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Reposted by Andrew Marderstein

Anshul Kundaje @anshulkundaje.bsky.social · Aug 19

@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

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Reposted by Andrew Marderstein

Greg Findlay @gregfindlay.bsky.social · Aug 18

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 (...

www.medrxiv.org

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Reposted by Andrew Marderstein

Caleb Lareau @caleblareau.bsky.social · Jul 22

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/

the treasure trove of all sequencing datasets

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Reposted by Andrew Marderstein

Tobi Alegbe @tobioinformatics.bsky.social · Jul 8

🚨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!

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Michael Montgomery @michaeltmont.bsky.social · Jun 11

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 · Jun 11

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

Measuring the effects of regulatory variants in an endogenous context

Nature Reviews Genetics, Published online: 11 June 2025; doi:10.1038/s41576-025-00863-wIn this Tools of the Trade article, Michael Montgomery presents Variant-EFFECTS, a high-throughput and generalizable approach that combines prime editing, flow cytometry, sequencing, and computational analysis to quantify the effects of regulatory variants.

www.nature.com

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Reposted by Andrew Marderstein

Kate (Kathryn) Lawrence @itskatelawrence.bsky.social · Jun 8

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”? 🧵 ⬇️

Standard methods are equivalent to a flashlight, looking at each gene independently. We combine signals from multiple genes, turning a floodlight onto the genome.

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Andrew Marderstein @amarderstein.bsky.social · Jun 5

Huge congrats Jeff!

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Reposted by Andrew Marderstein

Jacob Schreiber @jmschreiber91.bsky.social · Feb 24

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...

www.biorxiv.org

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Reposted by Andrew Marderstein

Jeremy Berg @jeremymberg.bsky.social · Feb 22

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

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Soumya Kundu @soumyakundu.bsky.social · Feb 19

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!

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Soumya Kundu @soumyakundu.bsky.social · Feb 19

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 · Feb 19

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...

www.biorxiv.org

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Andrew Marderstein @amarderstein.bsky.social · Feb 19

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...

www.biorxiv.org

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Andrew Marderstein @amarderstein.bsky.social · Feb 6

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: [email protected] Looking to make your mark on th...

www.ashg.org

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Andrew Marderstein @amarderstein.bsky.social · Jan 15

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...

www.nature.com

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Tim Coorens @timcoorens.bsky.social · Jan 15

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...

www.nature.com

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Reposted by Andrew Marderstein

Eric Topol @erictopol.bsky.social · Dec 14

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...

relationship of complete blood count setpoint metrics to 10-year mortality

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Eric Topol @erictopol.bsky.social · Dec 11

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...

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Andrew Marderstein @amarderstein.bsky.social · Dec 2

“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 · Dec 2

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

www.biorxiv.org

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bioRxiv Genetics @biorxiv-genetic.bsky.social · Dec 2

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

www.biorxiv.org

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Rosa Ma @rosaxma.bsky.social · Nov 25

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

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Christian Nefzger @nefzgerlab.bsky.social · Nov 18

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

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bioRxiv Genetics @biorxiv-genetic.bsky.social · Nov 24

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

www.biorxiv.org

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