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Fabien Burki

@fburki.bsky.social
1.5K followers 494 following 428 posts

Exploring the great microbial eukaryote diversity and evolution, one protist at a time. I’m fascinated by this question: how have #plastids evolved? #ProtistsOnSky | Associate Prof at Uppsala University. My lab: www.burki-lab.net

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Fabien Burki @fburki.bsky.social · 16h
www.biorxiv.org/content/10.6... #protistsonsky
biorxiv.org
Culture-free single-cell transcriptomics shows short-term functional and associative stability in non-model microeukaryotes under shading stress
Microeukaryotes 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...
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James McInerney @jomcinerney.bsky.social · 08/10/2026
I 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.com
CRAIC Features
YouTube video by James Talks Genetics
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Fabien Burki @fburki.bsky.social · 06/10/2026
Thanks to the committee for selecting this paper. Great surprise and particularly happy for Anders. This was part of his PhD thesis.
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Anna Karnkowska @ankarn.bsky.social · 04/10/2026
Postdoc 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
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Gabriela Montejo-Kovacevich @gmkov.bsky.social · 02/10/2026
4 years fully funded in a very fun department!
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David Berger @dbergerbiol.bsky.social · 01/10/2026
PhD-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.com
PhD-student in Evolutionary and Ecological Genetics
Do 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
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Bruce Taylor @brucedstaylor.bsky.social · 30/09/2026
Here'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 #Evolution
mjhickerson.github.io
Phylodiet
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Earlham Institute @earlhaminst.bsky.social · 26/09/2026
Drawing 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 #sequencing
okt.to
Unlocking the potential of protist research
A 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.
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Fabien Burki @fburki.bsky.social · 25/09/2026
This 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.com
Identification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (<fi>Margaritifera margaritifera</fi>) in Sweden
Freshwater 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 ....
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Fabien Burki @fburki.bsky.social · 25/09/2026
Thank 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.
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Fabien Burki @fburki.bsky.social · 23/09/2026
#protistsonsky (not to mention protistsonfire)
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Anthony M. Bonacolta @ambonacolta.bsky.social · 22/09/2026
Discovery of an Undocumented Symbiosis Between Arcellinida and a Flagellate Using Single-Cell Transcriptomics - Ani et al. (2026) Free link: onlinelibrary.wiley.com/share/QBTIVR... #ProtistsOnSky
onlinelibrary.wiley.com
Discovery of an Undocumented Symbiosis Between Arcellinida and a Flagellate Using Single‐Cell Transcriptomics
Symbiotic 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...
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paveltomancak.bsky.social @paveltomancak.bsky.social · 20/09/2026
21627 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.eu
MSCA Postdoctoral Fellowships 2026 receives record number of applications
The 2026 call has attracted considerable interest from the research community with 21,627 applications submitted.
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Jennifer Anderson @jandbio.bsky.social · 18/09/2026
I'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.se
Anne Walraven: Revealing the plastid symbioses in the marine centrohelid Meringosphaera: a novel model system for plastid evolution – Uppsala University
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Holly Moeller @mixotrophe.bsky.social · 17/09/2026
Thank 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).
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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
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ISEP @isepprotists.bsky.social · 17/09/2026
New #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
microscopic photos of microbial cells, upper row in normal light, lower in fluorescence
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Fabien Burki @fburki.bsky.social · 16/09/2026
Not 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
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Fabien Burki @fburki.bsky.social · 16/09/2026
Because 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?
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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
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Alexis Stamatakis @stamatak.bsky.social · 12/09/2026
The 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 course
biorxiv.org
RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics
RAxML-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...
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Fabien Burki @fburki.bsky.social · 11/09/2026
Well said
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Felix Mikus @fmikus.bsky.social · 11/09/2026
Are 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
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STCmicrobeblog @stcmicrobeblog.bsky.social · 09/09/2026
#SymbioSky #ProtistsOnSky
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Julia Van Etten @couchmicroscopy.bsky.social · 04/09/2026
Our 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
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John Burns @burnsajohn.bsky.social · 04/09/2026
I 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.
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Luis Javier Galindo @luisjagago.bsky.social · 04/09/2026
I 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!
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Fabien Burki @fburki.bsky.social · 04/09/2026
Yay
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Thibaut 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.org
Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals
Animal 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...
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Fabien Burki @fburki.bsky.social · 02/09/2026
I 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!
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Fabien Burki @fburki.bsky.social · 02/09/2026
Deeply 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.se
Priser | Kungl. Vetenskaps-Societeten
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Bigelow Laboratory for Ocean Sciences @bigelowlab.bsky.social · 01/09/2026
Bigelow 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-…
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Katharina Hoff @katharinahoff.bsky.social · 31/08/2026
A 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
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Fabien Burki @fburki.bsky.social · 28/08/2026
Warm congratulations @annewalraven.bsky.social on this big achievement. This is the nailing of the PhD thesis ahead of the defense
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Corey Holt @coreyholt.bsky.social · 27/08/2026
What'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.com
Evolution of complex organelles in ocelloid-bearing dinoflagellates
Abstract. Warnowiid dinoflagellates are known for possessing two of the most complex structures known in single cells: multi-projectile nematocysts and the
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 26/08/2026
If 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...
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Fabien Burki @fburki.bsky.social · 26/08/2026
Indeed: onlinelibrary.wiley.com/doi/full/10.... #protistsonsky
onlinelibrary.wiley.com
Long‐Read Metabarcoding With Optimized Bioinformatic Analysis Outperforms Short‐Read Metabarcoding for Assessing Soil Protist Diversity and Ecology
Comparing 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...
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Casey Dunn @caseywdunn.bsky.social · 25/08/2026
My 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.
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Lukas VF Novak @animalculum.bsky.social · 21/08/2026
Predator 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
fluorescence microscopy picture of a microbial cell
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Anthony M. Bonacolta @ambonacolta.bsky.social · 20/08/2026
Symbiotic capacity in a changing ocean: emerging questions around phytoplankton interactions- Zwahlen & Vincent 2026 - Trends in Ecology & Evolution www.cell.com/trends/ecolo...
cell.com
Symbiotic capacity in a changing ocean: emerging questions around phytoplankton interactions
Phytoplankton 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...
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Sergio Muñoz-Gómez @sergiophyceae.bsky.social · 18/08/2026
A 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.org
Green algal symbionts are stably retained and provisioned in the dark despite a clear physiological cost
Photosymbioses, 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...
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Fabien Burki @fburki.bsky.social · 17/08/2026
Brown 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
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Holly Moeller @mixotrophe.bsky.social · 07/08/2026
Freaking 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.org
Emergent metabolic parasitism driven by organelle sequestration
Chloroplast-stealing ciliates evolve, increasing reliance on their prey for all aspects of metabolism, including photosynthesis.
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Fabien Burki @fburki.bsky.social · 07/08/2026
Can't wait to hear from this meeting. Our lab will show first LOPIT data on glaucophytes (Cyanophora) #protistsonsky
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CGUE 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
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Ore Francis @orefrancis.bsky.social · 31/07/2026
Really 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.
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Fabien Burki @fburki.bsky.social · 31/07/2026
In London for this. Outside of my usual turf, daunting and exciting
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CGUE 2026 @cgue2026.bsky.social · 30/07/2026
Invited 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
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CGUE 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
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Fabien Burki @fburki.bsky.social · 28/07/2026
Nice :-)
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