Andrew Marderstein
@amarderstein.bsky.social
Human geneticist studying cancer at MSK. Prev. postdoc at Stanford and BS + PhD at Cornell. avid skier, runner, and Yankee fan.
Pinned
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
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...
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...
Reposted by Andrew Marderstein
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Andrew Marderstein
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
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
August 18, 2025 at 7:33 AM
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
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
Reposted by Andrew Marderstein
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/
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/
July 22, 2025 at 9:59 PM
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/
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/
Reposted by Andrew Marderstein
🚨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!
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!
July 8, 2025 at 8:52 AM
🚨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!
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!
Reposted by Andrew Marderstein
Had a lot of fun writing this “tools of the trade” highlight for our Variant-EFFECTS technology. Check it out! 🛠️
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
June 11, 2025 at 2:01 PM
Had a lot of fun writing this “tools of the trade” highlight for our Variant-EFFECTS technology. Check it out! 🛠️
Reposted by Andrew Marderstein
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”? 🧵 ⬇️
June 8, 2025 at 5:39 PM
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”? 🧵 ⬇️
Reposted by Andrew Marderstein
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...
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
February 24, 2025 at 4:45 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Andrew Marderstein
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.
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
February 22, 2025 at 10:19 AM
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.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
Reposted by Andrew Marderstein
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!
February 19, 2025 at 7:11 PM
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!
Reposted by Andrew Marderstein
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.
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...
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
February 19, 2025 at 7:11 PM
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.
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...
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
February 19, 2025 at 1:32 PM
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...
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...
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
February 6, 2025 at 7:25 PM
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...
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...
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
January 15, 2025 at 6:25 PM
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...
www.nature.com/articles/s41...
Reposted by Andrew Marderstein
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
January 15, 2025 at 4:40 PM
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...
Reposted by Andrew Marderstein
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...
erictopol.substack.com/p/your-lab-t...
December 14, 2024 at 7:55 PM
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...
erictopol.substack.com/p/your-lab-t...
Reposted by Andrew Marderstein
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...
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...
December 11, 2024 at 4:18 PM
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...
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”
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
www.biorxiv.org
December 2, 2024 at 4:52 PM
“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”
Reposted by Andrew Marderstein
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
www.biorxiv.org
December 2, 2024 at 4:35 PM
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
Reposted by Andrew Marderstein
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
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
November 25, 2024 at 8:08 PM
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
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
Reposted by Andrew Marderstein
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
Link: doi.org/10.1016/j.cmet.2024.06.006
Thread 🧵👇1/9
November 18, 2024 at 10:09 AM
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
Link: doi.org/10.1016/j.cmet.2024.06.006
Thread 🧵👇1/9
Reposted by Andrew Marderstein
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
www.biorxiv.org
November 24, 2024 at 10:32 AM
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1