Our paper is finally out in Cell! Years of work on one of biology's most beautiful tissue clocks, and finding an intrinsic oscillator that helps organize tissue dynamics. From my PhD work at @LongCai_Lab, with Shosei Yoshida and Ben Simons! 🧵(1/10) cell.com/cell/fulltext/S0092…

Our paper is finally out in Cell! Years of work on one of biology's most beautiful tissue clocks, and finding an intrinsic oscillator that helps organize tissue dynamics. From my PhD work at @LongCai_Lab, with Shosei Yoshida and Ben Simons! 🧵(1/10) cell.com/cell/fulltext/S0092…

Beautiful work @garber_manuel and co. Immunology is magical! nature.com/articles/s41590-0…

Thrilled to announce our new Nature Methods paper: Giotto Suite: an extensible, technology-agnostic ecosystem for spatial multiomics analysis. Big thanks to co-first authors @jiaji_g_chen & @josschavezf1, and all Giotto devs in @RnDries & @gc_yuan labs! nature.com/articles/s41592-0…

New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH bit.ly/46eTdez

Excited to share our new paper out in @Nature revealing cell-type specific nuclear organization and its link to gene regulation using new spatial multi-omics technologies! nature.com/articles/s41586-0…

Released my preprint! Here, we leverage spatial information to resolve temporal dynamics in male germ cell development! We reveal that Sertoli cells are precisely synchronized with periodic germ cell development and have an innate cyclic program independent of the germ cells!

Our new preprint with S.Yoshida and B.Simons! Led by @ChakraArun, we leverage spatial information to resolve temporal dynamics in spermatogenesis! biorxiv.org/content/10.1101/… Also check out a complementary preprint by S.Y. and B.S using live imaging! biorxiv.org/content/10.1101/… (1/10)

Thrilled to share our latest work on lipid nanoparticle (LNP) delivery of a stable CRISPR-Cas9 ribonucleoprotein (RNP) for in vivo genome editing, now published @NatureBiotech! 🧬 nature.com/articles/s41587-0… In this paper, we first engineered robust, efficient, and stable CRISPR-Cas9 genome-editing enzymes, iGeoCas9s, through #directedevolution of Cas9 from Geobacillus stearothermophilus (GeoCas9). We then developed an LNP-based delivery platform that successfully encapsulates and delivers iGeoCas9 RNP to various cell lines, achieving high-efficiency genome editing in vitro, including homology-directed repair (HDR) via codelivery of RNP and ssDNA templates. In the end, we demonstrated that different LNP formulations enabled tissue-specific genome editing in the liver and lungs after single intravenous injections of iGeoCas9 RNP–LNP complexes without triggering detectable immune responses. Overall, our results show that stable Cas9 RNP–LNP complexes can be a robust alternative to mRNA–LNP delivery and expand the therapeutic potential of CRISPR genome editing. Our previous study @CellCellPress illustrated why our engineered iGeoCas9 exhibits dramatic improvements in its genome editing function. The high protein stability and desired negative charge density are the key to the successful development of the LNP delivery strategy for iGeoCas9 RNPs, which outperforms mRNA sgRNA codelivery by LNPs for genome editing. We believe this LNP delivery platform can be further extended to other editing tools, such as base editors and prime editors. Huge thanks to my collaborators @doudna_lab and in the Murthy lab for making this possible! @igisci @berkeleyMCB

🚨𝐇𝐞 𝐋𝐚𝐛 job opportunity @UCSF 🚨: I'm hiring TWO postdocs - an experimentalist and a computational biologist. Join us to use cutting-edge single-cell and spatial technologies to unravel the mysteries of human tissues. opportunities.ucsf.edu/conte…

Just posted a preprint on our new spatial genomic recording system, baseMEMOIR. biorxiv.org/content/10.1101/… Motivation: Cells divide, differentiate, and migrate to form exquisitely organized tissues. Reconstructing the dynamic histories of individual cells, including their lineage relationships and ancestral states, is essential for understanding how intrinsic and extrinsic signals generate tissues during development and in regenerative medicine. Engineered genomic recording systems can reconstruct cell lineage histories from endpoint measurements. However, existing methods either require sequencing (disrupting spatial organization) or have been limited in memory size and scalability. To address this need, @ChadlyDuncan, Kirsten Frieda, and others in the lab created a high memory capacity image-readable recording system termed baseMEMOIR.

Why spatial? What can we learn from spatial transcriptomic analysis that we can't learn otherwise? Excited to present our collaboration with @AndyMcMahonLab led by @MichalPolonsky and @GerhardtLouisa : doi.org/10.1101/2023.11.22.5…

Thrilled to receive @SciLifeLabPrize in my category! Thanks again for the amazing support during my PhD @LongCai_Lab @Caltech. I am also super excited for the future of the spatial multi-omics field! science.org/doi/full/10.1126…

1/ Spatial Genomics is very excited to announce the launch of Gene Positioning System (GenePS), the first confocal end-to-end solution for spatial multiomics assays based on seqFISH technology! Please retweet! Check out more info at spatialgenomics.com/product/ #GenePS #seqFISH

Excited to release our preprint presenting two-layer DNA seqFISH to map over 100,000 genomic loci, beyond the 3660 loci we have previously demonstrated, and revealing subnuclear compartments in neurons and glial cells in the cerebellum.