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Jay Shendure

@jshendure.bsky.social
4.1K followers 169 following 48 posts

shendure lab |. krishna.gs.washington.edu

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Reposted by Jay Shendure
Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Sheri @sagrill.bsky.social · 19/09/2026
This work would not have been possible without the incredible snATAC-seq atlas of the Drosophila embryo from @diegoisworking.bsky.social @jshendure.bsky.social and @eileen-furlong.bsky.social which helped us discover that germ cells retain a totipotent chromatin state throughout development!
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Nozomu Yachie @nzmyachie.bsky.social · 04/09/2026
Maybe it’s time to say goodbye to UMAP and other low-dimensional embeddings (at least in many single-cell analyses). We developed MILK to encode single-cell populations into tree representations at unprecedented scales. www.biorxiv.org/content/10.6... Here’s what MILK is: 🧵
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Junhong Choi @choijunhong.bsky.social · 11/08/2026
Excited to share the first preprint from our lab! We combined a DNA Typewriter lineage recorder with clone-resolved founder profiling to find what makes metastatic potential heritable in lung cancer xenografts. 1/13 www.biorxiv.org/content/10.6...
biorxiv.org
Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential
Metastasis causes most cancer deaths, yet no recurrent mutation specifically drives it, raising the possibility that metastatic potential is a non-genetic yet heritable cell state. Classic experiments...
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Jonathan Pritchard @jkpritch.bsky.social · 09/08/2026
Must-know numbers in human genetics -- As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties. jkpritchard.substack.com/p/on-fermi-p...
jkpritchard.substack.com
On Fermi Problems in Human Genetics
and some very useful numbers about human genomes to get you started!
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Ran Blekhman @blekhman.bsky.social · 09/08/2026
Huge faculty recruitment effort at the University of Chicago -- a division-wide, open-rank search looking to hire about 20 faculty across 5 research areas in biology. Come be our colleague! Full announcement: uchicago.app.box.com/s/ckih9zv3rj...
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Harmit Singh Malik @harmitmalik.bsky.social · 06/08/2026
Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.
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Jay Shendure @jshendure.bsky.social · 31/07/2026
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
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Jay Shendure @jshendure.bsky.social · 30/07/2026
New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...
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William DeWitt @wsdewitt.github.io · 27/06/2026
Spectacular preprint led by @sydsat.bsky.social in @ohnolog.bsky.social lab, @uwgenome.bsky.social. Neutrophils precede gastrulation in killifish and rapidly patrol the yolk. (1/2)
doi.org
Early immune cell development precedes gastrulation in annual killifish
During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
22/n On a personal note, I’ll soon start an independent research group in the Genome Biology Unit at EMBL Heidelberg. If you enjoy this type of work and want to engineer genomes at the largest scale, please reach out! jonas-koeppel.github.io/koeppellab/ www.embl.org/groups/koepp...
jonas-koeppel.github.io
Koeppel Lab | Structural Variation and Genome Engineering
Genome engineering research led by Jonas Koeppel, developing scalable technologies to design structural variants and study mammalian genome function.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...
nature.com
Why a synthetic human genome is still worth building
A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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allen institute @alleninstitute.org · 02/06/2026
Brain disease is tragic, but it doesn’t have to be. It’s time for a new approach to #brainhealth research. That’s why we and our partners are launching the Brain Health accelerator. 🎥 youtu.be/wnTG5Sg8AKY?...
youtu.be
Brain Health accelerator: a new way to study brain disease to find new treatments for it
YouTube video by allen institute
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Hongkui Zeng @hongkuizeng.bsky.social · 04/06/2026
This week’s launch of the #BrainHealth accelerator marks an important step forward for neuroscience. I’m excited to see this ambitious effort rally teams around a shared goal: building a deeper understanding of brain disease and accelerating progress toward better therapies.
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Jay Shendure @jshendure.bsky.social · 30/05/2026
“AlphaFold 3's representational coherence is deeply tied to evolutionary scaffolding, suggesting it functions similarly to an advanced fold-recognition system and highlighting that protein structure prediction from sequence alone is not yet fully solved.”
biorxiv.org
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Kristian G. Andersen @kgandersen.bsky.social · 29/05/2026
And, here, in much more detail. This is an absolutely critical read for all federally funded scientists and institutions. Now is not the time to sit in the corner, hoping you won't be noticed - now is the time for action. elizabethginexi.substack.com/p/summary-of...
elizabethginexi.substack.com
Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule
Russell Vought is going destroy American Science
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BWJones @bwjones.bsky.social · 25/05/2026
NIH funded peeps: This is insane and coming for us.
For FY 2026 RPPRs:
If there are any publications with a foreign co-author, a statement submitted through the Signing Official (SO) confirming the author will no longer publish or collaborate with the foreign partner is sufficient to show the collaboration has ended. Also indicate that no IDeA money was transferred via subcontract to an institution in a foreign country. This path will minimize delays.For FY2027 RPPRs onward:
Pls are required to submit prior approval requests for any publication co-authored with individual(s) affiliated with a foreign institution(s).
Per NOT-OD-26-026, prior approval requests must be initiated and submitted by a SO for the recipient organization.
In addition to noting the foreign site and the name of the foreign investigator, the prior approval request should provide information about the nature of the research being conducted; why the involvement of the foreign site is necessary; and whether any data will be transferred.
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William DeWitt @wsdewitt.github.io · 20/05/2026
Game over, phylogeneticists! New DNA foundation model "Carbon" reconstructs the tree of life. 🙃 huggingface.co/spaces/Huggi...
Wildly incorrect phylogenetic tree
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Kurianlab @kurianlab.bsky.social · 15/05/2026
www.nature.com/articles/s41...
nature.com
Widespread DNA off-targeting confounds RNA chromatin occupancy studies - Nature Biotechnology
Many long noncoding RNA–DNA binding peaks detected using common assays arise from technical artifacts.
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Alfonso Martinez Arias @amartinezarias.bsky.social · 02/05/2026
Last year two preprints from @jshendure.bsky.social and @arjunraj.bsky.social www.biorxiv.org/content/10.1... and www.biorxiv.org/content/10.1... perhaps began to shed light on this question. One of them has been updated. Their findings are important.
biorxiv.org
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Saori Sakaue @saorisakaue.bsky.social · 28/04/2026
An important piece from my neighbor, colleague and friend Will DeWitt et al. @wsdewitt.github.io www.biorxiv.org/content/10.6...
biorxiv.org
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Saori Sakaue @saorisakaue.bsky.social · 28/04/2026
New preprint! 📣We performed the largest multi-ancestry GWAS of rheumatoid arthritis (RA), the most common autoimmune disease, by analyzing the VA Million Veteran Program (MVP) with international RA cohorts.
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Nature Biotechnology @natbiotech.nature.com · 28/04/2026
Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism - @jshendure.bsky.social @uwgenome.bsky.social go.nature.com/4cMTnLP
go.nature.com
Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism - Nature Biotechnology
Pooled production of recombinant AAV vectors leads to frequent genetic recombination.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
1/ Thrilled to share our latest: an exciting collaboration across the @jshendure.bsky.social, @leastarita.bsky.social, @nobuhamazaki.bsky.social and @dschweppe.bsky.social labs! 🧵 below- #SystemsBiology #SCBEM #MultiOmics #Gastruloids www.nature.com/articles/s41...
nature.com
The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology
Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.
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Devin Schweppe @dschweppe.bsky.social · 24/04/2026
Excited to see @riddhiman.bsky.social's gastruloid multiomics paper out now at Nature Cell Bio! Riddhiman used proteomics, phosphoproteomics, and RNAseq to profile stem-cell-derived embryo models to identify protein, complex, and signaling regulators of development. www.nature.com/articles/s41...
nature.com
The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology
Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.
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Harmit Singh Malik @harmitmalik.bsky.social · 16/04/2026
@hhmi-science.bsky.social's #FreemanHrabowski Scholars Program offers early career faculty up to $10M over 10 yrs, plus salary & benefits Stable, sustained support can transform your career: Senior Postdoc? This year's competition has a program for you too. Applications open 11/3! bit.ly/4vhC0LA
bit.ly
Early Career Faculty Program | Freeman Hrabowski Scholars | HHMI
The Freeman Hrabowski Scholars Program offers comprehensive support to outstanding early career faculty committed to scientific excellence in their own research, and to fostering labs that expand the ...
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Richard Sever @richardsever.bsky.social · 16/04/2026
HHMI CEO: "diamond funding should be deployed to sustain repositories [i.e. preprint servers] and connective infrastructure that focus on researcher-shared outputs" zenodo.org/records/1960...
zenodo.org
Realigning incentives for biomedical researchers and journals through researcher-shared outputs
In this preprint the authors propose a shift in what counts in the biomedical sciences: researchers should be recognized for what they choose to share on their own terms and timeline (for example as p...
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Junyue Cao @junyuecao.bsky.social · 16/04/2026
Excited to share our new paper @nature.com! We developed PerturbFate, a scalable single-cell platform to discover how diverse genetic perturbations converge on a shared drug-resistant cell state, and key programs driving it, led by our incredible Zihan Xu from @rockefeller.edu rdcu.be/fdC14
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Niklas Kempynck @niklaskemp.bsky.social · 08/04/2026
CREsted is finally out! You can find the article, together with a summarizing Research Briefing, in thread. 🦎
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Jay Shendure @jshendure.bsky.social · 10/04/2026
Latest from Shendure & Qiu labs (@cxqiu.bsky.social) )! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
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cxqiu.bsky.social @cxqiu.bsky.social · 09/04/2026
New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...
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Troy McDiarmid @troymcdiarmid.bsky.social · 02/04/2026
Stoked to announce that I’m starting a lab as an Assistant Professor in the School of Biomedical Engineering and Centre for Brain Health at UBC! mcdiarmid-lab.sbme.ubc.ca Recruiting at all levels - please share the word! Cheers and happy long weekend all!
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 24/03/2026
1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team! #napari #bioimageanalysis #MCP @biohub
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Waggoner Lab @labwaggoner.bsky.social · 20/03/2026
AP-1 mediates cellular adaptation and memory formation @natcomms.nature.com @pennmedicine.bsky.social @arjunraj.bsky.social @penngenetics.bsky.social www.nature.com/articles/s41...
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John Doench @johndoench.bsky.social · 15/03/2026
I mean, these are always good. But this is So Good. Nitrogen, Ammonia, and the Strait of Hormuz | Science | AAAS www.science.org/content/blog...
science.org
Nitrogen, Ammonia, and the Strait of Hormuz
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Alex Schier @schierlab.bsky.social · 12/03/2026
Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Will Chen @chenomics.bsky.social · 13/02/2026
We have significantly improved the protocol for recording CRE activities and orders with ENGRAM. We also designed new plasmids for easier cloning. Great work with @jennynathans.bsky.social, @troymcdiarmid.bsky.social and @jshendure.bsky.social . Happy recording!!
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Sudarshan Pinglay @sudpinglay.bsky.social · 23/01/2026
Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...
sciencedirect.com
Mammalian genome writing: Unlocking new length scales for genome engineering
The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…
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HHMI @hhmi-science.bsky.social · 18/11/2025
Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows
bit.ly
Summer Undergraduate Research Experience | HHMI
The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.
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allen institute @alleninstitute.org · 07/12/2025
Happy Birthday to the Seattle Hub for Synthetic Biology! 🎂🎉 OTD with @chanzuckerberg.bsky.social and @uwmedicine.bsky.social, we launched #SeaSynBio with the goal to build tech that allows cells to record their own histories. 🔗 alleninstitute.org/division/seattle…
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Zeitlinger Lab @zeitlingerlab.bsky.social · 19/11/2025
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)
biorxiv.org
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
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Troy McDiarmid @troymcdiarmid.bsky.social · 12/11/2025
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
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Nature Biotechnology @natbiotech.nature.com · 11/11/2025
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu
go.nature.com
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology
Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.
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Nick Page @nicholaspage.bsky.social · 06/11/2025
🚀 Very excited to share the first major work from my PhD!! We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬 www.biorxiv.org/content/10.1...
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.
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cxqiu.bsky.social @cxqiu.bsky.social · 04/11/2025
Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/
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Giulia Boezio @giulia-boezio.bsky.social · 26/10/2025
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions 🧵👇 www.biorxiv.org/content/10.1...
biorxiv.org
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
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Michael Hoffman @michaelhoffman.bsky.social · 22/10/2025
This is one of the coolest figures I've seen in a while
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