Assistant Professor @ Stanford Genetics & BASE Initiative. Mapping the regulatory code of the human genome to understand heart development and disease. www.engreitzlab.org
Jesse Engreitz
Hello #world, meet 1,000× Expansion Microscopy.
A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy.
Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us.
Story: www.biorxiv.org/content/10.6...
Ali Shaib
Exciting single cell eQTL study of IBD — showing how cell type resolved QTLs at scale find colocalized signals for over half of the GWAS signals
www.nature.com/articles/s41...
1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...
Jesse Engreitz
Video
How can researchers access and build on IGVF resources?
In this workshop presentation, Michael Love, PhD, highlights the IGVF data portal, catalog, APIs, and computational tools supporting reproducible functional genomics research.
youtu.be/W6Mr7O7gUNY
Planning a Perturb-seq experiment? Building virtual cells?
First step to good models is good data. How many cells to profile? How deeply to sequence? What statistical power?
Check out PerturbPlan — new tool from Ziang Niu in Katsevich Lab
www.perturbplan.com
www.biorxiv.org/content/10.6...
Now out @natbiotech.nature.com ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones.
🚨🧪🧵URGENT INPUT NEEDED: NIH asks input for next strategic plan-including emphasis on non-animal models (NAMs) to replace animals. Per NIH insider, anti-animal responses now outnumber scientists 200-700x. Please please provide input. Deadline: May 26, 11:59 PM ET.
grants.nih.gov/news-events/...
Super chuffed to see our latest preprint is out: Polygenic risk of cardiovascular disease manifests in cardiac structure and function 👉 www.medrxiv.org/content/10.6...
A collaborative study led by exceptional PhD student Benedetta Felici!
www.biorxiv.org
I'm excited to share that our work studying gene dosage response curves (GDRCs) is now out in Cell Genomics (@cellpress.bsky.social).
www.cell.com/cell-genomic...
[1/n]
Jesse Engreitz
Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵
www.science.org/doi/10.1126/...
Milind et al. explore why loss-of-function variants and duplications tend to have
average effects in the same direction on 94 complex traits. Using gene dosage response
curves (GDRCs), they gather evi...
Single-cell mapping of cis-expression quantitative trait loci in inflammatory bowel disease revealed distal, enhancer-enriched variants detected at the cell-type level more frequently co-loc...
How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...
A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from
Pieter Mestdagh in Ghent. TL;DR we show that many of lncRNA chromatin occupancy obtained are flawed www.biorxiv.org/content/10.1...
