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
Thanks for having me! I really enjoyed the discussion as well.
Ok, highly recommend this online journal club. The discussion was really thoughtful and the wide variety of perspectives was enlightening. Thank you @lavishaparab.bsky.social for organizing!
July 15, 2026 at 3:11 PM
Thanks for having me! I really enjoyed the discussion as well.
Reposted by Theoretical Biology & Bioinformatics @ UU
@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...
bsky.app/profile/paul...
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/...
www.science.org/doi/10.1126/...
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.
www.science.org
July 15, 2026 at 1:15 PM
@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...
bsky.app/profile/paul...
Reposted by Theoretical Biology & Bioinformatics @ UU
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!
Big thanks to @mfseidl.bsky.social and the TBB team, and to @femsmicro.org for the Research and Training Grant!
July 14, 2026 at 10:55 AM
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!
Big thanks to @mfseidl.bsky.social and the TBB team, and to @femsmicro.org for the Research and Training Grant!
Reposted by Theoretical Biology & Bioinformatics @ UU
For some reason people had less difficulty finding my poster than usual
July 11, 2026 at 11:08 AM
For some reason people had less difficulty finding my poster than usual
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
@ubc-uu.bsky.social @utrechtuniversity.bsky.social
July 6, 2026 at 10:10 AM
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
@ubc-uu.bsky.social @utrechtuniversity.bsky.social
Reposted by Theoretical Biology & Bioinformatics @ UU
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.
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.
July 1, 2026 at 8:48 PM
Reposted by Theoretical Biology & Bioinformatics @ UU
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 👇
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...
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 ...
www.biorxiv.org
June 23, 2026 at 6:25 PM
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 👇
Reposted by Theoretical Biology & Bioinformatics @ UU
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...
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 ...
www.biorxiv.org
June 22, 2026 at 12:20 PM
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...
Reposted by Theoretical Biology & Bioinformatics @ UU
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
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
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.
www.science.org
June 1, 2026 at 8:26 AM
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
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
Reposted by Theoretical Biology & Bioinformatics @ UU
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/...
www.science.org/doi/10.1126/...
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.
www.science.org
June 1, 2026 at 7:50 AM
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/...
www.science.org/doi/10.1126/...
Reposted by Theoretical Biology & Bioinformatics @ UU
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
www.evolbio.mpg.de/3884217/viru...
@jeroenmeijer.bsky.social @paulbrainey.bsky.social @uni-jena.de @utrechtuniversity.bsky.social @bedutilh.bsky.social
June 1, 2026 at 6:33 AM
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
www.evolbio.mpg.de/3884217/viru...
@jeroenmeijer.bsky.social @paulbrainey.bsky.social @uni-jena.de @utrechtuniversity.bsky.social @bedutilh.bsky.social
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!
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!
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! 🙏
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! 🙏
www.uu.nl
June 1, 2026 at 7:36 AM
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!
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!
Reposted by Theoretical Biology & Bioinformatics @ UU
Some snaps from trails around the SFU and UBC campuses from the last 2 months. Vancouver is beautiful 😭
May 28, 2026 at 3:11 AM
Some snaps from trails around the SFU and UBC campuses from the last 2 months. Vancouver is beautiful 😭
Reposted by Theoretical Biology & Bioinformatics @ UU
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! 🙏
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! 🙏
www.uu.nl
May 22, 2026 at 9:02 AM
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! 🙏
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! 🙏
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
Very well deserved, and congratulations!
@ubc-uu.bsky.social @utrechtuniversity.bsky.social
May 13, 2026 at 1:10 PM
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
Very well deserved, and congratulations!
@ubc-uu.bsky.social @utrechtuniversity.bsky.social
Reposted by Theoretical Biology & Bioinformatics @ UU
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/10.64898/202...
doi.org
May 13, 2026 at 9:48 AM
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/10.64898/202...
Reposted by Theoretical Biology & Bioinformatics @ UU
Our research work on using #singlecell co-mapping to study early embryonic development is now published: doi.org/10.7554/eLif....
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.
doi.org
April 23, 2026 at 3:27 PM
Our research work on using #singlecell co-mapping to study early embryonic development is now published: doi.org/10.7554/eLif....
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...
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...
www.biorxiv.org
May 5, 2026 at 12:15 PM
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...
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...
Reposted by Theoretical Biology & Bioinformatics @ UU
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...
www.jsmc-phd.de/admission/va...
Vacant Positions - JSMC Jena School for Microbial Communication
www.jsmc-phd.de
March 30, 2026 at 8:04 PM
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...
www.jsmc-phd.de/admission/va...
Reposted by Theoretical Biology & Bioinformatics @ UU
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...
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...
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!
www.uu.nl
March 23, 2026 at 7:41 PM
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...
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...
Reposted by Theoretical Biology & Bioinformatics @ UU
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...
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...
February 25, 2026 at 1:06 PM
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...
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...
Reposted by 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.
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.
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
academic.oup.com/femsre/artic... 🧵👇
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
academic.oup.com
February 13, 2026 at 1:04 PM
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.
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.
Reposted by Theoretical Biology & Bioinformatics @ UU
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
Read our reply here: tinyurl.com/n87myhpr
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...
tinyurl.com
February 13, 2026 at 12:45 PM
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
Read our reply here: tinyurl.com/n87myhpr