Yuval Simons
@yuvalsim.bsky.social
Assistant professor at the University of Chicago. Studying the population genetics of complex traits (mainly) and interested in using math to understand biology.
Join my lab, where science is fun and traits are complex!
Join my lab, where science is fun and traits are complex!
Reposted by Yuval Simons
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Simple scaling laws control the genetic architectures of human complex traits
Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...
journals.plos.org
October 24, 2025 at 1:51 AM
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Reposted by Yuval Simons
Population Biology Modeling & Theory (PBMT) is a peer-reviewed journal reporting advances in modeling and theory within population biology. Its scope spans demography, ecology, epidemiology, evolutionary biology, population genetics, and phylogenetics. PBMT will be online soon.
September 30, 2025 at 9:02 PM
Population Biology Modeling & Theory (PBMT) is a peer-reviewed journal reporting advances in modeling and theory within population biology. Its scope spans demography, ecology, epidemiology, evolutionary biology, population genetics, and phylogenetics. PBMT will be online soon.
My first paper as a PI is now out on PNAS!
www.pnas.org/doi/full/10....
www.pnas.org/doi/full/10....
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
September 25, 2025 at 6:59 PM
My first paper as a PI is now out on PNAS!
www.pnas.org/doi/full/10....
www.pnas.org/doi/full/10....
Reposted by Yuval Simons
Why do males and females often differ in traits?
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
August 23, 2025 at 11:12 PM
Why do males and females often differ in traits?
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
Reposted by Yuval Simons
I heard in the elevator a graduate student joking about destroying their lab and starting over, and I was just thinking that the lab I did my PhD. in was actually completely destroyed this week.
June 20, 2025 at 2:08 PM
I heard in the elevator a graduate student joking about destroying their lab and starting over, and I was just thinking that the lab I did my PhD. in was actually completely destroyed this week.
Reposted by Yuval Simons
Jennifer Blanc and @jeremyjberg.bsky.social use theory and simulations to study the process of testing for an association between polygenic scores and axes of ancestry variation when confounding factors are present.
Learn more about their findings in #GENETICS: buff.ly/EmKpXyP
Learn more about their findings in #GENETICS: buff.ly/EmKpXyP
June 3, 2025 at 10:02 PM
Jennifer Blanc and @jeremyjberg.bsky.social use theory and simulations to study the process of testing for an association between polygenic scores and axes of ancestry variation when confounding factors are present.
Learn more about their findings in #GENETICS: buff.ly/EmKpXyP
Learn more about their findings in #GENETICS: buff.ly/EmKpXyP
Reposted by Yuval Simons
Out today in @pnas.org! www.pnas.org/doi/10.1073/...
June 3, 2025 at 6:25 PM
Out today in @pnas.org! www.pnas.org/doi/10.1073/...
What is epistasis?
New preprint Blue-torial!
(Work by the wonderful postdocs Maryn Carlson and Bryan Andrews)
www.biorxiv.org/content/10.1...
New preprint Blue-torial!
(Work by the wonderful postdocs Maryn Carlson and Bryan Andrews)
www.biorxiv.org/content/10.1...
Robust detection of specific epistasis using rank statistics
The phenotypic effect of a mutation may depend on the genetic background in which it occurs, a phenomenon referred to as epistasis. One source of epistasis in proteins is direct interactions between r...
www.biorxiv.org
April 24, 2025 at 6:56 PM
What is epistasis?
New preprint Blue-torial!
(Work by the wonderful postdocs Maryn Carlson and Bryan Andrews)
www.biorxiv.org/content/10.1...
New preprint Blue-torial!
(Work by the wonderful postdocs Maryn Carlson and Bryan Andrews)
www.biorxiv.org/content/10.1...
Reposted by Yuval Simons
My most recent preprint, currently working on revising (some review suggestions were very helpful!). This comes from my NSF PRFB postdoc project in Annalise Paaby’s lab, on C. elegans regulatory rules from doing the first (we think) ASE study in this system. www.biorxiv.org/content/10.1...
Stabilizing selection and adaptation shape cis and trans gene expression variation in C. elegans
An outstanding question in the evolution of gene expression is the relative influence of neutral processes versus natural selection, including adaptive change driven by directional selection as well a...
www.biorxiv.org
January 11, 2025 at 9:43 PM
My most recent preprint, currently working on revising (some review suggestions were very helpful!). This comes from my NSF PRFB postdoc project in Annalise Paaby’s lab, on C. elegans regulatory rules from doing the first (we think) ASE study in this system. www.biorxiv.org/content/10.1...
Reposted by Yuval Simons
www.biorxiv.org/content/10.1...
Smart study to test whether lower prediction accuracy in non-Europeans is due to between-population differences in population structure, genetic nurture, or assortative mating.
Smart study to test whether lower prediction accuracy in non-Europeans is due to between-population differences in population structure, genetic nurture, or assortative mating.
Within-Family GWAS does not Ameliorate the Decline in Prediction Accuracy across Populations
As polygenic prediction extends beyond the research domain to involve clinical applications, the urgency of solving the "portability problem" becomes amplified -- that is, the fact that polygenic indi...
www.biorxiv.org
December 15, 2024 at 7:18 AM
www.biorxiv.org/content/10.1...
Smart study to test whether lower prediction accuracy in non-Europeans is due to between-population differences in population structure, genetic nurture, or assortative mating.
Smart study to test whether lower prediction accuracy in non-Europeans is due to between-population differences in population structure, genetic nurture, or assortative mating.
Reposted by Yuval Simons
New work by Andy Dahl and Michal Sadowski on using GxE to study genetics of drug response now out in Cell Genomics www.cell.com/cell-genomic...
Characterizing the genetic architecture of drug response using gene-context interaction methods
Sadowski et al. propose a framework to study the genetics of response to commonly prescribed drugs in large biobanks. They quantify the heritability of response to statins, metformin, warfarin, and methotrexate, and identify associated genes. Their analysis also shows the importance of accounting for drug use in genetic risk prediction.
www.cell.com
December 4, 2024 at 8:46 PM
New work by Andy Dahl and Michal Sadowski on using GxE to study genetics of drug response now out in Cell Genomics www.cell.com/cell-genomic...
Reposted by Yuval Simons
Excited to share a new preprint with @jnovembre.bsky.social ! We use a combination of population genetic theory, simulation, and data analysis to ask: how does study design in genetic studies (including biobanks) impact the discovery of rare, deleterious variants?
Study design and the sampling of deleterious rare variants in biobank-scale datasets https://www.biorxiv.org/content/10.1101/2024.12.02.626424v1
Study design and the sampling of deleterious rare variants in biobank-scale datasets https://www.biorxiv.org/content/10.1101/2024.12.02.626424v1
One key component of study design in population genetics is the "geographic breadth" of a sample (i.
www.biorxiv.org
December 4, 2024 at 5:17 PM
Excited to share a new preprint with @jnovembre.bsky.social ! We use a combination of population genetic theory, simulation, and data analysis to ask: how does study design in genetic studies (including biobanks) impact the discovery of rare, deleterious variants?
Reposted by Yuval Simons
Very interesting work by Tade Souaiaia et al on the non-polygenic architecture of the extremes of complex traits.
For many traits, polygenic scores show "regression to the mean" around the tails, as extreme traits are mostly due to rare alleles.
www.biorxiv.org/content/10.1...
For many traits, polygenic scores show "regression to the mean" around the tails, as extreme traits are mostly due to rare alleles.
www.biorxiv.org/content/10.1...
November 24, 2024 at 3:21 PM
Very interesting work by Tade Souaiaia et al on the non-polygenic architecture of the extremes of complex traits.
For many traits, polygenic scores show "regression to the mean" around the tails, as extreme traits are mostly due to rare alleles.
www.biorxiv.org/content/10.1...
For many traits, polygenic scores show "regression to the mean" around the tails, as extreme traits are mostly due to rare alleles.
www.biorxiv.org/content/10.1...
Reposted by Yuval Simons
We are accepting applications for the 2025 Evolution Seminar Series Early Career Award here at UW-Madison. Deadline November 30.
evolution.wisc.edu/seminars/ear...
Please share with grad students and postdocs working in evolutionary biology!
evolution.wisc.edu/seminars/ear...
Please share with grad students and postdocs working in evolutionary biology!
Early Career Award Seminar
The J.F. Crow Institute for the Study of Evolution at the University of Wisconsin-Madison is inviting early-career evolutionary biologists from outside UW-Madison to apply to participate in an early-c...
evolution.wisc.edu
November 14, 2024 at 6:22 PM
We are accepting applications for the 2025 Evolution Seminar Series Early Career Award here at UW-Madison. Deadline November 30.
evolution.wisc.edu/seminars/ear...
Please share with grad students and postdocs working in evolutionary biology!
evolution.wisc.edu/seminars/ear...
Please share with grad students and postdocs working in evolutionary biology!
Reposted by Yuval Simons
Supplemental Figure 3. The demographic model
November 24, 2024 at 5:31 AM
Supplemental Figure 3. The demographic model
Reposted by Yuval Simons
Optimist: The cup is half full.
Pessimist: The cup is half empty.
Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids.
bsky.app/profile/hutc...
Pessimist: The cup is half empty.
Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids.
bsky.app/profile/hutc...
Optimist: The cup is half full.
Pessimist: The cup is half empty.
Yorkshireman: A cup? Luxury!
Pessimist: The cup is half empty.
Yorkshireman: A cup? Luxury!
Optimist: The cup is half full
Pessimist: The cup is half empty
Science Fiction Writer: The cup is a crystalline super computer and the liquid is hyperintelligent, they want to know why humanity should be allowed to exist, you have 30 minutes to respond and the answer must be danced by a cat
Pessimist: The cup is half empty
Science Fiction Writer: The cup is a crystalline super computer and the liquid is hyperintelligent, they want to know why humanity should be allowed to exist, you have 30 minutes to respond and the answer must be danced by a cat
November 24, 2024 at 12:43 AM
Optimist: The cup is half full.
Pessimist: The cup is half empty.
Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids.
bsky.app/profile/hutc...
Pessimist: The cup is half empty.
Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids.
bsky.app/profile/hutc...
Reposted by Yuval Simons
A reminder for new folks. BlueSky does not have an algorithm to raise posts of interest. It is incumbent upon you to do so via reposting. Liking things only provides feedback to the poster but does not promote the post. The signal to noise ratio is taking a brief beating, so great to help curate.
November 22, 2024 at 10:58 PM
A reminder for new folks. BlueSky does not have an algorithm to raise posts of interest. It is incumbent upon you to do so via reposting. Liking things only provides feedback to the poster but does not promote the post. The signal to noise ratio is taking a brief beating, so great to help curate.
Going Blue feels like taking a fresh breath after a long nasty cold...
Happy to have a place to read, share, and talk about science. Welcome home!
Happy to have a place to read, share, and talk about science. Welcome home!
November 17, 2024 at 3:26 PM
Going Blue feels like taking a fresh breath after a long nasty cold...
Happy to have a place to read, share, and talk about science. Welcome home!
Happy to have a place to read, share, and talk about science. Welcome home!