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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

acritschristoph.bsky.social
Alex Crits-Christoph @acritschristoph.bsky.social · 2d
All you want for christmas is.... transposon mutagenesis!

Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.

Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.

Reposted by Simon Roux

sansculottid.es
The French Republican Calendar @sansculottid.es · 2d
Today is Quartidi the 4th of Nivôse in the year 234.
Nivôse is the month of snow.
Today we celebrate sulphur.#JacobinDay

More information on sulphur
An old time-y illustration of a Sulphur.

Reposted by Simon Roux

jgi.doe.gov
Joint Genome Institute @jgi.doe.gov · 2d
Don't miss Paul Jensen of @umich.edu at this year's Integrating Experimentation with Data Annual Meeting, during our session on AI in Action: Automating Experiments for Genomic Exploration.

More info: http://usermeeting.jgi.doe.gov
🖥️🧬
Promotional poster for EMSL and JGI event titled "Empowering Automated Laboratories: Integrating Experiment with Data." Features speaker Paul Jensen with portrait, Seattle Washington from March 3-5, and a Seattle cityscape. Includes QR code and registration link.

Reposted by Simon Roux, Mya Breitbart

cslamo.bsky.social
Claudio Slamovits 🇦🇷🇨🇦🏳️‍⚧️🏳️‍🌈 @cslamo.bsky.social · 2d
🎄 Just published 🎉! Our ongoing genome sequencing of the basal dinoflagellate Oxyrrhis marina uncovered a new lineage of endogenized Polinton-like viruses, OmPLV. Notably, OmPLV encodes ... [cont]
#VirEvol #MicroSky #Mevosky #SymbioSky #ProtistsOnSky
Endogenized polinton-like viruses in the dinoflagellate Oxyrrhis marina uncover novel PolB fusion
Marine viruses are ubiquitous entities that impact the biology of a large fraction of prokaryotic and eukaryotic diversity. Dinoflagellates are heterotrophic, mixotrophic and photosynthetic eukaryotes...
doi.org

Reposted by Simon Roux

pghphageprogram.bsky.social
Pittsburgh Phage Program @pghphageprogram.bsky.social · 3d
Pittsburgh Phage Program — 2025 Wrapped!

To our patients, clinicians, researches,
regulators, and partners— this work doesn’t happen without you. We screened, treated, delivered, learned—and even laid the groundwork for a 2026 trial!
#pittsburghphageprogram #phagetherapy #P3

Reposted by Simon Roux

dj-acid-reflux.bsky.social
Tom Cox @dj-acid-reflux.bsky.social · 3d
If I could say one sentence to cats and make them understand it, it would probably be "If you are going to puke, please do it on a hard surface."

Reposted by Simon Roux

berkeleyside.org
Berkeleyside @berkeleyside.org · 3d
Sauna Aid, a charity supported by many Bay Area saunas, has funded retreats for combat medics, led workshops for refugees and transported saunas to the frontlines in Kharkiv.
Ukrainian soldiers are relaxing in saunas set up by a former Berkeley resident
Sauna Aid, a charity supported by many Bay Area saunas, has funded retreats for combat medics, led workshops for refugees and transported saunas to the frontlines in Kharkiv.
www.berkeleyside.org

simrouxvirus.bsky.social
Simon Roux @simrouxvirus.bsky.social · 3d
Seems like IMG/PR may have some of what you need (img.jgi.doe.gov/cgi-bin/plas... / academic.oup.com/nar/article/...). Probably searching for "Direct terminal repeat" and "No close reference" ? @apcamargo.bsky.social does it sounds right ?
JGI IMG Home
Integrated Microbial Genomes. Bridging the Gap from Sequence to Biology
img.jgi.doe.gov

Reposted by Simon Roux, Ramon Rosselló‐Móra

lauraconsarnau.bsky.social
Laura GomezConsarnau @lauraconsarnau.bsky.social · 3d
Microbial rhodopsins are everywhere in the surface ocean, but were assumed to play a role mainly when nutrients are scarce. Our new study reveals unexpected rhodopsin dynamics tightly linked to phytoplankton blooms.

Reposted by Simon Roux

karthik-a.bsky.social
Karthik Anantharaman @karthik-a.bsky.social · 4d
News article from @uwmadison.bsky.social describing our recent study on viruses in peatland soils! news.wisc.edu/viruses-foun...
Viruses found in carbon-storing wetlands play an active role in shaping ecosystem health
The viruses could also help determine if a wetland has been damaged or if restoration efforts are working.
news.wisc.edu

Reposted by Simon Roux

phylogenomics.bsky.social
Jonathan Eisen @phylogenomics.bsky.social · 4d
Back in the day, I spent a lot of effort pointing out that many claims of lateral gene transfer between taxa were better explained by other phenomena, like gene loss, duplicaiton and deletion, convergence, bad informatics, etc 1/n

Reposted by Simon Roux

fsantoriello.bsky.social
Frank Santoriello @fsantoriello.bsky.social · 5d
The final form of my 2nd postdoc paper with the Bassler Lab! Turns out our favorite quorum-sensing phage isn’t a one-off, but rather a member of a globally dispersed family of phages that sense a universal autoinducer.

#phagesky #microsky

journals.asm.org/doi/10.1128/...
A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species | mBio
The discovery of quorum-sensing responsive linear plasmid phages has transformed understanding of phage-bacterial interactions by demonstrating inter-domain chemical communication. To date, however, e...
journals.asm.org

Reposted by Simon Roux

zaminiqbal.bsky.social
Zamin Iqbal @zaminiqbal.bsky.social · 5d
@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...

Reposted by Simon Roux

evbc.bsky.social
European Virus Bioinformatics Center @evbc.bsky.social · 6d
New study shows older siblings and urban/rural residence strongly shape the infant gut virome at one year, with most exposure-linked vOTUs being phages. 🔬👶🌍 #Virome #InfantHealth
📄 https://doi.org/10.1080/19490976.2025.2501194
👤 EVBC members: Marie-Agnès Petit
The influence of early life exposures on the infant gut virome
The factors influencing the establishment of the gut bacterial community in early life are fairly well studied. However, the factors shaping the infant gut virome remain elusive. Interestingly, ear...
doi.org

Reposted by Simon Roux

biorxiv-bioinfo.bsky.social
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 6d
Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1

Reposted by Simon Roux

jenarna.bsky.social
jenarna.bsky.social @jenarna.bsky.social · 7d
📣Excited to share our (first) VirJenDB publication!
🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration.
🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026!
📃 doi.org/10.1093/nar/...
💻 www.virjendb.org

Reposted by Francis Martin, Simon Roux

aeon.co
Aeon Magazine @aeon.co · 7d
The discovery of organisms that have been alive for many thousands of years requires a revolution in how we understand life. An Essay by @karenlloyd.bsky.social
The discovery of aeonophiles expands our definition of life | Aeon Essays
The discovery of organisms that have been alive for many thousands of years requires a revolution in how we understand life
aeon.co

Reposted by Simon Roux

kindrachukjason.bsky.social
Jason Kindrachuk @kindrachukjason.bsky.social · 7d
Sharing this here at the request of Dr. Florian Krammer:

semmelweisinstitute.ac.at/training-car...

Reposted by Jesse M. Shapiro, Simon Roux

microbiologysociety.org
Microbiology Society @microbiologysociety.org · 8d
Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.
Esther Lederberg in the laboratory in the 1950's. Credit: Estherlederberg.com

Reposted by Simon Roux

maitrejl.bsky.social
Jean Léon Maître @maitrejl.bsky.social · 8d
📣 #Job alert!
Looking to establish your own independent research in cell biology, development or evo-devo?
The @cnrs.fr is recruiting 7 scientists in that area of research.
Here are updated unofficial guidelines. Reach out to members of the committee if you have questions
c3n-cn.fr/section-24-w...

Reposted by Simon Roux

nature.com
Nature @nature.com · 8d
Nature research paper: Gene-specific selective sweeps are pervasive across human gut microbiomes

go.nature.com/48XAQL3
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to meet them.
go.nature.com

Reposted by Simon Roux

hollybik.bsky.social
Holly Bik @hollybik.bsky.social · 9d
Announcing our next #NSFfunded workshop on "Telling Stories Through Data", co-lead by myself + @vgwschutte.bsky.social! It’s half bioinformatics data viz & half #SciComm - this year’s focus is host-associated microbiome datasets. Apply here to join us (form closes 1/10) bit.ly/TSTD2026 #symbiosky

Reposted by Simon Roux

marcomauri.bsky.social
Marco Mauri @marcomauri.bsky.social · 9d
As my time as a researcher at FSU Jena and @microverse.bsky.social in the group of Rosalind Allen comes to an end, I warmly thank all collaborators and colleagues for the excellent science and discussions!

🚨I am (yes, again...) on the job market, looking for higher positions -->
Dr. Marco Mauri, Ph.D.
Postdoctoral Researcher in Biophysics in the "Theoretical Microbial Ecology" group of Prof. Rosalind Allen at the Friedrich-Schiller-University Jena
sites.google.com

Reposted by Simon Roux, Zen Faulkes

johnprensner.bsky.social
John Prensner @johnprensner.bsky.social · 9d
Wow this is a seriously serious supplementary figure from @cellpress.bsky.social today. Panels A through UU.

I get that Cell likes to minimize the number of supplementary figures. But is this really what is happening here?

www.cell.com/cell/fulltex...
Figure S7 with panels A through UU

Reposted by Simon Roux

biorxivpreprint.bsky.social
bioRxivpreprint @biorxivpreprint.bsky.social · 9d
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1

Reposted by Simon Roux

jgi.doe.gov
Joint Genome Institute @jgi.doe.gov · 9d
We're building a data lakehouse (data lake + data warehouse) to improve access to data — and want to hear about your experiences with our systems: https://jointgeno.me/PortalStoriesForm

🖥️ 🧬 🌱 🦠 🧪 🍄‍🟫 🍄
@berkeleylab.lbl.gov @danudwary.secondarymetabolism.com @axelvisel.bsky.social @biosci.lbl.gov

Reposted by Simon Roux, Meera Chand

edcoakes.bsky.social
Ed Cunningham-Oakes @edcoakes.bsky.social · 9d
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬

Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)

Reposted by Simon Roux

alibat.bsky.social
Dr Alison Peel @alibat.bsky.social · 10d
🦇 Two PhD positions available on our new ARC Discovery Grant: "From Diversity to Disease: Viral Ecology, Evolution and Persistence in Bats"

The project will investigate how viral diversity evolves and persists, with a particular focus on recently discovered henipaviruses in Australian flying foxes.
The torso and head of a black flying fox hanging upside down, looking directly at the camera, above the words "PhD positions available in bat viral ecology and evolution".

Reposted by Simon Roux

audeber.bsky.social
Aude Bernheim @audeber.bsky.social · 10d
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.

In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
www.biorxiv.org

Reposted by Simon Roux, Jason Stajich

danudwary.secondarymetabolism.com
Dan Udwary @danudwary.secondarymetabolism.com · 10d
DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form!
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
Tell Us Your JGI Portal Stories
The JGI Portal teams (IMG, Mycocosm, Phycocosm, Phytozome, and SMC) would love to sit with you (over Zoom) to hear your stories relating to your usage of the portals, your unsupported use cases, and p...
jointgeno.me