🚀Excited to start as Group Leader at the Institute of Human Biology in Basel! We want to accelerate organoid engineering, large scale screening & drug discovery with modern ML methods. Really looking forward to collab with great exp groups and work with complex & rich data from organoids.

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/

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.

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

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!

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

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...

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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?

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.

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!

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...

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...
 Find out how it can serve you ⏬
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A big day of output for the Human Cell Atlas, a global collaborative project with 100 countries to understand our ~37 trillion cells A Wikipedia of our cells, a "remarkable achievement" nature.com/articles/d41... nature.com/immersive/d4...

The integrated transcriptomic cell atlas of human neural #organoids, Barbara Treutlein's lab, @fabiantheis.bsky.social @graycamplab.bsky.social @sergiuppasca.bsky.social @giorgiaquadrato.bsky.social and colleagues: www.nature.com/articles/s41...

Hi bsky ✌️☀️