iiinova — where your digital self keeps evolving

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Alex de Mendoza @alexdemendoza.bsky.social · 12/10/2026

How can a #GiantVirus 👾 lurk inside the host genome undetected? We find that epigenetic conflict lies at the centre of the ⚖️ between infection and co-existence with the host. Great collaboration with the Aylward lab out in @biorxivpreprint.bsky.social: www.biorxiv.org/content/10.6...

biorxiv.org

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

🧬🧬🧬 Very happy to share our new preprint led by Fede Mantica (@fedemantica.bsky.social) on how tissue-specific alternative splicing (TS-AS) and gene expression (TS-GE) evolve across bilaterians! Thread below 🧵 1/11 www.biorxiv.org/content/10.6...

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

Thanks to all the co-authors: Antonio Torres (@antoniotorm.bsky.social ), Irene Bódalo, Luis P. Iñiguez (@luispiniguez.bsky.social ), Yamile Marquez, Violeta Morin and Jean-Yves Roignant!

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

In summary, TS-AS and TS-GE are not simply interchangeable routes to tissue specialization. Instead, they occupy distinct but complementary evolutionary niches, with recurrent neural exon evolution emerging as an important contributor to nervous-system diversification. 11/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

Finally, we asked whether this recurrent evolution was functionally relevant. We deleted two recurrent neural microexons in Drosophila: loss of the spg exon impaired climbing and strongly reduced lifespan, while loss of the syd exon caused age-dependent hyperactivity and reduced offspring. 10/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

Exon-level orthology revealed a second striking surprise. Most neural-specific exons lacking direct conservation were not unique events: neural exons repeatedly evolved in the same ancestral genes across distant bilaterian lineages. 9/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

But here came a first surprise: at the origins of both vertebrates and insects, gains of neural-specific splicing actually outnumbered gains of neural-specific gene expression, pointing to a major early contribution of TS-AS to nervous-system diversification. 8/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

We then asked how conserved these regulatory programs are. Overall, TS-GE was substantially more conserved than TS-AS, while neural tissue showed the highest conservation for both mechanisms. 7/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

Across evolution, the reach of these mechanisms was huge: together, TS-AS and TS-GE affected nearly 75% of ancestral bilaterian gene families. Some families used only one route, while ~30% evolved both across different species. 6/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

Yet, TS-AS and TS-GE largely targeted different genes. TS-AS preferentially affected long, exon-rich genes and shared intracellular functions, whereas TS-GE was associated with gene duplication and more tissue-defining functional programs (details in Fig 2b,d). 5/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

First, TS-AS and TS-GE affected remarkably similar numbers of genes within species. Neural tissues showed the strongest contribution of both, while muscle was more biased toward TS-AS and testis toward TS-GE. 4/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

To address this, we compared TS-AS and TS-GE across 8 homologous tissues, 20 bilaterian species and 7,178 ancestral gene families, spanning ~700 million years of evolution. 3/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

Specialized tissues often evolve by repurposing ancestral genes. TS-GE and TS-AS provide two ways to do this: changing how much of a gene is expressed, or which isoform is produced. But are these broadly interchangeable evolutionary solutions? 2/11

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Manuel Irimia @mirimiam.bsky.social · 05/10/2026

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Manuel Irimia @mirimiam.bsky.social · 03/09/2026

🚨🚨🚨 As part of the MSCA-DN DECODES, we're looking for a PhD student to study splicing programs in beta cells and diabetes at @melisupf.bsky.social @crg.eu Join 14 other PhD students across Europe to decipher the splicing code in human disease. More info below 👇 www.findaphd.com/phds/project...

findaphd.com

DECODES at University of Santiago de Compostela on FindAPhD.com

PhD Project - DECODES at University of Santiago de Compostela, listed on FindAPhD.com

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Manuel Irimia @mirimiam.bsky.social · 03/09/2026

Timeline: • Call opening: August 25, 2026. • Application deadline: October 1, 2026. • Remote evaluation results: October 10, 2026. • Interviews: October 10–31, 2026. • Notification: November 15, 2026. • Start date of the fellowship: January–December 2027. Interested? Get in touch! 😃

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Manuel Irimia @mirimiam.bsky.social · 03/09/2026

About DECODES: An European MSCA Doctoral Network whose overarching goal is to to decipher how alternative splicing drives human disease, from rare disorders and neurodegeneration to cancer and diabetes, and translate RNA biology into precision splicing therapies. 15 research groups in 9 countries!

Geographic distribution of DECODES groups

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Manuel Irimia @mirimiam.bsky.social · 03/09/2026

The PhD project: It aims to uncover how alternative splicing shapes pancreatic beta cell identity and function, how disruption of these regulatory programs contributes to beta cell failure and type 2 diabetes (T2D), and whether they can be therapeutically rewired to restore beta-cell fitness.

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Manuel Irimia @mirimiam.bsky.social · 03/09/2026

findaphd.com

DECODES at University of Santiago de Compostela on FindAPhD.com

PhD Project - DECODES at University of Santiago de Compostela, listed on FindAPhD.com

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Al Jord Lab @aljordlab.bsky.social · 21/08/2026

Transcription stops. RNA splicing takes over 🧬 ✨ Our new preprint uncovers the post-transcriptional RNA splicing landscape powering mammalian oocyte development. Read it here 👇 www.biorxiv.org/content/10.6...

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Isabel Almudi @isabelalmudi.bsky.social · 07/08/2026

What happens when evolution adds an extra pair of eyes? Male mayflies evolve an extra pair of dorsal compound eyes, the Turbanate eyes, thought to help males detect females during mating swarms. we have investigate how this remarkable evolutionary novelty develops. www.biorxiv.org/content/10.6...

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Alex de Mendoza @alexdemendoza.bsky.social · 03/08/2026

Sailing in @biorxivpreprint.bsky.social ready for summer, our study on the iconic Portuguese man o' war 🪼 is out: www.biorxiv.org/content/10.6.... We use (epi)genomics to understand a critter that fascinates me since childhood. Massive team effort with @obog.bsky.social, Cummins and Neely groups. 🧵

the indo-pacific bluebottle (Physalia utriculus)

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Ulrich Braunschweig @braunschweig.bsky.social · 20/07/2026

What happens if you delete large intronic regions? In human tissue culture cells, we found many deletions that decrease growth and some that increase it. In most cases, deletion affected expression or splicing of the gene. www.cell.com/cell-reports... 1/3

cell.com

A genome-wide functional analysis of conserved intronic regions reveals essential roles for speckle-associated retained introns

Farhangmehr et al. investigate functions of highly conserved intronic sequences in cell fitness using a CRISPR-based deletion screen. Deletions in FNBP4 intron lead to changes in p53 pathway genes. De...

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Barbara Pernaute @bpernaute.bsky.social · 24/06/2026

🚨 Early Bird registration and abstract submission deadline for #SEBD2026 extended!! 📅 Early registration and abstract submission deadline: 10th July 📅 Scholarship application deadline: 29th June www.sebd2026.com #SEBD #DevBio @sebioldev.bsky.social 👇👇👇

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tahneema.bsky.social @tahneema.bsky.social · 28/06/2026

Very excited to finally share my PhD! 🎉 Our paper, “Neuronal microexons modulate arousal via the cAMP-PKA-CREB pathway in zebrafish,” is now published in Science Advances. Many thanks to all of my co-authors, and especially to @mirimiam.bsky.social! 📄 www.science.org/doi/10.1126/...

science.org

Neuronal microexons modulate arousal via the cAMP-PKA-CREB pathway in zebrafish

Loss of the conserved splicing factor for neuronal microexons disrupts neuromodulatory signaling and drives hyperarousal.

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Parc de Recerca Biomèdica de Barcelona @prbb.org · 19/06/2026

🦟 Why don’t viruses kill the mosquitoes that transmit them? 🔬 A study reveals how these insects coexist with viruses such as dengue and Zika, and what this can teach us about their spread and control. Learn more: tuit.cat/uu8EJ @melisupf.bsky.social

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The Company of Biologists @biologists.bsky.social · 18/06/2026

Thank you to organisers to James Hombría and Antónia Monteiro @monteirolab.bsky.social and everyone who joined us at this week's Workshop on 'Novelty, Co-option and Divergence During Gene Network Evolution' biologists.com/workshops #BiologistsWorkshops

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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

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preLights @prelights.bsky.social · 02/06/2026

61 species, 13 phyla, one simple geometric rule that appears to set when every embryo starts speaking through its own genome. 🧬 Panagiotis Giannios highlights a recent #preprint from @mirimiam.bsky.social & collaborators. #EvolutionaryBiology #preLight: prelights.biologists.com/highlights/e...

prelights.biologists.com

Evolutionary landscapes of zygotic genome activation across animals - preLights

61 species, 13 phyla, one simple geometric rule that appears to set when every embryo starts speaking through its own genome.

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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 02/06/2026

Fin-catching prelight on @mirimiam.bsky.social et al.'s preprint on the animal zoo 🐟🧬

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EvoMG Program @evomg-bcn.bsky.social · 01/06/2026

We had a great seminar by Duncan Odom @odomlab.bsky.social today about mutagenesis and cancer evolution!

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Centre de Regulació Genòmica (CRG) @crg.eu · 31/05/2026

Huge congrats to the CRG's Mafalda Dias for being one of eight finalists for the 2026 Premio Vanguardia de la Ciencia, one of Spain's most visible science prizes. Voting is open now and closes on Sunday 28 June at 23:59 (peninsular time).

lavanguardia.com

La IA mejora el estudio de las enfermedades raras

Vota a las finalistas del premio Vanguardia de la Ciencia

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Gioia Quarantani @gioia-quarantani.bsky.social · 26/05/2026

1\ Excited to finally share some of my PhD work: OpenSplice! We measured how >590,000 mutations affect exon inclusion across 600 human exons, creating a resource to study splicing regulation, benchmark variant effect predictors, and support variant interpretation.

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Alex de Mendoza @alexdemendoza.bsky.social · 26/05/2026

New preprint! In an fun collaboration with @imaeso.bsky.social and @mirimiam.bsky.social led by Manu F-M, we set to explore the potential adaptation of transposable elements 👾 to host adenine DNA methylation by recruiting prokaryotic DAM methyltransferases: www.biorxiv.org/content/10.6.... 1/6

biorxiv.org

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Alejandro Burga @arburga.bsky.social · 18/05/2026

🧬 New research from the Burga lab! We took a closer look at a rogue selfish protein and caught evolution in the act of turning something old into something radically new 💡 (a.k.a. neofunctionalization) @imbavienna.bsky.social www.biorxiv.org/content/10.6... Curious? Here’s a breakdown:

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Schubeler Lab @schubelerlab.bsky.social · 07/05/2026

Excited to share our new study on CpG islands (CGIs) regulation by transcription factors (TFs)! CGIs drive most transcription initiation with unclear regulation. We find that chromatin-opening TFs are key players—following a surprisingly simple rule. 🧵 www.biorxiv.org/content/10.6... 1/9

biorxiv.org

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Isabel Almudi @isabelalmudi.bsky.social · 29/04/2026

Exhausted but extremely happy for the two past days of very exciting Science! The EvoDevOmics Spanish Network gathered together in BCN to discuss about evodevo & omics, lots of great talks, discussions and future collaborations. 🤩 #evodevo

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imaeso.bsky.social @imaeso.bsky.social · 29/04/2026

Amazing couple of days enjoying & discussing science in the best possible company during the Barcelona meeting of the 'EvoDevOmics Network', funded by @ageinves.bsky.social. Really happy to see how the EvoDevo community in Spain is thriving & fostering a fantastic new generation of PhDs & Postdocs.

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Johanna Joyce @johannajoyce.bsky.social · 22/04/2026

What should Europe do when demand for #ERC funding keeps rising? Restrict access or invest in excellence? Please read our open letter calling for reconsideration of the ERC 2027 resubmission restrictions & for constructive alternatives that preserve openness Consider to share & sign - see below 🧪

linkedin.com

#erc | Johanna Joyce

What should Europe do when demand for its most successful frontier research programme keeps rising? Restrict access, or invest in the excellence it has created? A new open letter, spearheaded by Sara...

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Ali Seleit @aliseleit.bsky.social · 20/04/2026

Really cool work ! Love the strong scaling of ZGA timing to genome size and egg volume. It's so simple and elegant. Highlights the strength of taking a comparative approach

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Manuel Irimia @mirimiam.bsky.social · 20/04/2026

Do you want to know when your favorite species activates its genome? Just input its genome size (🧬 in bp) and egg volumen (🥚 in um3) here! ZGA_onset = -2.37 * log10(gDNA/EggVol) + 11.74

media.tenor.com

a cartoon of spongebob saying magic with his hands up

ALT: a cartoon of spongebob saying magic with his hands up

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Cnidarian developmental mechanisms group @clytia-vlfr.bsky.social · 20/04/2026

This fits the general principle of ZGA being triggered by a 'universal' Genome: Cytoplasm ratio across animals! - and thus a highly conserved mechanism involving titration of a maternal cytoplasmic factor on chromatin.

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Cnidarian developmental mechanisms group @clytia-vlfr.bsky.social · 20/04/2026

So, by providing staged embryo mRNA for this beautiful wide comparative study, we now know that zygotic gene activation in Clytia occurs in the early blastula with 512 cells, at around 5hpf (Here termed ZGA cell cycle 9).

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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 20/04/2026

“Here, we generated a comprehensive transcriptomic atlas of early embryogenesis from 61 animal species, spanning 13 phyla. By applying a unified computational framework, we systematically inferred the timing of ZGA across species.” This is a big one from @mirimiam.bsky.social et al. 🔥🧪

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Manuel Irimia @mirimiam.bsky.social · 20/04/2026

Thanks so much to Jon Pemanyer and Cris Rodriguez and all our collaborators that provided all the essential embryo samples, without whom this project would have been impossible! (Those with handlers listed below!) 15a/15

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