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Ursula Oggenfuss

@oggenfussursula.bsky.social
729 followers 395 following 13 posts

🍄🧬 Screening trough fungal genomes to detect 🔻transposable elements🔻 and structural variation

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Reposted by Ursula Oggenfuss
Jolien van Hooff @jvhooff.bsky.social · 8h
We're looking for a PhD candidate who's eager to study how the genomes of fascinating eukaryotic microbes evolve and organize - and we have a fully funded PhD position available!
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Ursula Oggenfuss @oggenfussursula.bsky.social · 9h
Are you interested in learning how genomes of weird fungi and protists evolve and are you looking for an exciting PhD opportunity? Jolien van Hooff and I are looking for an enthusiasic PhD candidate at Wageningen University: www.wur.nl/en/vacancy/p... #TEworldwide #Fungi #Protists #Genome
wur.nl
PhD position in genome evolution and architecture in unicellular eukaryotes
Are you fascinated by how eukaryotic genomes evolve? Do you want to look beyond model organisms and point mutations to uncover the complexity of genome evolution?
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Ursula Oggenfuss @oggenfussursula.bsky.social · 04/09/2026
I can only recommend doing a PhD with Daniel. The position has transposons and fungi, the best combination! 🔻🍄 #TEworldwide #Fungi
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Daniel Croll @danielcroll.bsky.social · 04/09/2026
Our lab is looking for PhD students to join us in 2027 🎓🎉 The projects can be structured around our research directions: - Transposable element dynamics - Fungal pangenomics - ML/language model genomics applications - Pathogen adaptation More here pathogen-genomics.org ("Jobs") and please share! 🙏
pathogen-genomics.org
Evolutionary genomics of pathogens
Croll lab at University of Neuchatel. The lab of Daniel Croll wants to understand how pathogens evolve to cause disease. For this, we mainly focus on major crop pathogens to unravel mechanisms of rapi...
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Ursula Oggenfuss @oggenfussursula.bsky.social · 20/07/2026
I am happy to share that my NWO Veni project was awarded 🍄🧬🔻! In this project, I will study how transposons shape genome folding, evolution, and adaptation in a fungal salamander pathogen. I am incredibly thankful for all the support and look forward to this next chapter #fungi #transposons #TEsky
A sketch of two salamander species, with a zoomed in picture of a fungal fruit body releasing spores, leading to a small stretch of DNA which ends in a folded chromosome with many green triangles indicating transposon insertions
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Julian Vosseberg @julianvosseberg.bsky.social · 16/07/2026
I am very excited to share that I have received a Veni grant from the Dutch Research Council to start my own line of research on archaeal evolution at the Royal Netherlands Institute for Sea Research! www.nioz.nl/en/news-and-...
nioz.nl
Veni grant for research into evolution of archaea | NIOZ - Royal Netherlands Institute for Sea Research
Julian Vosseberg received a Veni grant to study the evolution of archaea. By characterizing similar genetic changes in their evolution, he aims to enlighten the predictability of the evolution process...
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The EMBO Journal @embojournal.org · 18/05/2026
Host-transposable element coexistence: a matter of resistance, tolerance and trade-off Read this new review by Séverine Chambeyron, Charlotte Grimaud, Mikiko Siomi et al link.springer.com/article/10.1...
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Genome Biology and Evolution @genomebiolevol.bsky.social · 10/03/2026
Fouché, @oggenfussursula.bsky.social, McDonald & @danielcroll.bsky.social retrace chromosomal degeneration in a fungal pathogen, identifying the exact sequence triggers that initiate chromosome instability and perpetuate degenerative cycles. 🔗 doi.org/10.1093/gbe/evag037 #genome #evolution
doi.org
Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen
Abstract. Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines.
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Tony Heitkam🌱🔍💚 @toheitka.bsky.social · 07/03/2026
Our lab member Sophie deep-dived into the genome of one of the plants we know best (sugar beet). She identified over 100 non-autonomous LTR retrotransposon families hiding in the genome. Many elements are rather long (length distribution ⬇️), often without any sequence similarity to coding TEs.
Length distribution of non-autonomous LTR retrotransposons
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Toby Baril @tobybarilbio.bsky.social · 05/03/2026
#TEworldwide #TEsky
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Dr. Tyler A. Elliott @transposableman.bsky.social · 06/03/2026
#TEsky a short paper from @mbonar.bsky.social , myself and others on our reannotation of TEs in the Octopus vulgaris genome. More work to come using genome ecology to analyze TEs in this species bsky.app/profile/bior...
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Reposted by Ursula Oggenfuss
Kassiani Panagiotou @kassipan.bsky.social · 05/03/2026
Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives. www.nature.com/articles/s41...
nature.com
Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology
The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...
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Genome Biology and Evolution @genomebiolevol.bsky.social · 18/02/2026
Dauphin et al. assembled a telomere-to-telomere reference genome for an ectomycorrhizal fungus with a large, repeat-rich genome, showing its genome expansion was driven by a few lineage-specific TE families in recent history. 🔗 doi.org/10.1093/gbe/evag017 #genome #evolution #TEsky
doi.org
Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism
Abstract. Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal spec
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PLOS Biology @plosbiology.org · 03/02/2026
#Azole resistance in #Candida albicans poses a growing threat, and is linked to #StressResponse. @annaselmecki.bsky.social &co show that mutations in the oxidative stress TF Cap1 promote #DrugResistance while exposing a lethal vulnerability at high azole doses @plosbiology.org 🧪 plos.io/4rOrfOz
Top: Subcellular localization of Cap1-GFP in wild-type background (top, tetO-CAP1-GFP/CAP1), Cap1-GFP with C446* (middle, TeO-CAP1C446*-GFP/CAP1) and wild-type Cap1-RFP (bottom, CAP1C446*/TeO-CAP1-RFP) in CAP1/CAP1C446* background. Scale bar, 5 μm. Bottom: Schematic of subcellular localization and transcription activation of CAP1 in wild-type (CAP1/CAP1, left) and CAP1/CAP1C446*. Figure generated with BioRender.
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/01/2026
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻 Please repost Apply here: www.wur.nl/en/vacancy/p...
wur.nl
Postdoctoral researcher Phylogenomics and metagenomics
Are you just as excited as we are about the fascinating world of microorganisms? Do you want to contribute to exploring and genomically characterize novel prokaryotic lineages? Do you have a PhD degre...
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Josje Romeijn @jromeijn.bsky.social · 09/12/2025
Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...
cell.com
Extensive horizontal transfer of transposable elements shapes fungal mobilomes
Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 06/12/2025
Extensive horizontal transfer of transposable elements shapes fungal mobilomes @currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social www.cell.com/current-biol...
cell.com
Extensive horizontal transfer of transposable elements shapes fungal mobilomes
Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...
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Reposted by Ursula Oggenfuss
Cecile Lorrain @ccilelorrain.bsky.social · 28/11/2025
Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...
link.springer.com
Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen - BMC Biology
Background Genome spatial organization plays a fundamental role in biological function across all domains of life. While the principles of nuclear architecture have been well-characterized in animals ...
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Ursula Oggenfuss @oggenfussursula.bsky.social · 29/10/2025
The best two things in one database: Transposons and Fungi
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Toby Baril @tobybarilbio.bsky.social · 29/10/2025
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start? We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes! www.biorxiv.org/content/10.1...
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Michael Habig @michaelhabig.bsky.social · 13/10/2025
Want to understand how entire fungal chromosomes can be horizontally transferred? Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available. fungal-evolutionary-genetics.de/open-positio...
fungal-evolutionary-genetics.de
Open Positions
ERC-funded project on the mechanism of horizontal transfer of entire fungal chromosomes PhD PostDoc
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PLOS Biology @plosbiology.org · 16/10/2025
Fungal #GenomeSize variation is largely driven by TEs & lineage-specific genome defenses. @tbadet.bsky.social & @danielcroll.bsky.social show that presence/absence of RIP mutation systems influences #genome architecture, identifying a likely novel defense mechanism @plosbiology.org 🧪 plos.io/4hcC5tx
 Widespread shifts in genome architecture and trophism across fungi. Phylogenetic positions of the shifts identified for genome size. Negative values denote an identified decrease in the genomic trait value while positive values denote an increase in the genomic trait value.
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ETH Zurich @ethz.ch · 18/09/2025
At its meeting of 17 and 18 September 2025 and upon application of Joël Mesot, President of ETH Zurich, the ETH Board appointed eight professors. The Board also awarded the title of "Professor of Practice" once. More info:
ethz.ch
Eight professors appointed
At its meeting of 17 and 18 September 2025 and upon application of Joël Mesot, President of ETH Zurich, the ETH Board appointed eight professors. The Board also awarded the title of
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Josje Romeijn @jromeijn.bsky.social · 20/06/2025
The first paper of my PhD is now available as a preprint! 🎉 Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.
biorxiv.org
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Ursula Oggenfuss @oggenfussursula.bsky.social · 16/06/2025
Happy Barbara Day, happy #TransposonDay2025 to all that celebrate! Every day we get to work on transposons is such a privilege and joy, and I will never not be amazed by these jumping weirdos -the neutral, the bad and the good. Share some black walnut brownies with your friends today!
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Ursula Oggenfuss @oggenfussursula.bsky.social · 28/03/2025
For those interested in repeat-induced point mutations (RIP) in fungi: Thomas Badet set up an amazing meeting in beautiful Neuchâtel #TEsworldwide #Transposon
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Thomas Badet @tbadet.bsky.social · 28/03/2025
🔥 The event will bring together molecular biologists, evolutionary geneticists, and bioinformaticians to explore RIP’s role in transposable element control, genome integrity, and fungal adaptation. Looking forward to seeing you in Neuchâtel! 🏔️ #RIPM2025 #FungalGenomics #EvolutionaryBiology
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Thomas Badet @tbadet.bsky.social · 28/03/2025
🔥 Exciting news! The first Symposium on Repeat-Induced Point mutations is happening June 30 – July 1 at the University of Neuchâtel🇨🇭! 🔹 Want to join? Register here > forms.gle/XWTd4gJAXZSx... 🚨 Limited spots available! So first come, first served! 🔹 More info > crolllab.github.io/ripm2025/
crolllab.github.io
RIPM 2025
Symposium on Repeat-induced Point Mutation research, 30.6 - 1.7, Neuchatel, Switzerland
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Daniel Croll @danielcroll.bsky.social · 25/03/2025
@guidopuccetti.bsky.social, Gabriel Scalliet and I are excited to share our latest work. Resistance in agriculture emerges fast, but we fail to grasp how the myriad mutations in pathogen populations contribute to this. Please check out and share our latest preprint: www.biorxiv.org/content/10.1...
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Kavita Mehta @kavitamehta.bsky.social · 01/03/2025
Honestly I am worried about the impact Trump policies will have on the future of third world PhD students who wants to do it abroad. Americans leaving for Europe will make the process even more harder for people coming from developing and underdeveloped nations.
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Aaron Vogan @fungage-lab.bsky.social · 11/02/2025
Interested in #fungal accessory chromosomes or toxin/antidote genes? Check out our new preprint! We show that the Spok gene family in Fusarium include active toxin/antidote genes. We present a model for how these genes influence the evolution of fungal genomes. www.biorxiv.org/content/10.1...
Illustration of FuSpok killing a cell which has lost an accessory chromosome. Core chromosome in blue, accessory chromosome in red. Black circle: FuSpok. Green circle: antidote function. Red triangle: toxin function.
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Ursula Oggenfuss @oggenfussursula.bsky.social · 23/12/2024
This goes on the top of my break reading list! It has everything that could be asked for: Starships! Transposable elements! Fungi! And an amazing group of scientists! #TEsky #transposons
link.springer.com
Starship Discovery: A Collaborative Approach to Uncover Massive Transposable Elements
The ability to generate high-quality fungal genomes brought with it new frontiers of scientific discovery and paved the way for answering outstanding biological mysteries. Recently, several independen...
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Dr. Tyler A. Elliott @transposableman.bsky.social · 23/12/2024
#TEsky Please circulate! The interdisciplinary research group I'm part of is looking for two postdocs to work on transposons with us here at the U of Guelph in Ontario Canada. philjobs.org/job/show/28330
philjobs.org
Postdoctoral Fellow , University of Guelph, Canada - PhilJobs:JFP Postdoctoral Fellow , University of Guelph, Canada
An international database of jobs for philosophers
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Anthony Amend @fungaloha.bsky.social · 26/11/2024
RP PLS! Iʻm hiring 3 postdocs at U Hawaiʻi to study yeast diversity and evolution, marine fungi, and the genomics of microbiomes in experimental foodwebs. All of these projects have existing datasets and LATITUDE to pursue individual interests and "blue sky" ideas www.dropbox.com/scl/fi/5d7u4...
A researcher on a boardwalk in a DANK hawaiian forest on Molokai.
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Clément Goubert @clementgoubert.bsky.social · 15/11/2024
If you like #Transposons 👾 check out this feed and tag your posts with #TEsky! Thanks @tobybarilbio.bsky.social 🤗 bsky.app/profile/did:...
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Martin Stervander 🏳️‍🌈🇸🇪🏴󠁧󠁢󠁳󠁣󠁴󠁿🏛️🦉🦤🪶 @stervander.com · 17/11/2023
I have asked ResearchGate over at the ex-platform to explain and to cancel the partnership with an unserious publisher like MDPI. If they don't, I too will delete my profile and leave the site. I suggest others in #science do the same. 🧪
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Tony Heitkam🌱🔍💚 @toheitka.bsky.social · 31/10/2023
🧬💚New preprint out, led by Ludwig and our fresh MSc graduate Kristin: Reliable repetitiveDNA consensus sequences from short reads -- do they exist and how can you do them? Is it worth in times of ONT/PacBio? Can newer genome assembly tools help? 🧬🖥️📈find out: doi.org/10.1101/2023...
a guide map through the manuscript
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Katie Emelianova @katieemelianova.bsky.social · 26/10/2023
Very cool work from @oggenfussursula.bsky.social on transposable element derived domains in fungal proteomes 🍄 I’m super excited to see more such insights into the fungal kingdom, so much more to learn www.biorxiv.org/content/10.1...
biorxiv.org
A systematic screen for co-option of transposable elements across the fungal kingdom
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Daniel Croll @danielcroll.bsky.social · 25/10/2023
Amazing work led by Ursula Oggenfuss @oggenfussursula.bsky.social and helped Thomas Badet now out as a preprint. Please check it out and tell us what you think. "A systematic screen for co-option of transposable elements across the fungal kingdom" www.biorxiv.org/content/10.1...
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