Stephan Köstlbacher
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stephkoe.bsky.social
Stephan Köstlbacher
@stephkoe.bsky.social
490 followers 320 following 34 posts
Scientific Computing Specialist @ AITHYRA
Opinions are my own
he/him
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stephkoe.bsky.social
Stephan Köstlbacher @stephkoe.bsky.social · Jul 20
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...
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...
www.biorxiv.org
Reposted by Stephan Köstlbacher
ettema.bsky.social
Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41...

Corrected paper: www.nature.com/articles/s41...

Importantly, the re-analyses of the corrected dataset are consistent with the original findings.
Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes - Nature
Nature - Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
www.nature.com
February 11, 2026 at 9:10 PM
Reposted by Stephan Köstlbacher
banoomalik.bsky.social
Postdoc position on Asgard archaea in Thiago’s new lab for someone well trained in biochemistry, cloning, and protein purification:
international.au.dk/about/profil...
Postdoc in Archaea Microbiology - Vacancy at Aarhus University
Vacancy at Department of Biology - Microbiology, Aarhus University
international.au.dk
February 10, 2026 at 2:36 PM
Reposted by Stephan Köstlbacher
ettema.bsky.social
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻

Please repost

Apply here: www.wur.nl/en/vacancy/p...
January 5, 2026 at 10:45 PM
Reposted by Stephan Köstlbacher
archaea-vienna.bsky.social
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)
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...
doi.org
December 18, 2025 at 2:08 PM
Reposted by Stephan Köstlbacher
kathikitzinger.bsky.social
🧪🦠🌊
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!
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...
www.nature.com
December 11, 2025 at 11:02 AM
Reposted by Stephan Köstlbacher
alextong.bsky.social
🔮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
December 10, 2025 at 9:37 PM
Reposted by Stephan Köstlbacher
aithyra.bsky.social
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
December 9, 2025 at 9:38 AM
Reposted by Stephan Köstlbacher
aithyra.bsky.social
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
December 9, 2025 at 9:39 AM
Reposted by Stephan Köstlbacher
archaea-vienna.bsky.social
🎄🧬 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! ✨
December 7, 2025 at 12:25 PM
Reposted by Stephan Köstlbacher
archaea-vienna.bsky.social
Asgard on the move ! Watch our videos!
Biorxiv.org/content/10.1101/2025.11.30.690169v1
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...
Biorxiv.org
December 3, 2025 at 8:22 PM
Reposted by Stephan Köstlbacher
wentsunghwang.bsky.social
#Archaea, #DPANN, #phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 13, 2025 at 7:28 PM
Reposted by Stephan Köstlbacher
biorxiv-evobio.bsky.social
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
November 12, 2025 at 11:32 PM
Reposted by Stephan Köstlbacher
fburki.bsky.social
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 1/2
November 12, 2025 at 9:50 AM
stephkoe.bsky.social
🧙‍♀️ 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...
October 31, 2025 at 9:59 AM
stephkoe.bsky.social
Congratttttttts!!!! So well deserved :)
October 23, 2025 at 1:14 PM
Reposted by Stephan Köstlbacher
fabaiwu.bsky.social
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
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.
www.nature.com
October 21, 2025 at 3:06 PM
stephkoe.bsky.social
#MicroSky #mevoSky
August 22, 2025 at 9:30 AM
stephkoe.bsky.social
If you want to mess around with some motifs, check out:
github.com/stephkoest/E...
GitHub - stephkoest/Ecoli_titration
Contribute to stephkoest/Ecoli_titration development by creating an account on GitHub.
github.com
August 22, 2025 at 9:16 AM
stephkoe.bsky.social
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!
August 22, 2025 at 9:07 AM
Reposted by Stephan Köstlbacher
martinsteinegger.bsky.social
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
July 7, 2025 at 8:21 AM
stephkoe.bsky.social
It was a pleasure to work with you! 😊
July 28, 2025 at 9:17 AM
stephkoe.bsky.social
Hey Felix, good question! Yeah it is different. In short: trimAl/ClipKit aim to remove uninformative sites. WitChi is a second step to remove misleading sites: those that can group unrelated taxa just because their sequence composition looks similar. Hope that helps!
July 21, 2025 at 4:11 PM
Reposted by Stephan Köstlbacher
asaflevylab.bsky.social
📢 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...
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...
www.biorxiv.org
July 21, 2025 at 6:40 AM
stephkoe.bsky.social
Thanks, jolien! ;)
July 21, 2025 at 6:26 AM
stephkoe.bsky.social
And of course the great work!
July 20, 2025 at 5:02 PM