Theoretical Biology & Bioinformatics @ UU
@binfutrecht.bsky.social
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 @ UU
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
Check it out here: tinyurl.com/4ectm9x4
tinyurl.com
December 1, 2025 at 2:53 PM
Reposted by Theoretical Biology & Bioinformatics @ UU
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
Check it out here: tinyurl.com/4ectm9x4
tinyurl.com
December 1, 2025 at 2:06 PM
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
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! 👇
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! 👇
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.
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.
www.biorxiv.org
December 9, 2025 at 9:34 AM
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! 👇
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 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...
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…
www.sciencedirect.com
December 9, 2025 at 9:21 AM
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 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...
Reposted by Theoretical Biology & Bioinformatics @ UU
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/...
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/...
December 8, 2025 at 10:00 AM
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/...
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 @ UU
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...
@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social
www.cell.com/current-biol...
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...
www.cell.com
December 6, 2025 at 9:22 AM
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...
@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social
www.cell.com/current-biol...
Reposted by Theoretical Biology & Bioinformatics @ UU
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.
Hoe is al het complexe leven op aarde eigenlijk ontstaan?
Wat DNA uit slootwater ons vertelt over jouw onbekende voorouders | VPRO Tegenlicht
YouTube video by VPRO Tegenlicht
youtu.be
October 28, 2025 at 8:32 AM
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
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...
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...
21 Vidi grants awarded to Utrecht-based researchers
21 researchers from Utrecht University, University Medical Center Utrecht, and Princess Máxima Center have each been awarded a Vidi grant worth up to €850,000.
www.uu.nl
October 23, 2025 at 1:30 PM
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
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-...
How do plant development and morphology mediate resource acquisition and costs?
🌿🌳🌺 💰💵📈
academic.oup.com/jxb/advance-...
October 23, 2025 at 10:13 AM
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-...
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!
Very well deserved, Paulien!
October 22, 2025 at 2:06 PM
Featuring Paulien Hogeweg (2nd from the right), founder and lifelong colleague at @binfutrecht.bsky.social @utrechtuniversity.bsky.social
Very well deserved, Paulien!
Very well deserved, Paulien!
Reposted by Theoretical Biology & Bioinformatics @ UU
Bram van Dijk @bramvandijk.bsky.social (@utrechtuniversity.bsky.social): How mobile genes reshape the microbial arms race
#NIME2025
#NIME2025
October 7, 2025 at 1:15 PM
Bram van Dijk @bramvandijk.bsky.social (@utrechtuniversity.bsky.social): How mobile genes reshape the microbial arms race
#NIME2025
#NIME2025
Reposted by Theoretical Biology & Bioinformatics @ UU
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!
October 8, 2025 at 1:54 PM
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!
Reposted by Theoretical Biology & Bioinformatics @ UU
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
Hoe is al het complexe leven op aarde eigenlijk ontstaan?
Wat DNA uit slootwater ons vertelt over jouw onbekende voorouders | VPRO Tegenlicht
YouTube video by VPRO Tegenlicht
youtu.be
October 9, 2025 at 8:46 AM
Very 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....
Great work by Rens Dijkhuizen, Bram van Eijnatten, Sarah Mehrem, @guidopmi.bsky.social & others!
doi.org/10.1111/tpj....
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,....
doi.org
September 3, 2025 at 9:26 AM
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....
Great work by Rens Dijkhuizen, Bram van Eijnatten, Sarah Mehrem, @guidopmi.bsky.social & others!
doi.org/10.1111/tpj....
Reposted by Theoretical Biology & Bioinformatics @ UU
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.
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.
www.biorxiv.org
June 20, 2025 at 7:39 PM
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.
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
rdcu.be/exBSp
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...
rdcu.be
July 24, 2025 at 10:40 AM
📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp
rdcu.be/exBSp
Reposted by Theoretical Biology & Bioinformatics @ UU
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!
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...
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...
Wound repair in plants guided by cell geometry
Mathew et al. show that growth conflicts reshape cells after injury, forming rhomboidal
geometries that trigger diagonal divisions. This reorients cell files to restore tapered
morphology. A two-step ...
www.cell.com
July 25, 2025 at 7:11 AM
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!
Reposted by Theoretical Biology & Bioinformatics @ UU
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...
🧵 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...
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...
www.biorxiv.org
July 20, 2025 at 1:04 PM
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...
🧵 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 @ UU
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 👇
📢 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...
🧵 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...
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...
www.biorxiv.org
July 28, 2025 at 7:18 AM
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 👇
📢 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 👇
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"
"First students are special, especially those who become a lifelong colleague, successor, and now, fellow emeritus"
June 12, 2025 at 8:39 AM
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"
"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!
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!
June 12, 2025 at 8:33 AM
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!
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 @ UU
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...
Apply before June 16 to join this exciting project with Kirsten ten Tusscher in the context of CropXR!! www.uu.nl/en/organisat...
PhD Position in Modelling Regulation of Plant Stress Responses across Species
Join us to model plant stress responses and help breed climate-resilient crops in a collaborative, interdisciplinary research environment!
www.uu.nl
May 12, 2025 at 6:42 PM
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...
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 @ UU
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.
Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published:
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods
Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.
www.nature.com
May 15, 2025 at 3:07 PM
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.
Reposted by Theoretical Biology & Bioinformatics @ UU
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...
➡️ www.lichtgedanken.uni-jena.de/en/3157/smal...
May 21, 2025 at 8:14 AM
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...
➡️ www.lichtgedanken.uni-jena.de/en/3157/smal...