Josh Popp
@jmpopp.bsky.social
Computational genomics PhD student at Johns Hopkins BME
Reposted by Josh Popp
We are excited to share the publication of our new paper "Univariate-guided sparse regression", with commentary by Larry Wasserman, Bin Yu, Lucas Janson, Cynthia Rudin and others.
hdsr.mitpress.mit.edu/pub/3i97j340...
Comments welcome!
hdsr.mitpress.mit.edu/pub/3i97j340...
Comments welcome!
Univariate-Guided Sparse Regression
hdsr.mitpress.mit.edu
October 23, 2025 at 6:52 AM
We are excited to share the publication of our new paper "Univariate-guided sparse regression", with commentary by Larry Wasserman, Bin Yu, Lucas Janson, Cynthia Rudin and others.
hdsr.mitpress.mit.edu/pub/3i97j340...
Comments welcome!
hdsr.mitpress.mit.edu/pub/3i97j340...
Comments welcome!
Reposted by Josh Popp
Exciting updates!!
(1) I just opened my lab at Boston Children’s Hospital (Harvard-affiliated)
(2) I’m hiring a postdoc focused on integrating GWAS and functional genomic data. Reach out if you’re interested or connect at ASHG next week!
(3) Learn more at stroberlab.com
(1) I just opened my lab at Boston Children’s Hospital (Harvard-affiliated)
(2) I’m hiring a postdoc focused on integrating GWAS and functional genomic data. Reach out if you’re interested or connect at ASHG next week!
(3) Learn more at stroberlab.com
Strober Lab
The Strober lab is a computational group at Boston Children's Hospital (a Harvard Medical School affiliated hospital) focused on developing statistical and machine learning tools applied to human gene...
stroberlab.com
October 7, 2025 at 6:55 PM
Exciting updates!!
(1) I just opened my lab at Boston Children’s Hospital (Harvard-affiliated)
(2) I’m hiring a postdoc focused on integrating GWAS and functional genomic data. Reach out if you’re interested or connect at ASHG next week!
(3) Learn more at stroberlab.com
(1) I just opened my lab at Boston Children’s Hospital (Harvard-affiliated)
(2) I’m hiring a postdoc focused on integrating GWAS and functional genomic data. Reach out if you’re interested or connect at ASHG next week!
(3) Learn more at stroberlab.com
Reposted by Josh Popp
I’ve spent a good chunk of my career relying on American science and engineering to keep me alive. Yesterday, RFK Jr. testified at the U.S. Senate Finance Committee. It was sad to see him try to destroy the life’s work of so many American scientists. He shouldn’t be in this job.
September 5, 2025 at 10:17 PM
I’ve spent a good chunk of my career relying on American science and engineering to keep me alive. Yesterday, RFK Jr. testified at the U.S. Senate Finance Committee. It was sad to see him try to destroy the life’s work of so many American scientists. He shouldn’t be in this job.
Reposted by Josh Popp
Excited to share our latest manuscript, "Exposure accumulation drives age-dependent disease architectures and polygenic risk scores," led by Xilin Jiang: www.medrxiv.org/content/10.1...
I am attempting an explainer thread for the first time here:
(I am usually too exhausted to post one)
I am attempting an explainer thread for the first time here:
(I am usually too exhausted to post one)
Exposure accumulation drives age-dependent disease architectures and polygenic risk scores
Our understanding of the dependence of the genetic and environmental architecture of common diseases on age is incomplete. Here, we use longitudinal data to quantify age-dependent genetic and environm...
www.medrxiv.org
September 2, 2025 at 11:08 PM
Excited to share our latest manuscript, "Exposure accumulation drives age-dependent disease architectures and polygenic risk scores," led by Xilin Jiang: www.medrxiv.org/content/10.1...
I am attempting an explainer thread for the first time here:
(I am usually too exhausted to post one)
I am attempting an explainer thread for the first time here:
(I am usually too exhausted to post one)
Reposted by Josh Popp
The startup named Herasightm after the goddess who threw her disabled child off a mountain, seems focused on public outreach using embryo selection for IQ to win over far rightwing pseuds & techbros
August 2, 2025 at 2:19 AM
The startup named Herasightm after the goddess who threw her disabled child off a mountain, seems focused on public outreach using embryo selection for IQ to win over far rightwing pseuds & techbros
Reposted by Josh Popp
Numerous FAQs & think pieces were written promising GWAS participants & the broader public that sociogenomics was focused on education improvement, environmental interventions, and away from the hereditarian past. All quickly betrayed.
August 2, 2025 at 2:15 AM
Numerous FAQs & think pieces were written promising GWAS participants & the broader public that sociogenomics was focused on education improvement, environmental interventions, and away from the hereditarian past. All quickly betrayed.
Reposted by Josh Popp
It is depressing, but all too predictable, how swiftly we’ve gone from the Social Science Genetic Association Consortium offering reassurances about the uses of behavioural polygenic scores to one of their lead authors marketing embryo selection for IQ
August 2, 2025 at 2:15 AM
It is depressing, but all too predictable, how swiftly we’ve gone from the Social Science Genetic Association Consortium offering reassurances about the uses of behavioural polygenic scores to one of their lead authors marketing embryo selection for IQ
Reposted by Josh Popp
This is what can be achieved today due to longstanding federal support of academic basic science alongside close partnership of universities, private industry and NIH intramural initiatives. An ecosystem worth not just saving but doubling down on!
innovativegenomics.org/news/first-p...
innovativegenomics.org/news/first-p...
First Patient Treated with Personalized CRISPR Therapy, Developed in Just Six Months
The first on-demand CRISPR therapy for an infant with a rare metabolic disease developed by the IGI and collaborators around the world.
innovativegenomics.org
May 15, 2025 at 5:40 PM
This is what can be achieved today due to longstanding federal support of academic basic science alongside close partnership of universities, private industry and NIH intramural initiatives. An ecosystem worth not just saving but doubling down on!
innovativegenomics.org/news/first-p...
innovativegenomics.org/news/first-p...
Reposted by Josh Popp
1/n 🚨Very excited to share our recent work!🚨
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
May 5, 2025 at 7:07 PM
1/n 🚨Very excited to share our recent work!🚨
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
Reposted by Josh Popp
Remember when you first learned about genetics at school? All those fascinating examples of human traits that are each apparently determined by just a single gene? Time to check in on some of your favourites to see how they’re doing. 🧬🧵🧪 1/n
May 2, 2025 at 2:50 PM
Remember when you first learned about genetics at school? All those fascinating examples of human traits that are each apparently determined by just a single gene? Time to check in on some of your favourites to see how they’re doing. 🧬🧵🧪 1/n
Reposted by Josh Popp
I keep coming back to this pithy 1854 statement by Abraham Lincoln about “the legitimate object of government,” which the Trump administration is undermining by offloading to individuals tasks, including life or death matters, that are more effectively, efficiently and fairly done collectively.
May 1, 2025 at 10:25 AM
I keep coming back to this pithy 1854 statement by Abraham Lincoln about “the legitimate object of government,” which the Trump administration is undermining by offloading to individuals tasks, including life or death matters, that are more effectively, efficiently and fairly done collectively.
Reposted by Josh Popp
This framing is their framing, and NYT took the bait. The correct and accurate framing is: “Deep cuts to medical research threatens progress on cancer and heart disease research, costs the economy $80B, and threatens 300,000 jobs across red and blue states”
February 8, 2025 at 7:17 PM
This framing is their framing, and NYT took the bait. The correct and accurate framing is: “Deep cuts to medical research threatens progress on cancer and heart disease research, costs the economy $80B, and threatens 300,000 jobs across red and blue states”
Reposted by Josh Popp
The website for the NIH Office of Research on Women's Health has nearly been dismantled between yesterday morning and today. Piece by piece throughout the day. What, the new administration will no longer support or tolerate discussion of research affecting the health of >50% of humans? Seriously?!?
The entire website for the NIH Office of Research on Women's Health (ORWH) is very nearly stripped bare. This is so, so devastating. orwh.od.nih.gov/research/fun...
orwh.od.nih.gov
January 31, 2025 at 6:37 PM
The website for the NIH Office of Research on Women's Health has nearly been dismantled between yesterday morning and today. Piece by piece throughout the day. What, the new administration will no longer support or tolerate discussion of research affecting the health of >50% of humans? Seriously?!?
Reposted by Josh Popp
Academic workers across the country are organizing to call on our congressional representatives on Thursday, 1/30, at 3pm ET / 12pm PT to demand these restrictions be lifted immediately.
There will be a training over zoom at the beginning of the event.
Join us!
form.jotform.com/250226137228...
There will be a training over zoom at the beginning of the event.
Join us!
form.jotform.com/250226137228...
Join researchers across the country in fighting restrictions on the NIH
Please click the link to complete this form.
form.jotform.com
January 28, 2025 at 3:49 AM
Academic workers across the country are organizing to call on our congressional representatives on Thursday, 1/30, at 3pm ET / 12pm PT to demand these restrictions be lifted immediately.
There will be a training over zoom at the beginning of the event.
Join us!
form.jotform.com/250226137228...
There will be a training over zoom at the beginning of the event.
Join us!
form.jotform.com/250226137228...
Reposted by Josh Popp
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 12:13 AM
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
Reposted by Josh Popp
Very excited about this new work from our lab! Explainer thread coming soon
@minetoota.bsky.social
@minetoota.bsky.social
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq https://www.biorxiv.org/content/10.1101/2025.01.22.634424v1
January 24, 2025 at 4:45 PM
Very excited about this new work from our lab! Explainer thread coming soon
@minetoota.bsky.social
@minetoota.bsky.social
Reposted by Josh Popp
How population stratification makes environments look like genes. A short 🧵:
January 20, 2025 at 7:09 PM
How population stratification makes environments look like genes. A short 🧵:
Reposted by Josh Popp
First post in the Good Place! Our preprint on cellular behavior analysis in TCR T cells & cancer cell live-cell imaging data is out! This 3-year collaboration led by pd Archit Verma w/ Alex Marson & Julia Carnevale, with segmentation & tracking by @davidvv & team! www.biorxiv.org/content/10.1...
Cellular behavior analysis from live-cell imaging of TCR T cell–cancer cell interactions
T cell therapies, such as chimeric antigen receptor (CAR) T cells and T cell receptor (TCR) T cells, are a growing class of anti-cancer treatments. However, expansion to novel indications and beyond l...
www.biorxiv.org
November 26, 2024 at 2:01 AM
First post in the Good Place! Our preprint on cellular behavior analysis in TCR T cells & cancer cell live-cell imaging data is out! This 3-year collaboration led by pd Archit Verma w/ Alex Marson & Julia Carnevale, with segmentation & tracking by @davidvv & team! www.biorxiv.org/content/10.1...
Reposted by Josh Popp
A great paper and a great thread! One point that I partcularly liked was this one:
"In particular, [GWAS] variants can be trait specific in two ways: they can either affect a trait-specific gene or affect a pleiotropic gene in a context-specific manner."
"In particular, [GWAS] variants can be trait specific in two ways: they can either affect a trait-specific gene or affect a pleiotropic gene in a context-specific manner."
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
www.biorxiv.org
December 17, 2024 at 3:11 PM
A great paper and a great thread! One point that I partcularly liked was this one:
"In particular, [GWAS] variants can be trait specific in two ways: they can either affect a trait-specific gene or affect a pleiotropic gene in a context-specific manner."
"In particular, [GWAS] variants can be trait specific in two ways: they can either affect a trait-specific gene or affect a pleiotropic gene in a context-specific manner."
Reposted by Josh Popp
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
www.biorxiv.org
December 17, 2024 at 7:05 AM
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Reposted by Josh Popp
Why do association studies prioritize trait-specific variants???
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
December 17, 2024 at 7:04 AM
Why do association studies prioritize trait-specific variants???
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
Reposted by Josh Popp
Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Central control of dynamic gene circuits governs T cell rest and activation - Nature
Resting and activated T cell states are established by context-specific regulators and dynamic gene circuits.
www.nature.com
December 11, 2024 at 8:46 PM
Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Josh Popp
Excited to share our first foray into (noncoding) rare variant association testing: a probabilistic model that learns functional annotation importance and finds associations missed by existing methods. Anjali did a fantastic job with model assessment and scaling! www.medrxiv.org/content/10.1...
Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere
The increasing availability of whole-genome sequencing (WGS) has begun to elucidate the contribution of rare variants (RVs), both coding and non-coding, to complex disease. Multiple RV association tes...
www.medrxiv.org
December 9, 2024 at 5:03 PM
Excited to share our first foray into (noncoding) rare variant association testing: a probabilistic model that learns functional annotation importance and finds associations missed by existing methods. Anjali did a fantastic job with model assessment and scaling! www.medrxiv.org/content/10.1...
Reposted by Josh Popp
Our study is up! Context-specificity galore -- we explore genetic regulation of gene expression across many cell types and temporal states simultaneously in an efficient experimental system + scRNA-seq:
Excited to see our study on genetic regulation in heterogeneous differentiating cultures out in final form!
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6
Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures
Popp et al. generate dozens of cell types from 53 human iPSC lines in order to characterize
the dynamic genetic regulation of gene expression across early stages of cellular
differentiation. Accessing...
www.cell.com
December 5, 2024 at 4:20 PM
Our study is up! Context-specificity galore -- we explore genetic regulation of gene expression across many cell types and temporal states simultaneously in an efficient experimental system + scRNA-seq:
Excited to see our study on genetic regulation in heterogeneous differentiating cultures out in final form!
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6
Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures
Popp et al. generate dozens of cell types from 53 human iPSC lines in order to characterize
the dynamic genetic regulation of gene expression across early stages of cellular
differentiation. Accessing...
www.cell.com
December 4, 2024 at 2:31 AM
Excited to see our study on genetic regulation in heterogeneous differentiating cultures out in final form!
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6