Rosa Fernández

I want to stress that I want AI to do my dishes and house work so that I can write and think, not all the other way around.

Permanent Research Group Leader Position, Crete, Greece: Interested to assume long-term responsibilities for the Biodiversity Computing Group www.biocomp.gr I have set up in Crete? Apply now via apella.minedu.gov.gr/en/node/5998 (PDF also in English) - for questions email to stamatak@ics.forth.gr

Article about melanistic fungi in #Chornobyl @bbcnews-world-rss.bsky.social including a comment about our study with dark frogs (@universidadoviedo.bsky.social @ebdonana.bsky.social )

bbc.com/future/artic...

Ctenophore Beroidae, a gelatinous zooplankton that moves using cilia and feeds on other ctenophores. Credit to the National Oceanic and Atmospheric Administration. Public domain license. Via Picryl.

🔦Shedding light on “dark biology”: a true FANTAS-IA?

📕A team led by Rosa Fernández from the @ibe-barcelona.bsky.social, and Ana Rojas from the @cabd-upo-csic.bsky.social, has developed an AI-based tool capable of predicting the unknown functions of animal proteins.🧵

👉https://shorturl.at/S9WjN

The Fractal Geometry of Innovation Why are some cities more innovative than others? Mapping more than a century of U.S. patents, our npj Complexity study reveals fractal and scaling patterns in innovation—showing how the distribution o...

Innovation isn’t random — it follows geometric laws.

Our new Behind the Paper post in @springernature.com Communities explores how innovation forms a fractal geometry — self-organizing like a living system.

communities.springernature.com/posts/the-fr...

9 days till registration closes!
bsky.app/profile/jlst...

Los equipos de @rosafernandez.bsky.social del @ibe-barcelona.bsky.social y de @amrojasm.bsky.social del #CABD han desarrollado #FANTASIA, una herramienta basada en #IA que es capaz de predecir funciones desconocidas de cualquier proteína.

Ctenophore Mnemiopsis leidyi. Credit: Bruno C. Vellutini. CC BY-SA 3.0. Via Wikimedia Commons.

📣Una herramienta basada en IA es capaz de predecir funciones desconocidas de cualquier proteína

📕 Un estudio del @ibe-barcelona.bsky.social y el @cabd-upo-csic.bsky.social ha revelado la función de 24 millones de genes codificantes para proteínas en animales.🧵

👉https://shorturl.at/O1x3m

Join us in Cesky Krumlov for this amazing workshop! Applications close in two weeks! 👇👇👇

CC @tonigabaldon.bsky.social, @rokaslab.bsky.social, @rosafernandez.bsky.social, @trayc7.bsky.social, Claudia Solis-Lemus, Bastien Boussau, @nclark.bsky.social, Kay Lucek, Tap Pupko, Ana Rojas, Frederik Ronquist & Ania Karnkowska

So many AMAZING instructors/organizers will be participating, including @tonigabaldon.bsky.social, @rokaslab.bsky.social, @rosafernandez.bsky.social, @trayc7.bsky.social, Claudia Solis-Lemus, Bastien Boussau, @nclark.bsky.social, Kay Lucek, Tap Pupko, Ana Rojas, Frederik Ronquist & Ania Karnkowska

Our lab has published a couple of major papers in the past few months, which I would like to highlight in this thread! 🧵

We are hiring a ✨ bioinformatics PhD student ✨ for fall 2026 as part of the @evomg-dn.bsky.social MSCA doctoral network!

Our project in a nutshell: can the evolution of gene expression in the uterus point us towards which genes are important for human uterine diseases?

To apply 👉 www.evomg-dn.eu

Now with @rosafernandez.bsky.social at @atlasea.bsky.social meeting in @mnhn.fr #Paris

@sesbe-org.bsky.social @csic.es @ibe-barcelona.bsky.social @official-smbe.bsky.social @eseb.bsky.social

Interested in phylogenomics and genome evolution? Join us in Cesky Krumlov next January! The list of topics and faculty is simply spectacular! 🧬🪾🧬🪲🦞🦐🌿🌾🦠🧫

Big shout out to all the collaborators, particularly @cefafalopodo.bsky.social @aubombarely.bsky.social @vargaschavezc.bsky.social Judit Salces-Ortiz & Nuria Escudero, for endless adventures together while working on this project! 🙏

This study is a core outcome of our @erc.europa.eu
project SEA2LAND, revealing how life’s move from sea to land was driven not by gene invention, but by genomic flexibility uncovered through a multi-omics, systems biology lens. 🌊➡️🌍 @ibe-barcelona.bsky.social @csic.es

To truly understand life’s major evolutionary transitions, counting genes isn’t enough. We need multi-omics, systems-level approaches that reveal how genomes are rewired to meet new ecological challenges. Only then can we see how evolution turns old parts into new solutions.

The transition to land was powered by flexibility, not innovation, with animals reshaping old genomic parts to solve new problems.

Machine learning identified a small set of ancient gene families whose copy-number shifts correlate with habitat, not via shared expansions, but through independent, lineage-specific trajectories across Metazoa. No common gene families between terrestrial lineages identified!

Adaptation to land thus emerged through functional convergence and genomic network reorganization, not through repeated invention of new genes.

Stress-response multiomics experiments in 17 species from 7 animal phyla revealed that different lineages recruit distinct genes to face similar challenges, yet converge in function, not gene identity.

Across 15 independent terrestrialization events, most adaptive genes (at least related to response to the environment) were ancient, predating land life.

Using comparative genomics, transcriptomics, proteomics & machine learning, we found that gene loss, not gain, dominates at the evolutionary nodes where animals transitioned to land.

Independent genomic trajectories shape adaptation to life on land across animal lineages How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared gen...

How did animals repeatedly conquer land? 🌊➡️⛰️ We analysed ~1,000 gene repertoires (24M genes!) from all animal phyla to uncover how this happened. Work led by @gemmaeling.bsky.social & Klara Eleftheriadi, both first coauthors of this titanic effort!
www.biorxiv.org/content/10.1...

#ERGAReads | Clitellates - terrestrial & freshwater annelids - underwent dramatic #genome reshuffling, losing synteny with their marine relatives. This rare burst of genomic change reshaped chromosome structure in the group
🔗 rdcu.be/euNbT
#genomics #evolution #Annelida @rosafernandez.bsky.social

FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...

Figure 1. From conserved macrosynteny to genome atomization in clitellates.

"Breaking bad: when clitellate genomes go rogue"
by Rosa Fernández (@rosafernandez.bsky.social) & colleagues

"Clitellate genomes are the result of a profound genome reshaping...What triggered such extreme rearrangements...?"

FREE till Aug. 24th at this link:
authors.elsevier.com/a/1lNmQcQbJF...

If you enjoyed our recent paper on massive genomic rearrangements in clitellates, don't miss our recent review on the topic, where we discuss some hypothesis and implications of our findings 👇🪱🧬💥👇 @cp-trendsgenetics.bsky.social @ibe-barcelona.bsky.social authors.elsevier.com/a/1lNmQcQbJF...