Sam von der Dunk
@derdunk.bsky.social
📤 334
📥 660
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Studying the evolution of complexity through modelling and phylogenomics
reposted by
Sam von der Dunk
Bram van Dijk 🏳️🌈
about 1 month ago
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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Sam von der Dunk
Jeroen Meijer
about 2 months ago
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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Sam von der Dunk
Edoardo Gianni
about 2 months ago
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
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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 ...
https://www.science.org/doi/10.1126/science.adt2760
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reposted by
Sam von der Dunk
Max Raas
about 2 months ago
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
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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...
https://tinyurl.com/n87myhpr
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Sam von der Dunk
Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
about 2 months ago
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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Sam von der Dunk
Liedewij Laan
about 2 months ago
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...
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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…
http://meetings.embo.org/event/26-cellular-evolution
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reposted by
Sam von der Dunk
Nature
3 months ago
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers
go.nature.com/4sEMwLH
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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.
https://go.nature.com/4sEMwLH
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reposted by
Sam von der Dunk
Christian Kost
3 months ago
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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Sam von der Dunk
Genome Biology and Evolution
5 months ago
@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
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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
https://doi.org/10.1093/gbe/evaf183
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reposted by
Sam von der Dunk
Jolien van Hooff
6 months ago
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel
@binfutrecht.bsky.social
!
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reposted by
Sam von der Dunk
Buzz Baum
6 months ago
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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Sam von der Dunk
Oxford Biology
7 months ago
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
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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.
7 months ago
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reposted by
Sam von der Dunk
Julian Vosseberg
7 months ago
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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reposted by
Sam von der Dunk
Marc Robinson-Rechavi
7 months ago
Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold
https://doi.org/10.1126/science.ade2574
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
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Original post on ecoevo.social
https://ecoevo.social/@marcrr/115071804016187245
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Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers!
#ESEB25
@julianvosseberg.bsky.social
7 months ago
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Interactive symbiosis in silico (back) and in vivo (front).
#ESEB25
8 months ago
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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...
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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...
https://www.biorxiv.org/content/10.1101/2025.07.30.667627v1.full.pdf+html
8 months ago
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Sam von der Dunk
Theoretical Biology & Bioinformatics @ UU
10 months ago
🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨
www.uu.nl/en/organisat...
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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!
https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-position-in-multiscale-mechanistic-modelling-of-animal-development
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reposted by
Sam von der Dunk
Julian Vosseberg
12 months ago
One week left to submit your abstract!
@eseb2025.bsky.social
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reposted by
Sam von der Dunk
Melissah Rowe
12 months ago
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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reposted by
Sam von der Dunk
Alvaro San Millan
about 1 year ago
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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#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
about 1 year ago
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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.
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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...
https://doi.org/10.1038/s41586-023-06974-w
about 1 year ago
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reposted by
Sam von der Dunk
Fabien Burki
over 1 year ago
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)
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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
https://uu.varbi.com/se/what:job/jobID:778680/
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reposted by
Sam von der Dunk
Ross Fitzgerald
over 1 year ago
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...
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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...
https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1001/job/11709
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reposted by
Sam von der Dunk
over 1 year ago
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
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Improving genome-scale metabolic models of incomplete genomes with deep learning
Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.
https://shorturl.at/REOm8
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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
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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...
https://t.co/IUCEnNcBkG
about 2 years ago
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