Jesse Engreitz
@jengreitz.bsky.social
Assistant Professor @ Stanford Genetics & BASE Initiative. Mapping the regulatory code of the human genome to understand heart development and disease. www.engreitzlab.org
Reposted by Jesse Engreitz
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Jesse Engreitz
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
Reposted by Jesse Engreitz
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 Jesse Engreitz
I'm happy to share that our gReLU package is now published in Nature Methods!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods
gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.
www.nature.com
October 15, 2025 at 9:21 PM
I'm happy to share that our gReLU package is now published in Nature Methods!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jesse Engreitz
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
nyti.ms
October 8, 2025 at 11:29 PM
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
Reposted by Jesse Engreitz
i desperately want everyone involved in the destruction of USAID to have to, st the very least, answer to the american people for the suffering and misery they have caused apnews.com/article/myan...
Starving children screaming for food as US aid cuts unleash devastation and death across Myanmar
U.S. Secretary of State Marco Rubio has repeatedly said “no one has died" because of his government’s decision to gut its foreign aid program.
apnews.com
October 8, 2025 at 2:59 PM
i desperately want everyone involved in the destruction of USAID to have to, st the very least, answer to the american people for the suffering and misery they have caused apnews.com/article/myan...
Reposted by Jesse Engreitz
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
www.nature.com
October 6, 2025 at 6:57 AM
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Reposted by Jesse Engreitz
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency
In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...
www.biorxiv.org
October 3, 2025 at 3:09 PM
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Reposted by Jesse Engreitz
HHMI adopts Plan U journals.plos.org/plosbiology/...
September 24, 2025 at 6:08 PM
HHMI adopts Plan U journals.plos.org/plosbiology/...
Reposted by Jesse Engreitz
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
September 24, 2025 at 9:45 PM
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
Reposted by Jesse Engreitz
Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!
An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates https://www.biorxiv.org/content/10.1101/2025.09.21.676939v1
September 22, 2025 at 7:05 PM
Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!
Reposted by Jesse Engreitz
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Jesse Engreitz
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 19, 2025 at 2:09 PM
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Reposted by Jesse Engreitz
Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
September 19, 2025 at 6:20 AM
Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
Reposted by Jesse Engreitz
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene by the @basvansteensellab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 19, 2025 at 7:50 AM
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene by the @basvansteensellab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
September 19, 2025 at 3:03 AM
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
Reposted by Jesse Engreitz
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks - Nature Genetics
Massively parallel reporter assay in primary human CD4+ T cells and bulk and single-cell CRISPR-interference screens identify candidate causal variants linked to autoimmune disease risk that modulate ...
www.nature.com
September 18, 2025 at 8:50 PM
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Reposted by Jesse Engreitz
@riyavsinha.bsky.social @jengreitz.bsky.social sky.social @anshulkundaje.bsky.social y.social have made the ENCODE-rE2G data available to browse through the E2G portal, a custom-built extension of the Platform 👇
We plan to further integrate their data 👀
e2g.stanford.edu
We plan to further integrate their data 👀
e2g.stanford.edu
E2G
E2G is a tool based on the Open Targets Platform for predicting enhancer-gene interactions.
e2g.stanford.edu
September 18, 2025 at 10:39 AM
@riyavsinha.bsky.social @jengreitz.bsky.social sky.social @anshulkundaje.bsky.social y.social have made the ENCODE-rE2G data available to browse through the E2G portal, a custom-built extension of the Platform 👇
We plan to further integrate their data 👀
e2g.stanford.edu
We plan to further integrate their data 👀
e2g.stanford.edu
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Jesse Engreitz
Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
Faculty Recruitment
chemh.stanford.edu
September 17, 2025 at 5:54 PM
Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
Reposted by Jesse Engreitz
www.cell.com/cell/abstrac...
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle integrates stolen chloroplasts for animal photosynthesis
Sea slugs steal foreign chloroplasts and store them in specialized organelles that
facilitate photosynthesis and eventual digestion to mediate starvation resistance.
www.cell.com
September 17, 2025 at 5:04 PM
www.cell.com/cell/abstrac...
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
Reposted by Jesse Engreitz
Most neurodevelopmental disorders are caused by having 1 functional gene copy. Using SCN2A, we show that upregulating the functional copy rescues neuronal phenotypes. Amazing work with @neurobender.bsky.social led by Serena Tamura, Andrew Nelson, Perry Spratt & others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CRISPR activation for SCN2A-related neurodevelopmental disorders | Nature
www.nature.com
September 17, 2025 at 3:13 PM
Most neurodevelopmental disorders are caused by having 1 functional gene copy. Using SCN2A, we show that upregulating the functional copy rescues neuronal phenotypes. Amazing work with @neurobender.bsky.social led by Serena Tamura, Andrew Nelson, Perry Spratt & others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jesse Engreitz
I am tremendously excited to share our work revealing the epigenomic landscape of single vascular cells. We discover that enhancers are not only cell type but vascular site specific and regulate the genetic drivers of disease risk. Let's dive in! 🧬👇 #epigenetics
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci | Molecular Systems Biology
imageimageVascular sites have distinct susceptibility to disease. Here, through single cell epigenomic profiling and predictive machine learning modeling, this study revealed that regulatory enhancers are vascular site specific, providing insight ...
www.embopress.org
September 10, 2025 at 3:54 PM
I am tremendously excited to share our work revealing the epigenomic landscape of single vascular cells. We discover that enhancers are not only cell type but vascular site specific and regulate the genetic drivers of disease risk. Let's dive in! 🧬👇 #epigenetics
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Reposted by Jesse Engreitz
Hard to understate how wonderful it is to see our manuscript in print today @natcardiovascres.nature.com. We discover ADAR1 to control dsRNA sensor MDA5 in atherosclerosis, creating a new paradigm of endogenous dsRNA sensing as a causal mechanism of disease. Let's get into it 👇 #RNAsky rdcu.be/eGEyu
Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of the RNA sensor MDA5 in atherosclerosis
Nature Cardiovascular Research - Weldy et al. show that smooth muscle expression of the RNA editing enzyme ADAR1 regulates activation of the double-stranded RNA sensor MDA5 in a novel mechanism of...
rdcu.be
September 16, 2025 at 12:48 PM
Hard to understate how wonderful it is to see our manuscript in print today @natcardiovascres.nature.com. We discover ADAR1 to control dsRNA sensor MDA5 in atherosclerosis, creating a new paradigm of endogenous dsRNA sensing as a causal mechanism of disease. Let's get into it 👇 #RNAsky rdcu.be/eGEyu
Reposted by Jesse Engreitz
Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...
Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design
The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...
www.biorxiv.org
September 7, 2025 at 5:02 PM
Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...