Happy to share a new preprint, where we studied the expected outcomes of polygenic embryo screening in real-world IVF patients.
Key conclusion: gains are very small for most infertility patients, with risk reductions under 5%.
🧵1/12
www.medrxiv.org/content/10.6...
Genome-wide genealogies reveal deep admixtures forming modern humans www.biorxiv.org/content/10.64898/2026.04...
Spread the word! UChicago BSD is currently searching for an instructional professor (open rank) to help develop and support graduate training in quantitative biology at UChicago. This is an Instructional Professor position (open rank). apply.interfolio.com/183517.
Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic www.biorxiv.org/content/10.64898/2026.04...
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...
General, orders-of-magnitude faster whole-genome analysis with genotype representation graphs www.biorxiv.org/content/10.64898/2026.04...
Very proud of this tour de force from two former students, Stephanie Tanis and Leah Simon, with help from a huge team, including @charlesdanko.bsky.social highlighting a novel-overlooked intervention point for male contraception
www.pnas.org/doi/10.1073/...
Delighted to share our latest research from the 23andMe Research Team, just published in @nature.com !
We looked at data from >27,000 participants to uncover how human genetics influences weight loss efficacy and side effects of GLP-1 medications like semaglutide. A short thread 🧵👇
Getting close to a robust pipeline for ARG inference for messy genomes.
1. get a vcf. Align short reads to a reference and GATK and pray, or use whole genome assemblies and github.com/baoxingsong/... followed by github.com/RILAB/argprep
Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀
I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵
seqeralabs.github.io/RustQC/
Why phylogenies compress so well: combinatorial guarantees under the Infinite Sites Model www.biorxiv.org/content/10.64898/2026.03...
We (with @yanwong.bsky.social) are advertising a 3 year postdoc position for a project on ARG inference and methods! Based at Oxford stats. Closing date noon 7 April, full details at my.corehr.com/pls/uoxrecru...
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/
🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳
The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.).
See github.com/snakemake/sn... for more
Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.
🙌 this looks awesome - and a good excuse for me to learn more jax too
Would genuinely welcome this - I’ve used some of the count-based GLMs in statsmodels and it’s never felt totally great to use in notebooks
Best wishes to @dannykellywords.bsky.social, host of The View From The Lane, after being diagnosed with esophageal cancer.
Be well, Danny. Hope you’re back behind the mic soon.
Up the Spurs.
📣Our paper is out! 🤩 We found that local modification of H3K9me3 using CRISPR/dCas9 at hotspots changes crossover activity, bringing us closer to targeted recombination in plants.🌱
Huge thanks to @szymanskalejman.bsky.social, Wojtek, Ania, and Karolina!
www.science.org/doi/10.1126/...
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...
This paper is bananas. I love everything about this. Such a fantastically smart design, signals popping out like nobody's business.
www.biorxiv.org/content/10.1...
If you're looking to build or deepen your knowledge in statistical genetics, the ISG Workshop (June 1–11) covers the full range: biometrics, GWAS, polygenic scores, causal inference, and more. Open to all levels, virtual, and international: www.colorado.edu/ibg/workshop...
Retweets appreciated 🙏
I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!)
link: www.sciencedirect.com/science/arti...
9/9 TRACE reveals hidden layers of modern human evolution using only contemporary genomes. We would greatly appreciate any comments or suggestions!
github.com/YulinZhang98...
Have you ever wondered how many archaic populations contributed DNA to modern humans? We know about Neanderthals and Denisovans, but the fossil and genetic evidence suggests a much more complex history!
www.biorxiv.org/content/10.6...
Happy to have co-led this work with @yulinzhang.bsky.social - where we leverage signatures in inferred ARGs to understand introgression from archaic hominins. See the explainer thread below, and thoughts/questions very much welcome!
A sedge. It may look unassuming but its genome has several unusual features.
Why do the chromosomes of cyperids (sedges & rushes) split and fuse so regularly on evolutionary timescales?
Is it because they have so many centromeres?
Our new preprint, the first major paper of my PhD, addresses this question. 🧵⬇️ 1/12
www.biorxiv.org/content/10.6...
Big News: I have revived Slime Soccer
Playable on mobile or desktop.
Play against the CPU or 1v1 against whoever is sitting next to you, just like the old days.
Includes World Cup and Premier League teams.
Sorry if you had any more work to do today.
trivialsports.com/games/slime-...
Great perspective by @philipcball.bsky.social.
Elementary genetics teaching (HS/college) focuses on Mendelian traits (single gene => single trait). However, it is now clear that polygenicity and pleiotropy are the norm. Curriculum must change accordingly.
www.sciencedirect.com/science/arti...
Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs www.biorxiv.org/content/10.64898/2026.02...