Arnau Sebé-Pedrós

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Our lab opens 2 PhD positions to investigate fungi's evolution: #Barcelona

Wet lab in Biochemistry/Structural Biology of cryo-tolerant fungi
www.upf.edu/documents/d/...

Computational in Physical Chemistry of cellular processes under extrem environments
www.upf.edu/documents/d/...

📣 Please spread: we’re hiring a Lab Manager! It is a critical position in our new lab. As our lab moves to Barcelona and joins the @crg.eu, we’re looking for a Lab Manager to help build the lab and set the lab atmosphere.
🔗 Apply here 👉 recruitment.crg.eu/content/jobs...

Epimutations: raw material for evolution? - The EMBO Journal Epigenetics is fundamental to cell differentiation as it enables cells with identical genomes to adopt distinct fates. Some epigenetic information can also be transmitted between generations, in a pro...

Need a bit of escapism? Not exactly Lord of the Rings, but in similar vein:
doi.org/10.1038/s443...

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

Un viaggio all’origine dei sistemi nervosi Il nuovo progetto GRNevo, finanziato con un grant FIS-3 Advanced da 1,9 milioni di euro, studierà come si formano i neuroni durante lo sviluppo in specie animali molto distanti tra loro: dal moscerino...

Thrilled to share that I’ve been awarded a FIS-3 Advanced Grant (ERC-inspired) to study the evolution of neurogenic GRNs.
Recruiting soon: 4 postdocs + 3 PhDs
Press release in Italian — to decolonise scientific language 😄
magazine.unibo.it/it/articoli/...
Email me if interested in joining the lab

Bravo Roberto! what a great way to start your new lab back in Italy.

Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history Sponges have a cryptic Ediacaran history because ancestral sponges were soft-bodied and had low fossilization potential.

Our latest: Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history, led by @meleonora-rossi.bsky.social with help from friends @bristolpalaeo.bsky.social including @anariesgo.bsky.social @evopalaeo.bsky.social Davide Pisani and many others

Looks super interesting. Congrats Nikos and team!

I am very happy (and a bit scared) to present to you what we have been working on over the last 4 years. This manuscript is exactly what I dreamt of when I started the lab and I could not be happier and prouder of the outcome!

Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes Nature Ecology & Evolution - Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms...

Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l

Open Senior Bioinformatician position at
@sangerinstitute.bsky.social
Tree of Life, to work on the Biodiversity Cell Atlas initiative with @marakat.bsky.social and me.

📅 Apply by January 18
🔗 sanger.wd103.myworkdayjobs.com/en-US/Wellco...

Please share with anyone who might be interested!

Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty

🚨🚨🚨

We're looking for a research tech to work on alt splicing, pancreatic islets and diabetes. The goal is to set a high-throughput platform to investigate the role of alternative exons in beta cell biology!

Interested in joining our lab at @melisupf.bsky.social? 👇

www.upf.edu/documents/d/...

The exciting next question is what these regulatory sequences can tell us about the evolution of cell types across species. We’ll be working on this in the coming years.

This is similar to what @tschopplab.bsky.social recently reported for skeletogenic cells in vertebrates. These approaches can be particularly useful to study cell type ontogenetic relationships in non-genetically tractable species and without access to dev stages.
www.nature.com/articles/s41...

We observed that while gene activity groups cell type functionally, whereas CREs and regulatory seqs group them ontogenetically. E.g. mesenteric and tentacle retractor muscles, a dev convergence described by @alisongcole.bsky.social and @ulrichtechnau.bsky.social.

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

With this TF-motif collection, we defined important TF in every cell type (expressed and with high motif accessibility) and we predicted TF-CRE regulatory links. In the example, the predicted cnidocyte GRN.

A major challenge was inferring TF binding motifs. We first derived multispecies motif archetypes from known and de novo motifs, then assigned archetypes to TFs by combining phylogenetic analysis (@zolotarg.bsky.social) with correlations between TF expression and motif accessibility.

Then, we used different sequence models to predict CRE activty. With the crucial help of @steinaerts.bsky.social and @lukasmahieu.bsky.social, who introduced us to the world of DL sequence models. In this example, top motif grammars defining cnidocyte CREs:

We map cell type-specific accessible regulatory landscapes in adult and gastrula stages, identifying over 112,000 candidate cis-regulatory elements (CREs), representing different types of promoters and non-promoter elements.

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...

Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social.

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

Evolutionary cell biology comes of age Summary: This Perspective discusses how the discipline of evolutionary cell biology, by integrating evolutionary theory, comparative physiology and modern molecular approaches, works to understand how...

Thanks @jcellsci.bsky.social for this opportunity to contribute to your centenary collection with our take on the state of the field - 10 years after its modern reincarnation 🧪🌍

W/ @alebenoit.bsky.social @eelcotromer.bsky.social @fritzlaylin.bsky.social

journals.biologists.com/jcs/article/...

Multistep genomics on single cells and live cultures in subnanoliter capsules Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, inclu...

@science.org Multistep genomics on single cells and live cultures in subnanoliter capsules | Science www.science.org/doi/10.1126/...

Point of no returns: researchers are crossing a threshold in the fight for funding With so little money to go round, the costs of competing for grants can exceed what the grants are worth. When that happens, nobody wins.

"How can funders avoid crossing the Szilard point?"

The Szilard point is "the threshold at which the total cost of competing for a grant equals (or surpasses) the value of the available funding."

Bravo @dudinlab.bsky.social!

Microbial eukaryotes keep challenging assumptions about eukaryotic cell and genome biology.

Our upcoming workshop explores the frontier of protist genomics and how it shapes cell biology, ecology and evolution.

Please save the date! Talks, posters and ECR events

Websites and details coming soon

It is amazing that @dudinlab.bsky.social beautiful #ExM composition has been selected to highlight our #6mA work for the cover of @natgenet.nature.com. #Protists (and ichthyosporeans in particular) in the cover of NG must be quite unique!

Everybody ready for #EMBOevoChromo25 ?
I, for one, cannot wait. It's like scientific Christmas come early :)

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution - Nature The Biodiversity Cell Atlas aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life, which will be phylogenetically informed, rely on high-quality genomes and use...

please share this postdoc job alert! come join the budding Biodiversity Cell Atlas initiative as a postdoc or senior postdoc at @sangerinstitute.bsky.social working closely with @arnausebe.bsky.social and me to make progress on what we cover in this paper www.nature.com/articles/s41...