Reposted by Zixuan (Eleanor) ZhangHanbin Lee @epigenci.bsky.social · 06/10/2026We 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. 15423
Reposted by Zixuan (Eleanor) ZhangRoshni Patel @roshnipatel.bsky.social · 06/10/2026So 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.orgLarge language model-based bibliometric evaluation of population descriptors in human geneticsAs 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... 12211
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 03/10/2026static.klipy.comSpongebob: Done And Done!ALT: Spongebob: Done And Done! 010
Reposted by Zixuan (Eleanor) ZhangYun S. Song @yun-s-song.bsky.social · 23/09/2026Please 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.eduBakar Computational Biomedicine Initiative | Bakar Computational Biomedicine Initiative 12937
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 10/09/2026Version 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.iojaxQTL - jaxQTLCell-type-specific eQTL mapping from single-cell pseudobulk expression. 0103
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 24/08/2026v0.2.0 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.comGitHub - mancusolab/jaxqtl: Flexible, scalable, QTL analyses using generalized linear models implemented in JAXFlexible, scalable, QTL analyses using generalized linear models implemented in JAX - mancusolab/jaxqtl 163
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 13/08/2026static.klipy.comTed Lasso says YES! (TheGoon BigOldGoon)ALT: Ted Lasso says YES! (TheGoon BigOldGoon) 010
Reposted by Zixuan (Eleanor) ZhangHanbin Lee @epigenci.bsky.social · 15/07/2026How 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 12712
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 24/06/2026Not ever seen this. But I have been using Jupyterlab. Not sure about rstudio 000
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 22/06/2026Genoio 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/ 183
Reposted by Zixuan (Eleanor) ZhangJeff Spence @jeffspence.github.io · 22/06/2026Excited 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.orgAllele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in HeterozygotesAbstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred 26844
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 18/06/2026I m 30mins in first episode. Shep scares me but I have to say it’s a smart delayed reveal. 010
Reposted by Zixuan (Eleanor) ZhangSasha Gusev @sashagusevposts.bsky.social · 07/06/2026I 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.comThoughts on AI in academiaPhD-level thinking, LLM bias, alignment, AGI, data centers, and AI politics 59336
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 06/05/2026Super 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 34516
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 14/04/2026Thrilled 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/fdl9krdcu.beMulti-ancestry genome-wide association study of severe pregnancy nausea and vomitingNature 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... 14419
Reposted by Zixuan (Eleanor) ZhangLior Pachter @lpachter.bsky.social · 13/04/2026If 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/🧵 13912
Reposted by Zixuan (Eleanor) ZhangApril Wei @aprilwei.bsky.social · 12/04/2026Very 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 24618
Reposted by Zixuan (Eleanor) ZhangArjun Bhattacharya @arjunbhattac.bsky.social · 26/03/2026Another 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! 074
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 24/03/2026I 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.ioglmaxGrammar-first generalized linear modeling in JAX. 3133
Reposted by Zixuan (Eleanor) ZhangJosh Weinstock @joshweinstock.bsky.social · 13/03/2026Here'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.ioHigh Performance GWAS Plotting And AnnotationMore about what it does (maybe more than one line). Continuation lines should be indented. 02414
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 11/02/2026I 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.comGitHub - mancusolab/jax_ldscContribute to mancusolab/jax_ldsc development by creating an account on GitHub. 283
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 27/01/2026Been 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.comGitHub - quattro/jax-numerics-agentContribute to quattro/jax-numerics-agent development by creating an account on GitHub. 111
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 18/01/2026hijack def adds fear of flying…very good show 000
Reposted by Zixuan (Eleanor) ZhangZeyun Lu 鲁泽沄 @zeyunlu.bsky.social · 05/01/2026Happy 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.orgIntegrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traitsMost 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... 13110
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 19/12/2025media.tenor.coma 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 . 100
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 05/12/2025Ah that’s why. I was confused for a sec when I pulled the branch earlier this morning and run it with —mode and —model. 😂 110
Reposted by Zixuan (Eleanor) ZhangHanbin Lee @epigenci.bsky.social · 30/11/2025www.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.orgGenetic prediction with ARG-powered linear algebraAncestral 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... 1199
Reposted by Zixuan (Eleanor) ZhangJeff 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.comHow do genetic association studies rank genes?Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology. 15322
Reposted by Zixuan (Eleanor) ZhangNicholas Mancuso @nmancuso.bsky.social · 18/11/2025Looking 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 3193
Reposted by Zixuan (Eleanor) ZhangJeff Spence @jeffspence.github.io · 07/11/2025How 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.comSpecificity, length and luck drive gene rankings in association studies - NatureGenetic association tests prioritize candidate genes based on different criteria. 517274
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 05/11/2025Very proud of you @tszfung.bsky.social for so many achievements!! 🎊 010
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 04/11/2025media.tenor.coma 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 . 000
Reposted by Zixuan (Eleanor) ZhangYuval Simons @yuvalsim.bsky.social · 24/10/2025Why 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.orgSimple scaling laws control the genetic architectures of human complex traitsGenome-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... 18738
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 23/10/2025media.tenor.coma bald man with a speech bubble that says ok on itALT: a bald man with a speech bubble that says ok on it 010