Jay Shendure

Today we release in @biorxivpreprint a pair of related methods, DNA Ticker Tape & ENGRAM, for multiplex, temporally ordered genomic recording of cell lineage histories, enhancer & signal transduction activities, respectively led by the brilliant @_Choi_Junhong & @wchenomics 1/25

Somite is building the blueprints to create any cell type for any person. We call it DeltaStem, our foundation model for the human cell. Our proprietary capsule technology allows us to generate cell signaling data 1,000x faster and more efficiently than current methods,…

Beyond thrilled to present our O-MAP—now *published* @naturemethods (!!!) O-MAP is a powerful new method for biochemically "dissecting" the subcellular microenvironment around an RNA of interest, using off-the-shelf parts and standard manipulations. 🧵 nature.com/articles/s4159…

🚨Big news! Five years in the making, our Zebrahub paper is now published in #Cell 🎉. We’ve built a timecourse atlas of zebrafish embryonic development, combining #scRNAseq data and #lightsheet live imaging, and delved deep into the dynamics of key progenitors.…

Excited to share my PhD work in @Agnelsfeir’s lab describing a method to engineer mitochondrial DNA deletions in human cells and our exploration of how cellular metabolism and transcription respond to deletion heteroplasmy. biorxiv.org/content/10.110… 1/19

Flexible differential expression analyses have always been neat in CZ #CellxGene. Now they’re next level! Quickly perform DE analysis across our entire data corpus. For ex: leveraging >125 relevant datasets to compare astrocytes with/without Alzheimer’s📷 bit.ly/4eDt9uU

New synthetic biology / gene regulation lab opening in Zurich! We’re studying how to control cell state transitions – for example, making diseased cells healthy or creating new cellular functions – using systematic perturbations, single-cell genomics and machine learning. 🧵1/4

📢 Check out our @teamstembryo @NatureCellBio News & Views with postdoc @alex_schauer_ on the latest feat in human stem-cell-based embryo models by @Nobu_Hamazaki, @JShendure & colleagues. Full text: rdcu.be/dWw3c nature.com/articles/s4155… #gastruloids

University of Washington biochemist David Baker has won the 2024 Nobel Prize in Chemistry for his pioneering work designing new proteins that can neutralize viruses, target cancer cells, and more. Read more from @uwmedicine: go.uw.edu/2024NobelPrize #NobelPrize #GoHuskies

BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

Beyond stoked to share our latest, entitled “Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording” ! biorxiv.org/content/10.110…

Incredibly proud to share that I recently joined @UCSF_BTS @UCSF as an Assistant Professor! This means that the Calderon Lab is now open! Or, more accurately, in the process of opening as I am still unboxing equipment and unraveling giant posters (a last @JSHendure lab gift) 🥳

(1/X) I hate doing these, but I feel like I'm being baited to do so. A few days ago Maggie H did an interview where she complained criticism of her reporting, James Fallows answered back (mentioning this account) and Jon Chait and some Reason bro took a shot at Fallows for...

Our paper describing a scalable method for Multiplex, single cell CRISPRa screening for cell-type specific regulatory elements is now published! rdcu.be/dUnoq nature.com/articles/s4146…

Genomic tech dev is my favorite area of science, and today our paper describing our multiplex CRISPRa screening method to identify cell type specific regulatory elements is published! rdcu.be/dUnoq

Published today in @Nature, we describe an approach for single-molecule protein reading on @nanopore arrays. By utilizing ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieved single-amino-acid sensitivity. nature.com/articles/s4158…

💫NEW: Hamazaki, Yang et al. report that an early pulse of #RetinoicAcid induces human #gastruloids with a neural tube, segmented somites and more advanced cell types than conventional gastruloids. #embryo_models @VinetteY @Nobu_Hamazaki @JShendure nature.com/articles/s4155…

Deluge of useful information @ proteomics, protein/mRNA correlations, comparative molecular landscapes and more. #gastruloids (#mouse and #human) biorxiv.org/content/10.110… Valuable resource. Huge effort from @dschweppe1 @Nobu_Hamazaki and colleagues #EmbryoModels #InNumbersWeTrust

Very happy to share our latest w/ @dschweppe1 and @Nobu_Hamazaki labs, where we map the temporal dynamics and proteomic landscape of mammalian gastruloids. Sneek Peak 🧵below #stembryo #gastruloid #proteomics biorxiv.org/content/10.110…

We are recruiting two computational biologists/bioinformaticians with ML expertise and a focus on genomics, variant effects and gene regulatory sequences in staff scientist and postdoc roles in Lübeck, Germany. Please find details here: kircherlab.github.io/contact.html

Excited to share my postdoc work from the @schierlab. This project was a joint effort with many collaborators @seeliglab, @castillohair,Lucia Du, @YiqunWang3,@adamcarte,@mcolomerr, Chris Yin. 1/20 biorxiv.org/content/10.110…