Sharon Zhou
@sharon-zhou.bsky.social
PhD student in evolutionary biology @UChicago
Spatial & temporal structure of biodiversity and morpho complexity; evolution and genetics of complex traits
Spatial & temporal structure of biodiversity and morpho complexity; evolution and genetics of complex traits
Reposted by Sharon Zhou
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...
It’s that magical time of the year again! This has been a very good year for fall colors here in Chicago.
November 2, 2025 at 11:50 PM
It’s that magical time of the year again! This has been a very good year for fall colors here in Chicago.
This view never gets old
(Hutchinson quad at uchicago - grateful to pass by this place every morning I go to work)
(Hutchinson quad at uchicago - grateful to pass by this place every morning I go to work)
October 29, 2025 at 11:56 PM
This view never gets old
(Hutchinson quad at uchicago - grateful to pass by this place every morning I go to work)
(Hutchinson quad at uchicago - grateful to pass by this place every morning I go to work)
Reposted by Sharon Zhou
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Sharon Zhou
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
doi.org
September 11, 2025 at 3:50 AM
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Reposted by Sharon Zhou
I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:
Beneath the surface of the sum
When genetic interactions matter and when they don't
open.substack.com
August 27, 2025 at 8:41 PM
I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:
Reposted by Sharon Zhou
Another fun year for the #mwpg, this year at the University of Minnesota! Great to see all the trainees participating with their cool work.
August 23, 2025 at 2:07 PM
Another fun year for the #mwpg, this year at the University of Minnesota! Great to see all the trainees participating with their cool work.
A windy sunset on Lake Michigan:
July 21, 2025 at 2:12 AM
A windy sunset on Lake Michigan:
A morning hike through the woods is like a refill for the soul.
June 28, 2025 at 1:29 AM
A morning hike through the woods is like a refill for the soul.
A very lucky morning in the Snoqualmie Falls (before hiking up the mountains)!
June 24, 2025 at 6:58 PM
A very lucky morning in the Snoqualmie Falls (before hiking up the mountains)!
Days and nights on the empire builder train from Chicago to Seattle:
June 21, 2025 at 11:30 PM
Days and nights on the empire builder train from Chicago to Seattle:
Beautiful strawberry moon tonight! That sliver of reflection over Lake Michigan adds even more to the moment’s tranquility.
June 11, 2025 at 2:13 AM
Beautiful strawberry moon tonight! That sliver of reflection over Lake Michigan adds even more to the moment’s tranquility.
Reposted by Sharon Zhou
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 Sharon Zhou
Excited for our publication on how the geographic scale of a sample affects the discovery of rare, deleterious variants to be out this week. With a mix of theory, simulation, and data analysis, we show when samples are narrow vs broad, the number of variants discovered and their frequencies change
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
June 5, 2025 at 5:55 PM
Excited for our publication on how the geographic scale of a sample affects the discovery of rare, deleterious variants to be out this week. With a mix of theory, simulation, and data analysis, we show when samples are narrow vs broad, the number of variants discovered and their frequencies change
Reposted by Sharon Zhou
The impact of background selection in mutation-selection-drift balance models of complex trait evolution https://www.biorxiv.org/content/10.1101/2025.05.27.656342v1
May 28, 2025 at 6:33 AM
The impact of background selection in mutation-selection-drift balance models of complex trait evolution https://www.biorxiv.org/content/10.1101/2025.05.27.656342v1
Reposted by Sharon Zhou
Mutation-selection-drift balance models of complex diseases https://www.biorxiv.org/content/10.1101/2025.05.18.654722v1
May 19, 2025 at 3:32 AM
Mutation-selection-drift balance models of complex diseases https://www.biorxiv.org/content/10.1101/2025.05.18.654722v1
Defended my thesis proposal this week and am now a PhD candidate! Incredibly grateful for the support from my mentors, friends, and everyone who came to the talk in person and on zoom. I’m so lucky to be around such amazing people and can’t wait to continue this journey!
May 2, 2025 at 8:08 PM
Defended my thesis proposal this week and am now a PhD candidate! Incredibly grateful for the support from my mentors, friends, and everyone who came to the talk in person and on zoom. I’m so lucky to be around such amazing people and can’t wait to continue this journey!
After a weekend that truly felt like summer (thunderstorms, sunshine, shorts and t-shirts), I just cannot believe that it’s going to dip below freezing again next week
(So says the weather app, which I wholeheartedly hope is wrong)
(So says the weather app, which I wholeheartedly hope is wrong)
March 30, 2025 at 11:31 PM
After a weekend that truly felt like summer (thunderstorms, sunshine, shorts and t-shirts), I just cannot believe that it’s going to dip below freezing again next week
(So says the weather app, which I wholeheartedly hope is wrong)
(So says the weather app, which I wholeheartedly hope is wrong)
Reposted by Sharon Zhou
I wrote about how population stratification in genetic analyses led to a decade of false findings and almost certainly continues to bias emerging results. But we are starting to have statistical tools to sniff it out. A 🧵:
How population stratification led to a decade of sensationally false genetic findings
Stratification makes environments look like genes
open.substack.com
March 28, 2025 at 9:54 PM
I wrote about how population stratification in genetic analyses led to a decade of false findings and almost certainly continues to bias emerging results. But we are starting to have statistical tools to sniff it out. A 🧵:
There’s no better getaway than the Oregon spring, and arguably no better therapy (at least for me!) than a few moist, crystal hours alone in the rain washed forest
March 23, 2025 at 7:46 PM
There’s no better getaway than the Oregon spring, and arguably no better therapy (at least for me!) than a few moist, crystal hours alone in the rain washed forest
Reposted by Sharon Zhou
My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.
It’s available on Amazon: tinyurl.com/mx2hewen
It’s available on Amazon: tinyurl.com/mx2hewen
January 17, 2025 at 2:30 PM
My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.
It’s available on Amazon: tinyurl.com/mx2hewen
It’s available on Amazon: tinyurl.com/mx2hewen
Finishing up 2024 with some amazing orchids and orchid mantis, hibiscus flowers (incl one very aptly named Hibiscus schizopetalus - look it up, please), butterflies, and so many other wildlife, all happily living under Malaysia’s lush, verdant tropical canopy!
December 30, 2024 at 2:35 PM
Finishing up 2024 with some amazing orchids and orchid mantis, hibiscus flowers (incl one very aptly named Hibiscus schizopetalus - look it up, please), butterflies, and so many other wildlife, all happily living under Malaysia’s lush, verdant tropical canopy!
An absolutely breathtaking sunset in Malaysia (with a double rainbow!) to make Christmas 2024 an incredible memory. Another day of feeling grateful for all the beauty in this world, and for being able to appreciate and understand them as much as we can.
December 25, 2024 at 2:22 PM
An absolutely breathtaking sunset in Malaysia (with a double rainbow!) to make Christmas 2024 an incredible memory. Another day of feeling grateful for all the beauty in this world, and for being able to appreciate and understand them as much as we can.
Every shade of rose over tonight’s blushing sky
December 8, 2024 at 5:04 AM
Every shade of rose over tonight’s blushing sky
Reposted by Sharon Zhou
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?