Sam von der Dunk
@derdunk.bsky.social
Studying the evolution of complexity through modelling and phylogenomics
Reposted by Sam von der Dunk
@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/10.1093/gbe/evaf183
#genome #evolution
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
doi.org
October 31, 2025 at 10:54 AM
@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/10.1093/gbe/evaf183
#genome #evolution
Reposted by Sam von der Dunk
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
Hoe is al het complexe leven op aarde eigenlijk ontstaan?
Wat DNA uit slootwater ons vertelt over jouw onbekende voorouders | VPRO Tegenlicht
YouTube video by VPRO Tegenlicht
youtu.be
October 9, 2025 at 8:46 AM
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
Reposted by Sam von der Dunk
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…
October 2, 2025 at 9:04 AM
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…
Reposted by Sam von der Dunk
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
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
September 15, 2025 at 8:20 AM
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
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
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.
September 1, 2025 at 10:35 AM
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.
Reposted by Sam von der Dunk
And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
August 22, 2025 at 2:27 PM
And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!
Reposted by Sam von der Dunk
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 […]
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
Original post on ecoevo.social
ecoevo.social
August 22, 2025 at 9:53 AM
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 […]
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
August 21, 2025 at 4:23 PM
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
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
August 5, 2025 at 9:35 AM
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...
Reposted by Sam von der Dunk
One week left to submit your abstract! @eseb2025.bsky.social
#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
April 17, 2025 at 10:16 AM
One week left to submit your abstract! @eseb2025.bsky.social
Reposted by Sam von der Dunk
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!
April 13, 2025 at 6:19 PM
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!
Reposted by Sam von der Dunk
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
March 13, 2025 at 5:30 PM
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
#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
March 17, 2025 at 6:09 PM
#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
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
March 17, 2025 at 12:44 PM
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.
Reposted by Sam von der Dunk
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
December 10, 2024 at 7:42 AM
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)
Reposted by Sam von der Dunk
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/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
December 4, 2024 at 9:56 AM
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/hcmUI/Candid...
Reposted by Sam von der Dunk
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
November 26, 2024 at 12:25 PM
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
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
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...
t.co
February 26, 2024 at 10:00 AM
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