Jonathan S. Weissman's lab at the @WhiteheadInst/@MIT. Account run by lab members.
Cambridge, MA
Joined October 2019
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Jonathan Weissman's Lab retweeted
the transcriptional state of a cell is not generally sufficient to predict its past or future. in our new preprint we show that conditioning on lineage context (sisters, cousins, etc) can help a lot.
this one was v fun :)
arxiv.org/abs/2610.40447
New preprint on generative modeling for mouse development! Rather than single cell trajectories, we set out to model embryos as trees.
Led by @gokl_g, @njwfish, @WilliamNColgan, w/ Philippe Rigollet, @stats_stephen, Zack Smith, @marinkazitnik, @lukekoblan and a wonderful team
New preprint on generative modeling for mouse development! Rather than single cell trajectories, we set out to model embryos as trees.
Led by @gokl_g, @njwfish, @WilliamNColgan, w/ Philippe Rigollet, @stats_stephen, Zack Smith, @marinkazitnik, @lukekoblan and a wonderful team
Overall, we're excited about the direction of modeling multicellular dynamics using lineage (and other kinds of) context, rather than one cell at a time. We hope that similar techniques can be applied to other systems: regeneration, inflammation, cancer and more.
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There's a lot more in the paper, and we also have a website w/ informal writeup of the method, code, data, and an interactive viewer for reconstructed dynamics. Looking forward to feedback!
Paper: arxiv.org/abs/2610.40447
Notes and interactive viewer: lineageinpainting.info
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Excited to share Pycea, a new Python toolkit for lineage analysis and visualization developed by @WilliamNColgan!
Pycea brings lineage trees into the scverse ecosystem, enabling seamless analysis of lineage, gene expression, and spatial data.
biorxiv.org/content/10.64898…
Jonathan Weissman's Lab retweeted
I'm also excited to share the first application of MeRN to study metabolic regulation in mouse embryos (including mutants)! Nick Dias of the Smith Lab led this work with me, in collaboration with the @jswlab. Now on bioRxiv! 🧵 1/
biorxiv.org/content/10.64898…
Thrilled to share that our work reconstructing a cell fate map of the mouse embryo is out now in @CellCellPress! doi.org/10.1016/j.cell.2026.…
🍾 Huge congratulations to @LukeKoblan @WilliamNColgan and many thanks to our wonderful collaborators Zachary Smith @YaleMed and MPIMG, @nir_yosef1 @WeizmannScience, @ZhuangLab @HarvardCCB, and Kyle Loh @Stanford
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Jonathan Weissman's Lab retweeted
This has been an incredible, collaborative effort co-led with @WilliamNColgan in the @JswLab and with Zach Smith’s group at Yale and the @maxplanckpress and his amazing group members @CAbiologist , Jason Hou, and Minming Wang and our other wonderful collaborators.
Jonathan Weissman's Lab retweeted
A fantastic collaboration with @LukeKoblan! Excited to see what the developmental biology community can learn from these data. Check out our CELLxLINEAGE explorer: mela.wi.mit.edu/explore/
Thrilled to share that our work reconstructing a cell fate map of the mouse embryo is out now in @CellCellPress! doi.org/10.1016/j.cell.2026.…