My postdoc work at Treutlein lab and @graycamplab.bsky.social with @jasperjanssens.bsky.social is out in @science.org ! We screen for neuron subtypes using pro-neural TFs + morphogen combinations + scRNA-seq and profiled over 700,000 cells in 480 conditions. www.science.org/doi/10.1126/...

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

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

8/ This work provides a comprehensive atlas for understanding neural regionalization & disease modeling. 🌍🧠 Check out our preprint for the full details! 🚀 Feedback & discussions welcome! #Neuroscience #Organoids #scRNAseq #DevelopmentalBiology

7/ Using differential condition abundance-informed trajectory inference, we also refined trajectories for posterior brain development.

6/ We used this rich data to infer morphogen-regulon relationships guiding neuronal fate.

5/ We performed a high-throughput morphogen screening using combinatorial barcoding scRNA-seq. With 48 conditions & 10 morphogens, we expand organoid diversity with emergence of previously underrepresented cell types, such as medulla glycinergic & cerebellum glutamatergic neurons.

4/ We inferred gene regulatory networks and, using single-cell CRISPR perturbations, validated key transcription factors controlling midbrain vs. hindbrain fate in human neural organoids.

3/ We developed a new approach to map the chromatin accessibility data to primary atlases using cisTopics loadings. We find that organoid cells recapitulate primary counterparts not only on transcriptomic, but also on chromatin accessibility level!

2/ We show that existing midbrain organoid protocols generate diverse cell types, covering ventral & dorsal midbrain and adjacent hindbrain regions, such as cerebellum.

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!