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Rosa Fernández

@rosafernandez.bsky.social
815 followers 532 following 40 posts

Evolutionary biologist, Inst. Evol. Biol. (CSIC, Barcelona). Invertebrate genomics, trying to understand how animals colonised land (and also caves). www.metazomics.com

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Reposted by Rosa Fernández
Adlung Lab @adlunglab.com · 20/08/2026
Great Nature Career piece on the "lottery" aspect of grant decisions, its pros and cons. Still liked the VolkswagenStiftung approach! www.nature.com/artic... 🧪
nature.com
When the best decision is no decision: the rise of randomization in grant funding
Nature - If reviewers can’t reliably tell the difference between top grant proposals, why should they pretend they can? A new wave of funders is turning to lotteries to break the tie.
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
This was funded by our @erc.europa.eu project SEA2LAND & couldn't have been possible without the incredible contribution of @klarael.bsky.social, Gemma, Judit Salces, Nuria Escudero, Carlos Vargas, @cefafalopodo.bsky.social and many other lab members and colleagues. Big shout out to all of them! 🧬🧬
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
Our main conclusion: Convergent adaptation does not require convergence on the same genes. Animals reached a similar ecological destination through different genomic trajectories, mainly by rewiring and co-opting ancient molecular systems🌊▶️🛘 11/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
Machine learning added another layer. Just 130 orthogroups could distinguish aquatic from terrestrial species with high-accuracy, but not through one universal expansion or loss pattern. Instead, habitat was encoded in complex, lineage-specific changes in gene copy number 10/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
Most stress-responsive genes were evolutionary ancient, often predating the origin of animals and appearing long before any lineage moved onto land. Terrestrialization was therefore less about inventing a new toolkit and more about teaching old genes new tricks 9/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
These convergent functions included metabolism, signalling, proteostasis, autophagy, apoptosis, cytoskeletal regulation and cellular homeostasis. The genes differed. The networks differed. But the biological outcomes converged 8/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
But when we looked beyond gene identify, a pattern emerged: different species recruited different genes into many of the same pathways and biological functions. Different molecular parts, similar functional machinery 7/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
Did independent lineages use the same genes to respond to terrestrial stresses? Mostly, no. Only 42 stress-associated orthogroups were shared across all 17 species. There was no universal "terrestrialization genetic toolkit" 6/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
First surprise: transitions to land were generally associated with far more gene loss than gene gain. Animals did not necessarily arrive on land with more genomic luggage. In many cases, it travelled light 🧬💼 5/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
We exposed aquatic and terrestrial animals from 7 phyla to challenges associated with life on land: osmotic stress, hypo/hyperoxia, UV radiation, visible light and chemical cues. Then we reconstructed their gene co-expression networks 4/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
So we went beyond gene counting: 🧬973 species across all animal phyla 🌍15 independent terrestrialization events 🧪796 stress-induced RNA-seq datasets 🧫17 experimentally studied species 🔬Iso-seq transcriptomes and proteomics From genomic inventories to functional responses 3/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
Gene gains & losses are an important part of the story. But a gene catalogue alone cannot tell us much the story. We also need to see those genes in action 🎬 2/n
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Rosa Fernández @rosafernandez.bsky.social · 28/07/2026
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...
nature.com
Convergent genomic trajectories shape adaptation to life on land across animal lineages - Nature Communications
Animals have moved from water to land many times, but whether they used the same genetic routes has remained unclear. This study shows that independent land transitions relied mostly on ancient, conse...
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Rosa Fernández @rosafernandez.bsky.social · 18/06/2026
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
sciencedirect.com
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Reposted by Rosa Fernández
Academia Joven de España @academiajoven.bsky.social · 11/06/2026
📢 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
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 26/05/2026
LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference www.biorxiv.org/content/10.64898/20…
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Rosa Fernández @rosafernandez.bsky.social · 28/05/2026
New paper from the lab! LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Rosa Fernández
Katharina Hoff @katharinahoff.bsky.social · 29/04/2026
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...
doi.org
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Jornadas Andaluzas de Bioinformática #JABI2026 @jabi-conference.bsky.social · 27/04/2026
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!
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Silvia Manrique @tank-silvia.bsky.social · 28/04/2026
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
Silvia Manrique smiling next to her poster entitled “Assessment of the impact of annotation quality on a transcriptomic analysis of Solanum melongena”. She is at the JABI2026 conference taking place in the headquarters of cordoba university.
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Reposted by Rosa Fernández
Genome Biology and Evolution @genomebiolevol.bsky.social · 31/03/2026
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
doi.org
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
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Silvia Manrique @tank-silvia.bsky.social · 25/03/2026
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! 🌸🌷🌻
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Rosa Fernández @rosafernandez.bsky.social · 24/03/2026
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...
sede.csic.gob.es
Convocatoria JAE INTRO 2026
Tipo: Ayudas a la formación. Subtipo: JAE INTRO  Categoría: Becas de Introducción a la Investigación. Número de ayudas: 240: 200 de la modalidad JAE INTRO ORGC y 40 de la modalidad JAE INTRO Momentum. Publicación: BDNS (892036) - BOE (11/03/2026)
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Reposted by Rosa Fernández
ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 18/03/2026
#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
nature.com
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…
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Reposted by Rosa Fernández
Raul Pacheco-Vega @raulpachecovega.bsky.social · 21/02/2026
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.
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Reposted by Rosa Fernández
Alexis Stamatakis @stamatak.bsky.social · 15/12/2025
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
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Germán Orizaola @gorizaola.bsky.social · 02/12/2025
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...
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Reposted by Rosa Fernández
Institut de Biologia Evolutiva (IBE) @ibe-barcelona.bsky.social · 10/11/2025
🔦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
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.
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Sergi Valverde @svalver.bsky.social · 06/11/2025
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...
communities.springernature.com
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...
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Reposted by Rosa Fernández
🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 06/11/2025
9 days till registration closes! bsky.app/profile/jlst...
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Centro Andaluz de Biología del Desarrollo @cabd-upo-csic.bsky.social · 05/11/2025
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.
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Institut de Biologia Evolutiva (IBE) @ibe-barcelona.bsky.social · 04/11/2025
📣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
Ctenophore Mnemiopsis leidyi. Credit: Bruno C. Vellutini. CC BY-SA 3.0. Via Wikimedia Commons.
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Rosa Fernández @rosafernandez.bsky.social · 03/11/2025
Join us in Cesky Krumlov for this amazing workshop! Applications close in two weeks! 👇👇👇
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Reposted by Rosa Fernández
🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 01/11/2025
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
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 01/11/2025
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
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Christophe Dessimoz @dessimoz.bsky.social · 23/10/2025
Our lab has published a couple of major papers in the past few months, which I would like to highlight in this thread! 🧵
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Camille Berthelot @camilleberthelot.bsky.social · 21/10/2025
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
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Rob Waterhouse @rmwaterhouse.bsky.social · 17/10/2025
Now with @rosafernandez.bsky.social at @atlasea.bsky.social meeting in @mnhn.fr #Paris
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Rosa Fernández @rosafernandez.bsky.social · 14/10/2025
@sesbe-org.bsky.social @csic.es @ibe-barcelona.bsky.social @official-smbe.bsky.social @eseb.bsky.social
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Rosa Fernández @rosafernandez.bsky.social · 14/10/2025
Interested in phylogenomics and genome evolution? Join us in Cesky Krumlov next January! The list of topics and faculty is simply spectacular! 🧬🪾🧬🪲🦞🦐🌿🌾🦠🧫
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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! 🙏
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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.
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
The transition to land was powered by flexibility, not innovation, with animals reshaping old genomic parts to solve new problems.
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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!
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
Adaptation to land thus emerged through functional convergence and genomic network reorganization, not through repeated invention of new genes.
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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.
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
Across 15 independent terrestrialization events, most adaptive genes (at least related to response to the environment) were ancient, predating land life.
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
Using comparative genomics, transcriptomics, proteomics & machine learning, we found that gene loss, not gain, dominates at the evolutionary nodes where animals transitioned to land.
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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...
biorxiv.org
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...
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