate phage can transmit both horizontally (lytic cycle) and vertically (lysogenic cycle). Many temperate phage have the ability to modify their lysis/lysogeny decisions based on various environmental cues. For instance, many prophage are known to reactivate when SOS stress responses of their host are triggered. Temperate phage infecting Bacilli can also use peptide signals (“arbitrium”) to control their lysis/lysogeny decisions. However, information from the arbitrium and SOS systems can be potentially conflicting, and it is unclear how phage integrate information carried by these two different signals when making lysis–lysogeny decisions. Here, we use evolutionary epidemiology theory to explore how phage could evolve to use both systems to modulate lysis/lysogeny decisions in a fluctuating environment. Our model predicts that it can be adaptive for phage to respond to both host SOS systems and arbitrium signaling, as they provide complementary information on the quality of the infected host and the availability of alternative hosts. Using the phage phi3T and its host Bacillus subtilis, we show that during lytic infection and as prophage, lysis–lysogeny decisions rely on the integration of information on host condition and arbitrium signal concentrations. For example, free-phage are more likely to lysogenise a stressed host, and prophage are less likely to abandon a stressed host, when high arbitrium concentrations suggest susceptible hosts are unavailable. These experimental results are consistent with our theoretical predictions and demonstrate that phage can evolve plastic life-history strategies to adjust their infection dynamics to account for both the within-host environment (host quality) and the external environment that exists outside of their host (availability of susceptible hosts in the population). More generally, our work yields a new theoretical framework to study the evolution of viral plasticity under the influence of multiple environmental cues.
dlvr.it

Reposted by Jay T. Lennon

simrouxvirus.bsky.social
Simon Roux @simrouxvirus.bsky.social · 10d
🚨 Reminder 🚨 Abstract deadline for ASM Microbe meetings, including the Applied and Environmental Microbiology Meeting, is *Jan 21* ! 👇👇
Join us in DC to share your latest research and hear about new discoveries on microbes in water, on land, and every place in between !
asm.org/events/asm-m...

Reposted by Simon Roux

bejalab.bsky.social
BejaLab @bejalab.bsky.social · 11d
Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...
Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection
Auxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...
www.cell.com

Reposted by Simon Roux, Mart Krupovìč

fnobrega.bsky.social
Franklin Nobrega @fnobrega.bsky.social · 11d
Preprint out: We characterise PUA-Cal-HAD, a widespread bacterial antiphage defence family. An infection cue switches a preassembled complex into an immune filament that drains dNTPs via a coupled two-enzyme cascade, and phage DNA mimics can block filament assembly (anti-polymerisation).
A methylome-derived m6-dAMP trigger assembles a PUA-Cal-HAD immune filament that depletes dNTPs to abort phage infection
Bacteria must distinguish phage attack from normal homeostatic processes, yet the danger signals that trigger many defence systems remain unknown. Here, we show that a PUA-Calcineurin-CE-HAD module from Escherichia coli ECOR28 confers broad anti-phage protection by binding Dam-methylated deoxyadenosine monophosphate (m6-dAMP) generated during phage-induced chromosome degradation. Ligand binding converts a preassembled PUA-Calcineurin-CE hexamer loaded with six HAD phosphatases into a polymerising filament. The filament acts as a high-flux dNTP sink through a two-enzyme cascade: HAD first dephosphorylates dATP to dADP, and Calcineurin-CE then converts dADP to dAMP. dNTP collapse halts phage replication and enforces abortive infection. Multiple mobile-element DNA mimic proteins block filament assembly, revealing a direct phage counter-defence. More broadly, our findings extend a conserved, cross-kingdom paradigm of immune filament assembly to nucleotide-depletion antiviral defence and suggest modified-nucleotide sensing by related PUA-Calcineurin-CE modules as a widespread, underappreciated bacterial strategy. ### Competing Interest Statement The authors have declared no competing interest. NIHR Southampton Biomedical Research Centre, https://ror.org/01qqpzg67, Postdoctoral Bridging Fellowship F.L.N. is supported by a Wessex Health Partners (WHP) and National Institute for Health and Care Research Wessex Experimental Medicine Network (NIHR WEMN), Seed fund National Institutes of Health, GM145888, U24 GM129539) Maloris Foundation Memorial Sloan Kettering Cancer Center, P30-CA008748 Simons Foundation, SF349247 New York State Assembly
www.biorxiv.org

Reposted by Simon Roux

chimerax.ucsf.edu
ChimeraX @chimerax.ucsf.edu · 12d
The ChimeraX DAQplugin computes DAQ scores showing the agreement between atomic models and cryoEM maps. Available from ChimeraX menu Tools / More Tools. cxtoolshed.rbvi.ucsf.edu/apps/chimera...
PDB 7jsn colored by DAQ scores of fit in cryoEM map.