GitHub - stephkoest/witchi: A compositional bias testing and pruning tool for multiple sequence alignments A compositional bias testing and pruning tool for multiple sequence alignments - stephkoest/witchi

9. TL;DR + link dump
WitChi is:
✔ Fast
✔ Interpretable
✔ Tree- and model-free
✔ Benchmark-validated
Designed to fix compositional bias at phylogenomic scale.
With: @kassipan.bsky.social, @danieltamarit.bsky.social, @ettema.bsky.social
💻 github.com/stephkoest/w...
📄 www.biorxiv.org/content/10.1...

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...

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...

Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109

I attended the exciting symposium organized by @floravincent.bsky.social @mwdorr.bsky.social, @nicoledubilier.bsky.social, @gautamdey.bsky.social & Susanna Coelho

LOTs of takeaways from the Symposium (from biology to climate change)

🚨Here are a few important ones in my listicle below 👇

With rapid changes in our environment and climate, there's an urgent need to better understand living systems and their interactions, going beyond the few well-established ‘model’ organisms. A recent EMBO | EMBL Symposium explored how we might do that.

Learn more: www.embl.org/news/science...

The Company of Biologists 100 logo to the left and QR code to the right. Portrait of Gautam Dey to the left, text to the right 100 extraordinary biologists Gautam Dey Gautam Dey co-organised the 2023 Development and 2024 Journal of Cell Science Meetings. Gautam’s research group frequently contributes to preLights. Gautam is a Group Leader at EMBL, Heidelberg, Germany, researching the evolutionary cell biology of mitosis and nuclear remodelling. #100biologists #biologists100

Our next extraordinary biologist for this week is Gautam Dey, who co-organised the 2023 @dev-journal.bsky.social and 2024 @jcellsci.bsky.social Journal Meetings. Gautam’s research group at @embl.org, Germany, frequently contributes to @prelights.bsky.social. #100biologists @gautamdey.bsky.social

Hanh Vu @hanhtkvu.bsky.social, Group Leader at the @embl.org DB unit presenting the diversity of size, pattern and colour of Life #EESWildModels #planarians #DevBio

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!

(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)

ecoevorxiv.org/repository/v...

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

I had a wild time presenting my coral work for the first time at EMBO/EMBL #EESWildModels.

Massive thanks to @embl.org @events.embl.org and the organisers for putting this together. It was a real pleasure to interact with so many weird and wonderful creatures...
...and their model organisms (!!)

Science by day, beats by night 🧬🎶
Sunset skies, science minds, and the EMBL DJ Club bringing the groove to the rooftop. Thanks to everyone who came out and made it such a special evening 🎧🌇 #EESWildModels
But the symposium isn't over yet! Time for the last talk of the day and poster prizes reveal 👀

That’s a wrap on the EMBO | EMBL Symposium: 'Wild frontiers of model organisms'! 🐠🌍🔍

Thanks to our scientific organisers and to all who shared their science and energy. Congrats to our poster prize winners—exceptional work! 👏 #EESWildModels

Let’s keep exploring the unknown and see you next time!

EvoChromo: Evolutionary approaches to research in chromatin Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…

Join us in Catalonia to discuss chromatin evolution across the tree of life and from all angles (metabolism, synthetic chromatin, you name it!) meetings.embo.org/event/24-evo...

Spotlight: Hot waters, shrinking fish | EMBL EMBL scientists investigate how zebrafish bodies change when grown at higher temperatures

Rising temperatures across Earth's oceans, rivers, and lakes are affecting the many creatures that call these home 🐟.

Mantha Lamprousi, a scientist in EMBL's Dorrity Group, investigates how zebrafish bodies change when grown at high temperatures.

www.embl.org/news/science...

How is mitochondrial volume maintained across successive generations of dividing cells? In our new preprint, we show how fission yeast cells use mitochondrial activity to control division timing and maintain mitochondrial homeostasis! (1/n)

📖 www.biorxiv.org/content/10.1...

Instead of believing the myth that three expensive, genetically modified wolves are “de-extinct” dire wolves, let’s look at animals humanity has actually brought back from the brink of extinction using proven science and dedicated hard work: 🧵/6

We give you the winners of yesterday's 'Wild frontiers of model organisms' pub quiz: Wildebeests 👏🏼🏆
Well done to all teams, it was a fun evening!
#EESWildModels

Very excited for this first of its kind EMBO/EMBL Symposium on the Wild Frontiers of Model Organisms.
So far Session 1 is a blast, from aiptasia symbiosis, oyster vibrio phage interactions, !!
#EESWildModels
@embldbunit.bsky.social
@embl.org

GODDAMIT. IT’S NOT A RESURRECTED DIRE WOLF. 20 edits in 19,000 genes.

IT’S NOT GOING TO AID CONSERVATION.

EVERY WRITE UP THAT SWALLOWS AND REGURGITATES THIS GUFFERY WOLFSHIT IS DOING PR FOR A FUNDING ROUND.

Kicked off the #EESWildModels at @embl.org 🐟🦠🍄‍🟫🪰🐟

@floravincent.bsky.social started the sessions with a little survey to sample the range of expertise/skills

Really diverse range of expertise amongst the attendees 💯

@events.embl.org

I say this every time de-extinction comes up: it makes no sense to devote science to bringing back extinct animals when we can’t be bothered to keep extant ones alive in the first place.

Tariffs xkcd.com/3073

The not-dire wolf is of course primarily just a PR invention, but perhaps it is also a good opportunity to think about the talismanic magical powers that get attributed to genes.

Dire wolves were the last of an ancient New World canid lineage - Nature Dire wolves split from living canids around 5.7 million years ago and originated in the New World isolated from the ancestors of grey wolves and coyotes, which evolved in Eurasia and colonized No...

Of course this is scientifically ridiculous, though not quite to the level of the "mammoth mouse" Read the linked paper to learn some science about the dire wolf genome that reveals how absurd the claim is 2/n
www.nature.com/articles/s41...

Cultivating the Ancestors… (1|4)

meet today the archaeon 𝘗𝘳𝘰𝘮𝘦𝘵𝘩𝘦𝘢𝘳𝘤𝘩𝘢𝘦𝘶𝘮 𝘴𝘺𝘯𝘵𝘳𝘰𝘱𝘩𝘪𝘤𝘶𝘮 MK-D1, and its syntrophic companions.

parts 2−4 in the coming weeks...

Read more > schaechter.asmblog.org/schaechter/2...
#MicroSky #Archaea #ArchaeaSky #SymbioSky

Jeremy keeps up--he's digging into the HHS grant details this is important--read on!

This is unconscionable! Subjecting eminent scientists to this uncertainty is crazy!!!

How can DOGE with their ‘coding errors’ be in charge of the US economy?! I hope each of these actions will be the subject of a punitive lawsuit collectively and individually

Friends, I know you're excited to try protesting, but under no circumstances should you ever sign up to attend one. I'm suspicious of any org asking people to put their name on a list that is easily accessible via warrant or may even be public. You can just show up day of.

@erictopol.bsky.social I think your Twitter account is hacked, or you have started believing in crypto😅

I remember when @archaeon-alex.bsky.social came to WashU last Fall to present this for a Biology seminar - completely blew my mind! 🤯 Happy to see this published!