Check out the latest paper by the Snoek lab in @theplantjournal.bsky.social, a genetics study involving a large field trial with 200 lettuce genotypes phenotyped by a drone. Great work by Rens Dijkhuizen, Bram van Eijnatten, Sarah Mehrem, @guidopmi.bsky.social & others! doi.org/10.1111/tpj....

The first paper of my PhD is now available as a preprint! 🎉 Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

It's alive!! 🌱 Check out our combination of experimental approaches and computational modeling, showing how growth conflicts among neighboring cell files underlie the orientation of cell divisions in root regeneration. Such a rewarding experience to be part of this collaboration!

1. 🧵 New preprint out! WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs. Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA. #ArchaeaSky #MEvoSky #MicroSky 🔗 doi.org/10.1101/2025... 💻 github.com/stephkoest/w...

Late due to vacation, but 📢 New preprint out, presenting a new approach to reduce compositional heterogeneity in alignments. A passion project led by the amazing @stephkoe.bsky.social 👀 Check out this great explanation thread below 👇

🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨 www.uu.nl/en/organisat...

Paulien Hogeweg was Rob's supervisor during his MSc and PhD. She kicks off the meeting by reminiscing about Rob's beginnings: "First students are special, especially those who become a lifelong colleague, successor, and now, fellow emeritus"

Today we celebrate over 40 years of research of Rob de Boer, chair Professor of Theoretical Biology. Rob complemented his tremendous scientific career with a deep impact in multiple roles, as a dedicated teacher, an inspiring mentor, and a kind and generous colleague. Thank you, Rob!

PhD Position in Modelling Regulation of Plant Stress Responses across Species!! 🌱🌽🌾🥬🌡️🌡️ Apply before June 16 to join this exciting project with Kirsten ten Tusscher in the context of CropXR!! www.uu.nl/en/organisat...

Faster && more accurate virus sequence clustering with Vclust! Thanks to Andrzej, Sebastian, et al. for the great collaboration. The author list also includes @prozwalak.bsky.social from the VEO Group.

Researchers led by @bedutilh.bsky.social at the Cluster of Excellence @microverse.bsky.social investigate #phages, showing how viruses not only cause harm but also create the basis for diversity & balance. Read more in the #UniJena research magazine. ➡️ www.lichtgedanken.uni-jena.de/en/3157/smal...

Are you interested in molecular plant microbe interactions and would like to study effector biology in Fusarium-lettuce patho-system? Consider this PhD position @uva.nl in the lab of Martijn Rep as part of our recently funded joint TKI project werkenbij.uva.nl/en/vacancies...

New paper by Arpit Swain, José Borghans and Rob de Boer, now in @plos.org Computational Biology. Using mathematical modeling, they show that estimating cell lifespans from deuterium labelling requires considering turnover rates of precursor cells. Find it here: journals.plos.org/ploscompbiol...

Great Mentor, Exciting project, Fun city. What more could you wish for!?

🌱 We're hiring! Join our team as a PhD candidate to explore plant–microbiota host specificity. Plant biology/microbiology background needed; bioinformatics skills a big plus💻! Apply by mid-June. www.uu.nl/en/organisat... #uubeta #plantmicrobiome #microbiota

Interested in microbial genome evolution? Consider applying for this exciting PhD project with a great mentor @danieltamarit.bsky.social embedded in a vibrant community @binfutrecht.bsky.social @utrechtuniversity.bsky.social

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

PhD position available at @binfutrecht.bsky.social. Join us if you are interested in modelling how plants respond to stress! www.uu.nl/en/organisat...

Come and join to work with @bramvandijk.bsky.social and others! Exciting PhD project between @rug.nl and @utrechtuniversity.bsky.social @binfutrecht.bsky.social with inspiring supervisors

🧩 PhD Position – Origins of Darwinian Inheritance 🧩 This joint PhD project between the @rug.nl (Rampal Etienne & Martijn Egas) and @utrechtuniversity.bsky.social (Bram van Dijk) explores how simple prebiotic systems could evolve reliable information transfer. Apply here: shorturl.at/WgYMF

New collaboration including Bas van den Herik and Kirsten ten Tusscher uses phenotyping, multiomics, and modelling to demonstrate the effect of brassinosteroids signalling on the integrated growth of both shoot and root. Now out in @natcomms.bsky.social! 👇

It's alive! Our work combining experiments and computational models to show that "Root stem cell homeostasis in Arabidopsis involves cell-type specific transcription factor complexes"! Amazing collaboration with Vivien Strotmann and @yvonnestahl.bsky.social! 🌱🌱 www.embopress.org/doi/full/10....

We are looking for a #postdoc to join the VEO Group @microverse.bsky.social @uni-jena.de and build an experimental research line into the dynamics and functioning of microbial communities: jobs.uni-jena.de/jobposting/1...

Are you interested in the distribution of microbes, viruses, and #phages throughout the Microverse? Come and do a PhD with us in experimental microbial ecology @microverse.bsky.social @uni-jena.de: jobs.uni-jena.de/jobposting/d...

Are you interested in the distribution of microbes, viruses, and #phages throughout the Microverse? Come and do a #bioinformatics PhD with us @microverse.bsky.social @uni-jena.de: jobs.uni-jena.de/jobposting/b...

📣 New, free webtool by the Snoek lab! Meet SpeSpeNet, an intuitive platform for automated network analysis of microbiomes to uncover complex interactions between microbes and their environments @ismepublications.bsky.social @isme-microbes.bsky.social doi.org/10.1093/isme... #microsky #mevosky

Ten days left to apply!!

Inspired by the work of @renskevroomans.bsky.social and @escolizzi.bsky.social on "selfish multicellularity", I made a very different type of model to replicate their results. Take that #replicationcrisis! (try it yourself here: tbb.bio.uu.nl/bvd/simulati...)

🚨 Now that @sultannazir.bsky.social has written about his work, let me try and summarise what we found. The question we worked on was inspired by Takeuchi et al. (2023) pubmed.ncbi.nlm.nih.gov/37339743/, who illustrated that (pro)phages are enriched in virulence factors compared to plasmids. [1/10]

📣 New preprint out by @sultannazir.bsky.social @bramvandijk.bsky.social studying the evolutionary association of phages with accessory genes using a mathematical model. Check out Sultan's fantastic thread describing the main findings 👇 #microsky #mevosky www.biorxiv.org/content/10.1...

Excited to share the first preprint from my PhD at @binfutrecht.bsky.social ! 1.5 years ago, @bramvandijk.bsky.social hired me to investigate: why do prophages preferentially carry virulence genes? Using mathematical models, we propose that spatial structure plays a key role. Here's a summary: 1/15

www.biorxiv.org/content/10.1... @sultannazir.bsky.social’s first preprint is on bioRxiv. He finds that regulated prophage induction and virion dispersal play a key role in understanding the accessory genes they carry as cargo. This can explain the prevalence of virulence genes on prophages.

I’m genuinely impressed (and proud) of what Sultan managed to unpack in a short amount of time. Watch out microbial peeps, there’s a new player in town! 🌠

Asgardarchaea & Alphaproteobacteria: key players for the assembly eukaryotic central carbon metabolism! Our new study reveals their gene contributions to glycolysis & TCA cycle, supporting synthrophic scenarios of eukaryogenesis. rdcu.be/eb0aK

📣 New article on the chimeric evolutionary origins of eukaryotic central carbon metabolism, by @santanamolina.bsky.social @tweethinking.bsky.social Berend Snel and @anja1.bsky.social Now out in @natureecoevo.bsky.social www.nature.com/articles/s41... #mevosky #microsky #archaeasky

SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks #ISMECommun from @binfutrecht.bsky.social @jwubs.bsky.social academic.oup.com/ismecommun/a...

Large crowds mobilising today to protest (we could not even fit in 3 different trains) in The Hague. The Dutch government wants to cut 1 billion euros to science and education. This policy will damage the country profoundly. Stop the budget cuts. Protect the future. @woinactie.bsky.social

Theoretical Biology and Bioinformatics at the protest against the budget cuts on education. This choice will cost - everyone - money in the long run. #WOinActie #wanbeleid

It’s easier to lie down and just let the idiocracy take over. But we won’t. We’re holding on to something. There's some good in this world... and it's worth fighting for! #WOinActie

The way is shut. It was made by those who are rich, and the rich keep it, until the time comes. The way is shut. #WOInActie

All the trains towards the protest against the budget cuts were full, so we’re taking a detour in this relatively empty train. This plan will not save money. This plan will cost money. It will cost - EVERYONE - money. #WOinActie @woinactie.bsky.social

The RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomics 🧬 into one microbial community profile with great sensitivity and precision. Read the article at www.nature.com/articles/s41.... 🧵 (1/5)

Do you want to know which virus discovery tool to use? Check out @lingyi.bsky.social 's new paper:

#Viromics #VirusDiscovery 🦠 by #Metagenomics 🧬! We used real metagenomic data from diverse biomes to #benchmark state-of-the-art #bioinformatics virus identification tools: genomebiology.biomedcentral.com/articles/10.... @goncalopiedade.bsky.social @bedutilh.bsky.social 🧵 (1/4)

Excited to share the last chapter of #XinZhang's PhD thesis on the evolution of secondary metabolite biosynthetic gene clusters in the fungal genus Aspergillus biorxiv.org/content/10.1... @binfutrecht.bsky.social #UUBeta #WesterdijkBiodiversity

Happy to see our most recent work on genome evolution of Fusarium isolates infecting banana published in @NewPhyt nph.onlinelibrary.wiley.com/doi/10.1111/... Congratulations especially to #AvWesterhoven and to all involved colleagues @binfutrecht.bsky.social #UUBeta #WURplant #PhytoWUR @keygene.com

It’s a wrap. Congratulations #XinZhang for submitting your PhD thesis - well done! Co-supervised by #JeromeCollemare #westerdijk @binfutrecht.bsky.social

TBB Paper alert! Sam (@derdunk.bsky.social) shows how genomes evolve intracellular signaling when enforcing endosymbiosis, and how this resolves the conflict between the two players!