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Zixuan (Eleanor) Zhang

@elezzx.bsky.social
351 followers 616 following 64 posts

Postdoc @UPenn working with Drs. Brielin Brown, Bogdan Pasaniuc, and Michael Gandal. Statistical genetics, functional architecture, single cell data. zixuanzhang.github.io

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Reposted by Zixuan (Eleanor) Zhang
Hanbin Lee @epigenci.bsky.social · 06/10/2026
We studied the evolution of genome-wide linkage disequilibrium and its influence on genetic architecture with genetic drift. We found that the Bulmer effect is population size and demography dependent. For nerds: genetic architecture follows from solving PDEs.
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Reposted by Zixuan (Eleanor) Zhang
Roshni Patel @roshnipatel.bsky.social · 06/10/2026
So excited about this work with @nasalab.bsky.social! Led by Stephanie Gogarten & with help from @daphmarts.bsky.social, we use LLMs as judges to evaluate the use of population descriptors in the entirety of the GWAS Catalog (~4,000 papers published 2007-2025) www.biorxiv.org/content/10.6...
biorxiv.org
Large language model-based bibliometric evaluation of population descriptors in human genetics
As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. M...
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 03/10/2026
static.klipy.com
Spongebob: Done And Done!
ALT: Spongebob: Done And Done!
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Reposted by Zixuan (Eleanor) Zhang
Yun S. Song @yun-s-song.bsky.social · 23/09/2026
Please help spread the word! We are recruiting multiple Postdoctoral Fellows as part of the recently launched Bakar Computational Biomedicine Initiative (BCBI) at UC Berkeley and UCSF. BCBI website: bcbi.berkeley.edu Apply by Nov 1, 2026: berkeley.infoready4.com#freeformComp... (1/n)
bcbi.berkeley.edu
Bakar Computational Biomedicine Initiative | Bakar Computational Biomedicine Initiative
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 11/09/2026
🍅 timer. Take a break every hour
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 10/09/2026
Version 0.3 of jaxQTL is out! We dramatically sped up ACAT-based scans by 3-6x. CD4+ OneK1K chr22 takes ~1m, down from ~15m. This fix improved memory consumption as well. There are various other numerical improvements made and improved documentation. Check it out! mancusolab.github.io/jaxqtl/
mancusolab.github.io
jaxQTL - jaxQTL
Cell-type-specific eQTL mapping from single-cell pseudobulk expression.
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 06/09/2026
Scene kid back then? Talk to DJ B lol
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 24/08/2026
v0.2.0 of jaxqtl is out! Now supports dosages, MAF filtering, and fixed a few bugs that could result in models not converging in rare cases. We're still actively developing and plan to get addition features (eg GxE, etc) integrated soon. github.com/mancusolab/j...
github.com
GitHub - mancusolab/jaxqtl: Flexible, scalable, QTL analyses using generalized linear models implemented in JAX
Flexible, scalable, QTL analyses using generalized linear models implemented in JAX - mancusolab/jaxqtl
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 13/08/2026
static.klipy.com
Ted Lasso says YES! (TheGoon BigOldGoon)
ALT: Ted Lasso says YES! (TheGoon BigOldGoon)
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 31/07/2026
🧙‍♂️
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 23/07/2026
😶‍🌫️😶‍🌫️
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Reposted by Zixuan (Eleanor) Zhang
Hanbin Lee @epigenci.bsky.social · 15/07/2026
How should we apply linear mixed models to populations under stabilizing selection? The first paper I wrote with my grad school advisor is published in Genetics. academic.oup.com/genetics/adv... 1/n
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 24/06/2026
Not ever seen this. But I have been using Jupyterlab. Not sure about rstudio
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 22/06/2026
Genoio has a v0.2.0 release. Performance is better across the board, beating most other libraries or matching highly performance ones (but with a single interface in Python now). Check it out mancusolab.github.io/genoio/
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Reposted by Zixuan (Eleanor) Zhang
Jeff Spence @jeffspence.github.io · 22/06/2026
Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...
doi.org
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
Abstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 18/06/2026
I m 30mins in first episode. Shep scares me but I have to say it’s a smart delayed reveal.
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 18/06/2026
No cue, not good for me 🥲
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Reposted by Zixuan (Eleanor) Zhang
Sasha Gusev @sashagusevposts.bsky.social · 07/06/2026
I wrote about AI in academia. "PhD-level thinking", LLM bias, grunt work, alignment, AGI, data center water use, AI politics -- something for everyone.
open.substack.com
Thoughts on AI in academia
PhD-level thinking, LLM bias, alignment, AGI, data centers, and AI politics
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 06/05/2026
Super excited to see this out! Fantastic collaboration with Luke O'Connor and trainees Amber Shen and Xinran Wang. Thread with details will come soon, but linear ARG provide a HIGHLY efficient representation of genotype data that can be treated as a linear operator www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 14/04/2026
Thrilled to see this out. What started out as a chat several years back with @drfejzo.bsky.social about leveraging publicly available data on hyperemesis gravidarum GWAS turned into a wonderful collaboration with April Shu, @mvaudel.bsky.social, @xwww.bsky.social and many others! rdcu.be/fdl9k
rdcu.be
Multi-ancestry genome-wide association study of severe pregnancy nausea and vomiting
Nature Genetics - Multi-ancestry GWAS meta-analysis identifies risk loci for severe nausea and vomiting of pregnancy. Downstream analyses explore maternal and fetal contributions of these loci and...
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Reposted by Zixuan (Eleanor) Zhang
Lior Pachter @lpachter.bsky.social · 13/04/2026
If you use dim. reduction, you may be interested in two recent preprints we've posted on contrastive PCA: The Rayleigh Quotient and Contrastive Principal Component Analysis I & II w/ Maria Carilli & Kayla Jackson. They cover a lot of ground from theory to practice. 1/🧵
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Reposted by Zixuan (Eleanor) Zhang
April Wei @aprilwei.bsky.social · 12/04/2026
Very proud to share our new work on General, orders-of-magnitude faster whole-genome analysis with genotype representation graphs (GRG). We topped ourselves in this one 🚀 and made GRG a practical foundation for biobank-scale population and statistical genetics. www.biorxiv.org/content/10.6...
biorxiv.org
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 27/03/2026
Good to know lol
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Reposted by Zixuan (Eleanor) Zhang
Arjun Bhattacharya @arjunbhattac.bsky.social · 26/03/2026
Another preprint from our group @mdanderson.bsky.social led by talented postdoc @seantbres.bsky.social! Joint with @jonhuang.bsky.social, exploring the intersection of environmental toxins, maternal/fetal health, and placental txomics. Tweet thread below!
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 24/03/2026
I used a combination of claude and codex, as well as the excellent base code from our jaxQTL project, to drive glmax. glmax is a jax-based GLM framework that is jit-compiled and end-to-end differentiable. It leverages implicit function theorem for improved autodiff. mancusolab.github.io/glmax/
mancusolab.github.io
glmax
Grammar-first generalized linear modeling in JAX.
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Reposted by Zixuan (Eleanor) Zhang
Josh Weinstock @joshweinstock.bsky.social · 13/03/2026
Here's our R package for interacting with WGS derived GWAS summary statistics with many rare variants (from e.g. UKB or AofUs). It uses duckdb underneath so it's fast. Includes some helpful tie ins to Open Targets / Encode Screen / Ensembl APIs for annotation. weinstocklab.github.io/gwasplot/ind...
weinstocklab.github.io
High Performance GWAS Plotting And Annotation
More about what it does (maybe more than one line). Continuation lines should be indented.
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 12/03/2026
The dynamic duo
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 24/02/2026
LoL child won’t lie :)
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 11/02/2026
I used my JAX-based skills for codex to port the excellent Python3 LDSC spec to JAX and Polars. My intent here was to stress test my JAX skill definitions and find how I could improve rules and contexts--NOT to develop a replacement github.com/mancusolab/j...
github.com
GitHub - mancusolab/jax_ldsc
Contribute to mancusolab/jax_ldsc development by creating an account on GitHub.
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 05/02/2026
Yeeess! Foot on table leaning back
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 27/01/2026
Been trying my hand with agents with varying degrees of success and placed some definitions into a repo. Feel free to fork/pull-req for improvements. I want to get a skill in there to generate code -> latex (and vice versa) for validation soon. github.com/quattro/jax-...
github.com
GitHub - quattro/jax-numerics-agent
Contribute to quattro/jax-numerics-agent development by creating an account on GitHub.
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 18/01/2026
hijack def adds fear of flying…very good show
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 16/01/2026
😂 mental breakdown within an hour lol
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 15/01/2026
🤩🤩
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Reposted by Zixuan (Eleanor) Zhang
Zeyun Lu 鲁泽沄 @zeyunlu.bsky.social · 05/01/2026
Happy to share our new preprint from @sashagusevposts.bsky.social and @nmancuso.bsky.social labs! We introduce Mr. PEG, a framework integrating perturbational screens, eQTL, and GWAS data to identify mediating genes for complex traits. (1/n) www.medrxiv.org/content/10.6...
medrxiv.org
Integrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traits
Most current GWAS-eQTL approaches prioritize genes whose mediating effects on complex traits act through cis-regulation, while trans-acting genes remain largely underexplored. Recent perturbational sc...
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 20/12/2025
LoL now I wanna add it to my watchlist
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 19/12/2025
media.tenor.com
a baby is screaming in a crowd of people while sitting in a stadium .
ALT: a baby is screaming in a crowd of people while sitting in a stadium .
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 05/12/2025
Ah that’s why. I was confused for a sec when I pulled the branch earlier this morning and run it with —mode and —model. 😂
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 04/12/2025
You got the bags! One step at a time :)
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Reposted by Zixuan (Eleanor) Zhang
Hanbin Lee @epigenci.bsky.social · 30/11/2025
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.
biorxiv.org
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...
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Reposted by Zixuan (Eleanor) Zhang
Jeff Spence @jeffspence.github.io · 19/11/2025
@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...
nature.com
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
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Reposted by Zixuan (Eleanor) Zhang
Nicholas Mancuso @nmancuso.bsky.social · 18/11/2025
Looking forward to presenting our work on characterizing eqtl architecture across ancestors and cells tomorrow at the Evolgenome seminar! Huge thanks for the invite @lindakachuri.bsky.social
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 12/11/2025
That will explain many GWAS hits
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Reposted by Zixuan (Eleanor) Zhang
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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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 05/11/2025
Very proud of you @tszfung.bsky.social for so many achievements!! 🎊
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 04/11/2025
media.tenor.com
a baby is being held by a woman in a crowd of people and screaming .
ALT: a baby is being held by a woman in a crowd of people and screaming .
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 01/11/2025
His Dudeness
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Reposted by Zixuan (Eleanor) Zhang
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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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 23/10/2025
media.tenor.com
a bald man with a speech bubble that says ok on it
ALT: a bald man with a speech bubble that says ok on it
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 11/10/2025
bon appétit Dr.🌶️
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