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Daniel Croll

@danielcroll.bsky.social
2.1K followers 874 following 157 posts

We want to understand how pathogens adapt and cause diseases. Also passionate about TEs, pangenomes & population genomics, bioinformatics and conservation genomics. Professor of Evolutionary Genetics @ University of Neuchatel 🇨🇭 Hobbies: 👧🏻👧🏼🏔️🏕️

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Daniel Croll @danielcroll.bsky.social · 15h
Golden glow early morning in Neuchâtel 🇨🇭
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Andrew Urquhart @starships-andrew.bsky.social · 24/09/2026
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...
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Sam Yeaman @samyeaman.bsky.social · 08/09/2026
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/...
Picture shows fireweed in foreground and Mt. Lougheed in background
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Mariana Schuster @marischuster.bsky.social · 07/09/2026
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!
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Rafal Mostowy @rafalmostowy.bsky.social · 04/09/2026
🧬 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-...
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Amelia Barber @ameliabarberphd.bsky.social · 04/09/2026
If I was eligibile, I would love to do a second PhD with @danielcroll.bsky.social!
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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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Tatsuya Nobori @tatsuyanobori.bsky.social · 03/09/2026
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
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Daniel Croll @danielcroll.bsky.social · 19/08/2026
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!
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Alice Laigle @alicelaigle.bsky.social · 23/07/2026
📝 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
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Rebecca Berrens @rberrens.bsky.social · 10/07/2026
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 !
join.slack.com
Join TransposonsWorldwide on Slack
Slack is a new way to communicate with your team. It’s faster, better organized, and more secure than email.
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Daniel Croll @danielcroll.bsky.social · 02/07/2026
That was such an inspiring and fun conference! Big thanks to everyone who helped make it happen!! #SMBE2026
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Ammar Abdalrahem @ammarabdalrahem.bsky.social · 01/07/2026
Happy to be at #SMBE2026 honored to give a talk about our research on fungal mitochondria 🍄. The energy here in Copenhagen is just incredible 🙌
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Edel Pérez-López 🇨🇦 @edelplopez.bsky.social · 30/06/2026
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. 👏
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Daniel Croll @danielcroll.bsky.social · 29/06/2026
True. You wrote "... the 1% is what exceptional science looks like..." 🤦‍♂️
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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 25/06/2026
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
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Ammar Abdalrahem @ammarabdalrahem.bsky.social · 19/06/2026
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 ☕ 💬
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Daniel Croll @danielcroll.bsky.social · 12/06/2026
Face of the guy who just pushed the "make myself even richer button" For context: www.youtube.com/watch?v=IHD8...
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Daniel Croll @danielcroll.bsky.social · 11/06/2026
🔔 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!
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Thomas Badet @tbadet.bsky.social · 11/06/2026
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.
Evolution of major eukaryotic genome defense systems.
The figure is organized along two axes representing core mechanistic features (homology recognition, small interfering RNA, and
heterochromatin assembly) and their lineage-specific elaborations. We hypothesize that a recombination-independent DNA
homology recognition system present in the eukaryotic common ancestor facilitated the emergence of both heterochromatin
assembly and small RNA-based repeat silencing. From this conserved ancestral core, lineage-specific gene neofunctionalizations
gave rise to distinct defense pathways: the RdDM pathway in plants; the piRNA and KRAB–ZFP pathways in vertebrates; and the
repeat-induced point mutation (RIP), methylation induced premeiotically (MIP), MSUD, and tandem repeat-induced sexual silencing
(TRISS) systems in filamentous ascomycete fungi. Question marks indicate steps for which the molecular mechanisms remain
unknown.
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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
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...
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Daniel Croll @danielcroll.bsky.social · 09/06/2026
Exactly this.
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Daniel Croll @danielcroll.bsky.social · 05/06/2026
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! ☺️
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Diana Gómez De La Cruz @dianagdlc.bsky.social · 05/06/2026
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/...
science.org
Molecular mimicry of a pathogen virulence target by a plant immune receptor
Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide-binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathog...
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Etienne Bucher 🌾🧬🇪🇺 @plantepigenetics.ch · 05/06/2026
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
nature.com
An active Helitron transposon family in wheat - Nature Plants
Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 04/06/2026
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
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Riccardo Baroncelli @riccardobaroncelli.bsky.social · 15/05/2026
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
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Nature Microbiology @natmicrobiol.nature.com · 12/05/2026
Out Now! Pooled CRISPRi screening reveals fungal-specific drug target candidates #MicroSky
go.nature.com
Pooled CRISPRi screening reveals fungal-specific drug target candidates
Nature Microbiology, Published online: 11 May 2026; doi:10.1038/s41564-026-02356-wThis study presents a pooled CRISPRi screening approach in Candida albicans to investigate essential genes at scale, revealing environment- and strain-dependent gene sensitivities and conserved vulnerabilities relevant to antifungal drug discovery.
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Daniel Croll @danielcroll.bsky.social · 11/05/2026
Wonderful thread and thinking on (bacterial) pangenomes
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Cecile Lorrain @ccilelorrain.bsky.social · 03/05/2026
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...
biorxiv.org
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Dr Emma Hodcroft @firefoxx66.bsky.social · 08/05/2026
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...
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Daniel Croll @danielcroll.bsky.social · 07/05/2026
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.
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Jana Sperschneider @jsperschneider.bsky.social · 07/05/2026
📢 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...
biorxiv.org
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Linda Horianopoulos @linder-surprise.bsky.social · 30/04/2026
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
communities.springernature.com
Learning the rules of metabolic innovation in yeast evolution
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Team Thomma @teamthomma.bsky.social · 30/04/2026
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
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Fantin Mesny @mesny.bsky.social · 29/04/2026
🎉 📰 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/...
science.org
Plant-associated fungi co-opt ancient antimicrobials for host manipulation
Fungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection.
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Daniel Croll @danielcroll.bsky.social · 17/04/2026
Professor in Epidemiology/Pathology for Agricultural Crop Plants at Aarhus University www.au.dk/om/stillinge...
au.dk
Professor in Epidemiology/Pathology for Agricultural Crop Plants - Ledig stilling på Aarhus Universitet
Ledig stilling ved Institut for Agroøkologi - Plantepatologi og Mikrobiologi, Aarhus Universitet
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Daniel Croll @danielcroll.bsky.social · 15/04/2026
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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Daniel Croll @danielcroll.bsky.social · 14/04/2026
👀
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Daniel Croll @danielcroll.bsky.social · 09/04/2026
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!
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Toby Baril @tobybarilbio.bsky.social · 09/04/2026
🎉 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
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Daniel Croll @danielcroll.bsky.social · 03/04/2026
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_...
crolllab.github.io
Home – genomepanel_nf
Nextflow pipeline for reference genome mapping, SNP calling and quality checks on large genome panels
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Daniel Croll @danielcroll.bsky.social · 03/04/2026
👀
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/03/2026
1/11 🔥 New preprint alert 🔥 We wanted to know what plants in the wild really care about. So we asked them 🎤. Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations” www.biorxiv.org/content/10.6...
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reemwheat.bsky.social @reemwheat.bsky.social · 09/03/2026
The International Symposium on Cereal Leaf Blights isclb.com/registration in beautiful Banff from May 26-29 is approaching with a deadline for early registration/oral abstract due on March 31. @wheatinitiative.bsky.social
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Daniel Croll @danielcroll.bsky.social · 10/03/2026
The latest work by @margaridasampaio.bsky.social is out as a preprint! Using an eQTL dataset for the fungal wheat pathogen Zymoseptoria tritici, we asked whether new regulatory mutations had a predominant effect towards up- or downregulation.
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bioRxivpreprint @biorxivpreprint.bsky.social · 10/03/2026
Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen www.biorxiv.org/content/10.64898/20…
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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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Edel Pérez-López 🇨🇦 @edelplopez.bsky.social · 10/03/2026
There is an old pattern that repeats itself when someone starts gaining visibility, sooner or later the narrative shifts. This tends to be more noticeable for people who do not come from the traditional centers of power. The only response is to keep working, keep building, and keep moving forward.
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