Zixuan (Eleanor) Zhang

LoL child won’t lie :)

GitHub - mancusolab/jax_ldsc Contribute to mancusolab/jax_ldsc development by creating an account on GitHub.

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...

Yeeess! Foot on table leaning back

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-...

hijack def adds fear of flying…very good show

😂 mental breakdown within an hour lol

🤩🤩

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...

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...

LoL now I wanna add it to my watchlist

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. 😂

You got the bags! One step at a time :)

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/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.

How do genetic association studies rank genes? Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.

@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...

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

That will explain many GWAS hits

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

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...

Very proud of you @tszfung.bsky.social for so many achievements!! 🎊

His Dudeness

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...

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/...

bon appétit Dr.🌶️

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!

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

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)

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.

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...

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...

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)

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.

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...

📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑‍🤝‍🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social