Stephan Köstlbacher
@stephkoe.bsky.social
📤 484
📥 321
📝 34
Scientific Computing Specialist @ AITHYRA Opinions are my own he/him
pinned post!
1. 🧵 New preprint out! WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs. Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky
#MEvoSky
#MicroSky
🔗
doi.org/10.1101/2025...
💻
github.com/stephkoest/w...
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WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
https://www.biorxiv.org/content/10.1101/2025.07.14.663642v1
5 months ago
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Stephan Köstlbacher
Archaea Biology Vienna
6 days ago
1. As we recently joined BlueSky, we want to repost this story for all newcomers! We sat down with
@radler92.bsky.social
to get more insight into the unique videos from his recent preprint on Promethearchaeota (formerly Asgard archaea).
doi.org/10.1101/2025...
(Videos and info below)
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Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota)
Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...
https://doi.org/10.1101/2025.11.30.690169
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Stephan Köstlbacher
Kathi Kitzinger
14 days ago
🧪🦠🌊 Curious on
#niche
differentiation of marine
#AOA
#Nitrosopumilus
and
#Nitrosopelagicus
?
#Urea
is (part of) the answer! Very happy this fun study led by
@mpimarinemicrobio.bsky.social
is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
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Urea use drives niche separation between dominant marine ammonia oxidizing archaea - Nature Communications
Two groups of ammonia-oxidizing archaea drive marine nitrification. Stuehrenberg et al. reveal that their distribution reflects substrate use, with one relying on urea and the other on ammonia to main...
https://www.nature.com/articles/s41467-025-67048-1
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Stephan Köstlbacher
Alex Tong
14 days ago
🔮Introducing OXtal – a new all-atom diffusion model for crystal structure prediction! We tackle a grand challenge in computational chemistry: predicting the structure of crystalline solids directly from their chemical composition. Paper:
arxiv.org/abs/2512.06987
Blog Post:
oxtal.github.io
1/8
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Stephan Köstlbacher
AITHYRA Research Institute of the Austrian Academy of Sciences
16 days ago
AITHYRA is seeking a PROCUREMENT MANAGER to establish and oversee our procurement processes, ensuring seamless support for our scientific teams.
aithyra.onlyfy.jobs/job/5kc6uod5...
Application deadline: 11.1.2026
#AITHYRA
#ProcurementManager
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Stephan Köstlbacher
AITHYRA Research Institute of the Austrian Academy of Sciences
16 days ago
AITHYRA is seeking a SCIENTIFIC ILLUSTRATOR to join our dynamic team and play a pivotal role in our mission.
aithyra.onlyfy.jobs/job/6vqx92se
Application deadline: 11.1.2026
#AITHYRA
#ScientificIllustrator
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Stephan Köstlbacher
Archaea Biology Vienna
18 days ago
🎄🧬 It’s December – time for an 'Immunocalendar': “CRISPR CRISPR KNÄUSCHEN”! Every day we open a new door onto a different prokaryotic immune system, with extra love for archaeal hosts. Crafted by the Zink Group within our department :) Have a wonderful Christmas time! ✨
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Stephan Köstlbacher
Archaea Biology Vienna
21 days ago
Asgard on the move ! Watch our videos!
Biorxiv.org/content/10.1101/2025.11.30.690169v1
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Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota)
Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...
https://Biorxiv.org/content/10.1101/2025.11.30.690169v1
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Stephan Köstlbacher
Wen-Cong Huang
about 1 month ago
#Archaea
,
#DPANN
,
#phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...
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Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages
The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...
https://www.biorxiv.org/content/10.1101/2025.11.11.687807v1
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Stephan Köstlbacher
bioRxiv Evolutionary Biology
about 1 month ago
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages
https://www.biorxiv.org/content/10.1101/2025.11.11.687807v1
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Stephan Köstlbacher
Fabien Burki
about 1 month ago
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more.
#protistsonsky
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🧙♀️ Something is brewing in the WitChi cauldron… After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments. Stay tuned for the next release! 🧙♀️ Can’t model it? Prune it!
github.com/stephkoest/w...
about 2 months ago
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Stephan Köstlbacher
Fabai Wu
2 months ago
Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”.
www.nature.com/articles/s41...
#microsky
#archaeasky
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Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution
Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.
https://www.nature.com/articles/s41559-025-02882-6
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#MicroSky
#mevoSky
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4 months ago
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Never thought I’d do real E. coli research, so far I used if only for cloning & protist snacks in my MSc 😅 But here I am simulating chromosomes & shuffling motifs. Watching
@loreoliv.bsky.social
and the lab turn those predictions into real data was pure magic.✨ Grateful to be part of this team!
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4 months ago
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reposted by
Stephan Köstlbacher
Martin Steinegger 🇺🇦
6 months ago
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄
www.biorxiv.org/content/10.1...
🌐
search.foldseek.com/folddisco
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Asaf Levy
5 months ago
📢 New preprint alert! We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...
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The Genetic Basis of Bacterial Adaptation to Hosts
Microbes colonize and interact with diverse multicellular hosts using specialized genes, many of which remain unidentified. Better understanding of host-associated gene functions is a key aspect of mi...
https://www.biorxiv.org/content/10.1101/2025.07.19.665706v1
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Stephan Köstlbacher
Kassiani Panagiotou
5 months ago
Excited to share our work on WitChi! 🛠️🖥️ We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h. The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics
#ArchaeaSky
#MSA
#opensource
#MEvoSky
#MicroSky
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Stephan Köstlbacher
Daan Speth
7 months ago
I'm happy to announce the latest release of the GlobDB, available at
globdb.org
. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
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home | GlobDB
https://globdb.org/
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1. 🧵 New preprint out! WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs. Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky
#MEvoSky
#MicroSky
🔗
doi.org/10.1101/2025...
💻
github.com/stephkoest/w...
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WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
https://www.biorxiv.org/content/10.1101/2025.07.14.663642v1
5 months ago
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reposted by
Stephan Köstlbacher
cemess_vienna
6 months ago
Exciting new research! Matthias Horn & Lukas Helmlinger from
#CeMESS
uncover how chlamydiae thrive in social amoebae by skipping their extracellular stage. Read their groundbreaking study in Current Biology (
@currentbiology.bsky.social
): 🔗
cemess.univie.ac.at/news/detail-...
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New Paper: Chlamydiae give up extracellular stage to thrive in social amoebae
Many intracellular bacteria rely on an extracellular stage to move between hosts – but what happens when that’s no longer needed? A new study, now published in Current Biology, reveals a striking exam...
https://cemess.univie.ac.at/news/detail-view/news/new-paper-chlamydiae-give-up-extracellular-stage-to-thrive-in-social-amoebae/
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Stephan Köstlbacher
Lukas Helmlinger
6 months ago
Excited to share our first paper on the symbiosis between chlamydiae and social amoebae showing in detail the adaptations of endosymbionts to the social life style of their host! 🎉
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Stephan Köstlbacher
STCmicrobeblog
6 months ago
a midsummer night's dream or understanding chromosome organization's deep evolutionary roots
#MicroSky
#Archaea
#ArchaeaSky
#ProtistsOnSky
et al.
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Stephan Köstlbacher
Nature Microbiology
6 months ago
#NewResearch
🚨Out Now Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by
@bbaker24.bsky.social
@deemteam.bsky.social
and team
#MicroSky
#Archaea
🦠
www.nature.com/articles/s41...
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Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology
Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
https://www.nature.com/articles/s41564-025-02024-5?utm_source=bluesky&utm_medium=social&utm_campaign=nmicrobiol
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Stephan Köstlbacher
Eduardo Rocha
8 months ago
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment
@pasteur.fr
for science, career building. Super collaborators
@celineloot.bsky.social
@amazeld.bsky.social
@fredoleroux.bsky.social
3 weeks to apply!
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Stephan Köstlbacher
Michael Brockhurst
9 months ago
Job alert ‼️ 2x professorships available
@uniofmanchester.bsky.social
- ecology
www.jobs.manchester.ac.uk/Job/JobDetai...
- organismal biology (inc genomics, evolution etc.)
www.jobs.ac.uk/job/DMI506/s...
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Senior Lecturer/Reader/Chair in Ecology:Manchester
https://www.jobs.manchester.ac.uk/Job/JobDetail?JobId=31704
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Stephan Köstlbacher
Pilhofer Lab 🦠❄️🔬
9 months ago
Asgard archaea have actin - but what about microtubules? Where do they come from? 🧐 Our new paper
www.cell.com/cell/fulltex...
by
@xujwet.bsky.social
&
@florianwollweber.bsky.social
, in collaboration with the Schleper & Wieczorek labs, describes tiny Asgard microtubules!
#TeamTomo
#ArchaeaSky
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Stephan Köstlbacher
Laura Eme
10 months ago
🚨 New paper alert! 🚨 A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/)
www.nature.com/articles/s41...
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A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature
The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...
https://www.nature.com/articles/s41586-025-08709-5
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Stephan Köstlbacher
Nancy Moran
10 months ago
Hi BlueSkyers! I'm an evolutionary biologist, microbiologist, entomologist, lover of nature, and long-time researcher on symbiosis. I'm realizing that BlueSky is useful and generally non-toxic so here I am (having quit Facebook in Jan 2017, and Twitter in Oct 2022).
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Stephan Köstlbacher
DEEMteam_Orsay
10 months ago
(1/2) Preprint alert! In collaboration with
@yifanzhou.bsky.social
and
@mkrupovic.bsky.social
we describe host-parasite layers in hypersaline systems of the Danakil Depression. Haloarchaea host nanohaloarchea and both are infected by viruses (12 new families found).
www.biorxiv.org/content/10.1...
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Stephan Köstlbacher
bioRxiv Evolutionary Biology
10 months ago
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea
https://www.biorxiv.org/content/10.1101/2025.02.13.637844v1
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Stephan Köstlbacher
Nico Claassens
11 months ago
And now our department can also be followed pn Bluesky!! Follow us!!
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Stephan Köstlbacher
Laboratory of Microbiology
10 months ago
Congratulations to our very own John van der Oost!!!!
#BeijerinckPrize
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Stephan Köstlbacher
Anja (she/her)
11 months ago
Are you interested in studying archaea with their diverse symbionts? We look forward hearing from you:
workingat.nioz.nl/o/postdoc-po...
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NIOZ - Postdoc position: “to elucidate the role of archaeal symbionts in cellular evolution and ecology”
The EvoSym Team within the Department of Marine Microbiology and Biogeochemistry (MMB) located at the Netherlands Institute for Sea Research (NIOZ), is looking for a postdoctoral researcher with a bac
https://workingat.nioz.nl/o/postdoc-position-to-elucidate-the-role-of-archaeal-symbionts-in-cellular-evolution-and-ecology
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Stephan Köstlbacher
Archaea Power Hour
11 months ago
Make sure to tune into Archaea Power Hour in just a few short hours! Sign up to receive the Zoom link here:
t.co/b17JFAaZQ6
. Checkout out our exciting schedule below:
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what a nice highlight of some excellent (archaea) researchers :)
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11 months ago
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Stephan Köstlbacher
Laura Eme
11 months ago
Fun little Q&A! Thank you for the opportunity Current Biology
@currentbiology.bsky.social
www.cell.com/current-biol...
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Stephan Köstlbacher
DaganLab
11 months ago
We have an open position PhD position in a project aiming to develop novel methodologies for phylogenomic reconstruction of plasmid evolution. See details and how to apply in the Ad. Candidates who will review the relevant literature (see Ad) have a higher chance to write a successful application.
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Stephan Köstlbacher
Sonja-Verena Albers
11 months ago
Would you expect that Bacteria use an archaellum for swimming? We didn't, but we found that some Chloroflexota do! Find the story here:
www.biorxiv.org/content/10.1...
A little thread below 1/n
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Horizontal gene transfer of the functional archaellum machinery to Bacteria
Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...
https://www.biorxiv.org/content/10.1101/2025.02.02.636118v1
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Stephan Köstlbacher
Ilnam Kang
11 months ago
"~demonstrating the successful expression and assembly of this (Archaeallum) machinery in Bacteria and its function in swimming motility." Horizontal gene transfer of the functional archaellum machinery to Bacteria
www.biorxiv.org/content/10.1...
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Horizontal gene transfer of the functional archaellum machinery to Bacteria
Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...
https://www.biorxiv.org/content/10.1101/2025.02.02.636118v1
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Maybe time to share this feed again, as many people recently joined here. If you are interested in the wonderful world of archaea, give it a follow :)
#Science
#MEvoSky
bsky.app/profile/did:...
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11 months ago
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Stephan Köstlbacher
NANO
11 months ago
#OceanOpportunities
PostDoc position: Elucidate the role of archaeal symbionts in cellular evolution and ecology” - Deadline 23 February 2025
nf-pogo-alumni.org/27012025-10/
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PostDoc position: Elucidate the role of archaeal symbionts in cellular evolution and ecology” - Deadline 23 February 2025 - NANO | NF-POGO Alumni Network for the Ocean
Job description The EvoSym Team within the Department of Marine Microbiology and Biogeochemistry (MMB) located at the Netherlands Institute for Sea Research (NIOZ), is looking for a postdoctoral resea...
https://nf-pogo-alumni.org/27012025-10/
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Stephan Köstlbacher
Eduardo Rocha
11 months ago
The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate :
doi.org/10.1101/2025...
(for the very busy: 1-6% of gene gains)
#MicroSky
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Stephan Köstlbacher
Martin Steinegger 🇺🇦
11 months ago
join us!
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Stephan Köstlbacher
SeqCode
11 months ago
Read more about the code:
doi.org/10.1038/s415...
Explore the SeqCode Registry:
registry.seqco.de
#SeqCode
#Nomenclature
#Genomes
#Bacteria
#Archaea
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SeqCode: a nomenclatural code for prokaryotes described from sequence data - Nature Microbiology
SeqCode is the result of a community effort to unify nomenclature for uncultured and cultured prokaryotes using genome sequences.
https://doi.org/10.1038/s41564-022-01214-9
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Stephan Köstlbacher
Cameron Thrash
11 months ago
The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics
www.nature.com/articles/s41...
#jcampubs
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The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics - Nature Microbiology
Eukaryotic Arf family proteins involved in endomembrane organelle dynamics arose from the Asgard archaeal ArfR GTPases, indicating this capability likely originated in the archaeal ancestor of eukaryo...
https://www.nature.com/articles/s41564-024-01904-6
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Stephan Köstlbacher
STCmicrobeblog
11 months ago
#MicroSky
#ArchaeaSky
#Archaea
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Stephan Köstlbacher
1000WomeninSTEM
11 months ago
7️⃣3️⃣ Laura Eme
@lauraeme.bsky.social
(1984- ) 🇫🇷
#womeninSTEM
Evolutionary biologist that studies the genomic diversity of micro-organisms in order to reconstruct the history of life. She helped to identify a new group of organisms, the Asgard archaea.
emelaura.com
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Wow!
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11 months ago
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Stephan Köstlbacher
Markel Martínez-Carranza
11 months ago
Super happy to see this work finally out in
@naturecomms.bsky.social
! Great team effort revealing how single-stranded DNA binding protein RPA interacts with the DNA polymerases in the archaeal replisome 🧵(1/4)
www.nature.com/articles/s41...
@sauguet-lab.bsky.social
@pasteur.fr
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Communication between DNA polymerases and Replication Protein A within the archaeal replisome - Nature Communications
The single stranded DNA binding protein RPA plays a pivotal role in DNA replication. The archaeal RPA hosts a WH domain that interacts with the DNA primase and the replicative polymerase PolD. Here th...
https://www.nature.com/articles/s41467-024-55365-w
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Joshua Hamm
11 months ago
In case you missed it the GRC and GRS for Archaea 2025 are both open for applications! Join us in Switzerland for the latest iteration of this awesome conference!
#archaeasky
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