Theoretical Biology & Bioinformatics @ UU
Our group consists of two research groups : Theoretical Biology (headed by Rob de Boer) and Bioinformatics (headed by Berend Snel) at @utrechtuniversity.bsky.social
- Reposted by Theoretical Biology & Bioinformatics @ UUWelcome to Bluesky, @pieterhart.bsky.social! Pieter just joined my group as a PhD student studying bacterial genome evolution—exciting years ahead! Here he is enjoying a chat about his MSc work (w/ @kassipan.bsky.social & @ettema.bsky.social) at Science4Life @utrechtuniversity.bsky.social 🧬🦠✨
- Reposted by Theoretical Biology & Bioinformatics @ UUNow officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...
- Reposted by Theoretical Biology & Bioinformatics @ UUNew preprint from our lab! Led by Emine Ali and @maxraas.bsky.social See the highlights below!
- Our story on the kinetochore composition of the ciliate Tetrahymena thermophila is out now on bioRxiv! We find surprisingly many orthologs of conventional kinetochore components, but also components that have very different evolutionary origins. A 🧵 (1/11) Check it out here: tinyurl.com/4ectm9x4
- Reposted by Theoretical Biology & Bioinformatics @ UUOur story on the kinetochore composition of the ciliate Tetrahymena thermophila is out now on bioRxiv! We find surprisingly many orthologs of conventional kinetochore components, but also components that have very different evolutionary origins. A 🧵 (1/11) Check it out here: tinyurl.com/4ectm9x4
- Now out in @currentbiology.bsky.social ! Screening over a thousand fungal genomes, @jromeijn.bsky.social, Iñigo Bañales Belaunde and @mfseidl.bsky.social find that horizontal transfer shapes the fungal mobilome 🍄🔄✈️🧬 @ubc-uu.bsky.social Don't miss Josje's thread for a summary of the findings! 👇
- Fighting virus with…virus? In a new paper, Griffin Kutler Dodd and Rob de Boer investigated whether defective virus particles could be used to treat HIV-1 infection. @ubc-uu.bsky.social @utrechtuniversity.bsky.social Now out at Journal of Theoretical Biology www.sciencedirect.com/science/arti...
- In this approach, the defective virus competes with the normal virus for shared proteins, which suppresses viral replication. Using mathematical modeling, they found that while this treatment is promising, a protective immune response drastically reduces its effectiveness. #mathbio #immunobio
- Reposted by Theoretical Biology & Bioinformatics @ UUMetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...
- Reposted by Theoretical Biology & Bioinformatics @ UUExtensive horizontal transfer of transposable elements shapes fungal mobilomes @currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social www.cell.com/current-biol...
- Reposted by Theoretical Biology & Bioinformatics @ UUThe mystery deepens: how did all complex life on Earth originate? In this intriguing VPRO Tegenlicht episode (in Dutch), PhD student Max Raas from the @kopslab.bsky.social talks about his collaboration with Berend Snel. They study the evolution of cell division machinery in single-celled organisms.
- Wonderful news for our team! Congratulations to Daniel on receiving this award, and looking forward to more archaeal research in our unit! 🦠 💻 📊 🧑🔬 @utrechtuniversity.bsky.social @ubc-uu.bsky.social
- Exultant to have been awarded a Vidi grant by the Dutch Research Council (NWO)! Can't wait to get started! Stay tuned for two upcoming (PhD student & postdoc) positions to study archaeal genome evolution. Also huge congrats to my colleague @dorotakawa.bsky.social! www.uu.nl/en/news/21-v...
- New review, result of a collaboration between researchers at @binfutrecht.bsky.social and Uni Groningen. How do plant development and morphology mediate resource acquisition and costs? 🌿🌳🌺 💰💵📈 academic.oup.com/jxb/advance-...
- Stoked to share our review advocating a whole plant perspective on resource balancing strategies with Joe Earle, Lucila Salvatore, Bas van den Herik and Kirsten ten Tusscher How coupling resources and development ensures whole plant homeostasis url: academic.oup.com/jxb/article/...
- Featuring Paulien Hogeweg (2nd from the right), founder and lifelong colleague at @binfutrecht.bsky.social @utrechtuniversity.bsky.social Very well deserved, Paulien!
- Reposted by Theoretical Biology & Bioinformatics @ UUBram van Dijk @bramvandijk.bsky.social (@utrechtuniversity.bsky.social): How mobile genes reshape the microbial arms race #NIME2025
- Reposted by Theoretical Biology & Bioinformatics @ UUYesterday the @biosb.bsky.social and Netherlands Integrative Microbial Ecology initiative organised a symposium on #MicrobialEcology. We hosted 80+ researchers, with 10 talks and 10 posters at @utrechtuniversity.bsky.social. A beautiful chance to hear more about exciting research across the country!
- Reposted by Theoretical Biology & Bioinformatics @ UUVery nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
- 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....
- They used an innovative GWAS approach involving the construction of many traits as ratios of the imaging data and quantifying these traits using various summary statistics. They then optimized the GWAS for computational efficiency to facilitate mapping this large number of traits.
- Using this methodology, they recovered both known and many novel QTLs for color and height, opening up new breeding targets. This study represents a blueprint for high-throughput genetics studies, with the entire methodology as well as all the raw data fully and conveniently available.
- Reposted by Theoretical Biology & Bioinformatics @ UUThe 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.
- Reposted by Theoretical Biology & Bioinformatics @ UU📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp
- Reposted by Theoretical Biology & Bioinformatics @ UUIt'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!
- Our new paper is out! 1/14 How does an organ rebuild its shape after injury? It's not just about making new cells, but aligning them in the right direction — like bricks shaping a structure. We show that it's all driven by Cell Geometry! www.cell.com/current-biol...
- Reposted by Theoretical Biology & Bioinformatics @ UU1. 🧵 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...
- Reposted by Theoretical Biology & Bioinformatics @ UULate 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 👇
- 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...
- 🚨 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!
- Reposted by Theoretical Biology & Bioinformatics @ UUPhD 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...
- Reposted by Theoretical Biology & Bioinformatics @ UUFaster && 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.
- Reposted by Theoretical Biology & Bioinformatics @ UUResearchers 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...
- Reposted by Theoretical Biology & Bioinformatics @ UUAre 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...
- Reposted by Theoretical Biology & Bioinformatics @ UUGreat Mentor, Exciting project, Fun city. What more could you wish for!?
- 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
- Reposted by Theoretical Biology & Bioinformatics @ UU🌱 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
- Reposted by Theoretical Biology & Bioinformatics @ UUInterested 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
- Reposted by Theoretical Biology & Bioinformatics @ UUNew 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
- Reposted by Theoretical Biology & Bioinformatics @ UUPhD position available at @binfutrecht.bsky.social. Join us if you are interested in modelling how plants respond to stress! www.uu.nl/en/organisat...
- Reposted by Theoretical Biology & Bioinformatics @ UUCome 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
- Reposted by Theoretical Biology & Bioinformatics @ UU🧩 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! 👇
- Root growth and branching are enabled by brassinosteroid-regulated growth anisotropy and carbon allocation www.nature.com/articles/s41...
- Reposted by Theoretical Biology & Bioinformatics @ UUIt'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....
- Reposted by Theoretical Biology & Bioinformatics @ UUWe 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...
- Reposted by Theoretical Biology & Bioinformatics @ UUAre 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...
- Reposted by Theoretical Biology & Bioinformatics @ UUAre 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
- Work led by Bram van Eijnatten, with researchers from @binfutrecht.bsky.social @niooknaw.bsky.social @uni-jena.de Find also the webtool here: utrecht-university.shinyapps.io/SpeSpeNet_v1/
- Late-tagging @bedutilh.bsky.social and the @microverse.bsky.social cluster, missing above
- Reposted by Theoretical Biology & Bioinformatics @ UUTen days left to apply!!
- Reposted by Theoretical Biology & Bioinformatics @ UUInspired 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...)
- Reposted by Theoretical Biology & Bioinformatics @ UU🚨 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
- Reposted by Theoretical Biology & Bioinformatics @ UUExcited 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
- Reposted by Theoretical Biology & Bioinformatics @ UUwww.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.
- Reposted by Theoretical Biology & Bioinformatics @ UUI’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! 🌠
- 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
- Reposted by Theoretical Biology & Bioinformatics @ UUAsgardarchaea & 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
- Don't miss the accompanying piece by John Archibald www.nature.com/articles/s41...
- Reposted by Theoretical Biology & Bioinformatics @ UUSpeSpeNet: 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...
- Reposted by Theoretical Biology & Bioinformatics @ UULarge 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
- 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
- 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
- Reposted by Theoretical Biology & Bioinformatics @ UUIt’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
- Reposted by Theoretical Biology & Bioinformatics @ UUThe 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)
- Did you ever wonder why you can find Tree Lizard 🦎 DNA at the bottom of the ocean? Read-based shotgun metagenomics profiles notoriously include random species that have no business being in a sample. Reads are often short can therefore falsely match surprising organisms. (2/5)
- RAT largely removes this issue by rigorously prioritizing taxonomic signals by annotation reliability: Read maps to a MAG? -> assign to the same organism as the MAG. Read maps to an unbinned contig? -> same procedure. Only unmapped reads are annotated directly. (3/5)
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View full threadCorresponding authors: @ehauptfeld.bsky.social @bedutilh.bsky.social
- Reposted by Theoretical Biology & Bioinformatics @ UUDo 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)
- Reposted by Theoretical Biology & Bioinformatics @ UU#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)
- Reposted by Theoretical Biology & Bioinformatics @ UUExcited 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
- Reposted by Theoretical Biology & Bioinformatics @ UUHappy 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
- Reposted by Theoretical Biology & Bioinformatics @ UUIt’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!
- The last chapter of my PhD is out now! #PLOSCompBio: Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis t.co/IUCEnNcBkG
- Paper alert: Van Eijnatten and colleagues find that C. elegans gene expression is confounded by what they call 'developmental age' (not chronological age). This complicates the interpretation of eQTL experiments, for which they provide a solution!
- Also see this nice summary on the Utrecht University website!
- With a complex developmental program, eQTL mapping can be challenging, as changes in gene expression complicate interpretation. Check out this new paper in G3 by Bram van Eijnatten, Basten Snoek and collaborators from Wageningen University & Research, and see how we can improve detection of eQTLs!
- Reposted by Theoretical Biology & Bioinformatics @ UUQ&A with Paulien Hogeweg #NatureComputationalScience www.nature.com/articles/s43...
