@kassipan.bsky.social
PhD candidate @Ettema lab | Laboratory of Microbiology (WUR)
Exultant to have been awarded a Vidi grant by the Dutch Research Council (NWO)! Can't wait to get started!
Stay tuned for two upcoming (PhD student & postdoc) positions to study archaeal genome evolution.
Also huge congrats to my colleague @dorotakawa.bsky.social!
www.uu.nl/en/news/21-v...
academic.oup.com/mbe/advance-...
Happy to share this one. We investigated the #phylogenetic placement and #genome_evolution of Pangui/Njordarchaea-unique #Asgardarchaea that might have undergone genome reduction...
Check out this beautiful work led by @stephkoe.bsky.social, with great teamwork from @danieltamarit.bsky.social and @ettema.bsky.social :
💻 github.com/stephkoest/w...
📄 doi.org/10.1101/2025.07.14.663642
🧂The placement of halophilic lineages was restored — Methanonatronarchaeia emerged outside Halobacteria, supporting independent origins of halophily
(in agreement with targeted analyses: doi.org/10.1038/s415... &
doi.org/10.1038/s415...)
🧩 Phyla representing the clades Acherontia and Stygia (Methanobacteriota_B + Hadarchaeota) shifted to sister TACK + Asgardarchaeota — consistent with site-heterogeneous models (doi.org/10.1186/s128...).
20.07.2025 16:58 — 👍 1 🔁 0 💬 1 📌 0Among the topological improvements:
🔥Thermophilic clades (e.g. JANJXX01, DRAE01, Korarchaeia) were repositioned in line with recent phylogenomic studies (doi.org/10.1038/s415... &
doi.org/10.1101/2025...).
→ The number of biased taxa dropped from 95.1% to just 2.3%
→ Pruning automatically stopped once further trimming risked loss of phylogenetic signal
Discrepancy between observed and expected amino acid frequencies in taxa:
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
Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
Our review on how thermophilic carbon monoxide(!)-eating microbes can aid the transition to renewable carbon-based products.
27.05.2025 18:10 — 👍 3 🔁 1 💬 0 📌 0
#Asgard,#phylogeny
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
Excited to share our recent work on the evolution of ectomycorrhizal plants! 🌳 🧬 🖥️
doi.org/10.1111/nph.70054
With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social
A thread: (1/5)
Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...
05.03.2025 11:56 — 👍 28 🔁 39 💬 0 📌 1
Not new here but will become more active at @bsky.app (I am no longer active on X)
Follow me to hear more about the wonderful world of microbes (evolution, archaea, symbiosis, new microbes, ...). Expect occasional rants about academia, 🇳🇱 politics, life, etc.
My research group: go.bsky.app/MzZPftE
