Puzzling over how tissues build themselves
UCSF, San Francisco
Joined November 2011
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Zev Gartner retweeted
Remembering Yoshiki Sasai, another scientist who made a mistake and took his life from the onslaught of media. Even worse, his death allows the community to continue "robbing" him from being credited adequately for making the first brain organoids in a stunning series of studies dating back to 2008-2011. sciencedirect.com/science/ar…
nature.com/articles/nature09…
nature.com/articles/nature10…
Zev Gartner retweeted
organs develop in a dynamic environment where their boundaries are constantly changing shape, relaxing, compressing, etc. in synchrony with the embryo.
see how this inspired us to create a material for optimal organoid bioprinting & self-organization!
nature.com/articles/s41563-0…
1. Excited to share CONCORD, now out in @NatureBiotech! It's an ML framework for single-cell analysis that solves integration, dimensionality reduction, and denoising in one go. Huge effort led by @qinzhu1.🔗 nature.com/articles/s41587-0… Check out this CONCORD atlas of worm development resolving detailed differentiation trajectories:
7. Best of all, it's fast (1M cells in <10 mins) and memory-friendly.
💻 Open Source: github.com/Gartner-Lab/Conco… 📖 Docs: qinzhu.github.io/Concord_doc… Try it out and let us know what you think!
8. We thank team member Zuzhi Jiang, collaborators Binyamin Zuckerman, Leor Weinberger, Matt Thomson, funding sources @cancerresearchinst (@CancerResearch) @NIH @czbiohub @czi @UCSF, the thoughtful reviewers for @NatureBiotech, and everyone else who shared data and feedback!
Zev Gartner retweeted
CONCORD: Revealing a coherent cell state landscape across single cell datasets biorxiv.org/content/10.1101/…
1. Struggling to integrate single-cell datasets? Finding it hard to resolve clear differentiation trajectories? Reveal the underlying structure in your data with CONCORD.biorxiv.org/content/10.1101/…
4. We validated CONCORD on an embryonic atlas of C. elegans and C. briggsae from @jisaacmurray. CONCORD captured known bifurcations, subtle cell states, and lineage convergence events missed by other methods (click here for interactive 3D UMAP! qinzhu.github.io/Concord_doc…...):
5. An intestinal development atlas demonstrated CONCORD's ability to resolve complex topologies, including differentiation trajectories intertwined with cell cycle loops (click here for interactive 3D UMAP! qinzhu.github.io/Concord_doc…...):
correct link: interactive 3D UMAP! qinzhu.github.io/Concord_doc…
9. While we focused on scRNA-seq, early results suggest CONCORD’s applicability to spatial transcriptomics & scATAC-seq. It’s open-source in Python. See galleries: qinzhu.github.io/Concord_doc….... Try it: github.com/Gartner-Lab/....
Zev Gartner retweeted
Thrilled to see our work highlighted by @GENbio! 🙏🏿🧬 Read the paper here: dlvr.it/TJfDpC #CRISPR #StemCells #SyntheticBiology
Epigenetic Editing of Mouse Stem Cells Generates Embryoids for Developmental Research
@ucsc scientists have used #CRISPR to develop programmable embryoids that can be used to study early embryo development and improve fertility.
hubs.li/Q03cV5mF0
