Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection.
Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social
www.nature.com/articles/s41...
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
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
the treasure trove of all sequencing datasets
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
🚨New preprint just dropped 🚨
medrxiv.org/content/10.1101/2025.06.24.25330216
The main output from my PhD is finally public and we’re SUPER excited about the findings! If you’re interested in what we learnt about IBD with a massive 700+ sample sc-eQTL dataset of the gut, read on!
Had a lot of fun writing this “tools of the trade” highlight for our Variant-EFFECTS technology. Check it out! 🛠️
11.06.2025 14:01 — 👍 13 🔁 7 💬 0 📌 1
Standard methods are equivalent to a flashlight, looking at each gene independently. We combine signals from multiple genes, turning a floodlight onto the genome.
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
08.06.2025 17:38 — 👍 91 🔁 33 💬 6 📌 4Huge congrats Jeff!
05.06.2025 01:47 — 👍 2 🔁 0 💬 0 📌 0
Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart
www.biorxiv.org/content/10.1...
I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
Excited to see this out, and really thankful for @anshulkundaje.bsky.social @sbmontgom.bsky.social and everyone in both of their labs who contributed to this work to make it possible!
19.02.2025 19:11 — 👍 5 🔁 2 💬 1 📌 0This was a really fun collaboration with @amarderstein.bsky.social where we explored some of the interesting relationships between context-specific non-coding variant effects, disease, and evolution using deep learning models of chromatin accessibility in the brain and heart.
19.02.2025 19:11 — 👍 15 🔁 8 💬 1 📌 0
New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social !
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
Submissions for ASHG 2025’s Featured Symposium are due Feb 10 at 5:00 pm ET!
Let me know if you have any questions. We're excited to see a wide range of proposals, ranging from AI/ML applications, clinical genetics, women's health, and more.
www.ashg.org/meetings/202...
Marker paper of the new dGTEx consortium is now published, describing the development of a new reference dataset for genomics research across human and non-human development!
www.nature.com/articles/s41...
Our new perspective article describing the human and non-human primate developmental GTEx projects is now out in
@nature.com! We outline the scope, vision, opportunities and challenges of these projects here:
www.nature.com/articles/s41...
relationship of complete blood count setpoint metrics to 10-year mortality
A new study this week showed how the most common blood test performed-—the CBC, complete blood count—contains a treasure chest of information that we are missing in reporting out to patients and doctors.
erictopol.substack.com/p/your-lab-t...
Our blood tests are interpreted by average reference values. That's missing a lot of rich information!
Each person has their own tightly regulated setpoints. One healthy person's complete blood count setpoint can be differentiated from 98% of other healthy adults.
www.nature.com/articles/s41...
“our analyses suggest that less than 1% of blastocysts are fully euploid, and that many embryos possess low-level mosaic clones that are not captured during biopsy”
02.12.2024 16:52 — 👍 1 🔁 0 💬 0 📌 0
Approximate Bayesian computation supports a high incidence of chromosomal mosaicism in blastocyst-stage human embryos https://www.biorxiv.org/content/10.1101/2024.11.26.625484v1
02.12.2024 16:35 — 👍 7 🔁 4 💬 1 📌 1
What cell types drive congenital heart defects (CHD)?
Some new answers in our latest preprint, where we explored:
1). Key cell types contributing to CHD genetics
2). Impact of noncoding variants on CHD risk
https://www.medrxiv.org/content/10.1101/2024.11.20.24317557v1
Our recent study in Cell Metabolism provides compelling evidence that chromatin accessibility and transcription factor network remodeling in aging reflect the predictable degrading effects of a mechanism initially driving organismal maturation.
Link: doi.org/10.1016/j.cmet.2024.06.006
Thread 🧵👇1/9
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
24.11.2024 10:32 — 👍 36 🔁 19 💬 0 📌 2