Yodai Takei
@yodai_takei
Research Scientist in Division of Biology and Biological Engineering @Caltech.
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/s4158…
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in @NatureGenet describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. nature.com/articles/s4158…
I'm happy to share a highlight from our recent work!
New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+ bit.ly/46eTdez
Nature research paper: Spatial multi-omics reveals cell-type-specific nuclear compartments go.nature.com/4i9uvyz
Out now in @CellCellPress! How to build the virtual cell with artificial intelligence: Priorities and opportunities. @Prof_Lundberg @StephenQuake @jure Aviv Regev @Tkaraletsos @_bunnech @YanayRosen @yusufroohani #CellBio2024 hubs.li/Q02_H8LG0
Ten years. Together we built a warm, tight-knit, international community, shared new computational and experimental technologies around the the world, posted >400 preprints, and catalyzed understanding of the mechanisms and functions of chromatin in development and disease.
Excited to finally share Perceptein, a PERCEPtron made of proTEINs: science.org/doi/10.1126/sc…
🚨 Exciting news! 🚨 Our latest paper is now published in Science Advances! 🎉 "Transcription-coupled changes in genomic region proximities during transcriptional bursting" 👉 Read it here: science.org/doi/10.1126/sc…
The lives of cells, recorded go.nature.com/4g2gRwG #Perspective by @AskaryLab, Wei Chen, @_Choi_Junhong, Lucia Y. Du, @ElowitzLab, @james_gagnon, @schierlab, @sophieseid, @JShendure, @TanjaStadler_CH & @tranmartink
We are happy to announce this year's winners of the @ScienceMagazine and SciLifeLab Prize for Young Scientists: Andrija Sente, @CasiratiG, @SabRondeau and @JarrodShilts! We'll see you in Stockholm in December! 👏💯 scilifelab.se/news/prizewinn…
In @CellCellPress, I share a major conceptual challenge for biology in the next decade, inspired by Crick’s Central Dogma: understanding information flow in the cell, the smallest indivisible unit of life bit.ly/4hQMmva
Glad to share our latest review article on #ChromatinTracing, published with @SpringerNature in Nature Reviews Methods Primers @MethodsPrimers! @GenomeTDCC @4DNucleome @sennetresearch @NIH_CommonFund @YaleMed @3D_Genome @The3DGenome @generegulation nature.com/articles/s4358…
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/10.110… Also check out a complementary preprint by S.Y. and B.S using live imaging! biorxiv.org/content/10.110… (1/10)
In case it's helpful to anyone, I posted the evolving set of talk tips that I share with my lab on our website. Scroll to bottom of this page: elowitz.caltech.edu/teaching. (It was once "10 commandments" but has since expanded to 25...the slide titles are currently number 5)
Thrilled to share our latest ChIL technology is finally out as single cell multiomics. The manuscript titled "Tracking chromatin structure changes by single-cell multi-epigenomics with RNA polymerase II binding profiles" is opened on doi.org/10.21203/rs.3.….
A long sought after hypothesis has been that organizing biomolecules in and around nuclear bodies is essential for functional RNA processing. We now provide direct evidence of this in @Nature for nuclear speckles and mRNA splicing. Check out this thread! nature.com/articles/s4158…
What are the functional roles of 3D genome organization? Our paper in @Nature led by @_prashantbhat demonstrates how dynamic 3D genome organization around nuclear speckles plays a crucial role in regulating mRNA splicing efficiency. rdcu.be/dHkez
Our new paper on “synpoptosis” circuits, led by the amazing @ShiyuXia, is now out: sciencedirect.com/science/articl… (1/3)
📢 Incredibly excited to share the peer-reviewed version of our lumenogenesis work. We developed a human epiblast model and discovered a new mechanism of lumen expansion that is driven by actin! @CellStemCell @theChaudhurilab 🧵 [1/17] doi.org/10.1016/j.stem…
Just posted a preprint on our new spatial genomic recording system, baseMEMOIR. biorxiv.org/content/10.110… Motivation: Cells divide, differentiate, and migrate to form exquisitely organized tissues. Reconstructing the dynamic histories of individual cells, including their lineage…