The Cai Lab at Caltech. We developed sequential FISH (seqFISH), seqFISH+, MEMOIR, and RNA SPOTs, apply them to study various biological questions.

Pasadena, CA
Joined October 2017
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.
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Check out Giotto Suite — our latest tool for spatial multiomics analysis. This is a complete overhaul of the original Giotto package, a result from years of making. Great collaboration with @RnDries team. Kudos to @jiaji_g_chen @josschavezf1 and the entire Giotto team!
Replying to @GiottoSpatial
Our dedicated Giotto team, led by the amazing @jiaji_g_chen & @josschavezf1 from the @RnDries and @gc_yuan labs, created a modular suite of R packages that can represent and analyze virtually any dataset.
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How neat. Researchers claim to have found, at long last, an "einstein" tile - a shape that tiles the plane in a pattern that never repeats. First two authors appear to have no academic affiliations. arxiv.org/abs/2303.10798
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Excited about this new grant from @NIH_NIAMS to support our vitiligo research for the next 5 years! We will collaborate with outstanding scientists @UMassChan and @LongCai_Lab at CalTech to synergize with us and make real progress to understand vitiligo and create new treatments. – at Sterling, MA
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How many chr1 fibers are in this mouse cell? Care to wager? Tempted to say 2, but our *SPATIAL GENOME ALIGNER* finds 4 chromatin fibers (sister chromatids!). Here’s how: 1/n biorxiv.org/content/10.1101/…
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Cai Lab retweeted
nature
@Nature21 Feb 2022
Revealing chromosome contours, one dot at a time go.nature.com/3tf03Mf
Squidpy 🌌🍤🐍🎉 is out in @naturemethods ! Truly collab effort with @HannahSpitzer1 Michal Klein @fabian_theis lab! nature.com/articles/s41592-0…
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Primordium is now offering everyone the chance to sample our full-plasmid sequencing service for FREE - never use Sanger sequencing again! Please retweet this message and we'll DM you a coupon to sequence 5 ENTIRE PLASMIDS 100% FREE, no CC or PO needed. primordiumlabs.com 5/
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What drives organization of RNA, DNA, and proteins in the nucleus? In our new paper out @CellCellPress, we show that non-coding RNAs play a central role through a unique RNA-based mechanism. authors.elsevier.com/c/1e132…
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A visual abstract for our latest publication in Science. Work at @LongCai_Lab @Caltech uncovers nuclear architectures within mouse brains–different imaging modalities form a picture of how proteins, DNA, &RNA interact across neurons. #spatialgenomics #medicalillustration #sciart
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New technique allows study of the dynamics within complex microbial communities #bacteria #spatialtranscriptomics. Image and research by @Danidiin et al @LongCai_Lab & Dianne Newman lab @Caltech in @ScienceMagazine. Read more on bpod.mrc.ac.uk/archive/2021/… with @MRC_LMS & @AntDLewis
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Ratiometric RNA labeling allows dynamic multiplexed analysis of gene circuits in single cells biorxiv.org/cgi/content/shor… #bioRxiv
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Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis go.nature.com/3DRM6rY
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Daniel Dar and Dr Nina Dar @CaltechN have developed a new technique dubbed par-seqFISH to understand microbial communities on our planet, from those in our gut to those that colonize plant roots caltech.edu/about/news/new-t…
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Cai Lab retweeted
A new technique developed at Caltech can examine the behavior of myriad microbial communities on our planet, from those deep under the ocean to those living in our gut, by surveying gene expression across a huge number of cells. caltech.edu/about/news/new-t…
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Join today and tomorrow @nih_nhlbi systems biology symposium. Keiji Zhao @youngricka Sunney Xie @AnnaGreka @eboyden3 @LongCai_Lab Hess Herald, @kadzuis Knepper @KSusztak @PerrimonLab and many more nhlbi.nih.gov/events/2021/20…
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