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Reposted by Sam von der Dunk

Buzz Baum @buzzbaum.bsky.social · 7d

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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Reposted by Sam von der Dunk

Oxford Biology @biology.ox.ac.uk · 24d

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 · Sep 1

Protein structures are not inherently robust, but natural proteins are substantially more robust than random sequences, representing a clear signature of adaptation. Mutational robustness is relatively low in newborn and viral proteins, and provides a new perspective on protein evolution.

Sam von der Dunk @derdunk.bsky.social · Sep 1

RNA structures are inherently evolvable and robust to mutations: random RNA molecules already show the same level of robustness and a similar distribution of secondary structures as natural RNA molecules. Hence, it is difficult to detect signatures of selection on the distribution of RNA structures.

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Sam von der Dunk @derdunk.bsky.social · Sep 1

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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Reposted by Sam von der Dunk

Julian Vosseberg @julianvosseberg.bsky.social · Aug 22

And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!

Sam von der Dunk @derdunk.bsky.social · Aug 21

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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Reposted by Sam von der Dunk

Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · Aug 22

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 […]

Original post on ecoevo.social

ecoevo.social

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Sam von der Dunk @derdunk.bsky.social · Aug 21

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 · Aug 19

Interactive symbiosis in silico (back) and in vivo (front). #ESEB25

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Sam von der Dunk @derdunk.bsky.social · Aug 5

We have found before, including in different models, that evolutionary conflict leads to better adaptive solutions. These challenges best expose the creativity of evolutionary processes. Or, borrowing from Nietzsche: "What doesn't kill you makes you stronger" (at the population level)!

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Sam von der Dunk @derdunk.bsky.social · Aug 5

Our main finding: Mixing of endosymbionts (sex) is dangerous but can stimulate beneficial regulatory integration of host and symbiont!

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Sam von der Dunk @derdunk.bsky.social · Aug 5

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...

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...

www.biorxiv.org

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Reposted by Sam von der Dunk

Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Jun 17

🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨

www.uu.nl/en/organisat...

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!

www.uu.nl

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Reposted by Sam von der Dunk

Julian Vosseberg @julianvosseberg.bsky.social · Apr 17

One week left to submit your abstract! @eseb2025.bsky.social

Sam von der Dunk @derdunk.bsky.social · Mar 17

#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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Reposted by Sam von der Dunk

Melissah Rowe @melissahrowe.bsky.social · Apr 13

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 @sanmillan.bsky.social · Mar 13

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 · Mar 17

#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 · Mar 17

In our study, we found that genome organization emerges, in which the positions of regulatory genes along the chromosome correlate with their temporal activity during the cell cycle...

Sam von der Dunk @derdunk.bsky.social · Mar 17

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.

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...

doi.org

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Reposted by Sam von der Dunk

Fabien Burki @fburki.bsky.social · Dec 10

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)

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

uu.varbi.com

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Reposted by Sam von der Dunk

Ross Fitzgerald @jrossfitz.bsky.social · Dec 4

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...

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...

elxw.fa.em3.oraclecloud.com

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Reposted by Sam von der Dunk

mdboer.bsky.social @mdboer.bsky.social · Nov 26

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

Improving genome-scale metabolic models of incomplete genomes with deep learning

Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.

shorturl.at

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Sam von der Dunk @derdunk.bsky.social · Feb 26

Hope that helps?

Sam von der Dunk @derdunk.bsky.social · Feb 26

Although we enforce the endosymbiosis, host and symbiont normally adapt in such a way that preserves their regulatory autonomy. Only when we include regulatory conflicts, do host and symbionts evolve to communicate and to establish control mechanisms between them.

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Sam von der Dunk @derdunk.bsky.social · Feb 26

Regulatory conflicts between host and symbionts (i.e. signaling molecules of host and symbiont interfering with each other) promote host--symbiont integration, providing a narrative for how a transition in individuality may take place in a tight endosymbiotic relationship.

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