jonas

Yeah, actually, why?

Yes yes I know. Most science has been hypey forever. But it's hyperaccelated now with this weird meld of academic science & startup culture + social media and highly skilled amplification by marketing & PR teams. 3/

One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/

That's totally fair. Just a very different point from "if they don't have the ambition for a career in science, they should not do a PhD". Not everyone who wants to learn how to do science also wants to pursue an academic career.

I'm just curious about your position. Is it "you should only do a PhD if you want to become a professor" or is wanting to becoming a "scientist" in industry also fine? Your objection to "careers outside universities" implies the former, but I wanted to clarify

Do you consider going into pharma/biotech R&D a "career in science"?

Thrilled to share our Human Endoderm-derived Organoid Cell Atlas (HEOCA). We compare organoids with primary tissues, assess culture strategies, and explore disease models. In collaboration with Lennard Halle, supervised by
@graycamplab.bsky.social, @fabiantheis.bsky.social & @TreutleinLab. @IHB.

Modular integration of epithelial, microbial, and immune components to study human intestinal biology. Amazing team project with Rubén López-Sandoval, Marius F. Harter, Qianhui Yu, Matthias Lütolf, Mikhail Nikolaev, and Nikolche Gjorevski! biorxiv.org/content/10.1...

The first two integrated HCA Organoid Cell Atlases, from brain and endoderm tissues, are available on the HCA Data Portal. Congratulations to all involved! 🖥️ 🧬 data.humancellatlas.org/hca-bio-netw...

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!

Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.

Massive thanks to brilliant co-lead @dominik1klein.bsky.social, Daniil, Aviv, as well as everyone else from the labs of @fabiantheis.bsky.social, @graycamplab.bsky.social & Barbara

What's really cool is that CellFlow enables screening organoid protocols entirely in silico, by learning from systematic organoid morphogen experiments (thx @nazbukina.bsky.social & Fatima!)

CellFlow is particularly good at modeling complex and heterogenous cell distributions. When applied to an iNeuron morphogen screen from @hsiuchuanlin.bsky.social & @jasperjanssens.bsky.social, it correctly predicts emergent cell populations arising from combinatorial morphogen treatment.

This was such a fun project! A while back, Daniil and I played with flow matching for pred. modeling of cell fate engineering and then teamed up with @dominik1klein.bsky.social and an amazing team @fabiantheis.bsky.social, to build a (close to) universal framework for modeling phenotypic screens 🧵

Happy to share our resource for blood vessel organoids!
@zhisonghe.bsky.social, Makiko Seimiya, Gustav Jonsson, Wuji Cao, Ryo Okuda, Reiner Wimmer, Ryoko Okamoto
Barbara Treutlein, @graycamplab.bsky.social, @penningerlab.bsky.social

Check it out -> cellflow.readthedocs.io

CellFlow enables generative single-cell phenotype modeling with flow matching High-content phenotypic screens provide a powerful strategy for studying biological systems, but the scale of possible perturbations and cell states makes exhaustive experiments unfeasible. Computatio...

Yay, we built a thing! With @dominik1klein.bsky.social Daniil, Aviv Regev, Barbara Treutlein @graycamplab.bsky.social @fabiantheis.bsky.social we use flow matching to enable generalised sc phenotype modeling. From cytokine screens to fate programming and organoid engineering tinyurl.com/3xhju7db

Excited to share our latest preprint, presenting a multi-omic human neural organoid cell atlas of the posterior brain! 🧠🔬
doi.org/10.1101/2025...
Great work with @hsiuchuanlin.bsky.social @zhisonghe.bsky.social @graycamplab.bsky.social and Barbara Treutlein!

Mapping cells through time and space with moscot - Nature Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...

Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep

Mapping cells through time and space with moscot - Nature Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...

Excited to see Moscot (moscot-tools.org) published in @Nature! We scaled Optimal Transport (OT) in single-cell genomics & added multimodality together with spatiotemporal trajectory inference, finding exciting new biology in the pancreas! 🚀 Read at www.nature.com/articles/s41...

💯

I’m always looking for things that explain a lot but that people have a hard time remembering.

Examples: Air is stuff. Pee comes from blood. All land vertebrates have a single common ancestor. Venus is bright enough to cast visible shadows. Clouds are heavy. Bones are alive.

Any others you know?

Meinung: »Human Cell Atlas«: Das wird die wichtigste Wissenschaft des 21. Jahrhunderts - Kolumne Gerade ist ein ganzes Bündel Publikationen aus einem einzigen Forschungsprojekt erschienen. Sie weisen in die Zukunft einer neuen Wissenschaft: Lernende Maschinen helfen jetzt, die Maschinerie des Leb...

If diving into scientific papers isn’t on your pre-Christmas to-do list, @spiegel.de has you covered! 📰 They featured our Neural Organoid Atlas in a piece on the Human Cell Atlas and related advancements in machine learning. 🤖🧬 It’s a great overview of this exciting field and the work behind it.

GitHub - devsystemslab/HNOCA-tools: Toolbox of the Human Neural Organoid Cell Atlas Toolbox of the Human Neural Organoid Cell Atlas . Contribute to devsystemslab/HNOCA-tools development by creating an account on GitHub.

Check out our HNOCA-tools python package, if you are interested in applying some of our analysis methods to your data! github.com/devsystemsla...

An integrated transcriptomic cell atlas of human neural organoids - Nature A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...

Bit late with this, but super happy that our neural organoid atlas is out in Nature! Really fun collab with @zhisonghe.bsky.social and @le-and-er.bsky.social between the Treutlein lab, @fabiantheis.bsky.social and @graycamplab.bsky.social.
www.nature.com/articles/s41...

📢 There are 2 open PhD positions in my group at CRG Barcelona! We are looking for candidates interested in cell fate engineering, gene regulation, and single-cell technologies with experience in both wet/dry labs.

Please help spread the word 🙌

Apply here ➡️ www.crg.eu/en/content/t...

Glad that our neural organoid atlas is out @Nature! Many interesting analyses for in vitro-in vivo comparisons beyond neural organoid setting - here eg fig 4e, where we visualize on primary reference which brain regions are not yet covered by organoids. Exciting for exp design!

An integrated transcriptomic cell atlas of human neural organoids - Nature A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...

Now in Nature! As a highly collaborative team with people from the Treutlein lab, @fabiantheis.bsky.social and @graycamplab.bsky.social, led by me, @le-and-er.bsky.social and @josch1.bsky.social, we generated the so far largest cell atlas of neural #organoid. www.nature.com/articles/s41...

An integrated transcriptomic cell atlas of human neural organoids - Nature A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...

Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...


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