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Yuval Simons

@yuvalsim.bsky.social
602 followers 215 following 57 posts

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!

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Reposted by Yuval Simons
Matthew Hahn @3rdreviewer.bsky.social · 15/09/2026
New paper with Trang Nguyen! Do you have only a single parent and offspring, but still want to calculate mutation rates? We've got the tool for you--OOPS github.com/TrangNg-Th/O... www.biorxiv.org/content/10.6...
biorxiv.org
Estimating de novo mutation rates using parent-offspring pairs
Existing pedigree approaches to identifying de novo mutations (DNMs) require at least two parents and a single offspring, limiting applicability. Here, we introduce OOPS (Only One Parent Sequencing), ...
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Yuval Simons @yuvalsim.bsky.social · 15/09/2026
The Carlson Lab at the University of Rochester is recruiting researchers at all levels! Please reach out to Maryn (marync.github.io/carlsonlab/i...) if you are interested in groundbreaking problems in population and quantitative genetics. Maryn is brilliant and will be a great mentor!
marync.github.io
Carlson Lab
The Carlson Lab works at the interface of population and quantitative genetics, statistics, and evolutionary biology.
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Yuval Simons @yuvalsim.bsky.social · 31/05/2026
Our new paper is out! Tweetorial coming soon!
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 31/05/2026
Accounting for recurrent mutation in the frequency spectrum of rare alleles www.biorxiv.org/content/10.64898/20…
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Eduardo Amorim @cegamorim.bsky.social · 08/05/2026
Yesterday our article was featured on the cover of Nature. I'm incredibly proud of this team, led primarily by Latin Americans, & the result of the decade-long work by @hunemeier.bsky.social & lab. Kudos to the 1st authors too (incl @macscastro.bsky.social here on 🟦☁️) www.nature.com/nature/volum...
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Huisheng (Julie) Zhu @huishengzhu.bsky.social · 30/03/2026
Why do schizophrenia GWAS signals look so flat across the genome? In our recent preprint, we explored why psychiatric disorders — and, more broadly, brain-related traits involving the central nervous system — appear to have unusual genetic architectures. 🧵1/n
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Shai Carmi @shaicarmi.bsky.social · 01/03/2026
Great perspective by @philipcball.bsky.social. Elementary genetics teaching (HS/college) focuses on Mendelian traits (single gene => single trait). However, it is now clear that polygenicity and pleiotropy are the norm. Curriculum must change accordingly. www.sciencedirect.com/science/arti...
sciencedirect.com
Should biology put complexity first?
The dictum “Everything should be made as simple as possible, but no simpler” poses a problem for biology. How simply can it be told without doing dama…
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Reposted by Yuval Simons
Yoav Gilad @ygilad.bsky.social · 19/12/2025
Faculty position at the department of medicine, University of Chicago. Please share.
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Jeff Spence @jeffspence.github.io · 07/11/2025
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...
nature.com
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
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Yuval Simons @yuvalsim.bsky.social · 24/10/2025
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/...
journals.plos.org
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...
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Reposted by Yuval Simons
Stanford University Press @stanfordpress.bsky.social · 30/09/2025
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.
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Yuval Simons @yuvalsim.bsky.social · 25/09/2025
My first paper as a PI is now out on PNAS! www.pnas.org/doi/full/10....
pnas.org
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...
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Laura K Hayward @lkhayward.bsky.social · 24/08/2025
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
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Yoav Gilad @ygilad.bsky.social · 20/06/2025
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.
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Genetics Society of America @genetics-gsa.bsky.social · 03/06/2025
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
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Maggie Steiner @maggiesteiner.bsky.social · 03/06/2025
Out today in @pnas.org! www.pnas.org/doi/10.1073/...
pnas.org
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...
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Yuval Simons @yuvalsim.bsky.social · 24/04/2025
What is epistasis? New preprint Blue-torial! (Work by the wonderful postdocs Maryn Carlson and Bryan Andrews) www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Avery Davis Bell @averydb.bsky.social · 11/01/2025
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...
biorxiv.org
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...
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Shai Carmi @shaicarmi.bsky.social · 15/12/2024
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.
biorxiv.org
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...
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Na Cai @caina89.bsky.social · 04/12/2024
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...
cell.com
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.
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Maggie Steiner @maggiesteiner.bsky.social · 04/12/2024
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?
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Shai Carmi @shaicarmi.bsky.social · 24/11/2024
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...
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Aaron Ragsdale @apragsdale.bsky.social · 14/11/2024
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
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...
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Justin Blumenstiel @bdelloid.bsky.social · 24/11/2024
Supplemental Figure 3. The demographic model
A Klein Bottle
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Graham Coop @gcbias.bsky.social · 24/11/2024
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...
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Patrick Phillips @patrickphillips.bsky.social · 22/11/2024
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.
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Yuval Simons @yuvalsim.bsky.social · 17/11/2024
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!
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