Daniel Croll
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: 👧🏻👧🏼🏔️🏕️
- Reposted by Daniel CrollHi everyone! The talk I had the chance to give with @fnucleosome.bsky.social last October is now out on Youtube! If you like evolution, 3D genomics, biodiversity and/or fungi, I think you might like it! 🧬🧪🍄 The submission of this paper has never been that close! www.youtube.com/watch?v=Plez...
- Reposted by Daniel CrollYesterday it was cows using tools, today its penguins using satellite imagery.
- Reposted by Daniel Croll1/🧵 Major milestone unlocked for mycology! 🍄 We just published a massive genomic resource in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐃𝐚𝐭𝐚, releasing 2,695 complete circular mitochondrial species assembled from public data This single dataset nearly 𝐓𝐑𝐈𝐏𝐋𝐄𝐒 📈the known mitochondrial diversity of the Kingdom Fungi rdcu.be/eYZ2h
- Reposted by Daniel CrollBeyond excited to see this work finally out in @narjournal.bsky.social! We show that epigenetic modifiers on fungal accessory chromosomes can contribute to the overall epigenetic profile. Many thanks to @gomezlucia93.bsky.social and our other amazing collaborators 👏🏻 academic.oup.com/nar/article/...
- Reposted by Daniel Croll🍄Transposon traffic in the mycocosmos🍄 Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu.... #TEworldwide
- Reposted by Daniel CrollSharing our lab’s first publication! Probing clinical isolates of Cryptococcus, a disease-causing fungus of the lungs and brain, we found multiple heat-mobile elements that ‘jump’ in the genome at body temperature (!) with the ability to drive adaptive changes. journals.plos.org/plosgenetics...
- Reposted by Daniel CrollEarlier this week, David Marques, my beloved PhD brother, died after a battle with cancer. He was an amazing person, friend, father, husband, scientist, collaborator, birder, among other things. I am immensely grateful for many years of friendship and close collaboration with him. We miss you!
- Reposted by Daniel CrollHave we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti... Thanks to those who already shared the link!
- Reposted by Daniel CrollDepends on the pathogen, I guess. However, generally, if the effector mutation that led to overcoming the R gene does not lead to a fitness or virulence penalty for the pathogen, that mutated allele wil be kept, and thus the R gene will not be "forgotten".
- Welcome to Bluesky Leila @leilaebrahimi.bsky.social!
- Reposted by Daniel CrollAlkemade, @timbarra.bsky.social et al. did temporal association analysis on three major fungal crop pathogens collected between 1956 and 2023, identifying genes linked to fungicide resistance and stress responses as frequent sites of adaptation. 🔗 doi.org/10.1093/gbe/evaf241 #genome #evolution
- Reposted by Daniel Croll
- A very warm welcome to Benjamin Adjei! pathogen-genomics.org/members/benj...
- A very warm welcome to Mélanie Echernier to the lab! pathogen-genomics.org/2025/11/17/M...
- A very warm welcome to the lab Joris Alkemade! pathogen-genomics.org/2025/12/05/J...
- A very warm welcome to the lab Jigisha! @jigisha1.bsky.social pathogen-genomics.org/2025/12/10/J...
- Reposted by Daniel CrollNow officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...
- Reposted by Daniel CrollThrilled to be hosting this session with @henriklicht.bsky.social and @agesiorska.bsky.social 🥳 Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! 🤩
- Organisers - Henrik H. de Fine Licht | University of Copenhagen - @drandiwilson.bsky.social | University of Copenhagen - @agesiorska.bsky.social | University of Copenhagen Invited Speaker - @danielcroll.bsky.social | University of Neuchatel
- Reposted by Daniel CrollOrganisers - Henrik H. de Fine Licht | University of Copenhagen - @drandiwilson.bsky.social | University of Copenhagen - @agesiorska.bsky.social | University of Copenhagen Invited Speaker - @danielcroll.bsky.social | University of Neuchatel
- Big congratulations @guidopuccetti.bsky.social !! Very proud of your achievement. It can feel like an eternity as a PhD student sometimes to see their first chapter in published form. Enjoy the moment!! 🎉
- Finally out! A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen journals.asm.org/doi/10.1128/... A big thanks to @danielcroll.bsky.social & @GabrielScalliet #azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
- Reposted by Daniel CrollFinally out! A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen journals.asm.org/doi/10.1128/... A big thanks to @danielcroll.bsky.social & @GabrielScalliet #azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
- Reposted by Daniel CrollOur paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...
- Reposted by Daniel CrollOur new collaborative work led by @taliamycota.bsky.social Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social and collaborators: @plantricia.bsky.social et al. tinyurl.com/5yx2wmz5 (1/n)
- Reposted by Daniel CrollThe number of Project funding applications and the requested amounts have risen to record levels, consequently decreasing researchers' chances of receiving a grant.📈⚠️ Evaluation is under way, and funding decisions will follow in spring 2026. ➡️ buff.ly/gEdD3OY #research #science
- Reposted by Daniel CrollResponses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....
- Reposted by Daniel CrollOur latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi www.biorxiv.org/content/10.1...
- On my way to visit the very impressive CAS Institute of Microbiology in Beijing. Then, on to the AMC in Guangzhou. Very excited about my first trip to China.
- Big congratulations @tobybarilbio.bsky.social! Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications www.nature.com/articles/s41...
- TEs aren’t just genomic parasites, they’re also engines of genomic novelty. Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion. With @danielcroll.bsky.social & @guidopuccetti.bsky.social 🧬 www.nature.com/articles/s41... #TEworldwide
- Reposted by Daniel CrollTEs aren’t just genomic parasites, they’re also engines of genomic novelty. Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion. With @danielcroll.bsky.social & @guidopuccetti.bsky.social 🧬 www.nature.com/articles/s41... #TEworldwide
- Reposted by Daniel CrollMy new Emmy Noether Group is recruiting! 🔬 Two PhD positions in plant pathogen evolution 🧬 Start: April 2026 (flexible) 📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de ⏰ Apply by 15 Dec 2025 🔗 More info: www.uni-kiel.de/personal/de/... Do get in touch or share 😊
- Very proud to see part of @luzia-stalder.bsky.social inspiring PhD work now published in Microbiome! We tackled the lack of resolution that affects many plant microbiome studies by designing new barcoding loci from scratch. Our multi-kb amplicons resolve Pseudomonas and fungal strain diversity.
- Still using 16S/ITS profiling? You might want to reconsider👀 Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable! microbiomejournal.biomedcentral.com/articles/10....
- Check out here our work: microbiomejournal.biomedcentral.com/articles/10.... There is even a neat video to an upbeat tune to watch! Follow @luzia-stalder.bsky.social for much more exciting research to come.
- Reposted by Daniel CrollStill using 16S/ITS profiling? You might want to reconsider👀 Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable! microbiomejournal.biomedcentral.com/articles/10....
- @tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom. 👉 Ready-to-use for your own genome with a simple tutorial! 👉 Metadata about TEs discovered in your genome! 👉 Contribute and get recognition!
- 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...
- Reposted by Daniel Croll1/ 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...
- Reposted by Daniel CrollI’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication. I’m recruiting PhD students to start in the first semester of 2026. Apply via EPFL PhD programs by Nov 1 drive.google.com/file/d/1cm-t...
- Reposted by Daniel CrollFungal #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
- Very excited to see the final version of our kingdom-scale fungal genome defense manuscript out in @plosbiology.org ! This work has been a major project of @tbadet.bsky.social during his time in our lab. We hope to stimulate much more exciting work on fungal TEs. journals.plos.org/plosbiology/...
- 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
- Reposted by Daniel CrollYoung lives cut short on an unimaginable scale: the 18,457 children on Gaza’s list of war dead "Far from comprehensive, the list does not include the thousands still buried under the rubble of destroyed buildings, as well as the war’s many indirect victims" www.theguardian.com/world/ng-int...
- Reposted by Daniel CrollNow with official press release. I'm very much looking forward to welcome @cbarragan.bsky.social in January www.uni-kiel.de/en/details/n...
- I am excited to share the news that Cristina Barragan @cbarragan.bsky.social got awarded an Emmy Noether Fellowship to start her own research group in my department @uni-kiel.de to explore population dynamics of fungal cereal pathogens!
- Reposted by Daniel CrollIf you saw my talk on the population structure of #Aspergillus flavus at Fungal Genetics in 2024, you might have heard someone ask "how does Aspergillus oryzae fit into the picture?" If so, you heard my answer was "wait and see--we're working on this exact topic" Well, the wait is over! Preprint ⬇️
- Population-Specific Transcriptomic Shifts Underlie Secondary Metabolic Diversification in Aspergillus flavus and the Domestication of Aspergillus oryzae biorxiv.org/content/10.1101/202…
- Neuchâtel morning glory - I love this time of the year!
- The🇨🇭Classics in full glory 🚴
- This is so exciting news, Megan!! Switzerland🇨🇭 is lucky to have you (again) and I am so looking forward to have you soon as a colleague close-by. We'll make sure to have you visit my beloved University of Neuchatel soon!
- Reposted by Daniel CrollCall for a tenure-track position at our Department of Plant Molecular Biology in Lausanne! We are searching for promising early-career researchers in the broad field of plant-organismal interactions. Deadline: November 30, 2025 - Please re-post! career5.successfactors.eu/career?caree...
- Cycling home time gets the autumn glow-up! 🚴♂️🍁
- What an amazing story of gut bacteria-fungi interactions! New paper out in Nature by @judith-behnsen.bsky.social's lab www.nature.com/articles/s41...
- Reposted by Daniel CrollUniversity of Calgary is hiring a tier I CRC professorship in crop genomics. Come work in one of the most beautiful corners of the world! careers.ucalgary.ca/jobs/1668764...
- Reposted by Daniel CrollThere's a lot happening in AI, and we made a way to keep up. @genomelybio.bsky.social will now post weekly reports about AI (& beyond). Eg, we examined & summarized 166 articles, 56 community posts (eg, from Reddit), and 10 trending topics (eg, from Bluesky) genomely.substack.com/p/ai-weekly-...
- Reposted by Daniel CrollI am excited to share the news that Cristina Barragan @cbarragan.bsky.social got awarded an Emmy Noether Fellowship to start her own research group in my department @uni-kiel.de to explore population dynamics of fungal cereal pathogens!
- Reposted by Daniel CrollWe have several open positions in my group, funded from the ERC Grant on the Early Sequestered Germline of Fungi. We search broadly for applicants at both PhD and master-level, with a dedicated interest in fungal evolutionary biology. Please forward and RT! Find the positions here: su.varbi.com
- Reposted by Daniel CrollSuper excited and honoured to have been awarded an ERC Starting Grant for CooPAIRation! How do plant immune receptors work together to trigger an immune response? Can we modulate immune responses for disease resistance? We will tackle these questions in CooPAIRation Positions to be announced soon!
- 📣 The ERC Starting Grant call results are out! Find out which early-career researchers will receive funding this year, what they will be investigating, where they will be based... plus lots of other #ERCStG facts & figures for 2025! ➡️ buff.ly/IsafuFh #FrontierResearch 🇪🇺#EUfunded #HorizonEurope
- Reproduction in ants 🐜 just keeps blowing my mind 🤯 But this here is the crown for sure... for now. www.nature.com/articles/s41... (go also check out obligate chimerism, social chromosomes, clonal production of females and males, and much more...)
- Reposted by Daniel CrollI’m super happy to present the first discoveries of the RIKEN-Cambridge Joint Crop Symbiosis Research Team, based in Japan 🇯🇵 doi.org/10.1101/2025... A thread 👇
- Reposted by Daniel CrollThrilled to share that the final chapter of my PhD with @rokaslab.bsky.social is now out in @natcomms.nature.com 🎉 Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪 rdcu.be/eAToj
- That is amazing tenacity! My success rate with zero ERC submissions and zero awards remains “undefined”.
- At the end of his #ESEB2025 plenary on deep-time palaeogenomes, Love Dalén shared his history of trying to obtain a big grant for his work. It eventually worked out!
- Reposted by Daniel Croll📣 NEW PREPRINT 📝 We identified evolutionary origins of many fungal effectors! We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression. www.biorxiv.org/content/10.1... cc @teamthomma.bsky.social
- Reposted by Daniel CrollLooking forward to attending my first #ESEB meeting in Barcelona next week #ESEB2025! Interested in the adaptive potential of transposons? I’ll be presenting my latest work in the Ecological Genomics of Coevolution satellite symposium on Weds 20th - feel free to join! #TESky #TEworldwide
- Could not agree more…
- Tobias Baril (@tobybarilbio.bsky.social) and I are very excited to share our Opinion piece in Trends in Microbiology. We were struck by the convergent phenomenon of hypermutation in fungal pathogens and hope that our piece helps connect puzzle pieces. Please check Toby's story below and share.
- 1/ Excited to share our latest opinion piece published today in Trends in Microbiology (@cp-trendsmicrobiol.bsky.social): Hypermutator fungal pathogens: from threat to meltdown Here, we argue that the origin of hypermutation follows defined principles, rather than...
- Reposted by Daniel CrollA pangenomics-enabled platform for the high-throughput discovery of antifungal resistance factors in crop pathogens biorxiv.org/content/10.1101/202…
- Reposted by Daniel CrollBring your #PlantScience publishing questions for our Editors! Catch Holly on our stand at #2025ISMPMI with @hacquardst.bsky.social, Ralph Panstruga, Ari Sadanandom, @pietrospanu.bsky.social and Ertao Wang! 📅 TODAY ⏰ 13:00–14:00 🗺 New Phytologist Foundation stand, poster hall
- Reposted by Daniel CrollWant to find out more about publishing your work in @mpmijournal.bsky.social? Please visit us at our @ismpmi.bsky.social stand at #2025ISMPMI
- Reposted by Daniel CrollFascinating talk by Dr. Talia Karasov (University of Utah) on how plant pathogens weaponize phage-derived tailocins to wipe out bacterial rivals. Microbes fighting microbes—nature’s own biotech. #ISMPMI2025 #Tailocins #MicrobialWarfare
- On my way to Köln for #2025ISMPMI watching a beautiful sunset after Mannheim. Looking forward to Monday!
- I very much appreciate the point you are making. With fixed budgets, my experience is that maintaining some non-tenure positions often helps people make the jump to a tenured position. We surely agree though that institutions need to do a lot more to support non-tenured academics on their path.
- Reposted by Daniel Croll🔥Postdoc opportunity 🌱 The Legris lab at the University of Neuchâtel 🇨🇭 is looking for a Postdoc to work on the regulation of branching by warm temperatures. If you have a background on plant physiology and development, and you're interested in shoot thermomorphogenesis, apply now!
- Reposted by Daniel CrollI am grieving the barbarism that is going to unfurl from all this. People are going to die. Livelihoods gone. All to feed a corrupt kleptocracy. I see every day up close how different it is from the first time around. There are no guardrails. A disaster. I’m sorry we have to live through this.
- “… they will have the ability to consult legal rights if they have that…”
- Reposted by Daniel CrollThe 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.
- Reposted by Daniel CrollThrilled to share that I'll be starting my lab @uofguelph.bsky.social this September! I'll be joining the Department of Food Science and I'm so excited to study yeast diversity in this context!
- Oded, our conveyor of painful truths... But it's early morning here though, so I am chilling at this lake here for the moment.
- Amazing to see @hannajohannesson.bsky.social on this list here! Big congratulations! Very much looking forward to your discoveries!
- 📣 Good news: 281 top researchers have just won ERC Advanced Grants! The new funding, worth nearly €721 million, is part of the 🇪🇺 EU’s #HorizonEurope programme. Find out more 👉 europa.eu/!JYKxkD #ERCAdG #FrontierResearch @ec.europa.eu
- Reposted by Daniel CrollHappy 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!
- 🧬🌽 Happy Transposon Day! 🌽🧬 Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025
- Reposted by Daniel CrollAfter 15 years of research, we're excited to share that the causative agent of White-Nose Syndrome/Disease is actually two cryptic fungal species, each showing host specialisation. We've also traced the introduction to North America back to Podillia, Ukraine.
- Amazing opportunity in an outstanding department! Could not recommend this place enough. Not least because of the amazing location. 🇨🇭🌊⛰️
- New tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...
- Reposted by Daniel CrollNew tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...
