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simrouxvirus.bsky.social
Simon Roux
@simrouxvirus.bsky.social
3.7K followers 1.7K following 170 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 Media Videos Starter Packs

Reposted by Simon Roux, Wolfgang Huber, Larry W. Hunter , and 1 more

ewanbirney.bsky.social
Ewan Birney @ewanbirney.bsky.social · 8h
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
embl.wd103.myworkdayjobs.com
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Reposted by Simon Roux

odedrechavi.bsky.social
Oded Rechavi @odedrechavi.bsky.social · 1d
Post docs who bring their own funding
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Reposted by Simon Roux, Alan McNally

lancetmicrobe.bsky.social
The Lancet Microbe @lancetmicrobe.bsky.social · 1d
New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
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Reposted by Simon Roux, Eric Thompson, Larry W. Hunter , and 1 more

crick.ac.uk
The Francis Crick Institute @crick.ac.uk · 1d
We're now recruiting early career group leaders at the Crick to lead ambitious research programmes and explore bold scientific questions.

Hear our Director, Edith Heard, explain why the Crick is a unique place for curiosity-driven research.

Apply now ➡️ www.crick.ac.uk/careers-stud...
110 130

Reposted by Simon Roux

anttikarkman.bsky.social
Antti Karkman @anttikarkman.bsky.social · 1d
Why not visit Helsinki next winter? There might be snow.

Abstract submission is open for the Nordic AMR Research Centre Conference 2026.

www.helsinki.fi/en/conferenc...
Nordic AMR Research Centre Conference 2026 | University of Helsinki
4-6 March 2026, Helsinki, Finland
www.helsinki.fi
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Reposted by Simon Roux

tweethinking.bsky.social
Tom Williams @tweethinking.bsky.social · 1d
There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)
The genomic basis of symbiotic integration at University of Bath on FindAPhD.com
PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com
www.findaphd.com
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Reposted by Simon Roux

edgigante.bsky.social
Eduardo Gigante @edgigante.bsky.social · 1d
There are amazing, once-in-a-generation people working at CDC and I am just so lucky to be married to one of them.

www.nature.com/articles/s41...
Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States - Nature Communications
Genomic deletions in poxviruses are not well understood, the authors found large deletions in >2% of Mpox virus genomes during routine surveillance, highlighting their role in poxvirus evolution and potential impact on diagnostics and therapeutics.
www.nature.com
2 5

Reposted by Simon Roux, Jason Stajich

robp.bsky.social
Rob Patro @robp.bsky.social · 1d
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
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Reposted by Simon Roux, Stephen D. Murphy

cathyhernandez.bsky.social
Cathy Hernandez @cathyhernandez.bsky.social · 1d
Very happy to share that I will be starting as an Assistant Professor in the department of Biological Sciences at the University of South Carolina in January! My group will be working on environmental phage ecology and evolution, and I am recruiting for the upcoming year (more info below).
A graphic advertising phage ecology and evolution research at the University of South Carolina, showing a central image of a tide pool flanked by a photo of an agar plate containing diverse microbes and a TEM image of a virus particle.
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Reposted by Simon Roux, Marc Strous

jcamthrash.bsky.social
Cameron Thrash @jcamthrash.bsky.social · 2d
Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope www.nature.com/articles/s41... #jcampubs
Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope - Nature Communications
Loretan and colleagues present a low-cost smartphone-based microscope capable of detecting single-molecule fluorescence. This approach opens doors to personalised and widely distributed applications in diagnostics, biosensing, and science education.
www.nature.com
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Reposted by Simon Roux

scilifelab.se
SciLifeLab @scilifelab.se · 2d
We’re launching a major #recruitment call for staff scientists in #ComputationalBiology, #DataScience, and #AI to strengthen Sweden’s life science research. 🧪🖥️

Positions are based at SciLifeLab sites across Sweden’s leading universities.

Learn more and apply ↓
www.scilifelab.se/news/scilife...
SciLifeLab launches major recruitment call for staff scientists in computational biology, data science and AI
Computational methods and artificial intelligence on large-scale molecular data are transforming the study of biological systems and processes, ranging from molecular structures and cellular processes...
www.scilifelab.se
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Reposted by Simon Roux

dumpyunc.bsky.social
Steven Cook @dumpyunc.bsky.social · 2d
Our group at the Allen Institute is recruiting a technician and postdoc to work on light microscopy-based connectomics. Please DM me or share with anyone you think may be interested in this NIH BRAIN CONNECTS funded project.
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Reposted by Simon Roux

clauswilke.com
Claus Wilke @clauswilke.com · 2d
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
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Reposted by Simon Roux

napaaqtuk.bsky.social
Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 3d
I have a fabulous undergrad who has a lot of experience with QIIME2 & using R to analyze microbiome data. She is looking for a job starting in January. Would love to learn more bench and field skills (will be getting some in her last 2 months). Open to academic, industry, government jobs in the US.
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Reposted by Simon Roux

bossdorf.bsky.social
Oliver Bossdorf @bossdorf.bsky.social · 3d
JOB ALERT! Do you also love large ecological experiments? Become coordinator of our big new geo-biosphere experiment in @terra-cluster.org. 7-year position! Follow link for details.
@gfoesoc.bsky.social
@britishecologicalsociety.org
@ecologicalsociety.bsky.social
@uslter.bsky.social

Please repost!
Stellenangebote: Universität Hohenheim
Aktuelle Stellenangebote der Universität Hohenheim.
www.uni-hohenheim.de
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Reposted by Simon Roux, Joshua S. Weitz

d2mory.bsky.social
David Demory @d2mory.bsky.social · 4d
Happy to share our new work on Temperature-driven biogeography of marine viruses infecting Micromonas:
academic.oup.com/ismecommun/a...
Temperature-driven biogeography of marine giant viruses infecting picoeukaryotes Micromonas
Abstract. Climate shapes the biogeography of microbial and viral communities in the ocean. Among abiotic factors, temperature is one of the main drivers of
academic.oup.com
1 4 9

Reposted by Simon Roux, Mart Krupovìč

daumlab.bsky.social
The Daum Lab @daumlab.bsky.social · 4d
Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...
Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail
This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.
www.science.org
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Reposted by Jesse M. Shapiro, Simon Roux, José R. Penadés , and 1 more

brockhurstlab.bsky.social
Michael Brockhurst @brockhurstlab.bsky.social · 4d
New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
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Reposted by Simon Roux, Elena Litchman, Jennifer Pett‐Ridge , and 2 more

erinrgreen.bsky.social
Erin Green @erinrgreen.bsky.social · 5d
Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404
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Reposted by Simon Roux

aventurini.bsky.social
Andressa M. Venturini @aventurini.bsky.social · 6d
Assembling MAGs from Amazonian soils is a challenge, but it has become one of our most useful tools to understand these complex communities. Check out our new paper at MRA @asm.org doi.org/10.1128/mra.... in collaboration with @louberrios.bsky.social @jubgontijo.bsky.social @mykophile.bsky.social
A catalog of metagenome-assembled genomes from Amazonian forest and pasture soils | Microbiology Resource Announcements
Our group previously recovered 64 bacterial and 5 archaeal metagenome-assembled genomes (MAGs) from Amazonian forest and pasture soils and evaluated their genomic traits (1). Here, we formally announc...
doi.org
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Reposted by Simon Roux

johninnescentre.bsky.social
John Innes Centre @johninnescentre.bsky.social · 7d
Shortlisted candidates will be invited to give a seminar at the Fellows Conference, which will be held on 10 March 2026.

Candidates who win Fellowships will be offered a Tenure Track Group Leader position from the outset, initially for 5 years.

Find out more: www.jic.ac.uk/training-car...
Independent Research Fellowships Leading to Tenured Faculty Positions | John Innes Centre
The John Innes Centre (JIC), is a world leading centre of excellence in plant and microbial sciences based on the Norwich Research Park, UK. We are inviting applications from outstanding researchers…
www.jic.ac.uk
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Reposted by Simon Roux

doradomoralesp.bsky.social
Pedro Dorado-Morales @doradomoralesp.bsky.social · 7d
A plasmid and an ICE teaming up... 🤯😱

www.nature.com/articles/s41...
The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications
Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin polymerization and biofilm formation in vivo.
www.nature.com
5 11

Reposted by Simon Roux

edrybicki.bsky.social
Ed Rybicki 🇿🇲🇿🇦🍷🚀 @edrybicki.bsky.social · 7d
And, I might add, an easily engineerable solution, given our (sadly now abandoned) patent detailing our discovery that you could get efficient transformation of microalgae with Agrobacterium tumefaciens if you immobilise them in a Celite matrix 😁
patents.google.com/patent/AU201...
AU2019389307A1 - Matrix-mediated cell culture system - Google Patents
The invention relates to a matrix-mediated algal cell culture system comprising a porous matrix, a microalgal cell culture comprising cells immobilised on the porous matrix, and a vector including a n...
patents.google.com
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Reposted by Simon Roux

harvardcellbio.bsky.social
Harvard Med Cell Biology @harvardcellbio.bsky.social · 7d
Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...
www.biorxiv.org
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Reposted by Simon Roux

vscooper.micropopbio.org
Vaughn Cooper @vscooper.micropopbio.org · 8d
DYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce?

We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE.

"Filamentous cheater phages drive bacterial and phage populations to lower fitness"

🔗 authors.elsevier.com/c/1lt5I3QW8S...
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Reposted by Simon Roux, Alan Richardson, Jon Agar , and 1 more

eayers0.bsky.social
Elaine Ayers @eayers0.bsky.social · 10d
Job at UC-Berkeley: Asst. Prof. in Global History of Technology, apps due 10/10 (so soon). #history #histSTM #histsci #histphilsci

aprecruit.berkeley.edu/JPF05065
Assistant Professor – Global History of Technology - Department of History
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
14 12

Reposted by Simon Roux

evbc.bsky.social
European Virus Bioinformatics Center @evbc.bsky.social · 10d
A nationwide #HTS survey of German hopyards identified HpLV, HpMV, ApMV, ArMV and viroids HLVd and CBCVd (CBCVd confined to Hallertau), highlighting HTS as a powerful tool for #PlantPathogenSurveillance and management #PlantViromics 🧬🌾🔬
📄https://doi.org/10.1371/journal.pone.0329289
👤EVBC: Ali Pasha
Virus and viroid diversity in hops, investigating the German hop virome
Germany is worldwide one of the largest hop (Humulus lupulus L.) producers, an essential crop for the brewing industry. However, infections caused by viruses and viroids can severely impact hop yield and quality. In 2019, citrus bark cracking viroid (CBCVd) – a highly aggressive pathogen in hop – was first reported in Germany, raising concerns about its spread and prompting a broader investigation of the German hop virome.To investigate the viro-diversity in German hops, we started with a pilot study in 2021 targeting three hopyards in the Hallertau region (Bavaria), where CBCVd was previously detected. This study was expanded in 2022 and 2023 to include other main hop growing regions of Tettnang (Baden-Wuerttemberg) and Elbe-Saale (Saxony, Saxony-Anhalt, Thuringia). Leaf samples were collected from hop as well as non-hop plants inside and outside the hopyard, pooled, and proceeded for double-stranded RNAs extraction. High-throughput sequencing (HTS) was used as a diagnostic tool, followed by RT-PCR confirmation. Our analysis identified four viruses infecting hops; hop latent virus (HpLV), hop mosaic virus (HpMV), apple mosaic virus (ApMV), arabis mosaic virus (ArMV) – and two viroids; hop latent viroid (HLVd) and CBCVd. HpLV, HpMV, and HLVd were consistently found across all targeted hopyards, while CBCVd was confined to the Hallertau region. ArMV was only detected in one hopyard at one sampling timepoint. ApMV was the only virus detected in both hop and non-hop plants. Additional analysis of hop pool datasets revealed the presence of other potential hop pathogens, i.e., fungi and bacteria. The results showed a low diversity of viruses and viroids infecting hops. However, this study provides a comprehensive overview on the major viruses and viroids in German hopyards. The results may serve as a useful resource for the development of disease management strategies in hop cultivation and highlight the valuable implementation of HTS in plant pathogen surveillance.
doi.org
2 5

Reposted by Simon Roux

raw937.bsky.social
raw9371 @raw937.bsky.social · 10d
Multiomic analysis of the only megaphage in culture. In press today.

Unlocking the genomic repertoire of a cultivated megaphage | npj Viruses share.google/HgU1cjRnaHWv...

#phage #bacteriophage
Unlocking the genomic repertoire of a cultivated megaphage - npj Viruses
npj Viruses - Unlocking the genomic repertoire of a cultivated megaphage
share.google
4 10

Reposted by Simon Roux

feldmanlab.bsky.social
Feldman Lab@WashU @feldmanlab.bsky.social · 10d
I said I will never work on phages, but having @micheleleroux.bsky.social next door made me change my mind. Here is Alexis's new paper showing how different phages deal with the capsular barrier to infect Acinetobacter! A great collaboration between our labs!
journals.plos.org/plospathogen...
Acinetobacter phages use distinct strategies to breach the capsule barrier
Author summary Acinetobacter baumannii causes life-threatening and often antibiotic-resistant infections thereby posing a global threat. Accordingly, there is an urgent need for alternative treatments...
journals.plos.org
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Reposted by Simon Roux

evolvedbiofilm.bsky.social
Ákos T Kovács @evolvedbiofilm.bsky.social · 11d
The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem

#CurrOpinMicrobiol from @lgbacteria.bsky.social

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