Fabien Burki @fburki.bsky.social · 16hwww.biorxiv.org/content/10.6... #protistsonskybiorxiv.orgCulture-free single-cell transcriptomics shows short-term functional and associative stability in non-model microeukaryotes under shading stressMicroeukaryotes are abundant, diverse, and morphologically and functionally complex. They represent one of the largest groups of primary producers and are involved in major ecosystem functions such as... 051
Reposted by Fabien BurkiJames McInerney @jomcinerney.bsky.social · 08/10/2026I have put this program online. I use it mostly for teaching about alignments, though it is a genuine aligner wrapper, as well as having a ProbCons-like aligner itself. www.youtube.com/watch?v=Zljs...youtube.comCRAIC FeaturesYouTube video by James Talks Genetics 197
Fabien Burki @fburki.bsky.social · 06/10/2026Thanks to the committee for selecting this paper. Great surprise and particularly happy for Anders. This was part of his PhD thesis. 080
Reposted by Fabien BurkiAnna Karnkowska @ankarn.bsky.social · 04/10/2026Postdoc opportunity! Join PERKFresh project and explore Perkinsea diversity, ecology & host–parasite interactions in freshwaters 📍 University of Warsaw ⏰ Deadline: 6 Nov 2026 🔗 euraxess.ec.europa.eu/jobs/466845 #protistonsky #postdoc 01210
Reposted by Fabien BurkiGabriela Montejo-Kovacevich @gmkov.bsky.social · 02/10/20264 years fully funded in a very fun department! 047
Reposted by Fabien BurkiDavid Berger @dbergerbiol.bsky.social · 01/10/2026PhD-position ALERT! Interested in the genomics of local adaptation and the evolution of niche breadth? 🪲🧬🪲🧬🪲🧬🪲🧬🪲🧬 Come join me and @gmkov.bsky.social at @animecol-uu.bsky.social, Uppsala University, by applying here: uu.varbi.com/en/what:job/... Deadline 1st of November!uu.varbi.comPhD-student in Evolutionary and Ecological GeneticsDo you want to conduct frontier research in an outstanding environment within evolutionary biology at Sweden’s largest faculty of science and technology? The Department of Ecology and Genetics at Up 02936
Reposted by Fabien BurkiBruce Taylor @brucedstaylor.bsky.social · 30/09/2026Here's a fun thing! Prof. Mike Hickerson @hickerlab.bsky.social has created Phylodiet, an app that reveals "How Much of the Tree of Life is on your plate": mjhickerson.github.io/phylodiet/ap... Enter your meal, and see how the ingredients are related. #phylogeny #TreeOfLife #Evolutionmjhickerson.github.ioPhylodiet 175
Reposted by Fabien BurkiEarlham Institute @earlhaminst.bsky.social · 26/09/2026Drawing on existing knowledge and success stories from the community, researchers are looking to tackle major technical barriers in protist sequencing, including extraction, cell lysis, and DNA amplification methods. 🦠🧬 #protists #sequencingokt.toUnlocking the potential of protist researchA new collaboration will tackle major technical challenges currently limiting protist genomics, helping to unlock the potential of protist research for biomanufacturing, sustainable agriculture and environmental applications. 0147
Fabien Burki @fburki.bsky.social · 25/09/2026This work involved coauthors: Anders Alfjorden, @ioanabrannstrom.bsky.social, Niklas Wengström, Arni Kristmundsson, @mjamy.bsky.social, David Persson Link to the paper: onlinelibrary.wiley.com/doi/10.1111/...onlinelibrary.wiley.comIdentification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (<fi>Margaritifera margaritifera</fi>) in SwedenFreshwater bivalves play key ecological roles in lakes and rivers, largely contributing to healthy ecosystems. The freshwater pearl mussel, Margaritifera margaritifera, is found in Europe and on the .... 010
Fabien Burki @fburki.bsky.social · 25/09/2026Thank you @dackslabecb.bsky.social for all your effort in making our (protistologists) society journal stronger. I am also particularly stocked to be among the recipients of the William Trager Award for the “outstanding paper in the Journal of Eukaryotic Microbiology” in 2024. 262
Reposted by Fabien BurkiAnthony M. Bonacolta @ambonacolta.bsky.social · 22/09/2026Discovery of an Undocumented Symbiosis Between Arcellinida and a Flagellate Using Single-Cell Transcriptomics - Ani et al. (2026) Free link: onlinelibrary.wiley.com/share/QBTIVR... #ProtistsOnSkyonlinelibrary.wiley.comDiscovery of an Undocumented Symbiosis Between Arcellinida and a Flagellate Using Single‐Cell TranscriptomicsSymbiotic interactions involving single-celled eukaryotes have been studied for over a century. This is in part because these microbes occupy nearly all environments and have adapted to survive throu... 0134
Reposted by Fabien Burkipaveltomancak.bsky.social @paveltomancak.bsky.social · 20/09/202621627 applications. Nothing to celebrate here. Impossible to evaluate fairly & safely. Neither the science (too diverse & possibly LLM generated) nor the soft criteria (likely LLM generated). Without an interview stage - a security risk! marie-sklodowska-curie-actions.ec.europa.eu/whats-new/ne...marie-sklodowska-curie-actions.ec.europa.euMSCA Postdoctoral Fellowships 2026 receives record number of applicationsThe 2026 call has attracted considerable interest from the research community with 21,627 applications submitted. 29844
Reposted by Fabien BurkiJennifer Anderson @jandbio.bsky.social · 18/09/2026I'm a huge fan of #AquaticFungi, but do you know what else are amazing, important, and understudied? #Protists. I'm having a protist-filled Friday, starting with the fantastic ongoing defense of soon to be 'Dr.' @annewalraven.bsky.social of the @fburki.bsky.social lab. Check out her fantastic work 🎉uu.seAnne Walraven: Revealing the plastid symbioses in the marine centrohelid Meringosphaera: a novel model system for plastid evolution – Uppsala University 0156
Reposted by Fabien BurkiHolly Moeller @mixotrophe.bsky.social · 17/09/2026Thank you for having me! Such a beautiful visit to Uppsala so far, with great scientific conversations (my favourite thing) and great running down tree-lined paths (my second-favourite thing). 0101
Fabien Burki @fburki.bsky.social · 17/09/2026@mixotrophe.bsky.social is in da house. First for a fantastic seminar today, and to lead the PhD defense as the opponent of @annewalraven.bsky.social tomorrow. Thank you so much for your visit 1131
Reposted by Fabien BurkiISEP @isepprotists.bsky.social · 17/09/2026New #ISEPpapers! The colorless dictyochophyte Ciliophrys sp. Baltic has lost a plastid but hosts a bacterial endosymbiont www.nature.com/articles/s42... #Protists #Algae #Symbiosis #Bacteria #Microbes #Evolution 1125
Fabien Burki @fburki.bsky.social · 16/09/2026Not to mention what’s going to happen when we realize that some/many of these new lineages are artefact? Will we have to stick to the existing names? Change names (God help me)? I think it is trying to fix a problem with a worse solution 130
Fabien Burki @fburki.bsky.social · 16/09/2026Because names don’t need to be arbitrary, they can reflect on the organisms once someone had actually seen it. What’s the value of “flooding the field” with names that no one can remember. Astronomers name stars with organised numbers, why not do something similar? 340
Fabien Burki @fburki.bsky.social · 15/09/2026💯% going the right way. I’m excited that the @earlhaminst.bsky.social recognizes the critical importance of protists for science and society #protistsonsky 0143
Reposted by Fabien BurkiAlexis Stamatakis @stamatak.bsky.social · 12/09/2026The RAxML-NG v2.0 preprint is out: www.biorxiv.org/content/10.6... v2.0 features integrated model testing, fast branch support metrics, automatic parallelization, phylogenetic difficulty prediction, genotype evolution models, to name but the most important features. And it is A LOT FASTER of coursebiorxiv.orgRAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metricsRAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w... 111557
Reposted by Fabien BurkiFelix Mikus @fmikus.bsky.social · 11/09/2026Are you interested in the nuclear envelope and are still lacking a dye for it? Try the lectin concanavalin A in #U-ExM! Together with @baukjeje.bsky.social, @gautamdey.bsky.social and @dudinlab.bsky.social and many collaborators sharing species with us we explored the versatility of this dye 12913
Reposted by Fabien BurkiSTCmicrobeblog @stcmicrobeblog.bsky.social · 09/09/2026#SymbioSky #ProtistsOnSky 0114
Reposted by Fabien BurkiJulia Van Etten @couchmicroscopy.bsky.social · 04/09/2026Our paper describing two new photosynthetic Paulinella species is out today in JPhycol! This is the kind of work I love to do and even it though took many years to finish, we had a lot of fun stomping around together in the marsh! onlinelibrary.wiley.com/doi/10.1111/... #protistsonsky 26523
Reposted by Fabien BurkiJohn Burns @burnsajohn.bsky.social · 04/09/2026I was late to the party, but it was super fun to contribute to this project. And what a beautiful result. And I got to see my first IRL paulinella, see the dedication and leadership of @couchmicroscopy.bsky.social, and make new friends! Bonus [probably] P. murrayi rolling around while dividing. 1172
Reposted by Fabien BurkiLuis Javier Galindo @luisjagago.bsky.social · 04/09/2026I am extremely happy to announce that I have been awarded an @erc.europa.eu ERC Starting Grant to lead the ProtistEye project! We will be diving into the function, architecture, and diversity of eye-like structures across different protists to better understand their evolution. Stay tuned for more! 15659
Reposted by Fabien BurkiThibaut Brunet @thibautbrunet.bsky.social · 02/09/2026🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️biorxiv.orgRapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animalsAnimal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho... 316777
Fabien Burki @fburki.bsky.social · 02/09/2026I am grateful to all colleagues and collaborators that have contributed to the body of work recognized by this price (for pioneering studies of the diversity and evolution of eukaryotes) in the last 20+ years. Thanks to all! 030
Fabien Burki @fburki.bsky.social · 02/09/2026Deeply honored to have received the 2026 Thuréus price in Natural history and medicine by the Royal Society of Sciences in Uppsala, the oldest learned society in Sweden and one of the oldest in Europe. www.vetenskapssocietetenuppsala.se/priser/vetenskapssocietetenuppsala.sePriser | Kungl. Vetenskaps-Societeten 5323
Reposted by Fabien BurkiBigelow Laboratory for Ocean Sciences @bigelowlab.bsky.social · 01/09/2026Bigelow Laboratory for Ocean Sciences is excited to announce new leadership and a bold vision for the future of the Single Cell Genomics Center (SCGC). SRSs Nicole Poulton and Julia Brown are now jointly leading the state-of-the-art facility. www.bigelow.org/news/articles/2026-… 093
Reposted by Fabien BurkiKatharina Hoff @katharinahoff.bsky.social · 31/08/2026A revolution in annotating protein coding genes in eukaryotes: Richard Krieg, Joscha Diehl & @masta.bsky.social developed Vipsania, a genome foundation model with integrated HMM-layer: www.biorxiv.org/content/10.6... 🎉💐 So impressive work! Congratulations!biorxiv.org 11513
Fabien Burki @fburki.bsky.social · 28/08/2026Warm congratulations @annewalraven.bsky.social on this big achievement. This is the nailing of the PhD thesis ahead of the defense 0161
Reposted by Fabien BurkiCorey Holt @coreyholt.bsky.social · 27/08/2026What's that? You wish we had more data on those bizarre dinoflagellates WITH EYES? Have no fear! With @protistwtmostest.bsky.social, Gordon Lax, and @pjkeelinglab.bsky.social, who also have eyes.academic.oup.comEvolution of complex organelles in ocelloid-bearing dinoflagellatesAbstract. Warnowiid dinoflagellates are known for possessing two of the most complex structures known in single cells: multi-projectile nematocysts and the 02917
Reposted by Fabien BurkiOmaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 26/08/2026If some of you are still wondering why we screen randomly purchased antibodies in ExM? Well, cuz we randomely find antibodies labelling key organelles and structures across many species... 4308
Fabien Burki @fburki.bsky.social · 26/08/2026Indeed: onlinelibrary.wiley.com/doi/full/10.... #protistsonskyonlinelibrary.wiley.comLong‐Read Metabarcoding With Optimized Bioinformatic Analysis Outperforms Short‐Read Metabarcoding for Assessing Soil Protist Diversity and EcologyComparing 18S metabarcoding of protist cultures and environmental samples with short and long read sequencing highlighted the advantages of each method. In particular, the study of 26 vineyard soil s... 171
Reposted by Fabien BurkiCasey Dunn @caseywdunn.bsky.social · 25/08/2026My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore. 12324164
Reposted by Fabien BurkiLukas VF Novak @animalculum.bsky.social · 21/08/2026Predator of #RedTide plankton reveals unusual bioluminescence today.ucsd.edu/story/ruthle... #Bioluminescence of the heterotrophic dinoflagellate Polykrikos kofoidii onlinelibrary.wiley.com/doi/10.1111/... #Protists #Algae #Plankton #Dinoflagellates #ProtistsOnSky 173
Reposted by Fabien BurkiAnthony M. Bonacolta @ambonacolta.bsky.social · 20/08/2026Symbiotic capacity in a changing ocean: emerging questions around phytoplankton interactions- Zwahlen & Vincent 2026 - Trends in Ecology & Evolution www.cell.com/trends/ecolo...cell.comSymbiotic capacity in a changing ocean: emerging questions around phytoplankton interactionsPhytoplankton fix half of global CO2 annually and drive key global nutrient cycles. They depend on interactions with bacteria, viruses, and protists. Yet our understanding of these interactions remain... 0126
Reposted by Fabien BurkiSergio Muñoz-Gómez @sergiophyceae.bsky.social · 18/08/2026A new preprint from the lab! "Green algal symbionts are stably retained and provisioned in the dark despite a clear physiological cost" www.biorxiv.org/content/10.6...biorxiv.orgGreen algal symbionts are stably retained and provisioned in the dark despite a clear physiological costPhotosymbioses, or associations between heterotrophs and photoautotrophs, are widespread and indispensable in today's ecosystems. The chloroplasts of algae and land plants, which are at the heart of m... 14618
Fabien Burki @fburki.bsky.social · 17/08/2026Brown algae as other ochrophytes (photosynthetic stramenopiles) have red algal derived plastids. We don’t know how it got there (there are several hypotheses) but it was certainly not from green algae 040
Reposted by Fabien BurkiHolly Moeller @mixotrophe.bsky.social · 07/08/2026Freaking finally! A massive compilation of data that sat on various desks for almost a decade is finally out. On the positive side, gave me time to learn expansion microscopy and make Fig 1 www.science.org/doi/10.1126/...science.orgEmergent metabolic parasitism driven by organelle sequestrationChloroplast-stealing ciliates evolve, increasing reliance on their prey for all aspects of metabolism, including photosynthesis. 26320
Fabien Burki @fburki.bsky.social · 07/08/2026Can't wait to hear from this meeting. Our lab will show first LOPIT data on glaucophytes (Cyanophora) #protistsonsky 0100
Reposted by Fabien BurkiCGUE 2026 @cgue2026.bsky.social · 04/08/2026📢 Meet our invited speaker: Mahwash Jamy, Uppsala University, @mjamy.bsky.social “New deep-branching environmental plastid genomes on the algal tree of life” How environmental plastid genomes reveal hidden algal diversity & evolution. #Protists #Protistology #Genomics #ProtistsOnSky #Microbiology 182
Reposted by Fabien BurkiOre Francis @orefrancis.bsky.social · 31/07/2026Really enjoyed the opportunity to share how useful #protists are when predicting orthologies of eukaryotic protein #complex components in my Planetary Biology Transversal Themes seminar at EMBL Heidelberg. Thanks so much to Nikki Cannon and the @jordivangestel.bsky.social lab for hosting me. 061
Fabien Burki @fburki.bsky.social · 31/07/2026In London for this. Outside of my usual turf, daunting and exciting 1100
Reposted by Fabien BurkiCGUE 2026 @cgue2026.bsky.social · 30/07/2026Invited speaker spotlight: Yuji Inagaki, University of Tsukuba “Phylogenomic illusions in the eukaryotic phylogeny” 📅 October 7 🕒 09:00–09:30 Full program: comparativegenomics2026.com #Phylogenomics #Protistology #Protists #ProtistsOnSky #Eukaryotes #Genomics #Microbiology 182
Reposted by Fabien BurkiCGUE 2026 @cgue2026.bsky.social · 28/07/2026🔬 Invited speaker spotlight: Fabien Burki, Uppsala University: Single cell genomics and fluorescence microscopy suggest a permanent plastid in a marine centrohelid. @fburki.bsky.social 👉 comparativegenomics2026.com #Genomics #SingleCellGenomics #Protistology #Protists #Microscopy #Eukaryotes 063