Sool Lee
@soley2260.bsky.social
Reposted by Sool Lee
Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
April 23, 2025 at 11:35 AM
Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
Reposted by Sool Lee
Our new study in Molecular Psychiatry, in 1528 children and their parents (@ntrbiopsy.bsky.social) shows that indirect genetic effects—where parental genetics shape offspring traits via environmental influences (genetic nurture)—impact DNA methylation of children. doi.org/10.1038/s413... (1/5)
Intergenerational transmission of complex traits and the offspring methylome - Molecular Psychiatry
Molecular Psychiatry - Intergenerational transmission of complex traits and the offspring methylome
doi.org
April 6, 2025 at 2:07 PM
Our new study in Molecular Psychiatry, in 1528 children and their parents (@ntrbiopsy.bsky.social) shows that indirect genetic effects—where parental genetics shape offspring traits via environmental influences (genetic nurture)—impact DNA methylation of children. doi.org/10.1038/s413... (1/5)
Reposted by Sool Lee
👇🎯 The public isn't going to understand this, unless the presidents of R1 universities around the country <loudly> & <collectively> get out into the public square & start explaining this & calling out the existential threat to the entire 🇺🇸 university system. The silence is deafening right now.
The public really needs to understand this. Every university system in the world rests on public funding, there has never been an alternative model at any time in history.
We have universities for literally the same reason that we have roads and armies.
We have universities for literally the same reason that we have roads and armies.
I don't disagree that the US university business model was/is fragile, but surely not for this reason?
There is no society in the history of humanity that has successfully built a good university system without massive govt subsidies. US had already pushed the idea very far.
There is no society in the history of humanity that has successfully built a good university system without massive govt subsidies. US had already pushed the idea very far.
March 8, 2025 at 8:45 PM
👇🎯 The public isn't going to understand this, unless the presidents of R1 universities around the country <loudly> & <collectively> get out into the public square & start explaining this & calling out the existential threat to the entire 🇺🇸 university system. The silence is deafening right now.
Reposted by Sool Lee
1/ I am beyond thrilled to share our new paper in @CellCellPress! We explored the regulatory principles underlying pleiotropy in psychiatric disorders.
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders
High-throughput experimental validation of genetic variants linked to eight psychiatric
disorders reveals the regulatory mechanisms underlying variants with pleiotropic and
disorder-specific effects.
www.cell.com
January 27, 2025 at 7:02 PM
1/ I am beyond thrilled to share our new paper in @CellCellPress! We explored the regulatory principles underlying pleiotropy in psychiatric disorders.
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
Reposted by Sool Lee
Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders
@cellcellpress.bsky.social @hyejungwon.bsky.social
cell.com/cell/fulltex...
@cellcellpress.bsky.social @hyejungwon.bsky.social
cell.com/cell/fulltex...
January 22, 2025 at 8:51 PM
Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders
@cellcellpress.bsky.social @hyejungwon.bsky.social
cell.com/cell/fulltex...
@cellcellpress.bsky.social @hyejungwon.bsky.social
cell.com/cell/fulltex...
Reposted by Sool Lee
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 Sool Lee
People often ask me what I use to create my plots. I use mostly R, but I have to admit that I cheat a little bit with Adobe Illustrator 🧑🏽🎨
See slide show below for some of my edits 👇🏽
See slide show below for some of my edits 👇🏽
January 10, 2025 at 12:20 PM
People often ask me what I use to create my plots. I use mostly R, but I have to admit that I cheat a little bit with Adobe Illustrator 🧑🏽🎨
See slide show below for some of my edits 👇🏽
See slide show below for some of my edits 👇🏽
Reposted by Sool Lee
Some thoughts about what I am looking forward this year from my vantage point of computational molecular biology. One mega-trend for me; we will definitely see more AI methods of all sorts emerge.
January 3, 2025 at 6:46 PM
Some thoughts about what I am looking forward this year from my vantage point of computational molecular biology. One mega-trend for me; we will definitely see more AI methods of all sorts emerge.
Reposted by Sool Lee
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
December 25, 2024 at 11:48 PM
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
Reposted by Sool Lee
2025 is 0% complete.
January 1, 2025 at 12:01 AM
2025 is 0% complete.
Reposted by Sool Lee
We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon!
Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?
www.cell.com/trends/genet...
Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?
www.cell.com/trends/genet...
Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?
Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term ‘ruler’ TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.
www.cell.com
December 9, 2024 at 11:03 AM
We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon!
Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?
www.cell.com/trends/genet...
Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?
www.cell.com/trends/genet...
Reposted by Sool Lee
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 Sool Lee
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1
December 16, 2024 at 10:33 AM
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1