Hello epithelia enthusiasts!

I’m @inesfournon.bsky.social and I study epithelial mechanics in sea anemones 🪼

Did you know epithelial cell extrusion had never been described outside bilaterian animals before? Well… not anymore 👀

Read ⬇️🧵1/9

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

Very happy to see this out. 👏 @yinanwan.bsky.social
Bogdan Bintu and team.
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

A poster in tones of blue with white text and pops of pink that reads: Michael Sars Symposium 2026 Living systems in a variable ocean In collaboration with the Computational Biology Unit, UiB June 4, 2026, Media City Bergen SPEAKERS Anne-Claude Gavin, Université de Genève Christian Jørgensen, Dept. of Biological Sciences, UiB Matthew Rockman, New York University Isabella Graf, EMBL Heidelberg Tom Michoel, Computational Biology Unit, UiB Anthony Mathelier, NCMBM, University of Oslo Susanna Röblitz, Computational Biology Unit, UiB Boris Lenhard, Imperial College London Jonas Brandenburg, Michael Sars Centre, UiB ORGANIZERS Lionel Christian, Michael Sars Centre, UiB Nathalie Reuter, Computational Biology Unit, UiB Below the text are the logos for the Michael Sars Centre, CBU, University of Bergen, EMBL with the mention 'Partners of', and the hashtag MSS2026

We are thrilled to announce that registration is now open for the Michael Sars Symposium 2026, co-organized with @cbubergen.bsky.social 🙌 Join us on June 4 in Bergen for a day of fantastic talks, with a focus on living systems in a variable ocean 🌊
🔗 tinyurl.com/joinMSS2026

Norway’s oil fund yielded NOK 2362 billions in 2025, enough to DOUBLE the current budget of Norwegian Research Council for the next 214 years. 🤷‍♂️
www.nbim.no/no/nyheter-o...

📡🧵 Excited to release an updated version of our preprint: Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis
🧪🧬🖥️🐠

doi.org/10.1101/2024...
A tour-de-force by @yangjoonkim with an unexpected discovery!

Here is the link to download the PDF of my course#5 on Biological computation. I present & discuss Self-tuning, Adaptation and Learning in biological (non-neuronal) systems, in particular during embryonic development.
This course contains various personal ideas/proposals.
tinyurl.com/hcpwsbtm

In this month's Creature Column, we feature the ascidian tunicate Ciona, a model for marine systems life sciences.

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

Thrilled to share the preprint from my PhD! 🥳 Where I characterised epithelial cell extrusion in a sea anemone
🔗 www.biorxiv.org/content/10.6...
Big thanks to my supervisor @prhsteinmetz.bsky.social and coauthors @noahbruderer.bsky.social @lionlchristiaen.bsky.social at🇳🇴 @msarscentre.bsky.social ⬇️🧵

Generative epigenetic landscapes map the topology and topography of cell fates | PNAS Epigenetic landscapes were proposed by Waddington as the central concept to describe cell fate dynamics in a locally low-dimensional space. In mode...

Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...

The tunicate Ciona - Nature Methods The ascidian tunicate Ciona, one of the closest relatives of the vertebrates, inhabits shallow temperate waters in the worldwide ocean. A unique combination of simple stereotyped embryogenesis, regula...

Very happy to see this piece on the Tunicate Ciona published. Grateful to @alexandrejan.bsky.social and @chiaracastelletti.bsky.social for the Illustrations, and to @natmethods.nature.com for the opportunity to showcase our ever emerging model organism www.nature.com/articles/s41...

Re-upping this with a Bluetorial in a shameless act of self-promotion. 1/n

» What is the macromolecular composition of the cell?Cell Biology by the Numbers Vignettes that reveal how numbers serve as a sixth sense to understanding our cells

Crowding more proteins per cytoplasm unit volume would hamper processes such as diffusion, which is already about ten fold slower inside the cell than in pure water.

Source: book.bionumbers.org/what-is-the-...

Intestinal villus cells extrude living, following a calcium pulse. Unlike from extruding apoptotic cells, Ca2+ messaging stops at the first neighbors! #FluorescenceFriday

Part of our TrepatLab preprint: www.biorxiv.org/content/10.1...

Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social

Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors | The EMBO Journal imageimageDuring development, multipotent cardiopharyngeal progenitors express both cardiac and pharyngeal muscle transcriptional programs. This study in the tunicate Ciona shows that cell cycle-regul...

Our latest on how cells get ready for fate transition! @noahbruderer.bsky.social @margauxfailla.bsky.social @lionlchristiaen.bsky.social

Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....

💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵
1/6 #iccv2025

Happy to share the last version of our story @currentbiology.bsky.social on the role of interfacial tension in mechanical cell competition led by @leovalon.bsky.social and Alexis Matamoro Vidal
www.sciencedirect.com/science/arti...

Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Emergence of cellular nematic order is a conserved feature of gastrulation in animal embryos - Nature Communications The morphogenetic events that occur during gastrulation involve dramatic cell- and tissue-level changes. Here they show that propagation of nematic order, leading to long-range spatial correlation, is...

Morphogenesis alert! A unifying physical principle links gastrulation in frogs, fish and flies! Stoked to be part of this new paper with Xin Li in Dave Thirumalai's lab and Robert Huebner in my group and a co-lab with @peiferlabunc.bsky.social and Margot Williams.
1/n

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

Introducing the Michael Sars Visitors Program The Michael Sars Centre is launching a Visitors Program designed to foster scientific exchange and collaborations across disciplines.

We are thrilled to announce the launch of the Michael Sars Visitors Program! ✨🧪 To spark new connections, we are opening our doors to visiting researchers who wish to conduct a project in #SunnyBergen. Applications are open, help us spread the word!

What a fantastic morning at #MSS2025 🤩 After an opening by BIO Dept. head @unibergen.bsky.social Ståle Ellingsen, three amazing talks by @lowelab.bsky.social, Georgia Rapti @embl.org and Camila Esguerra @ncmbm.bsky.social on System Evolution 👏

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse...

paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n

Conserved proteins link sensory input and metamorphosis in a marine chordate Anoctamins play a key role in sensory perception in mammals. A new article by the Chatzigeorgiou group reveals their dual role in perception and larval metamorphosis in the chordate Ciona.

📣 New article out in @cp-cellreports.bsky.social 🤩 Zonglai Liang and colleagues from the @mchatzigeorgiou.bsky.social group reveal a dual role for Anoctamins in sensory perception & metamorphosis in #Ciona larvae 🧪 Take a peek behind the scenes ⤵️

Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - Biohub SF) San Francisco, California, United States

🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍

job-boards.greenhouse.io/chanzuckerbe...

A man in a dark jumper stands similing in front of an audience in a seminar room. On a screen behind him, a slide that says 'optics' and 'biology', with a fluorescent microscopy image of a fish embryo, code, and a piece of equipment.

Loïc Royer @loicaroyer.bsky.social presented today the impressive work of his team @czbiohub.bsky.social in optical engineering and developing analysis tools to explore vertebrate development 🐟🧪 Thank you for an inspiring and visually stunning talk! 🤩

Picture of Loic Royer and Boah Bruderer in front of the first slide

We are in for a mindblowing treat today at @msarscentre.bsky.social with @loicaroyer.bsky.social from @czbiohub.bsky.social hosted by @noahbruderer.bsky.social for a seminar on “Building a virtual embryo, a single cell at a time”.

Now read Brave New World, mate it with the Orwellian distopia et voila: a beautiful 2025!

Graphical abstract of BioChatter

Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...

A poster in tones of blue and green. At the bottom, the logos of the Michael Sars Centre, University of Bergen, and EMBL with the mention "partner of" above. In the bottom right corner, the hashtag MSS2025. The following text is on the poster: Michael Sars Symposium 2025 Decoding signals and unveiling architectures, from molecules to organisms June 6, 2025, Media City Bergen Speakers: Georgia Rapti (EMBL Heidelberg) Ryan Hibbs (University of California San Diego) Ida Helene Steen (University of Bergen) Jingwei Xu (ETH Zürich) Ross Waller (University of Cambridge) Christopher Lowe (Stanford University) Yuhong Wang (Michael Sars Centre, University of Bergen) Ioannis Riziotis (The Francis Crick Institute, London/GSK) Paola Laurino (Okinawa Institute of Science and Technology)

We are excited to announce that registration for the Michael Sars Symposium 2025 is now open! 🤩 Join us on June 6th at Media City Bergen for a day of exceptional talks 🧪 #MSS2025
✨Learn more and register here: tinyurl.com/yc4jxdvz

Search is changing, using LLMs to reliably query your own data and public data bases will become the norm. Amongst other tools we use @langchain.bsky.social to drastically reduce hallucinations of LLMs.