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Simon Roux

@simrouxvirus.bsky.social
4K followers 1.9K following 245 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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Reposted by Simon Roux
Roland Hatzenpichler @environmicrobio.bsky.social · 17/09/2026
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
A manuscript title stating 'Better roughly right than precisely wrong: Fermi problems in biology curricula'
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Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
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
Machine learning workflow for GenoPHI platform
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
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...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The 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...
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Rob Patro @robp.bsky.social · 24/09/2026
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!
faculty.umd.edu
President's Postdoctoral Fellowship Program | Office of Faculty Affairs
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Maitreya Dunham @maitreya.bsky.social · 24/09/2026
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.
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Will Matlock @wtmatlock.bsky.social · 22/09/2026
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...
github.com
GitHub - wtmatlock/plasmid-model-cli
Contribute to wtmatlock/plasmid-model-cli development by creating an account on GitHub.
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H. B. Beryl Rappaport @hbrappap.bsky.social · 22/09/2026
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...
cell.com
A geothermal amoeba sets a new upper temperature limit for eukaryotes
The 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.
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Jim Shaw @jimshaw.bsky.social · 15/09/2026
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)
sylph-docs.github.io
Documentation for sylph - ultrafast, precise metagenomic profiling
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Simon Roux @simrouxvirus.bsky.social · 16/09/2026
2 more days for VEGA26 early-bird registration ! Get in before it's too late :-)
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Simon Roux @simrouxvirus.bsky.social · 11/09/2026
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...
jgi.doe.gov
VEGA Symposium | Joint Genome Institute
Berkeley, CA
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Simon 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
This image shows the VEGA logo (an Earth-shaped capsid colored with green continents and blue oceans), and the taglines: "VEGA Viral EcoGenomics & Applications", "Symposium hosted by the DOE Joint Genome Institute", "Novermber 18-19, 2026"
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Wikipedia @wikipedia.org · 08/09/2026
Imagine being responsible for founding and doing the first-ever edit to Wikipedia? Such a flex. 🎥 mister.tomfoolery on TikTok
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
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...
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Bas E. Dutilh @bedutilh.bsky.social · 07/09/2026
Join us and be part of the VirusREvolution! Study the link between the environment and phage host range in soil and groundwater systems 👇👇
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Royal Society Publishing @royalsocietypublishing.org · 05/09/2026
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
Pestilence and corruption of the air. Aldobrandino of Siena, Régime du corps. Paris, Bibliothèque nationale de France, Fr. 12323, f. 90v, detail. (© Bibliothèque nationale de France.)
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Andrew Heiss @andrew.heiss.phd · 05/09/2026
You can use this UN-approved Equal Earth projection right now in #rstats #gis #databs
library(tidyverse)
library(sf)
library(rnaturalearth)

world <- ne_countries() |> filter(sov_a3 != "ATA")

ggplot(data = world) +
  geom_sf() +
  coord_sf(crs = "+proj=eqearth") +
  theme_void()A basic world map using the Equal Earth projection
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Simon Roux @simrouxvirus.bsky.social · 03/09/2026
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 😁 🧬 🦠 🔬 🧫
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Rafal 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-...
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Hanna Kokko @kokkonut.bsky.social · 04/09/2026
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/...
lu.varbi.com
Senior Lecturer in Computational Biology
Lund 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
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Axel Visel @axelvisel.bsky.social · 03/09/2026
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
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Simon Roux @simrouxvirus.bsky.social · 03/09/2026
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 😁 🧬 🦠 🔬 🧫
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David 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.org
science.org
Ancient sheep virus found hiding in medieval parchment
Newly recovered sheeppox sequences reveal when and how the virus emerged
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 02/09/2026
Our 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...
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Patrick R. Secor @prsecor.bsky.social · 02/09/2026
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
jobs.montana.edu
Postdoctoral Researcher - Lyme Disease Bacteriophage Biology
The 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...
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Christophe 🔬 Leterrier @christlet.bsky.social · 01/09/2026
This is Marseille. We'll be recruiting soon 😎
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David Lowry @davidlowry.bsky.social · 31/08/2026
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...
careers.msu.edu
Postdoctoral Scholar-Fixed Term - East Lansing, Michigan, United States
Position 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...
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Claus Wilke @clauswilke.com · 30/08/2026
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...
blog.genesmindsmachines.com
I'm sorry, you're not going to die from an AI-engineered supervirus
God save us from economists who think they can competently talk about biology
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Jennifer Goff, PhD @jlgoff.bsky.social · 31/08/2026
New 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. 🧵
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Leticia Botella @letibosa.bsky.social · 31/08/2026
The 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.org
A single-stranded DNA virus replicates in the mitochondria of a marine oomycete
Abstract. A virus with a circular single-stranded DNA genome, HthCRESSV1, was discovered in an oomycete, Halophytophthora thermoambigua, isolated from brac
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Richard 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.com
I'm sorry, you're not going to die from an AI-engineered supervirus
God save us from economists who think they can competently talk about biology
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Jocelyn Poissant @jocelynpoissant.bsky.social · 05/08/2026
If 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.ca
VPR Postdoctoral Excellence Award
The Spring 2026 competition is now closed. Applications for the December 1 competition will open on October 1.
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Jocelyn 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!
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Kristian G. Andersen @kgandersen.bsky.social · 24/08/2026
We 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.com
About | Andersen Lab
Learn more about the Andersen Lab, as well as jobs and career opportunities.
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Christian Kost @kostchristian.bsky.social · 24/08/2026
Very 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/fBHAb
nature.com
Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology
Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...
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Rob Patro @robp.bsky.social · 23/08/2026
Can 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.com
Add seqproc 0.1.1 by rob-p · Pull Request #68400 · bioconda/bioconda-recipes
Adds 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...
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Sarah Whorley, Ph.D. 🦬⚔️ @dralgaegirl.bsky.social · 19/08/2026
Tenure 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 🧪🦠🧬
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vincentholst.bsky.social @vincentholst.bsky.social · 13/08/2026
In 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. 🧵
The average CD_5 index per year for Web of Science. The original Park et al. decline (top curve) becomes essentially flat (bottom curve) when removing papers with CD_5=1. Those papers largely correspond to dataset artefacts.
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Marc Somssich @somssich.bsky.social · 18/08/2026
We 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 #PlantScienceJobs
jobs.kws.com
Group Lead Wheat Research & Pre-Breeding (m/f/d)
Group Lead Wheat Research & Pre-Breeding (m/f/d)
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Antti Karkman @anttikarkman.bsky.social · 17/08/2026
Open 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.fi
Postdoctoral researcher in microbiology
Postdoctoral researcher in microbiology
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Xavier 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.org
Widespread immune systems protect bacteria against conjugative plasmids
Conjugative 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...
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Mark A. Hanson @hansonmark.bsky.social · 14/08/2026
HIRING 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... 1/2
careers.exeter.ac.uk
Postdoctoral Researcher Associate or Fellow in Cornwall | University of Exeter
View 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...
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Jonathan Eisen @phylogenomics.bsky.social · 13/08/2026
Job 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
POSITION DESCRIPTION

The College of Biological Sciences at the University of California, Davis invites applications and nominations for a 9-month, tenure-track position in the Department of Evolution and Ecology at the ASSISTANT PROFESSOR level. The Department of Evolution and Ecology is seeking a plant evolutionary biologist with interests in the evolution of plants at any taxonomic, geographic, organizational, or evolutionary scale. Candidates must have a Ph.D. (or equivalent) in the biological sciences, evolutionary biology, ecology, genetics, or a related field, and will be expected to complement and build upon existing faculty strengths in the Department of Evolution and Ecology and across UC Davis.

We welcome applicants working on any group of plants and using empirical, computational, experimental, and/or theoretical approaches. Possible areas of study are broad, and include macroevolutionary research on plant diversification, trait evolution in a phylogenetic context, major evolutionary innovations, comparative genomics, and evolutionary developmental biology, as well as research focusing at or below the species level including population biology, quantitative genetics, adaptive evolution, speciation, biogeography, and the evolution of life histories or species interactions.

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Xabier Vázquez-Campos @xabivc.bsky.social · 13/08/2026
Amazing 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 #microsky
biorxiv.org
Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions
Asgard 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...
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Emmanuele Severi @emmseveri.bsky.social · 14/08/2026
#microsky #phagesky #phage Phase variation FTW www.nature.com/articles/s41...
nature.com
Phage-encoded contingency loci enable bet-hedging against host defence mechanisms - Nature Microbiology
Diverse E. coli phage genomes have hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage, generating population heterogeneity that enables host exploita...
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Vivek Mutalik @vivekmutalik.bsky.social · 14/08/2026
Newest 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.
Phage art
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Thomas Mock @thomasmock.bsky.social · 13/08/2026
Our 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...
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James Pirruccello 🌉🇺🇸 @jamespirruccello.com · 13/08/2026
earthquake
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 12/08/2026
I 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/JPF07777
recruit.ucdavis.edu
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Curtis Suttle @virosphere.bsky.social · 13/08/2026
Professor 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...
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Kevin A. Scott, PhD @sculpturatus.bsky.social · 12/08/2026
derek 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.org
So How Is AI Drug Discovery Doing, Really?
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