Zixuan (Eleanor) Zhang
@elezzx.bsky.social
Postdoc @UPenn working with Drs. Brielin Brown, Bogdan Pasaniuc, and Michael Gandal. Statistical genetics, functional architecture, single cell data. https://zixuanzhang.github.io
Pinned
Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping
Population-scale single-cell transcriptomic technologies (scRNA-seq) enable characterizing variant effects on gene regulation at the cellular level (e.g., single-cell eQTLs; sc-eQTLs). However, existi...
www.medrxiv.org
Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Zixuan (Eleanor) Zhang
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...
Very proud of you @tszfung.bsky.social for so many achievements!! 🎊
Huge congratulations to @tszfung.bsky.social on successfully defending his PhD! (Co-advised with @charleston.bsky.social )
Plenty of cool insights and methods detailed in his dissertation, "Inferring genetic architecture of complex traits in admixed populations"
Plenty of cool insights and methods detailed in his dissertation, "Inferring genetic architecture of complex traits in admixed populations"
November 5, 2025 at 11:51 PM
Very proud of you @tszfung.bsky.social for so many achievements!! 🎊
Reposted by Zixuan (Eleanor) Zhang
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 Zixuan (Eleanor) Zhang
5 YEARS of HGG Advances! Mike, Jessica, Sara, and so many others have done such a fantastic job in shaping and expanding the journal.
Please consider submitting your work in genetics/genomics with us!
Please consider submitting your work in genetics/genomics with us!
Our October issue is online!
Check out the amazing cover from @comfortandadam.bsky.social to commemorate 5 YEARS of HGG Advances!
www.cell.com/hgg-advances...
Check out the amazing cover from @comfortandadam.bsky.social to commemorate 5 YEARS of HGG Advances!
www.cell.com/hgg-advances...
October 10, 2025 at 4:10 PM
5 YEARS of HGG Advances! Mike, Jessica, Sara, and so many others have done such a fantastic job in shaping and expanding the journal.
Please consider submitting your work in genetics/genomics with us!
Please consider submitting your work in genetics/genomics with us!
Reposted by Zixuan (Eleanor) Zhang
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
September 12, 2025 at 7:00 PM
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
Reposted by Zixuan (Eleanor) Zhang
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 Zixuan (Eleanor) Zhang
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 Zixuan (Eleanor) Zhang
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)
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...
www.medrxiv.org
September 2, 2025 at 11:08 PM
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)
I am attempting an explainer thread for the first time here:
(I am usually too exhausted to post one)
Reposted by Zixuan (Eleanor) Zhang
Please consider applying to be HGG new EiC! HGG is a fantastic avenue for publishing work in genetics and genomics, striving for fast turnaround and is committed to open access.
We're seeking our next EiC!
Are you passionate about human genetics & open science?
Apply at apply.ashg.org/a/page/hgga-...
Are you passionate about human genetics & open science?
Apply at apply.ashg.org/a/page/hgga-...
August 19, 2025 at 3:20 PM
Please consider applying to be HGG new EiC! HGG is a fantastic avenue for publishing work in genetics and genomics, striving for fast turnaround and is committed to open access.
Reposted by Zixuan (Eleanor) Zhang
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
Estimation of demography and mutation rates from one million haploid genomes
Samples of millions of genomes provide substantial information about recent demography
and mutation, but standard population-genetic methods make assumptions not met in
these data. We introduce DR EVI...
www.cell.com
August 13, 2025 at 2:40 PM
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
Huge congrats Roshni! Couldn’t wait to see what comes next in the new role!!
Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.
August 6, 2025 at 7:56 PM
Huge congrats Roshni! Couldn’t wait to see what comes next in the new role!!
Reposted by Zixuan (Eleanor) Zhang
I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!
July 25, 2025 at 8:29 PM
I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!
Reposted by Zixuan (Eleanor) Zhang
Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...
Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social
July 21, 2025 at 11:15 PM
Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...
Reposted by Zixuan (Eleanor) Zhang
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
📢OUT TODAY @natgenet.nature.com
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk - Nature Genetics
SuShiE is a multiancestry fine-mapping method for molecular quantitative trait loci that leverages linkage disequilibrium heterogeneity to improve resolution, infer cross-ancestry effect size correlat...
www.nature.com
July 21, 2025 at 6:54 PM
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
Reposted by Zixuan (Eleanor) Zhang
My talk from this year's probgen is finally out.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Modelling complex traits with ancestral recombination graphs https://www.biorxiv.org/content/10.1101/2025.07.14.664631v1
July 19, 2025 at 1:04 AM
My talk from this year's probgen is finally out.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Congrats on the first PhD work!! Very nicely done! @alnahid.bsky.social
traceax: a JAX-based framework for stochastic trace estimation https://www.biorxiv.org/content/10.1101/2025.07.14.662216v1
July 18, 2025 at 11:15 PM
Congrats on the first PhD work!! Very nicely done! @alnahid.bsky.social
Reposted by Zixuan (Eleanor) Zhang
Principled measures and estimates of trait polygenicity https://www.biorxiv.org/content/10.1101/2025.07.10.664154v1
July 16, 2025 at 4:45 PM
Reposted by Zixuan (Eleanor) Zhang
An insightful @cp-trendsgenetics.bsky.social perspective on our recent article about the early evolution of genome regulation in animals.
www.cell.com/trends/genet...
Thank you Omar and @ferdix.bsky.social!
www.cell.com/trends/genet...
Thank you Omar and @ferdix.bsky.social!
Animal origins: looping back in time
How did the chromatin folding mechanisms controlling gene regulation emerge during
animal evolution? Kim et al. surveyed chromatin folding at high-resolution in unicellular
relatives of animals as wel...
www.cell.com
July 15, 2025 at 11:38 AM
An insightful @cp-trendsgenetics.bsky.social perspective on our recent article about the early evolution of genome regulation in animals.
www.cell.com/trends/genet...
Thank you Omar and @ferdix.bsky.social!
www.cell.com/trends/genet...
Thank you Omar and @ferdix.bsky.social!
Reposted by Zixuan (Eleanor) Zhang
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Dissecting functional regulatory convergence over 160 million years of therian evolution https://www.biorxiv.org/content/10.1101/2025.07.10.662670v1
July 11, 2025 at 9:46 PM
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Reposted by Zixuan (Eleanor) Zhang
Very excited to see this out and delighted to have played a small part -- @courtsmithrun.bsky.social did a deep dive into the pleiotropy of the HLA locus and found tons of cool stuff, including lots of associations at the SNP, HLA allele, and haplotype levels.
📣New today!
📄Haplotype analysis reveals pleiotropic disease associations in the HLA region
🧑🤝🧑 @jkpritch.bsky.social @finngen.bsky.social & colleagues
📄Haplotype analysis reveals pleiotropic disease associations in the HLA region
🧑🤝🧑 @jkpritch.bsky.social @finngen.bsky.social & colleagues
Haplotype analysis reveals pleiotropic disease associations in the HLA region
The HLA region plays an important role in human health but is often excluded in large-scale
GWASs. We performed haplotype-based associations from genotype data to investigate
pleiotropy across thousan...
www.cell.com
July 10, 2025 at 11:15 PM
Very excited to see this out and delighted to have played a small part -- @courtsmithrun.bsky.social did a deep dive into the pleiotropy of the HLA locus and found tons of cool stuff, including lots of associations at the SNP, HLA allele, and haplotype levels.
Reposted by Zixuan (Eleanor) Zhang
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
July 7, 2025 at 3:27 PM
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
Reposted by Zixuan (Eleanor) Zhang
Delighted to share the first preprint of my postdoc in the @carlanderson.bsky.social lab www.medrxiv.org/content/10.1...! 🚨 A super exciting study I co-led with the very talented @tobioinformatics.bsky.social . Stay tuned to see what we learned about genetic susceptibility to complex disease. 🧬🧵 1/
Cell-type-resolved genetic regulatory variation shapes inflammatory bowel disease risk
Most genetic variants associated with complex diseases lie in non-coding regions, complicating efforts to identify effector genes and relevant cell types. Here, we map cis-eQTLs across 2.2 million sin...
www.medrxiv.org
July 8, 2025 at 8:51 AM
Delighted to share the first preprint of my postdoc in the @carlanderson.bsky.social lab www.medrxiv.org/content/10.1...! 🚨 A super exciting study I co-led with the very talented @tobioinformatics.bsky.social . Stay tuned to see what we learned about genetic susceptibility to complex disease. 🧬🧵 1/
Reposted by Zixuan (Eleanor) Zhang
I probably won't have time to make a video out of this.
But the materials are available online, and should be pretty self-explanatory.
Hope this is useful to some people.
privefl.github.io/statgen-cour...
But the materials are available online, and should be pretty self-explanatory.
Hope this is useful to some people.
privefl.github.io/statgen-cour...
July 4, 2025 at 3:27 PM
I probably won't have time to make a video out of this.
But the materials are available online, and should be pretty self-explanatory.
Hope this is useful to some people.
privefl.github.io/statgen-cour...
But the materials are available online, and should be pretty self-explanatory.
Hope this is useful to some people.
privefl.github.io/statgen-cour...
Reposted by Zixuan (Eleanor) Zhang
Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)
Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace
Deep mutational scanning (DMS) experiments interrogate the effect of genetic variants on protein function, often using fluorescence-activated cell sorting (FACS) to quantitatively measure molecular ph...
www.biorxiv.org
June 30, 2025 at 4:03 PM
Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)
Reposted by Zixuan (Eleanor) Zhang
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
June 18, 2025 at 5:56 PM
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22