Simon Roux

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

Now published! doi.org/10.1126/scia...

Show a picture on your phone that has your energy but isn’t a selfie.

🚨 New preprint 🚨 We’ve discovered millions of viruses from sequencing data but we don’t always know who they infect. Our new tool, VHAMSTeR generates broad virus host predictions across the tree of life (prokaryote, plant, animal, fungi and protist hosts) A thread 🧵👇 www.biorxiv.org/content/10.6...

No smoking in pubs. Craft ale. Wine imports. Computing hardware. More good music. More good films. More good art in general to be honest. Protein structure prediction. Air fryers. Climate change shitshitshitshitshit that wasn’t the brief. Roll that one back. Greggs vegan sausage rolls.

For this year's #WorldPhageDay we wanted to highlight the historical importance of #phage in Biology So we asked a panel of experts* for their favorite phage-based contributions accross history Here is their top 5 *members of the BBH lab (List of choices was based on doi: 10.1002/bies.201400152)

Happy World Phage Day to all who celebrate... ... delighted to share new work led by Jacopo Marchi, Chadiga Khalek & joint w/Remy Chait on stable coexistence of phage with migrating bacteria driven by the forces of infection, lysis, and chemotaxis. A 🧵 at the interface between known & unknown.

The latest from my lab is an announcement in MRA for our new R package {rchime} which is an R version of the popular uchime chimera detection algorithm journals.asm.org/doi/10.1128/...

Do you know any excellent young microbiologists who'd like to do a PhD on biofilms, microbial community assembly and antimicrobial resistance/tolerance? I'm advertising two projects to start in autumn 2027 warwick.ac.uk/fac/cross_fa... #MicroSky

Very nice discovery from the Jackson, Bravo and Basel labs. Cleaved tRNA ends, loaded with an amino acid, activate a form of bacterial immunity

Quick reminder: this is the last day to submit your abstract to VEGA26 if you want it to be considered for a short talk ! (final registration and poster abstract deadline is Nov. 4)

I will be advertising a 4-year postdoc soon. We're looking for a molecular biologist with interest in #AMR. You'll join researchers across the Universities of Warwick, Sheffield, Manchester and Leeds to study the emergence of vancomycin resistance in C. difficile. Contact me for more info! #microsky

Always wanted to fix microbial cells while still enabling downstream DNA sequencing? Try the new microbial fixative: DSP Preprint is out! doi.org/10.64898/202... Huge thanks to my collaborators @kennethwasmund.bsky.social & @loyteam.bsky.social & supervisors @sjmcilroy.bsky.social & Gene Tyson!

Really excited to be co-supervising this PhD project with Spyros Lytras through Institut Pasteur’s PPU programme! Virus evolution × comparative genomics × structural biology Applications are now open (rolling basis), deadline 14 November. Apply: ppu.pasteur.fr

Reminder, if you are applying for a NSF GRFP, recommendation letters are due this Friday at 8pm ET, well before the submission deadline for other materials (!!!) www.nsf.gov/funding/oppo...

The Predictive Biology Hub based within the University of Maryland - College of Computer, Mathematical, and Natural Sciences is welcoming applications from postdoctoral scientists across UMD interested in joining the inaugural Impact Fellowship cohort. Apply by 10/23

Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more! www.biorxiv.org/content/10.6... 1/n 🧵

My weekly reminder that there is still time to register for VEGA26, and come hang out with us to talk about everything virus/phage ecology, genomics, and applications ! And also still time to submit your abstract for poster/short talk, although this deadline is approaching :-)

I love me some Fermi problems! However, there are no good instructions on how to use them in classes. So I wrote it up! If you read this it, you will finally learn the answer to the question 'How much phosphorous is released each day by viruses lysing Prochlorococcus cells?' tinyurl.com/2njt9r8h

Happy to share that @averynoonan.bsky.social paper “Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning” is now published in @natmicrobiol.nature.com 🎉🎊 👉🏽 rdcu.be/nR2NizD7H5va

How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...

If you are a US citizen or permanent resident looking for a postdoc, the President's Postdoctoral Fellowship Program is a great opportunity faculty.umd.edu/presidentspo...! If you are eligible, working in computational genomics, and interested in my lab, let me know!

Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.

Want to explore host-plasmid and plasmid-plasmid distributions in your dataset? Or any tree with a set of binary traits? I’ve made a CLI for our model here: github.com/wtmatlock/pl...

Our description of fire amoeba, 𝘐𝘯𝘤𝘦𝘯𝘥𝘪𝘢𝘮𝘰𝘦𝘣𝘢 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴, is now online at Cell! Thanks @oliverio.bsky.social and amazing team for questioning the limits of eukaryotes! 🔥 www.cell.com/cell/fulltex...

The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)

2 more days for VEGA26 early-bird registration ! Get in before it's too late :-)

One week left to catch the early-bird rate for the VEGA26 symposium - Don't miss the deadline, and come share your research and thoughts about virus ecology, virus (meta)genomics, and virus applications ! (also, abstracts for posters and short talks are still open !) jgi.doe.gov/work-with-us...

Imagine being responsible for founding and doing the first-ever edit to Wikipedia? Such a flex. 🎥 mister.tomfoolery on TikTok

Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...

Join us and be part of the VirusREvolution! Study the link between the environment and phage host range in soil and groundwater systems 👇👇

The earliest medical images of the plague: manuscripts of Aldobrandino of Siena’s Régime du corps, pestilence, and the Black Death: doi.org/10.1098/rsnr... Image: Bibliothèque nationale de France #NotesandRecords #HistSci #HistMed

You can use this UN-approved Equal Earth projection right now in #rstats #gis #databs

Quick reminder - VEGA26 early-bird registration rates are on until Sept 19 ! If you are interested in virus/phage-host interaction, functional annotation of novel virus/phage genomes, and microbiome manipulations with virus/phages, you will have an amazing time Nov 18-19 in Berkeley 😁 🧬 🦠 🔬 🧫

🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...

Are you into mathematical modelling of ecological and evolutionary systems? Look at this job ad for a senior lecturer in Lund. I've visited many times, splendid compact city, splendid department! lu.varbi.com/en/what:job/...

Here is the Open Access paper: www.nature.com/articles/s41... Contributors included @aroneys.bsky.social @benjwoodcroft.bsky.social @drcronin.bsky.social @sullivan-lab.bsky.social and many more who are not on this platform

Quick reminder - VEGA26 early-bird registration rates are on until Sept 19 ! If you are interested in virus/phage-host interaction, functional annotation of novel virus/phage genomes, and microbiome manipulations with virus/phages, you will have an amazing time Nov 18-19 in Berkeley 😁 🧬 🦠 🔬 🧫

“I couldn’t have imagined they’d get all this data from parchment." Cool story by @andrewcurry.com for @science.org

This job ad is now live! Please share or apply here: jobs.montana.edu/postings/52780 Screening of applicants begins Sept 15, 2026 #MicroSky #PhageSky #ScienceJobs

This is Marseille. We'll be recruiting soon 😎

I am currently searching for a postdoc to work on the evolution of adaptations, cold acclimation, and freezing tolerance in switchgrass. The position entails lab, growth facility, bioinformatics, and fieldwork. careers.msu.edu/jobs/postdoc...

I'm really frustrated by the constant fear-mongering about AI-designed superviruses. Can we focus on the things that should actually worry us, such as measles? blog.genesmindsmachines.com/p/im-sorry-y...