Reposted by Daniel CrollAndrew Urquhart @starships-andrew.bsky.social · 24/09/2026Another 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... 05733
Reposted by Daniel CrollSam Yeaman @samyeaman.bsky.social · 08/09/2026I'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/... 05263
Reposted by Daniel CrollMariana Schuster @marischuster.bsky.social · 07/09/2026I'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! 18884
Reposted by Daniel CrollRafal 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-... 12529
Reposted by Daniel CrollAmelia Barber @ameliabarberphd.bsky.social · 04/09/2026If I was eligibile, I would love to do a second PhD with @danielcroll.bsky.social! 194
Daniel Croll @danielcroll.bsky.social · 04/09/2026Our 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.orgEvolutionary genomics of pathogensCroll 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... 23852
Reposted by Daniel CrollTatsuya Nobori @tatsuyanobori.bsky.social · 03/09/2026Excited 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 2212619
Daniel Croll @danielcroll.bsky.social · 19/08/2026Great 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! 0116
Reposted by Daniel CrollAlice 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 26021
Reposted by Daniel CrollRebecca Berrens @rberrens.bsky.social · 10/07/2026Hi #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.comJoin TransposonsWorldwide on SlackSlack is a new way to communicate with your team. It’s faster, better organized, and more secure than email. 13622
Daniel Croll @danielcroll.bsky.social · 02/07/2026That was such an inspiring and fun conference! Big thanks to everyone who helped make it happen!! #SMBE2026 0142
Reposted by Daniel CrollAmmar Abdalrahem @ammarabdalrahem.bsky.social · 01/07/2026Happy to be at #SMBE2026 honored to give a talk about our research on fungal mitochondria 🍄. The energy here in Copenhagen is just incredible 🙌 292
Reposted by Daniel CrollEdel Pérez-López 🇨🇦 @edelplopez.bsky.social · 30/06/2026The 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. 👏 1192
Daniel Croll @danielcroll.bsky.social · 29/06/2026True. You wrote "... the 1% is what exceptional science looks like..." 🤦♂️ 030
Reposted by Daniel CrollERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 25/06/2026ERGA 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 132
Reposted by Daniel CrollAmmar Abdalrahem @ammarabdalrahem.bsky.social · 19/06/2026Tickets 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 ☕ 💬 052
Daniel Croll @danielcroll.bsky.social · 12/06/2026Face of the guy who just pushed the "make myself even richer button" For context: www.youtube.com/watch?v=IHD8... 010
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! 02412
Reposted by Daniel CrollThomas Badet @tbadet.bsky.social · 11/06/2026Nearly 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. 14622
Reposted by Daniel CrollToni Gabaldón @tonigabaldon.bsky.social · 10/06/2026Our 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... 10278135
Daniel Croll @danielcroll.bsky.social · 05/06/2026Spent 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! ☺️ 080
Reposted by Daniel CrollDiana Gómez De La Cruz @dianagdlc.bsky.social · 05/06/2026So 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.orgMolecular mimicry of a pathogen virulence target by a plant immune receptorPlants 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... 1210359
Reposted by Daniel CrollEtienne Bucher 🌾🧬🇪🇺 @plantepigenetics.ch · 05/06/2026We 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... #TEskynature.comAn active Helitron transposon family in wheat - Nature PlantsHelitrons 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... 710249
Reposted by Daniel CrollSociety for Molecular Biology and Evolution @official-smbe.bsky.social · 04/06/2026Talks (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 121
Reposted by Daniel CrollRiccardo Baroncelli @riccardobaroncelli.bsky.social · 15/05/2026Thrilled 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 25330
Reposted by Daniel CrollNature Microbiology @natmicrobiol.nature.com · 12/05/2026Out Now! Pooled CRISPRi screening reveals fungal-specific drug target candidates #MicroSkygo.nature.comPooled CRISPRi screening reveals fungal-specific drug target candidatesNature 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. 0133
Daniel Croll @danielcroll.bsky.social · 11/05/2026Wonderful thread and thinking on (bacterial) pangenomes 041
Reposted by Daniel CrollCecile Lorrain @ccilelorrain.bsky.social · 03/05/2026New 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 12415
Reposted by Daniel CrollDr Emma Hodcroft @firefoxx66.bsky.social · 08/05/2026I'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... 56623
Daniel Croll @danielcroll.bsky.social · 07/05/2026Genomepanel_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. 060
Reposted by Daniel CrollJana 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 04328
Reposted by Daniel CrollLinda Horianopoulos @linder-surprise.bsky.social · 30/04/2026There'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.socialcommunities.springernature.comLearning the rules of metabolic innovation in yeast evolution 0126
Reposted by Daniel CrollTeam Thomma @teamthomma.bsky.social · 30/04/2026Delighted 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 13115
Reposted by Daniel CrollFantin 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.orgPlant-associated fungi co-opt ancient antimicrobials for host manipulationFungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection. 69649
Daniel Croll @danielcroll.bsky.social · 17/04/2026Professor in Epidemiology/Pathology for Agricultural Crop Plants at Aarhus University www.au.dk/om/stillinge...au.dkProfessor in Epidemiology/Pathology for Agricultural Crop Plants - Ledig stilling på Aarhus UniversitetLedig stilling ved Institut for Agroøkologi - Plantepatologi og Mikrobiologi, Aarhus Universitet 021
Daniel Croll @danielcroll.bsky.social · 15/04/2026Excited 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! 031
Daniel Croll @danielcroll.bsky.social · 09/04/2026Amazing 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! 040
Reposted by Daniel CrollToby 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 1158
Daniel Croll @danielcroll.bsky.social · 03/04/2026Resequencing 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.ioHome – genomepanel_nfNextflow pipeline for reference genome mapping, SNP calling and quality checks on large genome panels 23520
Reposted by Daniel CrollPlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/03/20261/11 🔥 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... 314781
Reposted by Daniel Crollreemwheat.bsky.social @reemwheat.bsky.social · 09/03/2026The 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 052
Daniel Croll @danielcroll.bsky.social · 10/03/2026The 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. 0103
Reposted by Daniel CrollbioRxivpreprint @biorxivpreprint.bsky.social · 10/03/2026Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen www.biorxiv.org/content/10.64898/20… 012
Reposted by Daniel CrollGenome Biology and Evolution @genomebiolevol.bsky.social · 10/03/2026Fouché, @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 #evolutiondoi.orgRecurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal PathogenAbstract. Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines. 0127
Reposted by Daniel CrollEdel Pérez-López 🇨🇦 @edelplopez.bsky.social · 10/03/2026There 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. 021