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jonas @josch1.bsky.social · Jul 23

Yeah, actually, why?

Pedro Beltrao @pedrobeltrao.bsky.social · Jul 23

New blog post: Why do we still publish in scientific journals ? What is holding us back from letting go of traditional publishing? No major insight here but I am curious what others think. www.evocellnet.com/2025/07/why-...

Why do we still publish in scientific journals ?

We publish in scientific journals to disclose our discoveries, such that others can build upon them. But we now have preprint servers and we...

www.evocellnet.com

Reposted by jonas

Anshul Kundaje @anshulkundaje.bsky.social · Jul 10

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/

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Anshul Kundaje @anshulkundaje.bsky.social · Jun 28

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/

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jonas @josch1.bsky.social · Jun 24

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.

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jonas @josch1.bsky.social · Jun 24

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

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jonas @josch1.bsky.social · Jun 24

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

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Quan Xu @quanxu.bsky.social · May 13

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.

Camp Lab @graycamplab.bsky.social · May 12

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

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Camp Lab @graycamplab.bsky.social · May 9

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...

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Human Cell Atlas @humancellatlas.org · Apr 28

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...

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Camp Lab @graycamplab.bsky.social · Apr 28

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!

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Stein Aerts @steinaerts.bsky.social · Apr 26

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.

VIB.AI @vibai.bsky.social · Apr 25

We are looking for additional Group Leaders to join the growing computational biology community at VIB.

If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!

https://vib.ai/en/opportunities#/job-description/110906

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jonas @josch1.bsky.social · Apr 24

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

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jonas @josch1.bsky.social · Apr 24

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!)

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jonas @josch1.bsky.social · Apr 24

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.

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jonas @josch1.bsky.social · Apr 24

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 🧵

dominik1klein.bsky.social @dominik1klein.bsky.social · Apr 23

From cell lines to full embryos, drug treatments to genetic perturbations, neuron engineering to virtual organoid screens — odds are there’s something in it for you!

Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1

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marinanikolova.bsky.social @marinanikolova.bsky.social · Apr 21

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

Cell - a Cell Press journal @cp-cell.bsky.social · Apr 17

Now online! Fate and state transitions during human blood vessel organoid development

Fate and state transitions during human blood vessel organoid development

Single-cell multiomic reconstruction of the human blood vessel organoid system allows for classifying and modeling disease and cell-type-specific states, demonstrating its potential for translational research.

dlvr.it

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jonas @josch1.bsky.social · Apr 18

Check it out -> cellflow.readthedocs.io

cellflow documentationContentsMenuExpandLight modeDark modeAuto light/dark, in light modeAuto light/dark, in dark mode

cellflow.readthedocs.io

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jonas @josch1.bsky.social · Apr 18

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

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Nadezhda Azbukina @nazbukina.bsky.social · Mar 24

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!

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dominik1klein.bsky.social @dominik1klein.bsky.social · Jan 23

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...

tinyurl.com

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Fabian Theis @fabiantheis.bsky.social · Jan 22

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...

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...

www.nature.com

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jonas @josch1.bsky.social · Jan 6

💯

Jacob Schreiber @jmschreiber91.bsky.social · Jan 6

The only sort of gatekeeper I wish we saw more of were those who wanted better software. Who cares if your model performs the best if it's unusable, or if your pipeline aligs reads faster if it only works on your local work computer? Or if there's no documentation on how to use any of it.

Reposted by jonas

Hank Green @hankgreen.bsky.social · Dec 28

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?

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Leander @le-and-er.bsky.social · Dec 19

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.

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...

www.spiegel.de

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jonas @josch1.bsky.social · Dec 13

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

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.

github.com

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