Zhisong He 何志嵩
@zhisonghe.bsky.social
Senior scientist & lecturer in Barbara Treutlein's Lab at D-BSSE, ETH Zürich. Computational biologist working on single-cell and spatial genomics, brain development and brain organoids
Very exited to be awarded my first SNSF Project Funding as the project PI. Huge thanks to @snsf.ch and the very supportive comments from the reviewers! The grant will support my project to decode human brain development and disease with AI-driven regulatory network modeling
October 8, 2025 at 2:36 PM
Very exited to be awarded my first SNSF Project Funding as the project PI. Huge thanks to @snsf.ch and the very supportive comments from the reviewers! The grant will support my project to decode human brain development and disease with AI-driven regulatory network modeling
Reposted by Zhisong He 何志嵩
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 2:29 PM
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
Reposted by Zhisong He 何志嵩
Integrated Organoid Atlas benchmarks new protocols, even more impressive as a Highly Variable Cohort for comparison against perturbation and disease models: nature.com/articles/s41... Lead by @quanxu.bsky.social, in collaboration with Lennard Halle and @fabiantheis.bsky.social
An integrated transcriptomic cell atlas of human endoderm-derived organoids - Nature Genetics
The human endoderm-derived organoid cell atlas (HEOCA) presents an integrative analysis of single-cell transcriptomes across different conditions, sources and protocols. It compares cell types and sta...
nature.com
May 12, 2025 at 9:23 PM
Integrated Organoid Atlas benchmarks new protocols, even more impressive as a Highly Variable Cohort for comparison against perturbation and disease models: nature.com/articles/s41... Lead by @quanxu.bsky.social, in collaboration with Lennard Halle and @fabiantheis.bsky.social
Reposted by Zhisong He 何志嵩
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...
May 9, 2025 at 12:54 PM
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...
Great to be part of the team! And this would not be the end of our efforts on exploring and characterizing the organoid systems
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...
May 3, 2025 at 6:14 AM
Great to be part of the team! And this would not be the end of our efforts on exploring and characterizing the organoid systems
Reposted by Zhisong He 何志嵩
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...
genomebiology.biomedcentral.com
April 20, 2025 at 4:14 PM
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Reposted by Zhisong He 何志嵩
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
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...
www.biorxiv.org
April 18, 2025 at 10:19 AM
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
Reposted by Zhisong He 何志嵩
New preprint from the @graycamplab.bsky.social & Treutlein labs, offering a single-cell multi-omic atlas and morphogen screen of human neural organoid models of the midbrain and hindbrain (#cerebellum) 🧪🧫🧬🧠
Project led by
@nazbukina.bsky.social @zhisonghe.bsky.social @hsiuchuanlin.bsky.social
Project led by
@nazbukina.bsky.social @zhisonghe.bsky.social @hsiuchuanlin.bsky.social
Multi-omic human neural organoid cell atlas of the posterior brain
Patterning of the neural tube establishes midbrain and hindbrain structures that coordinate motor movement, process sensory input, and integrate cognitive functions. Cellular impairment within these s...
www.biorxiv.org
March 21, 2025 at 8:38 AM
New preprint from the @graycamplab.bsky.social & Treutlein labs, offering a single-cell multi-omic atlas and morphogen screen of human neural organoid models of the midbrain and hindbrain (#cerebellum) 🧪🧫🧬🧠
Project led by
@nazbukina.bsky.social @zhisonghe.bsky.social @hsiuchuanlin.bsky.social
Project led by
@nazbukina.bsky.social @zhisonghe.bsky.social @hsiuchuanlin.bsky.social
It was really great to work with @nazbukina.bsky.social @hsiuchuanlin.bsky.social and all people involved in this project! It is cool to see how we can learn about posterior brain development from organoids and how we can extend the organoid protocols from existing ones!
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!
doi.org/10.1101/2025...
Great work with @hsiuchuanlin.bsky.social @zhisonghe.bsky.social @graycamplab.bsky.social and Barbara Treutlein!
March 24, 2025 at 2:13 PM
It was really great to work with @nazbukina.bsky.social @hsiuchuanlin.bsky.social and all people involved in this project! It is cool to see how we can learn about posterior brain development from organoids and how we can extend the organoid protocols from existing ones!
Reposted by Zhisong He 何志嵩
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...
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...
www.nature.com
December 13, 2024 at 2:27 PM
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...
www.nature.com/articles/s41...
Reposted by Zhisong He 何志嵩
Excited to announce that I will start my group at @crg.eu in Barcelona next April! We will decode and engineer cell fates using stem cell models, perturbation screening and single-cell multiomics. Looking forward to the new chapter ahead!
November 23, 2024 at 4:42 PM
Excited to announce that I will start my group at @crg.eu in Barcelona next April! We will decode and engineer cell fates using stem cell models, perturbation screening and single-cell multiomics. Looking forward to the new chapter ahead!
Reposted by Zhisong He 何志嵩
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!
November 22, 2024 at 5:25 PM
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...
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...
www.nature.com
November 21, 2024 at 10:20 PM
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...
Reposted by Zhisong He 何志嵩
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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Find out how it can serve you ⏬
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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...
www.nature.com
November 21, 2024 at 10:11 AM
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 ⏬
🧵1/8
Find out how it can serve you ⏬
🧵1/8