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Theoretical Biology & Bioinformatics @ UU

@binfutrecht.bsky.social
576 followers 35 following 43 posts

Our group consists of two research groups : Theoretical Biology (headed by Rob de Boer) and Bioinformatics (headed by Berend Snel) at @utrechtuniversity.bsky.social

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Jeroen Meijer @jeroenmeijer.bsky.social · 15/07/2026
Thanks for having me! I really enjoyed the discussion as well.
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 15/07/2026
@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...
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Reposted by Theoretical Biology & Bioinformatics @ UU
Sergio Alías Segura @seraliseg.bsky.social · 14/07/2026
Back in Madrid after 3 months at @utrechtuniversity.bsky.social! I recently wrapped up a research stay at @binfutrecht.bsky.social working on cereal metagenomics for my PhD thesis 🧬 Big thanks to @mfseidl.bsky.social and the TBB team, and to @femsmicro.org for the Research and Training Grant!
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Jeroen Meijer @jeroenmeijer.bsky.social · 11/07/2026
For some reason people had less difficulty finding my poster than usual
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Reposted by Theoretical Biology & Bioinformatics @ UU
Jeroen Meijer @jeroenmeijer.bsky.social · 09/07/2026
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
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 06/07/2026
Today we're enjoying a wonderful symposium hosted by Petros Skiadas & @mfseidl.bsky.social, as a prelude for Petros's PhD defence. Lots to learn about oomycetes and plant pathogenesis, immunity and effector biology! @ubc-uu.bsky.social @utrechtuniversity.bsky.social
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Reposted by Theoretical Biology & Bioinformatics @ UU
Vivek Bhardwaj @vivekbhr.bsky.social · 01/07/2026
We are #hiring! Come join us at Utrecht University (NL) and help centralize our ongoing #genomics efforts into a new core unit, embedded in our inter-divisional lab. We are looking for a Postdoc in molecular biology and a Bioinformatics engineer. Please apply/forward to those interested.
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Reposted by Theoretical Biology & Bioinformatics @ UU
Bas E. Dutilh @bedutilh.bsky.social · 23/06/2026
There are many types of urinary tract microbiomes, and UTIs can happen with most of them. Even more interesting is that healthy individuals have almost the same microbial communities! Check out David's new preprint to see the details 👇
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David Giron Villalobos @dagivi.bsky.social · 22/06/2026
1/4. Excited to share the first preprint from my PhD at @binfutrecht.bsky.social and @uti-revisited.bsky.social 🐥. In this work, we explored the urinary tract microbiome composition (urobiome) by combining data from multiple metagenomic sequencing studies 💛🦠. www.biorxiv.org/content/10.6...
biorxiv.org
Cross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infections
Background Urinary tract infections (UTIs) represent a major public health concern, increasingly complicated by rising antibiotic resistance, diminishing treatment efficacy, and increasing prevalence ...
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Reposted by Theoretical Biology & Bioinformatics @ UU
Jeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
science.org
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
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Reposted by Theoretical Biology & Bioinformatics @ UU
Paul Rainey @paulbrainey.bsky.social · 01/06/2026
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/...
science.org
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
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MPI for Evolutionary Biology @mpi-evolbio.bsky.social · 01/06/2026
New in Science Advances: A bacteriophage stayed genetically stable for months, then evolved rapidly in a new microbial community. www.evolbio.mpg.de/3884217/viru... @jeroenmeijer.bsky.social @paulbrainey.bsky.social @uni-jena.de @utrechtuniversity.bsky.social @bedutilh.bsky.social
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 01/06/2026
Application deadline coming up: June 7th 🔔 Interested in... 🧐 Fundamental biology? 🧩 Elucidating how evolution works? 🧬 Obtaining new insights from genome sequences? 🫥 Archaea, the least studied domain of life? Join us with an exciting PhD on archaeal genome evolution!
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Sultan Nazir @sultannazir.bsky.social · 28/05/2026
Some snaps from trails around the SFU and UBC campuses from the last 2 months. Vancouver is beautiful 😭
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 13/05/2026
Proud of @ehauptfeld.bsky.social for receiving the Young Investigator Award by @biosb.bsky.social, in recognition to her PhD achievements in research and education! Very well deserved, and congratulations! @ubc-uu.bsky.social @utrechtuniversity.bsky.social
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Carlos Santana Molina @santanamolina.bsky.social · 13/05/2026
Our preprint on the 'Origins of Eukaryotic Metabolism' is out! Take a look at some of the new findings on the origin of eukaryotic membranes, metabolic integrations between archaeal and bacterial ancestors, and other fascinating prokaryotic interactions during eukaryogenesis. doi.org/10.64898/202...
doi.org
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Vivek Bhardwaj @vivekbhr.bsky.social · 23/04/2026
Our research work on using #singlecell co-mapping to study early embryonic development is now published: doi.org/10.7554/eLif....
doi.org
Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development
A robust and quantitative map links chromatin modification and gene expression of cells during zebrafish embryogenesis.
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 05/05/2026
New preprint! Text by Bram van Eijnatten: Happy to share a collaboration between @binfutrecht.bsky.social and the Plant Stress Resilience Group from @utrechtuniversity.bsky.social and the Quint lab. We present the Arabidopsis thaliana 'EcoCore panel': www.biorxiv.org/content/10.6...
biorxiv.org
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Bas E. Dutilh @bedutilh.bsky.social · 30/03/2026
The VEO Group has a position open for a PhD student to investigate Fungi-bacteria interactions in complex communities! Check out this position and many more at the JSMC website 👇👇 www.jsmc-phd.de/admission/va...
jsmc-phd.de
Vacant Positions - JSMC Jena School for Microbial Communication
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 23/03/2026
Phd Position alert 🚨 Join our project ASTRAfun (Adaptation and Starship Traffic in Root-Associated fungi), in which we will use computational models to unveil the hidden dynamics of fungal evolution. It’s not going to be just regular fun. It’s going to ASTRAfun. 🤓 www.uu.nl/en/organisat...
uu.nl
PhD Position in Computational Modelling of Fungal Evolution
How do giant mobile elements called ‘Starships’ reshape fungal plant pathogens? Help us computationally model their spread and impact in nature and agriculture!
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 25/02/2026
In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...
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Jeroen Meijer @jeroenmeijer.bsky.social · 13/02/2026
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.
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Max Raas @maxraas.bsky.social · 13/02/2026
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
tinyurl.com
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...
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 13/02/2026
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 ! 🦠
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Bas E. Dutilh @bedutilh.bsky.social · 12/02/2026
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
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Bas E. Dutilh @bedutilh.bsky.social · 29/01/2026
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...
jobs.uni-jena.de
PhD student bioinformatics: Viral strategies in the global Microverse
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Simon van Vliet @simonvanvliet.bsky.social · 11/02/2026
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...
doi.org
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
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Reposted by Theoretical Biology & Bioinformatics @ UU
Wing Yui Ngan @yuingan.bsky.social · 12/02/2026
@bramvandijk.bsky.social (and many other)'s new paper covered insights in microbial ecology, evolution and theoretical biology.
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Daniel Tamarit @danieltamarit.bsky.social · 10/12/2025
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 🧬🦠✨
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Josje Romeijn @jromeijn.bsky.social · 09/12/2025
Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...
cell.com
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...
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Kops Lab @kopslab.bsky.social · 01/12/2025
New preprint from our lab! Led by Emine Ali and @maxraas.bsky.social See the highlights below!
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Max Raas @maxraas.bsky.social · 01/12/2025
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
tinyurl.com
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 09/12/2025
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! 👇
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 09/12/2025
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...
sciencedirect.com
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…
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Aldert Zomer @aldertzomer.bsky.social · 08/12/2025
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/...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 06/12/2025
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...
cell.com
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...
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Reposted by Theoretical Biology & Bioinformatics @ UU
Hubrecht Institute @hubrechtinstitute.bsky.social · 28/10/2025
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.
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 23/10/2025
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
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 23/10/2025
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-...
academic.oup.com
How coupling resources and development ensures whole plant homeostasis
Abstract. Plants maintain internal stability even amid fluctuating external conditions. For energy, nutrients, and fixed carbon, this relies on the dynamic
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 22/10/2025
Featuring Paulien Hogeweg (2nd from the right), founder and lifelong colleague at @binfutrecht.bsky.social @utrechtuniversity.bsky.social Very well deserved, Paulien!
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Ákos T Kovács @evolvedbiofilm.bsky.social · 07/10/2025
Bram van Dijk @bramvandijk.bsky.social (@utrechtuniversity.bsky.social): How mobile genes reshape the microbial arms race #NIME2025
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Daniel Tamarit @danieltamarit.bsky.social · 08/10/2025
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!
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Jolien van Hooff @jvhooff.bsky.social · 09/10/2025
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 03/09/2025
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....
doi.org
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,....
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Josje Romeijn @jromeijn.bsky.social · 20/06/2025
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.
biorxiv.org
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Team Thomma @teamthomma.bsky.social · 24/07/2025
📣 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
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...
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Monica L Garcia Gomez @moneralee.bsky.social · 25/07/2025
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!
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Stephan Köstlbacher @stephkoe.bsky.social · 20/07/2025
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...
biorxiv.org
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...
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