Josh Popp
@jmpopp.bsky.social
Computational genomics PhD student at Johns Hopkins BME
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!
Univariate-Guided Sparse Regression
hdsr.mitpress.mit.edu
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
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
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.
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)
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...
medrxiv.org
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
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.
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
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...
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
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...
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
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.
Kathleen Bachynski@bachynski.bsky.social · last yr.This public health nightmare continues. “Health Secretary Robert F. Kennedy Jr. advised parents of newborns to “do your own research” before vaccinating their infants during a televised interview in which he also suggested the measles shot was unsafe and repeatedly made false statements”
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”
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?!?
Dr. Becca@docbecca.bsky.social · 2y agoThe 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...
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...
Join researchers across the country in fighting restrictions on the NIH
Please click the link to complete this form.
form.jotform.com
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 🧵
Very excited about this new work from our lab! Explainer thread coming soon @minetoota.bsky.social
bioRxiv Genetics@biorxiv-genetic.bsky.social · 2y agoCausal 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
How population stratification makes environments look like genes. A short 🧵:
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...
biorxiv.org
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."
Jeff Spence@jeffspence.github.io · 2y agoWhat 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...
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...
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...
biorxiv.org
Why do association studies prioritize trait-specific variants??? A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
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...
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.
nature.com
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...
medrxiv.org
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:
Josh Popp@jmpopp.bsky.social · 2y agoExcited 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
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
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...
cell.com