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Levayer Lab

@levayerr.bsky.social
3.5K followers 503 following 249 posts

Epithelial cell death, cell extrusion, self-organisation, mechanotransduction and many other things

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Jean Léon Maître @maitrejl.bsky.social · 06/10/2026
📣Our department is hiring a new group leader!📣 Want to start your team in a vibrant scientific environment in the center of Paris? I was very lucky to do that 10 years ago, reach out if you have any question. Apply by December 18th: jpi-recruitment-curie-umr3215-u934.curie.fr
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Reposted by Levayer Lab
Jean-Yves Tinevez @jytinevez.bsky.social · 05/10/2026
We have a position open in our core facility in the @pasteur.fr . Please share it and / or apply! forum.image.sc/t/research-e...
forum.image.sc
Research engineer in Bioimage Analysis. Institut Pasteur, Image Analysis Hub - 2026
Dear all Below is an announcement for a permanent position as a Research Engineer in the Institut Pasteur, Paris. There is a flyer attached at the bottom. We are looking ideally for a Bioimage An...
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Levayer Lab @levayerr.bsky.social · 30/09/2026
Maybe the recurrent funding model will become popular again (combined with reccurent evaluation).... There could also be an engagement that if you get the grant, you'll have to "prescore" presubmissions falling in your expertise the year after (but this generates "self-similar" bias/club like bias)
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Levayer Lab @levayerr.bsky.social · 30/09/2026
Nothing indeed ! It is actually a real plan B...(and I hope we still have time before teachers get replaced by chatbot...)
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Levayer Lab @levayerr.bsky.social · 29/09/2026
The first step of evaluation is probably the main issue, but would prefer a millions times recruiting more man power rather than delegating this to LLM (+ strong neg. incentive for clear IA generated application). I am fine with bad english if this is something coming from a real person...!
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Levayer Lab @levayerr.bsky.social · 29/09/2026
Not sure how the community will be consulted, but if so this will be really critical and time to be vocal...delegating our peer judgement (admittedly imperfect) to LLM feels like removing the cornerstone of how science works. If this is the way it goes, I'd rather become a teacher or bake bread🤷‍♂️
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Levayer Lab @levayerr.bsky.social · 29/09/2026
I am all for it as well. But there is a real issue of man power to make the first bin classification if the current exponential increase of grant applications keeps going (see the Marie Curie for instance). I don't know what is the easiest solution here to be honnest
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Levayer Lab @levayerr.bsky.social · 28/09/2026
To be honnest, I would almost find it more acceptable to have a real random decision process as it was partially implemented in the SNF. At least, the "random" triage does not generate wrong incentive impacting the way you write a grant proposal and does not trigger such loop...
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Levayer Lab @levayerr.bsky.social · 28/09/2026
Here it is...by delegating decision to non transparent AI models we generate an incentive for grant applicants to use AI writing to tweak system and the vicious/absurd feedback loop is set (which all started by an overload of grant application driven by AI writing). www.science.org/content/arti...
science.org
U.K. funder uses ‘AI triage’ to reject grant proposals—leaving researchers dismayed
The AI-based assessment, which wasn’t explicitly described in the funding call, has raised privacy and fairness concerns
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John Stott @jpsastro.bsky.social · 24/09/2026
Had a UKRI funded grant proposal rejected at the "AI triage stage". "This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review." 🧪 #academicsky
I am writing to let you know that, unfortunately, your application was not successful.

Review process

As part of the initial triage of the 179 proposals submitted to this call, each was assessed using an AI-based review. Every proposal was read independently by several different AI models against the same seven criteria used to shape this call (including cyber security relevance, research quality and novelty, importance of the problem addressed, feasibility of the project plan, likely outputs and impact, value for money, and responsible research practice), with each model asked to give a score and a written justification with supporting quotations from the text. To guard against any one model's idiosyncrasies, we also ran a second, independent process in which different AI models debated the merits and weaknesses of each proposal before reaching a judgement, again against the same criteria. Scores from both processes were combined to produce an overall ranking. 

This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review.  Projects selected for funding were drawn from those that progressed to the full human review stage. We recognise that AI-assisted assessment is a new and evolving part of the review process, and we are continuing to evaluate how well it aligns with the judgements of human reviewers on this call. We will soon produce a document detailing our method, so that others can build upon it and improve it.

Feedback on your application

Your application was not selected to progress beyond the AI triage stage.  To provide transparency on the outcome of this assessment, we are sharing below the scores (out of 5) from each of the two AI review processes described above, together with the mean score across the two processes.
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Reposted by Levayer Lab
Marion Baraban @marionbaraban.bsky.social · 24/09/2026
A funded postdoctoral position is available at the IBPS, Sorbonne University/CNRS/INSERM in Paris, to investigate the formation of the olfactory organ in zebrafish. We are looking for an postdoctoral researcher with expertise in transcriptomics and bioinformatics, (scRNAseq analysis).
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Levayer Lab @levayerr.bsky.social · 24/09/2026
Only one week left to apply ! Check below for more details but the course will be great. Please spread the word 🙏
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Levayer Lab @levayerr.bsky.social · 24/09/2026
well by "obvious" I meant a single pathway/regulators whose depletion completly block this memory effect. We tried know pathways than can be modulated by caspases and feedback on cell death mostly. Nothing noticable for Diap1 which would be downstream of Yki but can't exclude more subtle PTM indeed
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Levayer Lab @levayerr.bsky.social · 24/09/2026
Yes it seems so but the integral from the past only matters of there is caspase activity in the "present".
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Levayer Lab @levayerr.bsky.social · 23/09/2026
A big thanks for the essential support provided by @erc.europa.eu, la ligue contre le caner and @pasteur.fr !
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Levayer Lab @levayerr.bsky.social · 23/09/2026
This work was a pretty long process initiated at the end of @avillars.bsky.social PhD and taken over by @tomcumming.bsky.social with the essential contribution of Andela Davidovic. It is a small step, but it helps to get closer to a "predictive" understanding of cell death in vivo.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Most likely this could be based on partial cleavage of numerous substrates affecting the susceptibility to extrusion and where timescale is defined by protein turnover (but this still remains to be proven).
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Levayer Lab @levayerr.bsky.social · 23/09/2026
You may wonder how this "memory" is molecularly encoded ? Well...we do as well and despite trying many candidates (that you will find in the big supp fig. Supp 5 and 6) we could not find anything obvious.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Overall, this revealed complex business taking place downstream of terminal caspase activation. There is a lot of heterogeneity between cells that encompass temporal information and relative information between neighbours.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Can we now use it to "bias" apoptosis ? We performed a very mild activation of optocaspase in clones and let them develop. Cells in the clones were 3x more likely to die compared to neighbouring cells, suggesting that this previous priming sensitise them to "later" developmental caspase activation.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
So can we predict who among neighbours will be the first ? Using time serie forest (machine learning adapted to use temporal features) we could predict in close to 80% of the case who will the first using relative present and past caspase activity among neighbours
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Can we now also better predict the physiological death ? We previously found a negative feedback where the first extruding cell blocks apoptosis in the direct neighbours through ERK activation. This implies that cell death decision is not fully autonomous and is about who is the "fastest" to die.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
This also explains a good deal of cell to cell heterogeneity. Accordingly, the cells that are more likely to die upon a pulse of optogenetic caspases are the one that were already exposed in the past.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Can we go back to the previous experiment and explain the heterogeneity we observed ? Actually the domain of high sensitivity revealed by the global pulse of caspase are mostly explained by the history of cells. Doing the same expt. after "erasing" past caspase removed most of the spatial bias.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
In other words, cells already exposed to caspase in the last 3-5 hours die at lower caspase activity. We used again the optogenetic caspase to validate this prediction using pulses of activation separated in time comparing contralateral regions exposed 1 or 2 times and confirming the "priming"
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Levayer Lab @levayerr.bsky.social · 23/09/2026
So what explains then this heterogeneity ? We looked systematically at geometrical/signaling/spatial features that may correlate with the caspase activity at which cells engage in apoptosis. The correlation matrix you see below outlines a clear neg. correlation with past caspase activation.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Not only we found cell to cell differences, but also global spatial pattern of caspase sensitivity. Using an optogenetic caspase that we previously developed (optoDronc) and doing mild global activation revealed zones much more sensitive to caspases.
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Levayer Lab @levayerr.bsky.social · 23/09/2026
We checked this in the Drosophila pupal notum segmenting ~20,000 cells and checking systematically at which caspase activity cells engage in cell extrusion and cell death. Using the "derivative" of the GC3Ai caspase sensor was quite predictive but revealed a large heterogeneity of thresholds
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Works over the past decades outlined numerous non-apoptotic functions of caspases, and the large proportion of cells surviving to effector caspase activation during development. But what makes the difference between a surviving and dying cell ? Maybe a simple threshold ?
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Not every cell react the same way to caspase activation. In our recent study (led by @tomcumming.bsky.social and initiated by @avillars.bsky.social ), we tried to better understand what explains this difference and outlined a role of past caspase exposure 👇 www.nature.com/articles/s41...
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Marco MILAN LAB @milanlab.bsky.social · 16/09/2026
Milan Lab is recruiting a new PhD student. Deadline: October 30th. Please, spread the news. www.irbbarcelona.org/en/careers/y...
irbbarcelona.org
IRB Barcelona International PhD Fellowships - Extraordinary call 2026
The following will be offered in this call:Up to 8 FPI positions associated with the “Proyectos de Generación de Conocimiento 2025” Call (funded by the Agencia Estatal de Investigación AEI- MICINN).Ch...
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Terence Tao @teorth.bsky.social · 11/09/2026
A group of 25 Fields Medalists, including myself, have made a joint declaration on Math and AI: mathandai.org . We welcome additional signatories. See also this article in the Economist announcing the declaration: www.economist.com/science-and-...
mathandai.org
Declaration — Math and AI
Read the declaration and add your name.
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Levayer Lab @levayerr.bsky.social · 11/09/2026
I see a huge problem with interoperability and long term coconstruction. If everyone develop from scratch their own pipeline using existing one, who will make the new common "bricks" used by these agents (specially if no one is trained anymore) ? No more long term envt construction=empoverishment!
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Prisca Liberali @priscaliberali.bsky.social · 08/09/2026
What if we stop asking only how cells build tissues and ask how tissues shape cells? That’s what we’ll explore at Modelling Life from Tissues to Cells 🇨🇭 lakeconferences.org/conf/8334d9b...
lakeconferences.org
Conference - Modelling Life from Tissues to Cells: Coordination and Robustness - Lake Conferences
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Levayer Lab @levayerr.bsky.social · 08/09/2026
Institut Curie, Paris, symposium: Where Form Takes Shape October 27-28th 2026 (after the yearly International Developmental Biology course) Registration before October 10th (for free !): docs.google.com/forms/d/e/1F... There will be short talks and posters selected from abstracts.
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Levayer Lab @levayerr.bsky.social · 04/09/2026
Deadline is approaching very fast (end of september). Don't hesitate to spread the word 🙏.
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Levayer Lab @levayerr.bsky.social · 04/09/2026
📢master or PhD student interested in cell biology ? There are spots left for the Molecular Biology of the Cell course @pasteur.fr. Check the amazing list of lecturers + 1 week practical pocking choano cytokeleton with @thibautbrunet.bsky.social team. Registration 👇 www.pasteur.fr/fr/nous-conn...
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Development @dev-journal.bsky.social · 04/09/2026
The role of geometry in morphogenesis Read this Review from our special issue #DevSIextracellular by Ryan Harrison, Olivier Hamant and @timesaunders.bsky.social. journals.biologists.com/dev/article/...
Role of geometry in shaping tissues. Multiple factors, including cell shape (top left), boundary constraints (top right), topological inputs (bottom left) including from different cell alignment defects (±1/2) and biophysical factors (bottom right) impact how the final tissue form emerges (centre). Centre shows images of a 48 h neuruloid (left; magenta, DAPI; green, actin) and a young Arabidopsis flower (right) treated with oryzalin (depolymerised microtubules) thus showing isotropic growth, but no defect in patterning (organs are still initiated in the right position).
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Levayer Lab @levayerr.bsky.social · 03/09/2026
The last version of our EpiCure tool is now out in @dev-journal.bsky.social, a user friendly Napari plugin for epithelial segmentation curation. A bit thanks to @gaellel.bsky.social for carrying all along this joint department effort (check the details below). Feel free to use it and expand it !
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Thibaut Brunet @thibautbrunet.bsky.social · 02/09/2026
🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️
biorxiv.org
Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals
Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...
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Levayer Lab @levayerr.bsky.social · 01/09/2026
Amazing ! Good luck for this new adventure.
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Cells & Development @cellsdev.bsky.social · 28/08/2026
A very intriguing story by Joao F. Botelho et al shows that in bird, the digit formation (their ✋) is not only governed by apoptosis but also due to changes in the rate of growth extension and cell division between the interdigital zone and the digital zone. So cool! #devbio doi.org/10.1016/j.cd...
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Levayer Lab @levayerr.bsky.social · 28/08/2026
I guess that's where I should include the link of the meeting report now that it is out 🙂 (very nice thread by the way) : journals.biologists.com/jcs/article/...
journals.biologists.com
Meeting report – CellExIt#1, the first international symposium on cell extrusion
Summary: The CellExIt#1 symposium gathered for the first time investigators working on cell extrusion. This report offers a panoramic view of the research teams and ongoing projects of the field.
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Carolina Rezaval @crezaval.bsky.social · 26/08/2026
We’re recruiting postdocs to join our @wellcometrust.bsky.social , Decoding Competition in the Brain. How does the brain resolve competing needs and prioritise behaviour? 📅 New deadline: 15 September 🔗 Apply: rezavallab.org Please share!
rezavallab.org
Home
​ ​Animals must make crucial behavioural choices on a minute by minute basis to survive in a changing environment. A long-standing enigma is, how are alternative options evaluated in the brain...
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Kate Cavanaugh @katecavanaugh.bsky.social · 25/08/2026
🧵 What if one reason fertility declines with age isn’t just genetic-but mechanical? Thrilled to share our new paper in @NatureCellBio : Elevated contractility drives implantation failure in mouse embryos from aged females… here’s what we found 👇 www.nature.com/articles/s41... 1/11
nature.com
Elevated contractility drives implantation failure in mouse embryos from aged females - Nature Cell Biology
Cavanaugh et al. show that embryos from aged mice have increased contractility and tissue viscosity on embryonic day 4.5, which leads to poor spreading and attachment. Similar age-associated mechanica...
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Delarue Research @delarueresearch.bsky.social · 25/08/2026
Please save the date: The Microphysio Conference is back and will be held in Cargèse from April 25th to April 30th! With a great lineup of speakers, it’s an excellent opportunity to exchange ideas in fields related to organ-on-chip, organoids, bioprinting, mechanobiology, and much more! Stay tuned.
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Stefano Di Talia @ditalialab.bsky.social · 24/08/2026
Happy to see Ashley's paper out @natphys.nature.com www.nature.com/articles/s41...
nature.com
Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration
Nature Physics - Zebrafish can regenerate amputated fins back to their original size. It is now shown that gradients in extracellular signal-regulated kinase activity act as rulers during fin bone...
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FlyBase @flybase.bsky.social · 20/08/2026
Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...
nature.com
Treat biological databases as infrastructure, not projects
Letter to the Editor
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Levayer Lab @levayerr.bsky.social · 20/08/2026
So cells do count eventually (still need to check the details but the abstract sounds very appealing) www.nature.com/articles/s41...
nature.com
Intestinal stem cells count self-renewal divisions to switch multipotency - Nature
In Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing ...
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Levayer Lab @levayerr.bsky.social · 20/08/2026
This 👇, and Europe should also have more scheme to finance those essential "infrastructures" (rathen than implementing 10 millions single person grant...) www.nature.com/articles/d41...
nature.com
Treat biological databases as infrastructure, not projects
Letter to the Editor
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