We're looking for a PhD candidate who's eager to study how the genomes of fascinating eukaryotic microbes evolve and organize - and we have a fully funded PhD position available!

Ursula Oggenfuss@oggenfussursula.bsky.social · 5d ago

Are you interested in learning how genomes of weird fungi and protists evolve and are you looking for an exciting PhD opportunity? Jolien van Hooff and I are looking for an enthusiasic PhD candidate at Wageningen University: www.wur.nl/en/vacancy/p... #TEworldwide #Fungi #Protists #Genome

In my latest for @undark.org, I compare AI adoption in science to the Ship of Theseus: "If you swap out every wooden plank on a ship over time, is it still the same vessel?" I argue that science derives authority from something more than data generation + publication. undark.org/2026/09/25/o...

AI Presents Science with a ‘Ship of Theseus’ Problem

Opinion | AI can replace each part of the scientific process, leaving the enterprise recognizable but devoid of human judgment.

undark.org

“I’ve heard from a bunch of people in our field who say, ‘Uh oh, are they training on my prompts?’” Dr. Shipman said. “We can’t not think about it.” ... '[A]fter Anthropic’s announcement last week, he is winding down his projects with Claude.' “I’m shutting down everything,” [Dr. Mestre] said.

Carl Zimmer@carlzimmer.com · 2w ago

Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc

Are you into sequence graphs and looking for a PhD position in viral ecology? Join the VEO Group in beautiful Jena, Germany! 👇👇 jobs.uni-jena.de/jobposting/a...

Ken je Hyves nog? Het sociale platform van de krabbels en dansende bananen maakt een comeback. Deze week kondigde De Telegraaf aan Hyves nieuw leven in te blazen. Volgens de hoofdredacteur draait het platform op Europese software. Maar dat klopt niet. www.ftm.nl/artikelen/hy...

Hyves draait wél op Amerikaanse tech, in tegenstelling tot wat eigenaar De Telegraaf beweert

Deze week kondigde De Telegraaf aan Hyves nieuw leven in te blazen. Volgens de hoofdredacteur draait de socialenetwerksite ‘voor de veiligheid, voor de zekerheid’ op Europese software. Maar dat klopt ...

ftm.nl

🌱 Systems Ecology is now live! A new independent, researcher-run, diamond OA journal for ecological research through systems science. Free to read. Free to publish. No APCs. We are now open for submissions: systems-ecology.org Please help spread the word!

Any other bioinformaticians feel they’re the temporary, meat-flavored glue between experimental biologists and LLMs like Claude?

Wonderful tool that solves the problem that "Conventional research papers require readers to understand...the paper’s code, data and methods to their work"

Bram van Dijk 🏳️‍🌈@bramvandijk.bsky.social · 3w ago

Hey folks, let’s go to the gym with a forklift, the weights will be so much easier to lift! We’ll look super strong and productive! 🤦

Authors!🚨 While you scramble for scarce $ 🤔 “Springer Nature reports revenue growth of 6.2%..and adjusted operating profit growth of 7.7%. They reported even more stunning submission growth of 30% and published article growth of 13%.” Publishing in society journals helps YOU not them👇🏻. Pass it on.

Man Lying on a Pile of Money

ALT: Man Lying on a Pile of Money

static.klipy.com

🧬 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-...

Delighted to share news that our preprint “Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics” is now online, led by Akash Arani (UMD-BEES PhD), Paul Fremont (UMD-Biology postdoc) and Emma Wachter (former UMD Honors Bio student) www.biorxiv.org/content/10.6...

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

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...

nature.com

Rewilded land remains green amid drought-stricken English countryside, images show. Excellent work by the National Trust at Holnicote. #MakeBritainWetAgain www.theguardian.com/environment/...

Rewilded land remains green amid drought-stricken English countryside, images show

National Trust’s Holnicote estate says restored wetlands and rivers offer proof of resilience to drought, wildfires and flooding

theguardian.com

Join us and become part of PhageOrder: study the evolution of phage genetic modules!

Jessica Andreani@jessicaandreani.bsky.social · 2mo ago

🚨📣 Hiring a postdoc in bioinformatics 🧬🧑‍💻 Join our team at @i2bcparissaclay.bsky.social to explore biomolecular interactions and improve protein function prediction in bacteriophages! 📍 Gif-sur-Yvette, France ⏳ 13 months (+ possible extension) 📅 Apply here: emploi.cnrs.fr/Offres/CDD/U...

A third-year student draws poster PS3.20.305 -- far corner, farthest wall -- and commits to standing there two hours. Barely anyone makes it that far. Two floors up, a senior colleague is having the week of his life. Same conference. A new essay. academicrenewal.substack.com/p/why-we-sti...

Why we still fly

The scientific conference was invented to solve a transport problem we no longer have. What is it for now?

academicrenewal.substack.com

I wrote about a reason not to use generative AI in your writing that I haven't seen anyone talking about. Once I realized this, banning GenAI in our lab's writing became a no-brainer. Feel free to share, I think this is probably useful especially for trainees: www.carlsonlab.bio/thoughts/the...

The only reason you’ll ever need not to write with AI — The Carlson Lab

Over the last year, our lab has been developing a policy on AI use. To do this, we did three main things: We read a lot of academic publications and tech news. We set up an #ai channel on our la...

carlsonlab.bio

🚨 New paper with @bramvandijk.bsky.social, out now in Genome Biology and Evolution! Why do accessory genes so often hitch a ride on temperate phages? We show that spatial structure alone can tip selection toward a prophage locus over a chromosomal one. doi.org/10.1093/gbe/... 🧵 Two mechanisms:

Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages

Abstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The

doi.org

Nazir & @bramvandijk.bsky.social demonstrate how phage lifecycle dynamics and spatial heterogeneity drive mobile genetic element–gene associations, providing new insights into the evolution of phage-encoded virulence. 🔗 doi.org/10.1093/gbe/evag181 #societyjournal #virus

Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages

Abstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The

doi.org

Happy to share our latest review on @isme-microbes.bsky.social. We discussed how (intra- or interpopulation) cell-cell distances shape microbial interactions and enable community-level outcomes. Several hypotheses are proposed and we are testing them! doi.org/10.1093/isme...

Influence of cell-cell distance on the ecology and evolution of microbial communities

Abstract. Microorganisms assemble into spatially structured communities in which neighboring cells are separated by highly heterogeneous cell-cell distance

doi.org

🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiology

Bacteria organise themselves to hitchhike across large distances

Microbes rarely travel alone. In any given environment, millions of microbial species compete with each other for resources while locked in an endless state of warfare […]

dlvr.it

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiology

Bacteria organise themselves to hitchhike across large distances

Microbes rarely travel alone. In any given environment, millions of microbial species compete with each other for resources while locked in an endless state of warfare […]

dlvr.it

Bacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.

Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics

Theory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data.

science.org

Thanks for having me! I really enjoyed the discussion as well.

Dr. Kat Napaaqtuk❄️@napaaqtuk.bsky.social · 3mo ago

Ok, highly recommend this online journal club. The discussion was really thoughtful and the wide variety of perspectives was enlightening. Thank you @lavishaparab.bsky.social for organizing!

@jeroenmeijer.bsky.social is presenting today on this paper. They studied the eco-evo dynamics in 10 paired open and closed communities with a focus on viral communities. bsky.app/profile/paul...

Paul Rainey@paulbrainey.bsky.social · 4mo ago

Pleased to see this beautiful paper out. Kudos to @jeroenmeijer.bsky.social who took @stevenquistad.bsky.social data and dug deep, revealing a new phage that erupts to astonishing abundance. As theory predicts, the life of SGEs is fuelled by encounters with new hosts www.science.org/doi/10.1126/...

If you are interested in microbiomes, this is an excellent group of international researchers coming together to discuss current research.

Lavisha Parab@lavishaparab.bsky.social · 5mo ago

Hi #microbiomesky and #mevosky and also #phagesky maybe? Some of us want a microbiome journal club to catch up on microbiology/evolution related microbiome research. Monthly@15:00 CET/09:00 EST/18:30 IST or so Please text my LMU email address if you're interested (not typing it here to avoid spam)

Bacterial community adaptation after brackish and freshwater coalescence academic.oup.com/ismecommun/a... #jcampubs

For some reason people had less difficulty finding my poster than usual

Excited to share our new paper! Emanuele and @benjaminraach.bsky.social combine experiments and modelling to show that phage-mediated lysis can increase the growth rate of surviving bacteria by releasing resources back into the environment. 👇 www.cell.com/iscience/ful...

Phage-mediated lysis increases growth rate of surviving bacterial cells

Microbiology

cell.com

Enjoyed speaking about viruses driving state shifts in microbial communities at #VoM2026. All 120 seconds of it. Catch me this afternoon at poster 236 if you want to know more. #phagesky