Damien M. de Vienne

Le saviez-vous ? 😜🤩😅

(repéré par @virhostnet.bsky.social)

Metazooa Become an evolutionary detective to find the Mystery Animal!

🦨 Animal #917 🦓
I figured it out in 10 guesses!
🟧🟨🟨🟨🟨🟨🟩🟩🟩🟩
🔥 1 | Avg. Guesses: 10

metazooa.com
#metazooa

The abstract submission deadline for the 2026 Mathematical and Computational Evolutionary Biology Meeting on Crete mceb2026.sciencesconf.org has been extended until February 6

The website mentions March 15th for registration deadline?!

Did you rephrase these types of sentences? In my case it was impossible...

I realized this recently as well when submitting a draft. In addition to the paper already on biorxiv, the tool presented in the paper (whose name was in the title) was on my GitHub account!...

Captured d'écran de la barre de navigation chrome montrant l'url de Lifemap et le bouton télécharger permettant d'installer l'app sur son bureau

Lifemap is now installable as an app on your desktop (PWA). 🖥️

Just one click from your browser!

lifemap.cnrs.fr

#Lifemap #CNRS #LBBE

We are recruting an assistant engineer for 18 months at LBBE (Lyon, France) in molecular biology of Drosophila. The project is to study the interactions between response to viral infections and control of transposable elements.
emploi.cnrs.fr/Offres/CDD/U...

Vue de pylifemap n°1

Vue de pylifemap n°2

Vue de pylifemap n°3

Vue de pylifemap n°4

Our tool **pylifemap** for mapping data onto the complete Tree of Life is ready !!
Explore YOUR datasets (metagenomics, ecology, genomics, outreach...) in a FULL taxonomy-aware context with a few lines of code !
The doc: lifemap-tol.github.io/pylifemap/
The draft: www.biorxiv.org/content/10.6...

...If you think that other languages could be useful, please let me know!?

📢
Following many requests, we prepare translation in Chinese for Lifemap (lifemap.cnrs.fr).
- For taxa name, we will use @inaturalist.bsky.social 👌
- For the interface, we look for a chinese-speaking 🇨🇳colleague to check that the automatic translation is correct. Just 1 small file!

CAN YOU HELP!? 🙏

There’s still work ahead to turn this proof of concept into a method usable on real data. This is one of the focus of Enzo Marsot’s PhD, co-first author on this article, where he develops deep learning models for this goal.
Stay tuned! (2/2)

Finally! Thrilled to share our new work on ghosts and horizontal gene flow!
After showing that ghost lineages (extinct, unknown, unsampled) can distort gene flow detection, we now show that gene flow signals can be used to detect, quantify, and place ghost species in the Tree of Life!(1/2)

And here is the Institute in Crete! First day today!!

TODAY is my Last day at LBBE in Lyon (for a while)!!
From September, I’ll be in Heraklion 🇬🇷 for a year-long stay in Alexis Stamatakis’ lab @stamatak.bsky.social at FORTH @forth-ite.bsky.social .
Can’t wait for this new adventure 🏖️ ☀️🖥️👻

Our new work on the overlooked impact of ghosts for HGT detection and simulation has just been published in MBE @molbioevol.bsky.social !

Hi, tonight I will give my conference on "Exploring the tree of Life", a special type of immersive experience with animations projected under the dome of the planetarium!!

#Évènement🎟️|
Les #ÉchappéesInattendues du @cnrs.fr reviennent ‪au planétarium de @vaulx-en-velin.bsky.social avec la conférence immersive de @damdevienne.bsky.social "Voyage au cœur de l’arbre du vivant "🦠🍄
📅le 3 juin
🕢à 19h30
🤩gratuit SANS inscription 👇 echappeesinattendues.cnrs.fr/event/voyage...

March was the first complete month since the update of Lifemap (lifemap.cnrs.fr). Time for some statistics!

In March we had 17,880 (unique) visitors, who spent on average 4 min 49s on the website. France and USA were the top visitor countries.

Let's continue to talk about Lifemap!

🙏THANKS🙏

The new Lifemap is out: explore the full Tree of Life with an interactive interface à la Google Maps! lifemap.cnrs.fr
Give it a try!

🪧 My Lab (LBBE) is looking for a communication officer (1 year contract)! Deadline March 7th.
Apply here: emploi.cnrs.fr/Offres/CDD/U...

Do you think marine evolution #MarEvol is cool? Maybe you were at the 2018 Marine Evolution meeting in Strömstad, Sweden? And surely you'd like us to do it again and organise MarEvol2? Why not in the South of France? Then fill in this questionnaire and spread the word:
framaforms.org/my-interest-...

📢 A new version of Lifemap will soon be available at a new URL. Automatic redirection will be implemented, but if you develop or use tools or applications that could be affected, please contact me to ensure a smooth transition: damien.de-vienne@univ-lyon1.fr. 🚀

multistrap: boosting phylogenetic analyses with structural information - Nature Communications Phylogenetic trees provide key information to elucidate basic aspects of functional genomics. This method, multistrap, offers a way to combine sequence and structural protein information that improves...

Just out!
Ooooold collaboration finally led to a (nice!) publication!
www.nature.com/articles/s41...

LAST DAY to send an abstract to ALPHY-AIEM!
alphy-aiem-2025.sciencesconf.org

Gene flow can reveal ghost lineages Ghost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden diversity has been shown to influence the study of hor...

New preprint to (finaly) present the proof of concept that detection of HGTs can help reveal invisible (ghost) lineages along the branches of a species tree. More work on that coming soon!
www.biorxiv.org/content/10.1...

HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting When a gene is horizontally transferred (HGT), under the “replacement” model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the ...

New preprint on a funny obvservation: treating horizontal gene transfers (HGTs) as Subtree Pruning and Regrafting (SPRs) operations (as is commonly done) assumes that no ghost lineages are around... which is unlikely!

www.biorxiv.org/content/10.1...

Hi everybody! Just landed here!

My goal is to post and read information regarding science, mostly evolutionary biology : articles, comments, ideas...