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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

hannahgreich.bsky.social
Hannah Reich @hannahgreich.bsky.social · 5h
It's that time of year again! I'm looking for suggestions of 'emerging' model organisms for my #CellBio course's final proj:

Organism nomination form here (links to blog on proj info): forms.office.com/r/v8zYgqVe8W

#cellbiology #biology #academicsky #microsky #archaeasky #protistsonsky 🧪 (1/n)

Reposted by Simon Roux

microdarren.bsky.social
Darren Dunlap @microdarren.bsky.social · 2d
It's Friday. Find your motivation.
Screenshot from World of Warcraft of a speech text box from an Orc named "Overworked Peon". He is saying "Work is da poop. Too hard, make me tired. Life sad. But then, burger. Burger worth it"

Reposted by Simon Roux, Mart Krupovìč

ingrida.bsky.social
Ingrida Olendraite @ingrida.bsky.social · 2d
Save the date for phylogenetics!

RNA virus Journal Club returns ( @rdrpsummit.bsky.social ) with @evogytis.bsky.social intro to his "Baltic" - python module to visualise phylogenetic trees.

January 15th (Thu) - EEST Vilnius Time 3:00 PM

Join slack for updates: join.slack.com/t/rdrp-io/sh...

Reposted by Simon Roux, Daniel S. Goldberg

napaaqtuk.bsky.social
Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 2d
I'm really proud of this article. Quyanakpuq @redped.bsky.social for including me on this project. In this discussion between 5 Indigenous academic women, we discuss the intersection between feminism and Indigenous studies, with lots of suggested readings that shaped our thinking in this area.
onlinelibrary.wiley.com

Reposted by Simon Roux

brunlabcaulo.bsky.social
Yves Brun lab @brunlabcaulo.bsky.social · 3d
Canada Research Chairs www.canada.ca/en/impact-pl...: $1M/year for 8 years, plus up to $6M in CFI infrastructure support. Looking for leading researchers abroad interested in AMR research, antibiotic discovery (Pandemicstopai.ca), phages. Email short vision + CV. Tight deadlines: March 10 & June 15
Canada Impact+ Research Chairs - Canada.ca
www.canada.ca

Reposted by Simon Roux

jcamthrash.bsky.social
Cameron Thrash @jcamthrash.bsky.social · 3d
Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊
Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients
Oxygen Minimum Zones (OMZs) are pivotal ocean regions where both lateral and depth-based variations may influence microbial biogeochemical cycling. We used metagenome sequencing to investigate these ...
enviromicro-journals.onlinelibrary.wiley.com

Reposted by Simon Roux, Paul Matthews

jon276.bsky.social
Jon Nichols @jon276.bsky.social · 4d
I’m in this meme and I don’t like it.
#academicsky #academiclife

Reposted by Simon Roux, Joshua S. Weitz

kakape.bsky.social
Kai Kupferschmidt @kakape.bsky.social · 4d
“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪
Fresh conflicts erupt around giant database for flu and COVID-19 sequences
Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic
www.science.org

Reposted by Simon Roux

anthbyte.bsky.social
Sterling L. Wright @anthbyte.bsky.social · 4d
Are you involved in oral microbiome research? 🧬
We’re conducting a brief survey to understand how researchers report metadata for their oral microbiome studies. You must be 18 or older. To be eligible, you must have conducted research on the oral microbiome (past or currently).
Building Consensus on Reporting Oral Microbiome Metadata: A Community Survey
Building Consensus on Reporting Oral Microbiome Metadata: A Community Survey
asu.questionpro.com

Reposted by Simon Roux

Heng Li @lh3lh3.bsky.social · 5d
Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.

Reposted by Simon Roux

environmicrobio.bsky.social
Roland Hatzenpichler @environmicrobio.bsky.social · 5d
We stress the importance of remaining agnostic about the physiology of MCR-encoding Thermoproteota (don't call them methanogens [yet]) in the absence of experimental data because most of these archaea also carry the genetic potential to grow non-methanogenically. #testthymetagenomichypotheses

Reposted by Simon Roux

environmicrobio.bsky.social
Roland Hatzenpichler @environmicrobio.bsky.social · 5d
New paper out in Current Opinion in Microbiology: MCR-encoding (potentially methanogenic) Thermoproteota are widespread and transcriptionally active in diverse anoxic ecosystems! @dr-zj.bsky.social, Matthew Kellom & @emileyeloe-fadrosh.bsky.social. Funded by DOE BER program. tinyurl.com/2fsyxswj 🦠🧪
Phylogeny and ecology of MCR-encoding archaea

Reposted by Simon Roux

vscooper.micropopbio.org
Vaughn Cooper @vscooper.micropopbio.org · 5d
Congratulations to Sean Yu-Hao Wang, Will DePas, @catarmbruster.bsky.social and colleagues on their use of experimental evolution to identify regulators of Mycobacterium abscessus biofilm production!
www.sciencedirect.com/science/arti...
Experimental evolution in the cystic fibrosis chemical environment reveals early TCA cycle flux as a central regulator of Mycobacterium abscessus biofilm formation
Mycobacterium abscessus (MAB) is an emerging opportunistic pathogen that can cause severe, recalcitrant pulmonary infections in susceptible groups, in…
www.sciencedirect.com

Reposted by Simon Roux

ettema.bsky.social
Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 6d
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻

Please repost

Apply here: www.wur.nl/en/vacancy/p...

Reposted by Simon Roux

jgi.doe.gov
Joint Genome Institute @jgi.doe.gov · 6d
In honor of the IMG/M data portal's 20th anniversary, we want to hear how you use it in your work and what type of science it has enabled you to do.

You can share how IMG has helped your science using this form: https://jointgeno.me/IMGStoriesForm

@berkeleylab.lbl.gov @axelvisel.bsky.social 🖥️🧬 🦠

Reposted by Simon Roux

asm.org
ASM @asm.org · 6d
The latest virology research shapes public health in real time. 🌍

Join us to explore how traditional food markets sustain millions but also pose zoonotic risks—and how One Health strategies can reduce them without disrupting livelihoods.

asm.social/2KR
Zoonotic Disease Risk at Traditional Food Markets January 29, 2026 Frida E. Sparaciari, Ph.D., Institut Pasteur du Cambodge, Phnom Penh, Cambodia Tuli Mukhopadhyay, Ph.D. (moderator), Indiana University Stacey Schultz-Cherry, Ph.D. (host), Co-Editor in Chief, Journal of Virology, St. Jude Children's Research Hospital journals.asm.org

Reposted by Simon Roux

ashleyweiss.bsky.social
Ashley Weiss (she/her) @ashleyweiss.bsky.social · 6d
Excited to share my publication, showing that co-residing bacteria in the gut alters population heterogeneity in C. difficile. Thank you to my co-author, Jilarie Santos-Santiago, and our collaborative team from the labs of @joeyzacks.bsky.social and @ritatamayo.bsky.social! 
doi.org/10.1128/jb.0...
Enterococcus faecalis modulates phase variation in Clostridioides difficile | Journal of Bacteriology
Clostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.
journals.asm.org

Reposted by Simon Roux

epcrocha.bsky.social
Eduardo Rocha @epcrocha.bsky.social · 6d
The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky

Reposted by Jesse M. Shapiro, Simon Roux

lcatherines.bsky.social
Laura Suttenfield @lcatherines.bsky.social · 6d
Happy new year! The second big project of my PhD in Rachel Whitaker's lab is now up! 🎉 We look at how provirus infection affects the evolution of the bacterial chromosome with different types of viral induction – with CRISPRs or antibiotics. Take a peek 🦠 www.biorxiv.org/content/10.6...
Provirus induction diversifies adaptive variation in Pseudomonas aeruginosa lysogen populations
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that forms chronic infections in people with cystic fibrosis. Often P. aeruginosa strains are lysogens, infected with proviruses, that ...
www.biorxiv.org

Reposted by Simon Roux

carolynbertozzi.bskyverified.social
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 8d
A tribute to Stuart Kornfeld, pioneering #glycotime scientist whose work on mannose-6-phosphate receptor lysosomal trafficking (among many other contributions) was highly influential to our work 🫡

www.jci.org/articles/vie...
JCI - A tribute to Stuart A. Kornfeld (1936–2025)
www.jci.org

Reposted by Simon Roux

jgi.doe.gov
Joint Genome Institute @jgi.doe.gov · 9d
Deadline Jan. 9: Submit your abstract to give a short talk at our 2026 "Empowering Automated Laboratories" joint meeting with the Environmental Molecular Sciences Laboratory. 🖥️🧬

More info: usermeeting.jgi.doe.gov
Registration: bit.ly/EMSLJGIusermeeting2026

@berkeleylab.lbl.gov @biosci.lbl.gov
Integrating Experimentation with Data | Joint Genome Institute
Join the Joint Genome Institute and the Environmental Molecular Sciences Laboratory for “Empowering Automated Laboratories: Integrating Experimentation with Data.”
usermeeting.jgi.doe.gov

Reposted by Simon Roux, William G. Wade

natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · 9d
#NewResearch

While oral bacteria rarely colonize the healthy gut, they dominate the gut microbiome of patients with chronic liver disease. Here a bacterial gene encoded by microbial translocators is linked to gut barrier disruption and fibrosis

#MicroSky 🦠

www.nature.com/articles/s41...
Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease - Nature Microbiology
While oral bacteria rarely colonize the healthy gut, they dominate the gut microbiome of patients with chronic liver disease. Here a bacterial gene encoded by microbial translocators is linked to gut ...
www.nature.com

Reposted by Simon Roux

wintherhave.bsky.social
Caroline Winther-Have @wintherhave.bsky.social · 9d
New paper! Host-specific phage diversity in Atlantic salmon gut microbiota shows distinct viral patterns. Phage pressure was minimal in host-dependent Mycoplasma-dominated guts but high with opportunistic Aliivibrio. Thanks to all co-authors! doi.org/10.1093/isme...
Ecological strategies of bacteria shape inherent phage diversity in Atlantic salmon gut microbiomes
Abstract. Understanding host-specific phage diversity is essential for deciphering the complex dynamics shaping microbial ecology and evolution. However, t
doi.org

Reposted by Simon Roux, Smith

surtlab.bsky.social
Dave Baltrus 🦦 @surtlab.bsky.social · 10d
I know many of you know Joe James (of Binning Singletons)

Joe and his family had a terrible tragedy occur on Christmas. If you can give, this is a good family to help out

gofund.me/5cbfe22fe
Donate to Honoring Sarah James Through Education, organized by Joe James
Honoring Sarah James & Supporting Her Children’s Future On Christmas, our com… Joe James needs your support for Honoring Sarah James Through Education
gofund.me

Reposted by Simon Roux

marjanghotbi.bsky.social
marjanghotbi.bsky.social @marjanghotbi.bsky.social · 11d
Think you need large volumes for microbial experiments?
Our recent publication introduces HiMEx, a simple, scalable method for microbial ecology. academic.oup.com/ismecommun/a...
🦠 it provides an easy, efficient approach to capturing viral diversity, opening new opportunities for virome analysis.
From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology
Abstract. Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating th
academic.oup.com

Reposted by Simon Roux

doctorbou.bsky.social
Mehdi Bouhaddou @doctorbou.bsky.social · 11d
Thrilled to share the first major preprint from the lab. Viruses are classically viewed as targets of host sensing. Do viruses also sense and respond to the host? We propose viruses may act as “biosensors” of the host signaling state. A thread👇🏾 www.biorxiv.org/content/10.1...
Global Landscape of Human Kinase Motifs in Viral Proteomes
Viruses are classically viewed as targets of host sensing, yet whether they also sense and respond to host cues remains largely unexplored. We propose that host-driven post-translational modification ...
www.biorxiv.org

Reposted by Simon Roux

bffo.bsky.social
BF Francis Ouellette @bffo.bsky.social · 11d
From @jchowning.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for running a virtual program to introduce computational biology at the high school level | #Education #Bioinformatics #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...
Ten simple rules for running a virtual program to introduce computational biology at the high school level
journals.plos.org

Reposted by Simon Roux

jonathanwosen.bsky.social
Jonathan Wosen @jonathanwosen.bsky.social · 12d
If you're a first-year biomedical Ph.D. student, I'd like to hear how your first few months of grad school have been going. I'm a science journalist at @statnews.com and got my Ph.D. in immunology before going into journalism. You can reach me at [email protected]. #journorequest

Reposted by Simon Roux

kgandersen.bsky.social
Kristian G. Andersen @kgandersen.bsky.social · 12d
If you have been following the African swine fever "mystery" in Catalonia, you would have noticed that this had the early hallmarks of a "lab leak" from a nearby facility.

Turns out it wasn't, however.

h/t @acritschristoph.bsky.social @flodebarre.bsky.social

www.infobae.com/espana/2025/...
La Generalitat descarta que el origen del brote de peste porcina africana en Cataluña comenzara en un laboratorio de Barcelona
“La secuenciación genética nos dice que no coinciden las muestras de jabalí con las del IRTA-CResa”, ha declarado el conseller de Agricultura, Òscar Ordeig
www.infobae.com

Reposted by Simon Roux

emggroupucph.bsky.social
emggroupucph.bsky.social @emggroupucph.bsky.social · 13d
[1/3] Is your favorite bacterial isolate hiding a surprise lytic virus with a VERY different lifestyle? Finally I can proudly say that our paper on persistent phages is out in Nature Microbiology. rdcu.be/eWJEp. Well done @peterdoug.bsky.social
Persistent virulent phages exist across bacterial isolates
Nature Microbiology - The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical...
rdcu.be