Daniel Croll

Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache! Here's my solution that used to be lab-internal but that I am happy to share: crolllab.github.io/genomepanel_...

Interesting insights on plant pathogen emergence from @danielcroll.bsky.social #ICBPI2026

Golden glow early morning in Neuchâtel 🇨🇭

Another step in the #Starship story - they move via a circular intermediate. Helps explain how these elements horizontally transfer and means that we can modify them into transformation vectors (starmids). www.biorxiv.org/content/10.6...

I'm looking to hire a postdoc to work on the RepAdapt + MacroMar projects, analysing genomic data from >130 species of plants, animals, and fungi (VCFs are processed, ready to go). Lots of potential for creativity and collaboration! yeamanlab.weebly.com/uploads/5/7/...

I'm excited to share that my newly funded #ERCStG FRONTERA is recruiting two postdoctoral researchers at @ipbhalle.bsky.social 🌱🔬 If you are passionate about plant immunity, proteolysis, membrane proteins, or proteomics, I'd love to hear from you. 🧵 Please RT/share!

🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...

If I was eligibile, I would love to do a second PhD with @danielcroll.bsky.social!

Excited to launch our ERC project ImmuneCellState 🚀 We’ll investigate how individual plant cells respond to pathogens and explore new dimensions of plant immunity research by integrating single-cell/spatial omics, deep learning and genome editing. @thesainsburylab.bsky.social @erc.europa.eu

Great work out by @alicelaigle.bsky.social on her investigation of 3D genome architectures across the fungal kingdom! Big thanks to our excellent co-authors @camillecornet.bsky.social @crazychipkali.bsky.social @tobybarilbio.bsky.social, also to Darwin Tree of Life for making their data accessible!

📝 NEW PREPRINT It’s with an immense joy that our preprint is finally out and it’s my first first co-author paper!!! 🧬🍄 What is the diversity of 3D genome architectures in fungi? We reconstructed the 3D genome architecture of public Hi-C data from 55 fungal. Preprint: lnkd.in/enxTh2Cm

Hi #TEsky, please remember that we have an amazing community in the TransposonsWorldWide slack channel (join.slack.com/t/transposon...), which I encourage you to join. Another great resource is tehub.org. Please share !

That was such an inspiring and fun conference! Big thanks to everyone who helped make it happen!! #SMBE2026

Happy to be at #SMBE2026 honored to give a talk about our research on fungal mitochondria 🍄. The energy here in Copenhagen is just incredible 🙌

The Genome Plasticity and Evolutionary Innovations session was absolutely outstanding! 🤯🧬 So many exciting ideas for new projects… at this rate, we might go from 25 to 50 people in the lab after #SMBE2026! 😅🫣 Incredible science, inspiring presentations, and an amazing lineup of researchers. 👏

True. You wrote "... the 1% is what exceptional science looks like..." 🤦‍♂️

ERGA member Daniel Croll @danielcroll.bsky.social will present @official-smbe.bsky.social June 30 in session "S03 – Genome Plasticity and Evolutionary Innovation (Part 1)" #SMBE2026

Tickets to Copenhagen are booked! I’m going to #SMBE2026 to talk about our work on fungal mitogenome diversity 🍄 📄 Read the paper: rdcu.be/fpjru Looking forward to catching up and grabbing a coffee during the breaks ☕ 💬

Face of the guy who just pushed the "make myself even richer button" For context: www.youtube.com/watch?v=IHD8...

🔔 Our synthesis on what’s going on in the field of TE control and RIP in the fungal world! Out now in Trends in Genetics!

Nearly a year after our symposium on Repeat-Induced Point (RIP) mutations, I’m happy to share the fruit of some of our discussions. The fungal RIP hypermutator mechanism has deep eukaryotic roots www.sciencedirect.com/science/arti... We hope to spark interest in this underappreciated mechanism.

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

Exactly this.

Spent this week with an amazing cohort of Scandavian and Baltic PhD students. NOVA is a wonderful tradition and the future for plant 🌱 pathology 🍄 is bright! ☺️

So proud to see this story finally out!🎉 We added new data since our previous preprint—transgenic barley plants with an engineered immune receptor that fights off two fungal pathogens at once. Short 🧵 and link to the original preprint thread on X👇 www.science.org/doi/10.1126/...

We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky

Talks (Part 1): @danielcroll.bsky.social @jrotwitguez.bsky.social Aaryan Bhatia @mtoll8.bsky.social Ana Lindeza Máire Ní Leathlobhair @iglavincheska.bsky.social @marcelauliano.bsky.social Julien Dutheil @a-mack-s.bsky.social Shu Zhang

Thrilled to see this finally out!! Our new work suggests #Starships helped #Colletotrichum acquire the genes needed to infect lupin. A glimpse into how fungal pathogens emerge through horizontal transfer and genome reshaping. biorxiv.org/content/10.6... #Fungi #Genomics #Pathogenicity #evolution

Out Now! Pooled CRISPRi screening reveals fungal-specific drug target candidates #MicroSky

Wonderful thread and thinking on (bacterial) pangenomes

New preprint out! We generated haplotype-phased genome assemblies for two poplar rust fungi. These resources open new opportunities to explore rust genome architecture, haplotype diversity, and TE-driven evolution. www.biorxiv.org/content/10.6...

I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland. Please interpret with caution. By segment: S: nextstrain.org/groups/hodcr... M: nextstrain.org/groups/hodcr... L: nextstrain.org/groups/hodcr...

Genomepanel_nf v 1.0.8 is out! Includes a nice summary html in addition to the tsv files, more robust GATK implementation, even more aggressively saves on storage space and includes now a fully functional example dataset. crolllab.github.io/genomepanel_... Please get in touch if you have feedback.

📢 EffectorGeneP is finally here! Stop missing small, single-exon or orphan genes from your favourite pathogen genome. Current tools only annotate 15%-78% of effector genes, EffectorGeneP finds 95% - including the large AvrSr26 family in stem rust. #Bioinformatics 📖 www.biorxiv.org/content/10.6...

There's a story behind every project that doesn't get fully captured in the final paper. Check out our "behind the paper" accompanying our paper on convergent evolution of aerobic fermentation in yeast. communities.springernature.com/posts/learni... @hittingerlab.bsky.social @rokaslab.bsky.social

Delighted to see this work out in #ScienceAdvancesResearch @science.org where we uncover a surprising evolutionary origin of fungal effector proteins as ancient antimicrobials. Led by the super-star @mesny.bsky.social in the frame of @ceplas.bsky.social @mibinet.bsky.social & @madfungi.bsky.social

🎉 📰 Very happy to share the journal publication of our manuscript "Plant-associated fungi co-opt ancient antimicrobials for host manipulation"! #ScienceAdvancesResearch @science.org @teamthomma.bsky.social www.science.org/doi/10.1126/...

Professor in Epidemiology/Pathology for Agricultural Crop Plants at Aarhus University www.au.dk/om/stillinge...

Excited to have Carlos Lax @clax8.bsky.social and Ghizlane Tahiri @ghizlane-tahirizn.bsky.social recently join our lab. Give them a follow to not miss out on their fantastic science!

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Amazing new tool out by @tobybarilbio.bsky.social ! We think this is going to be a super useful tool to annotate TEs in a pangenome context!

🎉 EarlGrey ParTEA v0.1.6 is here! Huge thanks to everyone who's tried the pipeline and shared feedback — your suggestions directly shaped these new features. 🍵 #TEworldwide #transposableelements #bioinformatics #genomics