New paper from the lab out! How did animals move repeteadly from water to land? We compared ca. 1,000 animal genomes across the animal kingdom to ask whether evolution reused the same genomic solutions. The answer: same challenge, but many genomic routes 🧵1/n www.nature.com/articles/s41...

New paper out! With @amrojasm.bsky.social @bombarelya.bsky.social @svalver.bsky.social Ildefonso Cases, Scott Handley & yours truly @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @ibmcp.bsky.social @csic.es

Trends in Genetics@cp-trendsgenetics.bsky.social · 2mo ago

"Rethinking molecular evolution through protein language model embeddings" by Rosa Fernández, Ana M. Rojas, & colleagues FREE till Aug. 4th at authors.elsevier.com/a/1nGxPcQbJI...

📢 Nos complace anunciar la incorporación de Rosa Fernández @rosafernandez.bsky.social como nueva Vocal de la Junta de Gobierno de la @academiajoven.bsky.social . ¡Mucho éxito en esta nueva etapa! 🤝 #AcadémicaJoven

LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference https://www.biorxiv.org/content/10.64898/2026.05.26.727789v1

New paper from the lab! LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference www.biorxiv.org/content/10.6...

Post 1/2 Our new preprint is out! 🧬 We’ve extended #Tiberius for accurate ab initio gene prediction across the eukaryotic tree, including Plants, Fungi, Insects, and Diatoms. doi.org/10.64898/202...

Impresionante la presentación de @bombarelya.bsky.social en las #JABI2026. Rigor por la calidad de los datos y una claridad comunicativa que no dejó a nadie indiferente. ¡Un lujo contar con ponentes así!

I am participating in #JABI2026 with a poster on the impact of annotation quality in the analysis of transcriptomic experiments, when working with non-model organisms. This is a collaboration with @bombarelya.bsky.social lab. @jabi-conference.bsky.social

Carbonetto, @rosafernandez.bsky.social et al. explored genetic changes supporting terrestrial adaptation in planarians, identifying a major burst of gene gain preceding the radiation of terrestrial planarians. 🔗 doi.org/10.1093/gbe/... #genome #evolution

Genomic Exaptation and Regulatory Landscape Shifts as Key Mechanisms Enabling Flatworm Terrestrialization

Abstract. Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering th

doi.org

Desde que empecé a hacer ikebana en 2019 durante una estancia de investigación en Japón, tenía el sueño de hacer divulgación combinando #ikebana y #botánica. Aprovechando la visita a Europa de mi sensei, #KayokoKondo, hemos organizado unos talleres en @irnasa.bsky.social. No os lo perdáis! 🌸🌷🌻

IRNASA-CSIC@irnasa.bsky.social · 4mo ago

🌺"Botánica e #Ikebana. Entre tallos y vacíos", un taller gratuito en el que vamos a fusionar ciencia y arte floral. 👩‍🔬👩‍🔬Con Kayoko Kondo y @tank-silvia.bsky.social. 🗓️17 de abril. 📍#IRNASA-CSIC (Salamanca). 🔗Más info: www.irnasa.csic.es/el-csic-fusi... ✍️Inscripción: forms.gle/JhBwdZvqbASC...

Finishing your bachelor or master's? Interested in doing a paid internship in our lab @ibe-barcelona.bsky.social ? Check out the JAE-Intro fellowships! 20 hours/week, 7 months, 600€/month. Ping me if you're interested! sede.csic.gob.es/tramites/pro...

#ERGAReads | FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life www.nature.com/articles/s42... @rosafernandez.bsky.social @commsbio.nature.com @csic.es @ibe-barcelona.bsky.social #LLM #proteome #functional #annotation #genomes

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 non-model organisms beyond…

nature.com

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...

🔦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

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...

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...

communities.springernature.com

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

🧬Jacob L Steenwyk@jlsteenwyk.bsky.social · 9mo ago

The full list of workshop instructors is available here. Registration closes November 15 🥳🥳 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.

CSIC@csic.es · 9mo ago

🖥️Una herramienta basada en IA es capaz de predecir funciones desconocidas de cualquier proteína 🦠Un estudio del IBE-CSIC-UPF y el @cabd-upo-csic.bsky.social ha revelado la función de 24 millones de genes codificantes para proteínas  ➡️ https://f.mtr.cool/cuowksioyo

📣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! 👇👇👇

🧬Jacob L Steenwyk@jlsteenwyk.bsky.social · 9mo ago

🎉 A flyer for the 2026 workshop on #phylogenomics and #genome evolution We have #instructors and #organizers from top-tier universities around the globe who will share their experiences in a two-week intensive course. Register here while there are still seats available! evomics.org/apply-worksh...

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

EVOMG-Doctoral Network@evomg-dn.bsky.social · 10mo ago

The #EvoMG Doctoral Network brings together leading research institutions from Spain, France, Germany, the United Kingdom, Ireland, Portugal and Sweden to train 15 #PhD researchers in #evolutionarymedicine. To find out more about the secondments for each position, visit👉 www.evomg-dn.eu

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

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

Workshops@evomics.bsky.social · 10mo ago

The 2026 Workshop on Phylogenomics will take place between the 25th of January and 7th of February, in Cesky Krumlov, Czechia. 🧬🌳 Applications are now open! Deadline: 15th of November, 2025. Do not miss the chance to attend! Spread the word among colleagues! 🤗 evomics.org/apply-worksh...

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...

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...

biorxiv.org

#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'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...

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...

nature.com