I am deeply honoured to have been recognized by the European Research Council with a #StartingGrant. @erc.europa.eu With this support, my team and I will launch #MOVIOLA. Our goal is to understand how human neural progenitors decide their fate during brain development.

uMAIA offers an analytical framework designed to enable construction of high-resolution metabolic atlases using mass spec imaging data. @gioelelamanno.bsky.social www.nature.com/articles/s41...

Excited to share #uMAIA, our method to create 4D lipidomic atlases, now published in @natmethods.nature.com We demonstrate that with uMAIA, the field is ready for atlas-level analyses capable of uncovering histological metabolic heterogeneity in both space and time. [1/2]

And he made it again!...tour the force from JIa-Wei´s Wang lab using comparative sc-transcriptomes, and developing new analytical tools, to tackle evolutionary trajectories of plant cell types!. Amazing work as usual! www.cell.com/cell/abstrac...

A little over two weeks to the deadline! 20 positions, generous startup funding, a great community and fantastic infrastructure. Come join us!

Join us at the FENS Single-Cell & Spatial Omics Winter School with: @sarabiz86.bsky.social @rongfan8.bsky.social @gokcegroup.bsky.social @gioelelamanno.bsky.social @sj-marzi.bsky.social @jplopez-atalaya.bsky.social Ana Falcão Florian Rosenberger Gabriel Baró Bosiljka Tasic Barbara Treutlein

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social www.nature.com/articles/s41...

Hey, it's out! doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

Wowee! Super-resolution stimulated X-ray Raman spectroscopy | Nature share.google/Mdn4Z0ddIy2t...

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab. www.biorxiv.org/content/10.1... 1/

I love the idea of "micropublications" www.micropublication.org (preparing one now)

Super thrilled to give a full day #DeepLabCut Workshop in Okinawa today! We had a packed house and everyone got models trained 🚀 - even then used #CEBRA 🦓 and/or #DLC2Action on the outputs! Thank you #OIST for hosting us!! 🥳

A major step forward in organoid technology–producing liver tissue that grows its own internal blood vessels #TakebeLab @cincyresearch.bsky.social @natbiomedeng.nature.com scienceblog.cincinnatichildrens.org/liver-organo... www.nature.com/articles/s41...

There is absolutely no reason to think that such models are actually learning biology. So maximizing the perturbation prediction objective does not necessarily result in a "virtual cell". 3/

A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)

Call from 6 Swiss Fields Medal laureates to preserve science funding science-under-threat.com

Almost all Nobel Prizes are awarded for work that is exploratory, or absolutely basic science with no obvious commercial or medical benefit. You cannot predict where advancements come from, so you have to invest in science and scientists. Targeted (corporate) science investment will never do this.

Check out our Spotiflow to accurately identify any spot-like objects (and more)! First output of an amazing colaboration experience with @maweigert.bsky.social

Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com! Since the pre-print, we have added many features, notably native 3D detection! @maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social Paper: rdcu.be/epIB7 (1/N)

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social www.nature.com/articles/s41... rdcu.be/epIB7

Another case showing we must be wary of Gell-Mann amnesia in evaluating molecular bio applications of AI. rachel.fast.ai/posts/2025-0...

The special thing about US labs and science was the huge amount of funding available for labs, top-notch infrastructure, & lab work culture. The scientists themselves came from a global pool, incl. Europe. Bringing the best scientists from US to the comparatively underfunded European academic…1/n

I’ve just spent a few days in Barcelona and the ALBA #synchrotron, where I’ve been imaging, studying and admiring complex structures of many sorts. I haven’t been this excited about a project in a very very long time! 🤩 🧠 🪰🔬🧪 #neuroskyence

Since we are still talking about interactions, I worked with some ecologists a couple of years ago on measurement scale, interactions and interpretation issues. I think some problems arise from failure to distinguish prediction from inference, a chronic problem in ecology imo doi.org/10.1111/brv....

🧠 Few spots left! Join us at Neuromics Approaches in Development and Disease, June 24–25 @EPFL. @graeffjohannes.bsky.social @gioelelamanno.bsky.social @sebastianwaszak.bsky.social ⏳ Register by May 31! 👉 www.epfl.ch/schools/sv/b... #BMISymposium2025 #Neuroscience #Genomics #EPFL

Join us this summer for the Neuromics Symposium, a truly exciting international lineup. Only few spots left!

It was fun to learn about blood vessel organoids together with @marinanikolova.bsky.social and Barbara Treutlein! Thanks to Reiner Wimmer and @penningerlab.bsky.social for introducing us to this system! www.cell.com/cell/fulltex... Great support from editors and reviewers @cellpress.bsky.social!

The common argument is that we are the "GPT2" stage of these models. If so maybe we shouldn't pretend they are GPT10 stage in the papers & social media posts. Honest, self-critical accounts of science in papers & scicomm is essential for rapid progress.

As a candidate last year, Trump promised “to unleash the power of American innovation” to super-charge U.S. scientific research.
 He’s instead unleashed cuts and chaos, researchers and scientists warn. Our look at the abrupt changes — and the consequences. With @dtkeating.bsky.social

The success of LLMs has inspired their extension to genomics data. A preprints reports that such models lack understanding of genomics and provide minimal utility, even for basic tasks such as sequence classification. www.biorxiv.org/content/10.1...

"Simulate, Don't Label": My WashU colleagues have put out a new spatial omics tool that automatically maps anatomical regions samples. Cool example of training a model with synthetic data inspired by biophysics. www.biorxiv.org/content/10.1...

Yes, a couple of billion per year, out of which only 1/3rd goes to life science, is a very low figure Europe-wise. Compare to NIH's 47 billion... Of course there's a lot of country-specific funding, but I would love to see European funding for biomedical research match that in US.

35% increase in applications to the ERC consolidator grants. This is not sustainable and it will result in too low acceptance rates. The ERC budget needs to be drastically increased. erc.europa.eu/news-events/...

I started working on genetic therapies for Mendelian disease in 2000 - and in the subsequent 25 years have never seen a disease where the molecular aetiology has undergone as giant an "OH WOW" moment as this. www.cell.com/cell/fulltex...

Liu, ... Rouhanifard have optimized nuclear FISH to the point where it's now possible to sort cells based on transcript production. They sort cells into bins and measure chromatin state at the locus whose tx was sorted on. www.biorxiv.org/content/10.1...

RNA control of reverse transcription in a diversity-generating retroelement www.nature.com/articles/s41...

Trying to retrofit all types of scientific work into that ancient format is a horrible approach. One should write papers in formats and styles that are optimal for the type of scientific work that is being presented.

I am usually not fan of atlases… but this one is actually useful, as it demonstrates the value of protein-level measurements to identify functional cell states. #Brain #Development www.nature.com/articles/s41...

People: please don't ML for the sake of ML. I keep seeing manuscripts using fancy machine learning on brain-imaging data, where, in my opinion (having processed a lot of brain-imaging data), the method is way too complex for the richness of the data. Fancier is not better per se

Example of when a career opportunity is so great that I would want to be at an earlier career step to seize it! Amazing PI, amazing science, the right moment to apply is yesterday!

📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...

Will read with much interest as I am profoundly skeptical of this approach. Will be interested to see what is their goal but a cell is not just a bag of molecules. We are still learning what a cell is and how it works so, perhaps is a bit premature to try to simulate what we don't understand

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇 biorxiv.org/content/10.1101/2024.12.11.627935v1

Jian Shu, presenting GenVinci translating from and to modalities. Deep learning speaks the language of cells! Now live Jonhatan Sweedler, tracking the history of single cell MS to arrive to the most recent technologies his lab develops! So cool!

Peter Nemes talk was a blast! Metabolites can control developmental fates!

It really is terrific!

It is happening! Exciting start already with an field-highlights talk, and contributions from the HCA and HuBMAP consortium!

Single-cell and Spatial Metabolomics Online Day is Live youtube.com/live/9uM0ltT... via @YouTube, organized by @gioelelamanno.bsky.social at #EPFL See you there!

Last minute call !! Join us soon for the first Single-cell and spatial metabolomics online day! We have more than 700 registrations! Zoom, doors open 14.30 CET = 8.30 Boston, registration (mandatory) below. It's time for the program reveal! 1/4