Stephan Köstlbacher
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stephkoe.bsky.social
Stephan Köstlbacher
@stephkoe.bsky.social
Scientific Computing Specialist @ AITHYRA
Opinions are my own
he/him
Pinned
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
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
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
🧪🦠🌊
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
🔮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 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 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
🎄🧬 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
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
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
🧙‍♀️ 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
Reposted by Stephan Köstlbacher
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
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
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
Reposted by Stephan Köstlbacher
📢 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
Reposted by Stephan Köstlbacher
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
July 20, 2025 at 4:58 PM
Reposted by Stephan Köstlbacher
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.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
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
July 20, 2025 at 1:04 PM
Reposted by Stephan Köstlbacher
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-...
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...
cemess.univie.ac.at
July 8, 2025 at 9:58 AM
Reposted by Stephan Köstlbacher
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! 🎉
July 9, 2025 at 1:03 PM
Reposted by Stephan Köstlbacher
a midsummer night's dream
or
understanding chromosome organization's deep evolutionary roots
#MicroSky #Archaea #ArchaeaSky #ProtistsOnSky et al.
June 22, 2025 at 12:42 AM
Reposted by Stephan Köstlbacher
#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...
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.
www.nature.com
June 18, 2025 at 1:53 PM
Reposted by Stephan Köstlbacher
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!
April 16, 2025 at 7:14 AM