Yun Deng
@yundeng.bsky.social
Postdoc in Pritchard lab at Stanford University. Previous PhD co-advised by Yun Song and Rasmus Nielsen at UC Berkeley.
Reposted by Yun Deng
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 6:42 PM
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Reposted by Yun Deng
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 7:27 PM
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Reposted by Yun Deng
New preprint alert: we use sign errors as a test of how well TWAS works.
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:48 AM
New preprint alert: we use sign errors as a test of how well TWAS works.
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Reposted by Yun Deng
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:30 AM
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
Reposted by Yun Deng
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado
In avocado and certain wild relatives in Lauraceae, pollination occurs via a synchronized rhythm of floral sex timing between two hermaphroditic flowering types. A-type plants present female-phase flo...
www.biorxiv.org
December 29, 2025 at 7:13 PM
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Reposted by Yun Deng
Congrats @jeffgroh.bsky.social et al. Some avocado trees open female-phase flowers in the morning & then male in afternoon. Others show complementary pattern (m->f), to synchronize pollination of two types. Jeff show this to be a >45Mya polymorphism at a transcription factor across 100s of species.
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
December 25, 2025 at 6:47 PM
Congrats @jeffgroh.bsky.social et al. Some avocado trees open female-phase flowers in the morning & then male in afternoon. Others show complementary pattern (m->f), to synchronize pollination of two types. Jeff show this to be a >45Mya polymorphism at a transcription factor across 100s of species.
Reposted by Yun Deng
How much better is an ancestral recombination graph (ARG) than a site frequency spectrum (SFS)? For recovering mutation rate history, we can answer fairly precisely because both ARG and SFS are linear transforms of mutation rate history. This blog post uses spectral analysis to clarify the picture.
Observability of mutation rate histories from ancestral recombination graphs
This post explores mathematical aspects of recovering mutation rate histories from an ancestral recombination graph (ARG) Vs a sample frequency spectrum (SFS), expanding on a recent collaborative pape...
dewitt-lab.github.io
December 22, 2025 at 6:19 PM
How much better is an ancestral recombination graph (ARG) than a site frequency spectrum (SFS)? For recovering mutation rate history, we can answer fairly precisely because both ARG and SFS are linear transforms of mutation rate history. This blog post uses spectral analysis to clarify the picture.
Reposted by Yun Deng
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
www.biorxiv.org
December 22, 2025 at 3:09 PM
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
Reposted by Yun Deng
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:53 PM
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Yun Deng
Preprint online right before the holidays! Excited to share the first piece of work from the Zhang Lab, led by my absolutely stellar postdoc Michelle Kim! In this work, we ask how admixture, selection and demography shape complex trait genetics and GWAS performance www.biorxiv.org/content/10.6...
Determining the driving factors shaping genetic architecture of complex traits in recently admixed populations
Understanding the genetic architecture of complex traits in admixed populations remains challenging due to heterogeneous genetic backgrounds and demographic histories. Mischaracterizing admixture can ...
www.biorxiv.org
December 16, 2025 at 1:47 PM
Preprint online right before the holidays! Excited to share the first piece of work from the Zhang Lab, led by my absolutely stellar postdoc Michelle Kim! In this work, we ask how admixture, selection and demography shape complex trait genetics and GWAS performance www.biorxiv.org/content/10.6...
Reposted by Yun Deng
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 13, 2025 at 4:45 PM
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Reposted by Yun Deng
As a (to me very enjoyable) part of this paper, we worked out what mutation-selection balance looks like in finite populations with varying degrees of inbreeding.
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 13, 2025 at 10:43 PM
As a (to me very enjoyable) part of this paper, we worked out what mutation-selection balance looks like in finite populations with varying degrees of inbreeding.
Reposted by Yun Deng
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
With @szhan.bsky.social, @yulinzhang.bsky.social, Chao Zhang and Bingjie Chen, we wrote a Perspective about unifying the tree-based method across phylogenetics, population genetics and cell biology: arxiv.org/abs/2512.05499.
Reposts are greatly appreciated!
Reposts are greatly appreciated!
Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and ...
arxiv.org
December 9, 2025 at 3:26 AM
With @szhan.bsky.social, @yulinzhang.bsky.social, Chao Zhang and Bingjie Chen, we wrote a Perspective about unifying the tree-based method across phylogenetics, population genetics and cell biology: arxiv.org/abs/2512.05499.
Reposts are greatly appreciated!
Reposts are greatly appreciated!
Reposted by Yun Deng
BAPG 2025 was a blast. Looking forward to seeing folks in Davis in Spring 2026! bapg2025.github.io/bapg2025stan...
BAPG Fall 2025
Bay Area Population Genomics Conference @ Stanford
bapg2025.github.io
December 7, 2025 at 3:59 AM
BAPG 2025 was a blast. Looking forward to seeing folks in Davis in Spring 2026! bapg2025.github.io/bapg2025stan...
Reposted by Yun Deng
Our new ancient DNA paper has just been published!
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
Homo sapiens-specific evolution unveiled by ancient southern African genomes - Nature
The genomes of 28 ancient southern African individuals dated to between 10,200 and 150 years before present offer insights into the evolution of Homo sapiens.
www.nature.com
December 3, 2025 at 4:42 PM
Our new ancient DNA paper has just been published!
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
Reposted by Yun Deng
Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)
Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix
Observational studies are commonly used in psychology and epidemiology to identify risk factors correlated with health outcomes. However, these studies are vulnerable to confounding when shared geneti...
www.biorxiv.org
December 1, 2025 at 7:09 PM
Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)
Reposted by Yun Deng
www.biorxiv.org/content/10.1...
We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
Genetic prediction with ARG-powered linear algebra
Ancestral recombination graphs (ARGs) are an attractive means for quantitative genetic analysis of complex traits because they encode the realized genetic relatedness between a sample of individuals i...
www.biorxiv.org
November 30, 2025 at 5:08 PM
www.biorxiv.org/content/10.1...
We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
Reposted by Yun Deng
Interested in pleiotropy dissection but not sure where to start, which methods are useful, which studies offer illustrative examples, or how to robustly validate your results? Look no further 👀 rdcu.be/eSfAZ
Dissecting pleiotropy to gain mechanistic insights into human disease
Nature Reviews Genetics - Genome-wide association studies of increasing scale have revealed the prevalence of pleiotropic genetic variants that affect multiple traits. In this Review, the authors...
rdcu.be
November 28, 2025 at 1:10 PM
Interested in pleiotropy dissection but not sure where to start, which methods are useful, which studies offer illustrative examples, or how to robustly validate your results? Look no further 👀 rdcu.be/eSfAZ
Reposted by Yun Deng
We've got a really cool preprint out in collaboration with @lpachter.bsky.social's awesome student Cat Felce. Using biophysical models and RNA-seq data, we explore the mechanisms of selective constraint on mRNA abundance, finding constraint on decay rate www.biorxiv.org/content/10.1...
Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances
Evolutionary changes to gene expression are understood to be a major driver of phenotypic divergence between species. Researchers have investigated the drivers of this divergence by fitting evolutiona...
www.biorxiv.org
November 26, 2025 at 5:25 PM
We've got a really cool preprint out in collaboration with @lpachter.bsky.social's awesome student Cat Felce. Using biophysical models and RNA-seq data, we explore the mechanisms of selective constraint on mRNA abundance, finding constraint on decay rate www.biorxiv.org/content/10.1...
Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to.
Check it out & consider reposting to support a great young scientist!
Check it out & consider reposting to support a great young scientist!
We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1....
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
1/7
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
1/7
Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors
Ancestral Recombination Graphs (ARGs) are fundamental population genetic structures that encode the genealogical history of a sample of haplotypes along the genome. They have recently received substan...
biorxiv.org
November 26, 2025 at 5:12 PM
Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to.
Check it out & consider reposting to support a great young scientist!
Check it out & consider reposting to support a great young scientist!
Reposted by Yun Deng
Hitting refresh on biorxiv for a paper to appear... realized my first biorxiv preprint was more than 12 years ago, and on arXiv two years before that! Preprinting sure seemed strange at the time, but it's become my favorite part of the process!
www.biorxiv.org/content/10.1...
arxiv.org/abs/1208.0634
www.biorxiv.org/content/10.1...
arxiv.org/abs/1208.0634
Complex patterns of local adaptation in teosinte
Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requi...
arxiv.org
November 26, 2025 at 5:27 AM
Hitting refresh on biorxiv for a paper to appear... realized my first biorxiv preprint was more than 12 years ago, and on arXiv two years before that! Preprinting sure seemed strange at the time, but it's become my favorite part of the process!
www.biorxiv.org/content/10.1...
arxiv.org/abs/1208.0634
www.biorxiv.org/content/10.1...
arxiv.org/abs/1208.0634
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
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
November 25, 2025 at 8:27 PM
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
Reposted by Yun Deng
In an earlier project simulating quantitative traits/stabilizing selection in a human-Neanderthal model, I became a bit curious about some observed fitness dynamics that I wasn’t expecting.
I’m not sure if this is all that interesting or relevant, but at least it’s short.
I’m not sure if this is all that interesting or relevant, but at least it’s short.
Mean fitness is maximized in small populations under stabilizing selection on highly polygenic traits https://www.biorxiv.org/content/10.1101/2025.11.17.688329v1
November 21, 2025 at 11:09 AM
In an earlier project simulating quantitative traits/stabilizing selection in a human-Neanderthal model, I became a bit curious about some observed fitness dynamics that I wasn’t expecting.
I’m not sure if this is all that interesting or relevant, but at least it’s short.
I’m not sure if this is all that interesting or relevant, but at least it’s short.
Reposted by Yun Deng
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
www.nature.com
November 19, 2025 at 6:43 PM
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...