@sbmontgom.bsky.social and I wrote a Research Briefing on our recent Nature Genetics paper! We summarize the study, along with some behind-the-scenes thoughts on how the project came together and what we learned along the way. www.nature.com/articles/s41...

Non-coding variant prioritization based on cell type, developmental stage and evolutionary constraint - Nature Genetics

By using deep learning sequence models, we predict non-coding variant effects across the allele frequency spectrum in over 100 fetal and adult cell types. Linking these data with evolutionary constrai...

nature.com

Andrew Marderstein@amarderstein.bsky.social · 2mo ago

Our latest is out in Nature Genetics with @soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social ! We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects. www.nature.com/articles/s41...

Our latest is out in Nature Genetics with @soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social ! We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects. www.nature.com/articles/s41...

Decoding common and rare noncoding variant effects across cellular and developmental contexts - Nature Genetics

This study contributes a resource of predicted effects of noncoding variants on chromatin accessibility and a method to identify noncoding variants with extreme regulatory effects, with application to...

nature.com

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...

Population-scale sequencing resolves determinants of persistent EBV DNA - Nature

Population-scale WGS reveals genetic determinants of persistent EBV DNA, linking immune regulation—especially antigen processing and MHC class II variation—to EBV persistence and heterogeneous di...

nature.com

@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

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 (...

medrxiv.org

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! 🛠️

Nature Reviews Genetics@natrevgenet.nature.com · last yr.

New online! Measuring the effects of regulatory variants in an endogenous context

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”? 🧵 ⬇️

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...

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal...

biorxiv.org

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.

the word irony is written on a white background

ALT: the word irony is written on a white background

media.tenor.com

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!

This 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.

Andrew Marderstein@amarderstein.bsky.social · last yr.

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...

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...

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal...

biorxiv.org

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...

Featured Symposia

ASHG’s Featured Symposium are a part of the most premier science at the Annual Meeting, featuring 8,000 of the world’s leading geneticists. Questions: programs@ashg.org Looking to make your mark on th...

ashg.org

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...

The human and non-human primate developmental GTEx projects - Nature

The developmental Genotype-Tissue Expression (dGTEx) projects will catalogue and integrate gene expression, regulation and genetics data across 120 human donors from birth to adulthood with developmen...

nature.com

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...

The human and non-human primate developmental GTEx projects - Nature

The developmental Genotype-Tissue Expression (dGTEx) projects will catalogue and integrate gene expression, regulation and genetics data across 120 human donors from birth to adulthood with developmen...

nature.com

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”

bioRxiv Genetics@biorxiv-genetic.bsky.social · 2y ago

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

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

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

Chromosome mis-segregation is common in human meiosis and mitosis, and the resulting aneuploidies ar

biorxiv.org

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

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1

Mapping enhancers and their target genes in specific cell types is crucial for understanding gene re

biorxiv.org