Theoretical Biology & Bioinformatics @ UU

Space is the place (for microbes 🦠)!
Delighted to have contributed to this review on spatial structure in microbial communities by @marcelbaecker.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others.

The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature – a critical evaluation of Akiyoshi, 2025 Summary:Akiyoshi, 2025 presented a hypothesis with implications for the early evolution of eukaryotes and eukaryotic cell division machinery. In this Correspondence, the authors conclude that this hyp...

Recently, a Hypothesis was posed in @jcellsci.bsky.social in which the root of eukaryotes was placed between kinetoplastids and all other eukaryotes. From this, it was implied that LECA did not have a kinetochore. We argue this is highly unlikely. A 🧵(1/12)

Read our reply here: tinyurl.com/n87myhpr

Please check out our review on the impact of spatial structure in microbial ecosystems! In it, we discuss how spatial patterns impact microbial ecology and evolution, eventually impacting everything we see around us!

See @marcelbaecker.bsky.social's amazing summary below :)

🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠

Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social

We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...

Spatial structure: shaping the ecology and evolution of microbial communities Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

Wrapping up a productive week: very glad to have contributed to this review on how spatial structure shapes microbial ecology and evolution, led by @marcelbaecker.bsky.social, @bedutilh.bsky.social, @bramvandijk.bsky.social and many others. doi.org/10.1093/fems...

@bramvandijk.bsky.social (and many other)'s new paper covered insights in microbial ecology, evolution and theoretical biology.

Welcome 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 🧬🦠✨

Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social

www.cell.com/current-biol...

New 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

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! 👇

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

Immune responses may make HIV-1 therapeutic interfering particles less effective The current standard treatment for HIV-1 infection is antiretroviral therapy, which effectively suppresses viral replication but requires a lifelong d…

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...

MetaPointFinder:
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/...

Extensive horizontal transfer of transposable elements shapes fungal mobilomes Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...

Extensive 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...

The 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

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-...

Featuring Paulien Hogeweg (2nd from the right), founder and lifelong colleague at @binfutrecht.bsky.social @utrechtuniversity.bsky.social

Very well deserved, Paulien!

Bram van Dijk @bramvandijk.bsky.social (@utrechtuniversity.bsky.social): How mobile genes reshape the microbial arms race
#NIME2025

Yesterday 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!

Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!

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.

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.

From aerial drone to quantitative trait locus: leveraging next‐generation phenotyping to reveal the genetics of color and height in field‐grown Lactuca sativa Understanding the genetic basis of lettuce color is important because these traits correlate with metabolites such as anthocyanins, which are known to have strong antioxidant properties. Furthermore,....

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.

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 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!

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

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...