(@martaig) — Bluesky Profile

1 week ago

Efficient genome editing using CRISPR–Cas9 in reef-building corals - Nature Protocols In this protocol, the authors present straightforward and efficient methods to genetically modify corals and study gene function throughout various life-history stages using CRISPR–Cas9-based mutagene...

To increase the use of gene editing in corals, we have made a comprehensive methods paper describing the protocol. We hope this helps the field of functional genetics in corals. www.nature.com/articles/s41...

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3 weeks ago

Introducing a Clytia planula cell atlas, and demonstrating broad-level relations with medusa cells via another updated atlas. By @annaferraioli.bsky.social with @juliarmateu.bsky.social and collaborators in a project led by @rcply.bsky.social @biodev-vlfr.bsky.social www.biorxiv.org/content/10.6...

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3 weeks ago

We‘re looking for a motivated Master student to join our team!

Do you want to optogenetically control metabolic activity to see how metabolism affects patterning and morphogenesis? 💡🧫🧬🔬

Then please apply!
#optogenetics #metabolism #devbio #hESCs

Please RT. Thank you!🙏

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1 month ago

How have concerted and mosaic evolutionary mechanisms shaped the expansion of the human cerebellum?

Our review with @tyamadat.bsky.social and @ioansarr.bsky.social available free till March 29:
authors.elsevier.com/a/1ma2wFzn7a...

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1 month ago

Brain with puzzle overlay to show that our study provides missing pieces of the puzzle of human brain development by delivering the most comprehensive picture of hindbrain development to date. We have strived to go beyond just another multi-omics atlas to gain deep insights by:
1. Meticulously annotating cell clusters
2. Extracting regulatory programs in terms of coordinated gene sets and accessible regulatory elements
3. Using deep learning to identify regulatory syntax
4. Resolving context-specific TF activity

Excited to share our preprint on our new multi-omic atlas of human hindbrain development. Led by postdoc Piyush Joshi, in collaboration with @kaessmannlab.bsky.social and Pfister labs, our atlas represents the first comprehensive view of human hindbrain development. www.biorxiv.org/content/10.6...

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2 months ago

@arnausebe.bsky.social has put together a fantastic thread explaining the work—check it out here 👇 bsky.app/profile/arna...

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2 months ago

A particularly exciting finding is that, while effector gene usage groups functionally similar cell types, regulatory similarities beautifully reflect known ontogenetic relationships!

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2 months ago

We dissect the regulatory logic underlying cell identity in the cnidarian Nematostella, laying a foundation for comparative regulatory genomics.

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2 months ago

And to @xgrau.bsky.social, @zolotarg.bsky.social, @lukasmahieu.bsky.social, @steinaerts.bsky.social, plus Didac Cañas and the Genomics, FACS & ALMU teams at @crg.eu for amazing support

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2 months ago

Decoding cnidarian cell type gene regulation - Nature Ecology & Evolution This study reconstructs the gene regulatory networks that define cell types in the sea anemone Nematostella vectensis, providing a valuable resource for comparative regulatory genomics and the evoluti...

Lovely Xmas gift 🎄—our paper is out today in @natecoevo.nature.com www.nature.com/articles/s41...! Huge thanks to everyone who made it possible, especially @aelek.bsky.social and @arnausebe.bsky.social

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2 months ago

Whole body regeneration deploys a rewired embryonic gene regulatory network logic - Nature Communications To what extent regeneration recapitulates embryonic development is a longstanding question. Here, they show that embryonic gene modules are re-used, rewired, and interconnected to specific injury-indu...

Stoked that this paper, summarizing a vast series of experiments from past and present members of the team is out. A great way to end this year.

www.nature.com/articles/s41...

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2 months ago

Two nerve nets are formed in Hydra vulgaris: the endodermal (cyan) and the ectodermal (purple) net. (B) Intraepithelial neurons are randomly scattered between the epithelial cells of the two germ layers. (C) Two types of connections have been found between Hydra’s neurons. (D) Endodermal neurons are in physical touch with each other by forming neural handshakes by digiform endings, which get intertwined. (E) In other places, clusters of vesicles of different types can be released to mediate volume transmission between neurons and between neurons and other cells.

Our dispatch:

https://www.sciencedirect.com/science/article/pii/S0960982225014691

on the recent Hydra volume EM paper by Zhang, Rafa Yuste and colleagues:

#connectomics, without synapses

https://www.sciencedirect.com/science/article/pii/S0960982225013090

#neuroscience

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3 months ago

Ectopic head regeneration after nervous system ablation in a sea anemone Via genetic ablation of neurons, Mazloumi Gavgani et al. show that the nervous system is essential for defining axial polarity during whole-body regeneration in the sea anemone Nematostella vectensis.

Our paper on the role of neurons in Nematostella head regeneration is now out at @currentbiology.bsky.social Big thank you to all collaborators, it was a pleasure!

Ectopic head regeneration after nervous system ablation in a sea anemone: Current Biology www.cell.com/current-biol...

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3 months ago

Separation of the Early gastrula into oral and aboral halves shows that some neural cell tupes derive from aboral ectoderm, and others from i-cells

Drawing together findings from several projects over many years, we make a case that neural cell types in the Clytia larva have two embryological origins: i-cells and ectodermal.
bioRxiv 2025.11.17.688882; doi: doi.org/10.1101/2025...

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3 months ago

We are pleased to announce our next #SEBD2026 meeting! The meeting will take place in El Rompido, Huelva, from the 28th to the 30th of October 2026 #savethedate @cabd-upo-csic.bsky.social @isdb.bsky.social @gfeev.bsky.social @ijdb.bsky.social @devbiol.bsky.social @devdynamics.bsky.social

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5 months ago

Staufen2 modulates the temporal dynamics of human neurogenesis in vitro RNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly u...

🚨New preprint from the lab! This work led by @akshayjg.bsky.social & @smfernandezmoya.bsky.social shows how the RNA binding protein STAU2 regulates the timing of neurogenesis in iPSC-derived human cells
www.biorxiv.org/content/10.1...

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7 months ago

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...

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8 months ago

Decoding cnidarian cell type gene regulation Animal cell types are defined by differential access to genomic information, a process orchestrated by the combinatorial activity of transcription factors that bind to cis -regulatory elements (CREs) to control gene expression. However, the regulatory logic and specific gene networks that define cell identities remain poorly resolved across the animal tree of life. As early-branching metazoans, cnidarians can offer insights into the early evolution of cell type-specific genome regulation. Here, we profiled chromatin accessibility in 60,000 cells from whole adults and gastrula-stage embryos of the sea anemone Nematostella vectensis. We identified 112,728 CREs and quantified their activity across cell types, revealing pervasive combinatorial enhancer usage and distinct promoter architectures. To decode the underlying regulatory grammar, we trained sequence-based models predicting CRE accessibility and used these models to infer ontogenetic relationships among cell types. By integrating sequence motifs, transcription factor expression, and CRE accessibility, we systematically reconstructed the gene regulatory networks that define cnidarian cell types. Our results reveal the regulatory complexity underlying cell differentiation in a morphologically simple animal and highlight conserved principles in animal gene regulation. This work provides a foundation for comparative regulatory genomics to understand the evolutionary emergence of animal cell type diversity. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, ERC-StG 851647 Ministerio de Ciencia e Innovación, https://ror.org/05r0vyz12, PID2021-124757NB-I00, FPI Severo Ochoa PhD fellowship European Union, https://ror.org/019w4f821, Marie Skłodowska-Curie INTREPiD co-fund agreement 75442, Marie Skłodowska-Curie grant agreement 101031767

I am very happy to have posted my first bioRxiv preprint. A long time in the making - and still adding a few final touches to it - but we're excited to finally have it out there in the wild:
www.biorxiv.org/content/10.1...
Read below for a few highlights...

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