Alberto Perez-Posada

Congratulations, amazing work! I remember when you explained to me the TF/motif strategy in the Sevilla meeting. I'm happy it worked well!

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...

A single-cell ATACseq atlas of our favourite sea anemone, Nematostella vectensis! By @aelek.bsky.social @martaig.bsky.social

Congratulations to the new PhD at #CABD: Marta Moreno Oñate!

Dr. Moreno did an amazing job explaining the projects of her PhD work! Marta's thesis was done with @pablodeolavide.upo.es’s PhD program and was co-supervised by @martinfranke.bsky.social and Juan Tena!

I am very proud of you, Marta. You did outstanding work in the lab, and your defence was spotless. I am also very happy to now know an expert in gene compensation between paralogous genes!

Decoding cnidarian cell type gene regulation https://www.biorxiv.org/content/10.1101/2025.07.01.662323v1

And, if it turns out these long computation times are not due to lack of parallelisation, then there is something very strange going on that should be investigated. Functions like FindVariableFeatures, ScaleData, and others, are now reported to take several hours for 10K~30K cells datasets.

What is the current status of parallelisation support in Seurat? It was dropped last year with v5 and so far nothing has changed. It is not good that multiple people are reporting very slow runtimes (myself included).
github.com/satijalab/se...
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Proud to present the peer-reviewed version of our Cell Type Allometry paper, out today in Science Advances!

www.science.org/doi/10.1126/...

Are animals of different sizes made of the same cell types?

Here’s an update of the main points and revision items

(with memes!)

Thread 👇🧵

Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...

I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...

Lungfish xkcd.com/3064

Y'all so excited to build this world lol

Oxford historian faces deportation from UK after doing research on India … in India Home Office told Manikarnika Dutta to quit Britain for spending too many days abroad for study

This. A thousand times this.

"If the UK genuinely seeks to position itself as a global leader in academia and innovation, it must foster an environment that is welcoming to top talent."

A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...

🚨 New paper alert! 🚨

A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...

A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation Spermatogenesis is the biological process by which male sperm cells (spermatozoa) are produced in the testes. Beyond facilitating the transmission of genetic information, spermatogenesis also provides...

Ever wondered how sperm are formed? Spermatogenesis is a microscopic marathon that starts in the testes and ends with fully functional sperm! Our new preprint bitly.cx/jC4Qg takes a deep dive into zebrafish spermatogenesis, mapping out every fascinating step. 🧵👇 1/7

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

23/46 This contrasts with the view that polyploidy is unstable and transient, and shows that sustained environmental selection can maintain polyploidy, even without evolving genome-stabilizing mutations.

Small, perky snail with head poking out between its two shells. The snail has a pair of long, tubular tentacles. The shells are like clam shells, except they are vivid green. The hinge is at the top. Julia exquisita: Kwajalein Atoll, Marshall Islands. © uwkwaj CC BY-NC https://www.inaturalist.org/photos/166680082

In this photo, the snail is lying on its side with the hinge of the two shells pointing towards the camera. The shell and snail are both very bright green. The snail has white blotches on its back. Julia exquisita: Kwajalein Atoll, Marshall Islands. © uwkwaj CC BY-NC https://www.inaturalist.org/photos/263219540

We’ve looked at snails with one shell and slugs with no shells. Now let’s have a look at a snail with two shells, because Nature laughs at our puny attempts to pigeonhole.

In today’s #AtoZ – J is for Julia (Juliidae) (1/9)

Pic: © uwkwaj CC BY-NC

The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality - Nature Communications Here they generate a cell type atlas of the colonial cnidarian Hydractinia symbiolongicarpus, which reveals that distinct colony parts are mostly made from unique combinations of shared cell types, an...

Happy to present the peer-reviewed version of our Hydractinia Cell Atlas paper out today in Nature Communications! As I presented this back when we were in “that other” social network, let me recap the basic findings and revision items in this thread:

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

The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality - Nature Communications Here they generate a cell type atlas of the colonial cnidarian Hydractinia symbiolongicarpus, which reveals that distinct colony parts are mostly made from unique combinations of shared cell types, an...

Very glad of having been part of this fantastic collaboration now available at Nature Communications! congrats especially to @hrhorkan.bsky.social and @drsalamander.bsky.social !! www.nature.com/articles/s41...

AI-driven automated discovery tools reveal diverse behavioral competencies of biological networks A novel methodology, using diversity search AI algorithms, for exploring the space of possible behaviors of gene regulatory networks, from the perspective of generic problem-solving agents navigating ...

The version of record is out in eLIFE - elifesciences.org/articles/92683 - the hard work of Mayalen Etcheverry, Clement Moulin-Frier, and
@pyoudeyer.bsky.social as we try to develop tools to characterize the behavior space of gene-regulatory networks (and pathways more broadly)

This will be a wonderful conference - come discuss the origin of metazoans and enjoy fruits de mer with us in Roscoff!

Scientists need more time to think

Good piece by @natureportfolio.bsky.social. The erosion of thinking time—driven by admin, bureaucracy, industry agendas, and unrealistic output targets—stifles curiosity-led science. These pressures undermine innovation and the intellectual freedom vital for real progress. 🧪🌱🌍 #ScienceIsNotBusiness

congratulations Omaya! Well deserved!

🍾Our small #UExM adventure is only starting! #ProtistsOnSky

We are happy to announce that the Moore Foundation will be funding our efforts in creating an Expansion Microscopy atlas of #Microbial #Eukaryotes with @gautamdey.bsky.social @UNIGE
@embl.org

LINK: www.unige.ch/sciences/chi...

1/4

Also I'm happy I finally managed to download what for a while was the only dataset of cell cycle gene expression in mouse (fibroblasts), from back in 2001. This had been previously inaccessible but I guess there's now a copy in archive.org?

The 2019 version of me is happy and can finally rest.

Re-reading the introduction of my PhD thesis, which I defended 5 years ago (time flies...). Trying to find some inspiration for writing new proposals, and I'm surprised why I never bothered to submit it as a bibliographical review somewhere.

... I might do it at some point I think.

I think most of it is inhabiting the data.. if you are really trying to get a full understanding of a mechanism, then every piece of data either fits or doesn't fit.. it's always trying to live inside the data and use it to test the structure. – Ellen Rothenberg

The intrinsic dimension of gene expression during cell differentiation Waddington’s epigenetic landscape has long served as a conceptual framework for understanding cell fate decisions. The landscape’s geometry encodes the molecular mechanisms that guide the gene express...

"[...]pluripotent cells as cells in a “high-temperature” state. In fact, they should be able to freely navigate the landscape, only to become progressively con strained into a specific valley when they commit to a differentiation path. [...]"

www.biorxiv.org/content/10.1...