Reposted by Simon RouxRoland Hatzenpichler @environmicrobio.bsky.social · 17/09/2026I 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 53111
Reposted by Simon RouxVivek Mutalik @vivekmutalik.bsky.social · 29/09/2026Happy 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 16522
Reposted by Simon RouxVaughn Cooper @vscooper.micropopbio.org · 27/09/2026How 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...biorxiv.orgConvergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patientsThe patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati... 14521
Reposted by Simon RouxRob Patro @robp.bsky.social · 24/09/2026If 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!faculty.umd.eduPresident's Postdoctoral Fellowship Program | Office of Faculty Affairs 099
Reposted by Simon RouxMaitreya Dunham @maitreya.bsky.social · 24/09/2026Exciting 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. 110398
Reposted by Simon RouxWill Matlock @wtmatlock.bsky.social · 22/09/2026Want 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...github.comGitHub - wtmatlock/plasmid-model-cliContribute to wtmatlock/plasmid-model-cli development by creating an account on GitHub. 0155
Reposted by Simon RouxH. B. Beryl Rappaport @hbrappap.bsky.social · 22/09/2026Our 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...cell.comA geothermal amoeba sets a new upper temperature limit for eukaryotesThe amoeba Incendiamoeba cascadensis demonstrates that eukaryotic life can withstand temperatures beyond what was thought possible and sheds light on molecular strategies for survival in extreme heat. 211655
Reposted by Simon RouxJim Shaw @jimshaw.bsky.social · 15/09/2026The 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)sylph-docs.github.ioDocumentation for sylph - ultrafast, precise metagenomic profiling 26330
Simon Roux @simrouxvirus.bsky.social · 16/09/20262 more days for VEGA26 early-bird registration ! Get in before it's too late :-) 001
Simon Roux @simrouxvirus.bsky.social · 11/09/2026One 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...jgi.doe.govVEGA Symposium | Joint Genome InstituteBerkeley, CA 053
Reposted by Simon RouxSimon Roux @simrouxvirus.bsky.social · 12/06/2026🚨 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 12717
Reposted by Simon RouxWikipedia @wikipedia.org · 08/09/2026Imagine being responsible for founding and doing the first-ever edit to Wikipedia? Such a flex. 🎥 mister.tomfoolery on TikTok 18314
Reposted by Simon RouxTami Lieberman @contaminatedsci.bsky.social · 08/09/2026Two 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... 15320
Reposted by Simon RouxBas E. Dutilh @bedutilh.bsky.social · 07/09/2026Join us and be part of the VirusREvolution! Study the link between the environment and phage host range in soil and groundwater systems 👇👇 0210
Reposted by Simon RouxRoyal Society Publishing @royalsocietypublishing.org · 05/09/2026The 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 0308
Reposted by Simon RouxAndrew Heiss @andrew.heiss.phd · 05/09/2026You can use this UN-approved Equal Earth projection right now in #rstats #gis #databs 727081
Reposted by Simon RouxSimon Roux @simrouxvirus.bsky.social · 03/09/2026Quick 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 😁 🧬 🦠 🔬 🧫 0115
Reposted by Simon RouxRafal Mostowy @rafalmostowy.bsky.social · 04/09/2026🧬 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-... 12529
Reposted by Simon RouxHanna Kokko @kokkonut.bsky.social · 04/09/2026Are 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/...lu.varbi.comSenior Lecturer in Computational BiologyLund University welcomes applicants with different backgrounds and experiences. Gender equality, equal opportunities and diversity are fundamental principles in all parts of the University’s activit 04156
Reposted by Simon RouxAxel Visel @axelvisel.bsky.social · 03/09/2026Here 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 031
Simon Roux @simrouxvirus.bsky.social · 03/09/2026Quick 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 😁 🧬 🦠 🔬 🧫 0115
Reposted by Simon RouxDavid Grimm @david-grimm.bsky.social · 03/09/2026“I couldn’t have imagined they’d get all this data from parchment." Cool story by @andrewcurry.com for @science.orgscience.orgAncient sheep virus found hiding in medieval parchmentNewly recovered sheeppox sequences reveal when and how the virus emerged 03611
Reposted by Simon RouxRachel M. Wheatley @rachelmwheatley.bsky.social · 02/09/2026Our special issue on the social lives of bacteria is out today 🎉 it was a pleasure to edit this collection over the last year with @friendlymicrobe.bsky.social. Read our editorial here: portlandpress.com/essaysbioche... 24218
Reposted by Simon RouxPatrick R. Secor @prsecor.bsky.social · 02/09/2026This job ad is now live! Please share or apply here: jobs.montana.edu/postings/52780 Screening of applicants begins Sept 15, 2026 #MicroSky #PhageSky #ScienceJobsjobs.montana.eduPostdoctoral Researcher - Lyme Disease Bacteriophage BiologyThe Secor Lab seeks a postdoctoral researcher to investigate bacteriophage biology in the Lyme disease spirochete Borrelia burgdorferi. The successful candidate will help define how phiBB-1 controls h... 02929
Reposted by Simon RouxChristophe 🔬 Leterrier @christlet.bsky.social · 01/09/2026This is Marseille. We'll be recruiting soon 😎 0453
Reposted by Simon RouxDavid Lowry @davidlowry.bsky.social · 31/08/2026I 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...careers.msu.eduPostdoctoral Scholar-Fixed Term - East Lansing, Michigan, United StatesPosition Summary The Lowry Lab at Michigan State University is searching for a postdoctoral research associate to conduct field and laboratory experiments to understand the causes of genetic variation... 16189
Reposted by Simon RouxClaus Wilke @clauswilke.com · 30/08/2026I'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...blog.genesmindsmachines.comI'm sorry, you're not going to die from an AI-engineered supervirusGod save us from economists who think they can competently talk about biology 412557
Reposted by Simon RouxJennifer Goff, PhD @jlgoff.bsky.social · 31/08/2026New preprint! This one is actually from my class! We did metagenomic sequencing on a Winogradsky column. In my Microbial Biochemistry class, the students learned to assemble and analyze the MAGs, directly applying what they learned in lecture to make predictions about their organism’s metabolism. 🧵 36714
Reposted by Simon RouxLeticia Botella @letibosa.bsky.social · 31/08/2026The most interesting studies often begin with random observations, but it takes a great team to publish them. Thanks to @excellentia.bsky.social, all coauthors @phytophthorarc.bsky.social, and especially Kohei and Mart @mkrupovic.bsky.social, for this amazing joint journey! doi.org/10.1093/ve/v...doi.orgA single-stranded DNA virus replicates in the mitochondria of a marine oomyceteAbstract. A virus with a circular single-stranded DNA genome, HthCRESSV1, was discovered in an oomycete, Halophytophthora thermoambigua, isolated from brac 0155
Reposted by Simon RouxRichard Sever @richardsever.bsky.social · 31/08/2026"When you find yourself writing such a statement about a topic you’re not an expert in, there are only two possibilities: 1. You are not talking to the right people. 2. You are talking to the right people but you’re not listening" blog.genesmindsmachines.com/p/im-sorry-y...blog.genesmindsmachines.comI'm sorry, you're not going to die from an AI-engineered supervirusGod save us from economists who think they can competently talk about biology 14518
Reposted by Simon RouxJocelyn Poissant @jocelynpoissant.bsky.social · 05/08/2026If you would be interested to apply for a fellowship to join the lab to work on fecal microbiome MAG assembly and/or mGWAS in caribou and feral horses, please get in touch. We have had great success with this competition so far (3/3 funded) research.ucalgary.ca/postdocs/fun...research.ucalgary.caVPR Postdoctoral Excellence AwardThe Spring 2026 competition is now closed. Applications for the December 1 competition will open on October 1. 046
Reposted by Simon RouxJocelyn Poissant @jocelynpoissant.bsky.social · 28/08/2026🦌💩🦠 PhD opportunity! I am recruiting a fully-funded PhD student at the University of Calgary Faculty of Veterinary Medicine to study the causes and consequences of gut microbiome variation in caribou. Start date is flexible. Please share! 13953
Reposted by Simon RouxKristian G. Andersen @kgandersen.bsky.social · 24/08/2026We have a (dry lab) Postdoc Position in Viral Genomics & Pathogen Surveillance here in wonderful and sunny San Diego 🏄♂️☀️! We're looking to continue to build our AI and broader infectious disease surveillance efforts, with a focus on our outbreak.info platform. Read more: andersen-lab.com/about/andersen-lab.comAbout | Andersen LabLearn more about the Andersen Lab, as well as jobs and career opportunities. 13531
Reposted by Simon RouxChristian Kost @kostchristian.bsky.social · 24/08/2026Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAbnature.comObligate cross-feeding of metabolites is common in soil microbial communities - Nature MicrobiologyCultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic... 814256
Reposted by Simon RouxRob Patro @robp.bsky.social · 23/08/2026Can a #bioconda team member please merge github.com/bioconda/bio... when they have a chance? It's the initial release of seqproc! combine-lab.github.io/seqproc/github.comAdd seqproc 0.1.1 by rob-p · Pull Request #68400 · bioconda/bioconda-recipesAdds the first Bioconda recipe for seqproc, a programmable preprocessing engine for sequencing reads. Release: https://github.com/COMBINE-lab/seqproc/releases/tag/v0.1.1 Crates.io: https://crates.i... 131
Reposted by Simon RouxSarah Whorley, Ph.D. 🦬⚔️ @dralgaegirl.bsky.social · 19/08/2026Tenure Track job alert! We're hiring someone to teach Microbiology and Genetics! Know someone on the job market? Must have a PhD. Position is mostly teaching (65%) but research expected. Send them my way! Will have official ad details soon 🧪🦠🧬 22840
Reposted by Simon Rouxvincentholst.bsky.social @vincentholst.bsky.social · 13/08/2026In 2023, @nature.com published 'Papers and patents are becoming less disruptive over time', receiving world-wide media attention. Our Matters Arising, published after a 32 month delay (more on that soon), shows that the reported decline can largely be attributed to dataset artefacts. 🧵 9351172
Reposted by Simon RouxMarc Somssich @somssich.bsky.social · 18/08/2026We are looking for a Group Leader in #Wheat research for pre-breeding here @kwsgroup.bsky.social. This is a full-time, permanent position at KWS France. You would be working on a research station near Lille or Paris. jobs.kws.com/job/Mons-en-... #PlantScience #PlantSciJobs #PlantScienceJobsjobs.kws.comGroup Lead Wheat Research & Pre-Breeding (m/f/d)Group Lead Wheat Research & Pre-Breeding (m/f/d) 02538
Reposted by Simon RouxAntti Karkman @anttikarkman.bsky.social · 17/08/2026Open postdoc position in my group. I’m looking for someone with computational and/or wet-lab experience. Previous work on (environmental) AMR is considered a plus. Please share. jobs.helsinki.fi/job/Helsinki...jobs.helsinki.fiPostdoctoral researcher in microbiologyPostdoctoral researcher in microbiology 029
Reposted by Simon RouxXavier Charpentier @labxc.bsky.social · 07/07/2026#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️biorxiv.orgWidespread immune systems protect bacteria against conjugative plasmidsConjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi... 410355
Reposted by Simon RouxMark A. Hanson @hansonmark.bsky.social · 14/08/2026HIRING MICROBIOLOGIST: effective start asap! The PDRA/PDRF (per xp) will investigate the interactions of bumblebee antimicrobial peptides (AMPs) with the gut microbiota & more. Our work has shown AMPs have striking specificity for ecological microbes. careers.exeter.ac.uk/vacancies/13... 1/2careers.exeter.ac.ukPostdoctoral Researcher Associate or Fellow in Cornwall | University of ExeterView details and apply for this Postdoctoral Researcher Associate or Fellow vacancy in Cornwall. Postdoctoral Research Associate / Fellow This job is part of an Advanced Research + Inventio... 24359
Reposted by Simon RouxJonathan Eisen @phylogenomics.bsky.social · 13/08/2026Job Opening. Faculty Position in Plant Evolutionary Biology at University of California, Davis in the Department of Evolution and Ecology (EVE, my home department). More detail here. recruit.ucdavis.edu/JPF07777 26170
Reposted by Simon RouxXabier Vázquez-Campos @xabivc.bsky.social · 13/08/2026Amazing first first-author work by @juliameltzer.bsky.social. Shout out to the lab heads @brendanburns999.bsky.social @belindaferrari.bsky.social @kmichie.bsky.social and Debnath Gosal #archaea #phage #asgard #microskybiorxiv.orgViruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial InteractionsAsgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Her... 1124
Reposted by Simon RouxEmmanuele Severi @emmseveri.bsky.social · 14/08/2026#microsky #phagesky #phage Phase variation FTW www.nature.com/articles/s41...nature.comPhage-encoded contingency loci enable bet-hedging against host defence mechanisms - Nature MicrobiologyDiverse E. coli phage genomes have hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage, generating population heterogeneity that enables host exploita... 23610
Reposted by Simon RouxVivek Mutalik @vivekmutalik.bsky.social · 14/08/2026Newest preprint 🎉 from phagefoundry.org Here we built one of the most comprehensive K. pneumoniae phage–host interaction datasets to date, an atlas of 8,484 interactions testing 84 taxonomically diverse phages vs 101 globally sourced clinical strains, including some of the most resistant kinds. 34917
Reposted by Simon RouxThomas Mock @thomasmock.bsky.social · 13/08/2026Our new paper just out @natmicrobiol.nature.com led by Yumary Vasquez & Frederik Schulz @jgi.doe.gov @norwichmicro.bsky.social Genomic catalogue of giant #viruses reveals expanded diversity and functional potential www.nature.com/articles/s41... 1177
Reposted by Simon RouxJeffrey Ross-Ibarra @jrossibarra.bsky.social · 12/08/2026I am excited to announce a job for an Asst Prof in Plant Evolution in the dept. of Evolution and Ecology at @ucdavis.bsky.social. We're looking broadly, from macro (speciation, comparative genomics, evo-devo) to micro (pop biology, adaptive evolution, evo-eco). recruit.ucdavis.edu/JPF07777recruit.ucdavis.edu 2126158
Reposted by Simon RouxCurtis Suttle @virosphere.bsky.social · 13/08/2026Professor in Bacteriophage Biology & Evolution at the University of British Columbia (UBC). Closing date 1 October, with an expected start date no earlier than January 1, 2027, and a salary within the range of $200,000 to $270,000 per year. For details: ubc.wd10.myworkdayjobs.com/en-US/ubcfac... 25585
Reposted by Simon RouxKevin A. Scott, PhD @sculpturatus.bsky.social · 12/08/2026derek lowe strikes again - we may not be as far along as hype seems to suggest, in terms of AI in drug discovery. www.science.org/content/blog...science.orgSo How Is AI Drug Discovery Doing, Really? 042