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Sam von der Dunk

@derdunk.bsky.social
358 followers 684 following 21 posts

Studying the evolution of complexity through modelling and phylogenomics

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Reposted by Sam von der Dunk
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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Timothy Fuqua @timothyfuqua.bsky.social · 29/05/2026
Our study comparing promoter existence and emergence in random vs genomic DNA is finally published!!! TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
science.org
De novo promoters emerge more readily from random DNA than from genomic DNA
Promoters emerge three times more readily from random DNA than from genomic DNA.
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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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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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Christian Kost @kostchristian.bsky.social · 14/04/2026
@shrylishreekar.bsky.social and me wrote a commentary on Chunhui Hao's and @stuwest.bsky.social et al.'s recent paper "Cooperation and the evolution of bacterial niche breadth" in PNAS. Please find our commentary here: www.pnas.org/doi/10.1073/...
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Sam von der Dunk @derdunk.bsky.social · 09/04/2026
Very excited with the online publication of our modeling work on the evolution of sexual reproduction during obligate endosymbiosis: doi.org/10.1098/rstb.... The first publication of Alkmini Zania 🎉; together with Paulien Hogeweg.
doi.org
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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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Edoardo Gianni @edogia.bsky.social · 13/02/2026
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n
science.org
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
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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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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 12/02/2026
Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!
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Liedewij Laan @liedewijlaan.bsky.social · 12/02/2026
Meeting alert! EMBO workshop about molecular and physical principles in evolution in Portugal, 2-5 June 2026. Deadline for registration is March 1st. Check out the website it should be a fun and informative workshop bridging evolutionary biology and physics of life meetings.embo.org/event/26-cel...
meetings.embo.org
The rules of the game: biophysical & molecular principles in cellular evolution
Cells are the fundamental units of life, shaped by evolution into a remarkable diversity of forms and functions. Much is known about the roles of genes and proteins, the regulation of molecular proce…
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Nature @nature.com · 14/01/2026
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers go.nature.com/4sEMwLH
go.nature.com
Genomic clues to the origin of eukaryotic cells
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers.
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Christian Kost @kostchristian.bsky.social · 30/12/2025
Less than two 2 weeks to apply for this PhD position in my group. Please do not miss the opportunity to apply if the topic is of interest to you 👇
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Genome Biology and Evolution @genomebiolevol.bsky.social · 31/10/2025
@guyleonard.bsky.social et al. report a near-complete genome and transcriptome sequence dataset for green algae host Paramecium bursaria, an endosymbiotic model system. 🔗 doi.org/10.1093/gbe/evaf183 #genome #evolution
doi.org
De Novo Genome Sequence Assembly of the RNAi-Tractable Paramecium bursaria 186b: An Endosymbiotic Model System
Abstract. How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a use
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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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Buzz Baum @buzzbaum.bsky.social · 02/10/2025
LMB PhD studentship available in the Baum lab to use informatics to infer cell structure from genomic data in collaboration with the brilliant Tom Williams. If you write to me and I don’t reply - try again - the spam filter is hungry…
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Oxford Biology @biology.ox.ac.uk · 15/09/2025
Oxford Biology is growing 📢 We’re appointing 3 Associate Professors in: 🌱 Plant Sciences 🦉 Animal Behaviour 🔬 Molecular Cell Biology 3 fields. 3 opportunities. One new home for Oxford Biology. Learn more 👉 bit.ly/41S2Tc7 Apply now 👉 bit.ly/488CNW3
Photo showing the inside atrium of the new Life and Mind Building
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Sam von der Dunk @derdunk.bsky.social · 01/09/2025
Excited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.
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Julian Vosseberg @julianvosseberg.bsky.social · 22/08/2025
And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 22/08/2025
Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold doi.org/10.1126/science.ade2574 Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
ecoevo.social
Original post on ecoevo.social
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Sam von der Dunk @derdunk.bsky.social · 21/08/2025
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
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Sam von der Dunk @derdunk.bsky.social · 19/08/2025
Interactive symbiosis in silico (back) and in vivo (front). #ESEB25
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Sam von der Dunk @derdunk.bsky.social · 05/08/2025
The exciting project of Alkmini Zania on the impact of sex on endosymbiosis reveals complex evolutionary dynamics. What could this mean for early eukaryotes? www.biorxiv.org/content/10.1...
biorxiv.org
The risk of sexual reproduction promotes the evolution of regulation between host and symbionts
Sexual reproduction is a widely spread feature of eukaryotes and was already present in the last eukaryotic common ancestor (LECA). Most extant eukaryotes inherit mitochondria from a single parent, bu...
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 17/06/2025
🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨 www.uu.nl/en/organisat...
uu.nl
PhD Position in Multiscale Mechanistic Modelling of Animal Development
How do protein interactions at the subcellular scale regulate the morphology of an entire organ? Join us to explore this question with computer models!
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Julian Vosseberg @julianvosseberg.bsky.social · 17/04/2025
One week left to submit your abstract! @eseb2025.bsky.social
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Melissah Rowe @melissahrowe.bsky.social · 13/04/2025
Share your work on host-associated microbiomes in our symposium @eseb2025.bsky.social - with speakers Hassan Salem @hassansalem.bsky.social and Carola Petersen. Abstract deadline April 25th. Florent, Klara, and I would love to see you there!
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Alvaro San Millan @sanmillan.bsky.social · 13/03/2025
Join us in at #ESEB2025 Barcelona for our symposium on microbial adaptation to changing conditions. Organised by @mtoll8.bsky.social @javierdelafuente.bsky.social and me. Amazing invited speakers @saramitri.bsky.social and Itzik Mizrahi!! @eseb2025.bsky.social
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Sam von der Dunk @derdunk.bsky.social · 17/03/2025
#ESEB2025 Exciting symposium alert: (S50) Unravelling the origin of eukaryotes. 🦑🌴 With speakers Purificación López-García and Mark Field. We are looking forward to your abstract submissions! eseb2025.com/list-of-symp... @julianvosseberg.bsky.social
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Sam von der Dunk @derdunk.bsky.social · 17/03/2025
Here's a cool article doi.org/10.1038/s415..., which supports my evolutionary model of a prokaryotic cell cycle (doi.org/10.1093/gbe/...), in which we allow evolution to exploit the changes in gene dosage induced by replication to improve cell-cycle regulation.
doi.org
Transcription–replication interactions reveal bacterial genome regulation - Nature
Single-cell expression data from bacteria are used to classify gene regulatory architectures in relation to gene expression dynamics and the cell cycle, revealing distinct categories of gene regulator...
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Fabien Burki @fburki.bsky.social · 10/12/2024
I would really appreciate a wide sharing of this post, as the candidate profile I am looking for is outside of my regular circle. Thank you so much. More info and how to apply here: uu.varbi.com/se/what:job/... (2/2)
uu.varbi.com
Postdoktor inom i proteomik och eukaryotisk evolution
Postdoktor i proteomik och eukaryotisk evolution Detta projekt är en del av ett ERC Consolidator-anslag (PlastidOrigin) som tilldelats Fabien Burki och syftar till att studera en av de mest omvälvan
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Ross Fitzgerald @jrossfitz.bsky.social · 04/12/2024
New MRC-funded postdoc with me on comparative bacterial genomics/phylodynamics @roslininstitute.bsky.social university of Edinburgh. Great multidisciplinary team and collaboration with partners at Shanghai Jao Tong University. elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
elxw.fa.em3.oraclecloud.com
PDRA in Bacterial Genomics
We are looking for a Post-Doctoral Research Associate in Bacterial Genomics at the Laboratory for Bacterial Evolution and Pathogenesis (www.ed.ac.uk/roslin/research/divisions/bacteriology/lbep) at The...
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mdboer.bsky.social @mdboer.bsky.social · 26/11/2024
Exciting news! 🎉 My article is out in iScience presenting DNNGIOR, a deep learning tool advancing gap-filling in metabolic models. Huge thanks to co-authors @cmelkonian.bsky.social, @hariszaf.bsky.social, Daniel Garza, Andreas Haas and @bedutilh.bsky.social. Read at shorturl.at/REOm8
shorturl.at
Improving genome-scale metabolic models of incomplete genomes with deep learning
Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.
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Sam von der Dunk @derdunk.bsky.social · 26/02/2024
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
t.co
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis
Author summary Virtually all life forms visible by the naked eye are eukaryotes, complex cells with a nucleus, mitochondria and many other subcellular structures as well as the regulatory mechanisms t...
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