Jay Shendure
@jshendure.bsky.social
shendure lab |. krishna.gs.washington.edu
Reposted by Jay Shendure
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
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
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.
go.nature.com
November 12, 2025 at 6:06 PM
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
Reposted by Jay Shendure
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
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.
go.nature.com
November 11, 2025 at 4:36 PM
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
Reposted by Jay Shendure
🚀 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...
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...
November 6, 2025 at 11:57 PM
🚀 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...
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...
Reposted by Jay Shendure
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.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
November 5, 2025 at 3:09 PM
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.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
Reposted by Jay Shendure
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/
November 4, 2025 at 3:10 PM
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/
Reposted by Jay Shendure
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...
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...
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...
www.biorxiv.org
October 26, 2025 at 5:15 PM
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...
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...
Reposted by Jay Shendure
This is one of the coolest figures I've seen in a while
Transcriptional interferences ensure one olfactory receptor per ant neuron
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
October 22, 2025 at 8:44 PM
This is one of the coolest figures I've seen in a while
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 14, 2025 at 6:45 PM
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jay Shendure
Developmental Biology and Disability.
“Developmental biology is fundamentally beautiful. We are no less beautiful for our variation. Instead, perhaps we are more so. Perhaps we are remarkable. Perhaps we are full of wonder.”
Insightful post by Bethan ⬇️👀
thenode.biologists.com/developmenta...
“Developmental biology is fundamentally beautiful. We are no less beautiful for our variation. Instead, perhaps we are more so. Perhaps we are remarkable. Perhaps we are full of wonder.”
Insightful post by Bethan ⬇️👀
thenode.biologists.com/developmenta...
Developmental Biology and Disability - the Node
Hopeful monsters. Morphospace. Mutation. Natural variation. Mutagenesis screens. Polymorphism. Deformity. Phenotype. Disease. Adaptation. Anomaly.
thenode.biologists.com
October 6, 2025 at 12:05 PM
Developmental Biology and Disability.
“Developmental biology is fundamentally beautiful. We are no less beautiful for our variation. Instead, perhaps we are more so. Perhaps we are remarkable. Perhaps we are full of wonder.”
Insightful post by Bethan ⬇️👀
thenode.biologists.com/developmenta...
“Developmental biology is fundamentally beautiful. We are no less beautiful for our variation. Instead, perhaps we are more so. Perhaps we are remarkable. Perhaps we are full of wonder.”
Insightful post by Bethan ⬇️👀
thenode.biologists.com/developmenta...
Reposted by Jay Shendure
awesome new work by my @gladstoneinst.bsky.social and @ucsanfrancisco.bsky.social colleagues incl @vram142.bsky.social on how chromatin remodelers affect mesoscale chromatin organization www.science.org/doi/10.1126/...
ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes
Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...
www.science.org
October 2, 2025 at 6:18 PM
awesome new work by my @gladstoneinst.bsky.social and @ucsanfrancisco.bsky.social colleagues incl @vram142.bsky.social on how chromatin remodelers affect mesoscale chromatin organization www.science.org/doi/10.1126/...
Reposted by Jay Shendure
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
September 26, 2025 at 6:06 PM
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
Reposted by Jay Shendure
Hugely thankful for this 🙏. We will do our best to make the most of it. @erc.europa.eu!
Congratulations to @gregfindlay.bsky.social on being awarded a €1.5 million Starting Grant from the @erc.europa.eu to take a closer look at possible disease variants hiding in the dark genome.
www.crick.ac.uk/news/2025-09...
www.crick.ac.uk/news/2025-09...
€1.5 million to uncover disease risk hiding in non-coding DNA
Greg Findlay, Group Leader of the Genome Function Laboratory at the Francis Crick Institute, has been awarded a Starting Grant from the European Research Council for €1.5 million to take a deep dive i...
www.crick.ac.uk
September 4, 2025 at 6:40 PM
Hugely thankful for this 🙏. We will do our best to make the most of it. @erc.europa.eu!
Reposted by Jay Shendure
Our latest research is out today on @medrxivpreprint.bsky.social:
www.medrxiv.org/content/10.1...
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk.
Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
www.medrxiv.org/content/10.1...
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk.
Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk
Germline pathogenic BRCA1 variants predispose women to breast and ovarian cancer. Despite accumulation of functional evidence for variants in BRCA1 , over half of reported single-nucleotide variants (...
www.medrxiv.org
August 18, 2025 at 7:33 AM
Our latest research is out today on @medrxivpreprint.bsky.social:
www.medrxiv.org/content/10.1...
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk.
Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
www.medrxiv.org/content/10.1...
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk.
Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
Thrilled at the news of @10xgenomics.bsky.social ' acquisition of Scale Bio which I co-founded with Frank Steemers (ex-Illumina), @coletrapnell.bsky.social and Garry Nolan . Further thrilled to joining 10X Genomics as an scientific advisor and for the synergies that lie ahead!
This acquisition will bring together two pioneering companies with a shared vision: to make single cell analysis more powerful, affordable and accessible to researchers worldwide.
Learn more: bit.ly/4mAWAS8
Learn more: bit.ly/4mAWAS8
August 7, 2025 at 11:32 PM
Thrilled at the news of @10xgenomics.bsky.social ' acquisition of Scale Bio which I co-founded with Frank Steemers (ex-Illumina), @coletrapnell.bsky.social and Garry Nolan . Further thrilled to joining 10X Genomics as an scientific advisor and for the synergies that lie ahead!
Reposted by Jay Shendure
Two new preprints from the @arjunraj.bsky.social on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
July 15, 2025 at 1:28 PM
Two new preprints from the @arjunraj.bsky.social on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
Reposted by Jay Shendure
🚨 Most variant screens measure growth or abundance. What do they miss? That variants impact a spectrum of protein and cellular phenotypes. Variant in situ sequencing (VIS-seq) finds what’s missing: image cells 🔬 first, decode later, revealing multi-scale phenotypes for thousands of variants.👇
1/9
1/9
July 7, 2025 at 2:44 AM
🚨 Most variant screens measure growth or abundance. What do they miss? That variants impact a spectrum of protein and cellular phenotypes. Variant in situ sequencing (VIS-seq) finds what’s missing: image cells 🔬 first, decode later, revealing multi-scale phenotypes for thousands of variants.👇
1/9
1/9
Reposted by Jay Shendure
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
June 28, 2025 at 10:38 AM
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
Reposted by Jay Shendure
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae | Science www.science.org/doi/10.1126/... 😍
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous ...
www.science.org
June 20, 2025 at 10:36 AM
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae | Science www.science.org/doi/10.1126/... 😍
Reposted by Jay Shendure
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
June 13, 2025 at 4:30 AM
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
Reposted by Jay Shendure
Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...
Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens
Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular str...
www.biorxiv.org
May 25, 2025 at 11:00 AM
Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...
Reposted by Jay Shendure
New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)
Lineage recording in monoclonal gastruloids reveals heritable modes of early development
Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully contr...
www.biorxiv.org
May 27, 2025 at 2:57 PM
New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)
Reposted by Jay Shendure
CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
A multi-kingdom genetic barcoding system for precise clone isolation - Nature Biotechnology
A barcoded CRISPR base editing system isolates target clones from complex mammalian, yeast and bacterial populations.
www.nature.com
May 21, 2025 at 1:56 PM
CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
Reposted by Jay Shendure
Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Massively parallel jumping assay decodes Alu retrotransposition activity - Nature Communications
Here, the authors develop a high-throughput assay to measure the jumping potential of thousands of transposons in parallel.
www.nature.com
May 9, 2025 at 3:50 AM
Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jay Shendure
Very grateful to receive the Searle Scholars Award, especially during this challenging time! This support will help our lab realize our vision of genomic recording for reconstructing the mammalian cell fate decision. searlescholars.org/2025/04/14/s...
SEARLE SCHOLARS PROGRAM NAMES 15 SCIENTISTS AS SEARLE SCHOLARS FOR 2025
Members of the new class of Searle Scholars pursue ground-breaking research in chemistry and the biomedical sciences. Each receives an award of $300,000 in flexible funding to support his, her, or …
searlescholars.org
May 6, 2025 at 2:46 PM
Very grateful to receive the Searle Scholars Award, especially during this challenging time! This support will help our lab realize our vision of genomic recording for reconstructing the mammalian cell fate decision. searlescholars.org/2025/04/14/s...
Reposted by Jay Shendure
Happy to share our new review on molecular circuits for genomic recording with @chenomics.bsky.social! Here, we present our views on the remaining challenges in the field of genomic recording for reconstructing cell-fate decisions. (1/2)
Online now -- a new Review:
"Molecular circuits for genomic recording of cellular events"
by Wei Chen & Junhong Choi (@choijunhong.bsky.social)
FREE to read till June 25th using this link:
authors.elsevier.com/a/1l2gMcQbJF...
"Molecular circuits for genomic recording of cellular events"
by Wei Chen & Junhong Choi (@choijunhong.bsky.social)
FREE to read till June 25th using this link:
authors.elsevier.com/a/1l2gMcQbJF...
May 6, 2025 at 2:39 PM
Happy to share our new review on molecular circuits for genomic recording with @chenomics.bsky.social! Here, we present our views on the remaining challenges in the field of genomic recording for reconstructing cell-fate decisions. (1/2)