Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests. We describe a critical concept that we call *specificity*. Led by Jeff Spence and Hakhamanesh Mostafavi:

One of the coolest papers I’ve read. Changed the way I think about GWAS and burden testing.

Exciting work by Jeff and Hakhamanesh is now published!

Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled

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...

How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.

Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...

Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring! Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu Travel grants available - register here: emgm2026.sciencesconf.org?lang=en

Everything Jeff said except since we're hosting at Stanford it's pronounced BAP-G bsky.app/profile/jros...

The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.

Revisiting last week’s open problems scandal, I wrote about LLMs as Lore Laundering Machines and why some are blind to the novelty whitewashing.

Please share/repost widely: I have a postdoc position available. Please see ad below and reach out to apply. academicpositions.harvard.edu/postings/15449

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/...

reminder that my (wonderful, diverse, interdisciplinary) department at the University of Oregon is seeking applications for an Associate/Full Professor of Data Science -- deadline 10/31 and only cover letter/CV needed to apply academicjobsonline.org/ajo/jobs/30328

I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini. 📄: shorturl.at/BgXqq Github: shorturl.at/b49Wa

I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!

For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6. Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT! docs.google.com/forms/d/e/1F...

New study in #GENETICS from @anaignatieva.bsky.social and @linoafferreira.bsky.social shows how ancestral recombination graphs can help detect "phantom" genetic interaction signals that arise due to genealogy and not because of epistasis. buff.ly/TQARoDp

We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT

Very excited for Jeannette Tenthorey! @packardfdn.bsky.social @ucsfhealth.bsky.social

Hi #ashg2025! Lookin forward to another exciting event! If any trainee would like to chat, either about career advice or submitting their work to @hggadvances.bsky.social pls don't hesitate to reach out!

An open-rank faculty search in AI + Engineering (Bioengineering included) at UC Berkeley. Due date: Monday, Nov 3, 2025 at 11:59pm (PT) Please help spread the news. aprecruit.berkeley.edu/JPF05144

I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.

We have a postdoc position in my team. Join us if you are passionate about genomics, human genetics, synthetic biology and agentic AI! careers.gene.com/us/en/job/20...

📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).

This paper is bananas and shows there is still so much to be learned about gradient descent behavior. [ODEs are so hot right now] centralflows.github.io

My lab is seeking to co-hire a postdoctoral fellow with the @shaonsengupta.bsky.social team. See details below! I'll be #ASHG2025, so open to discuss further there if interest. careers.chop.edu/us/en/job/10...

Do check out our new manuscript, now out in G3 on modelling theoretical expectations of ghost introgression in sampled genomes. Just in time for Halloween! 🎃 👻

Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we: 1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs bsky.app/profile/bior...

Fine-tuning sequence to function deep learning models on large-scale proteomic data improves the accuracy of variant effect prediction https://www.biorxiv.org/content/10.1101/2025.09.26.678908v1

New paper alert 🚨 w/ @NoahRosenberg, out in EJHG (www.nature.com/articles/s41...) 🧵

Any academic folks on H1B visas (even with stamps in passports) please get legal advice from your University attorneys before leaving the US.

/2 OUTRAGEOUS! Fri. afternoon (night in most of the US), providing less than 25 hr notice of a BIG new fee. Looks like it is not just new post-docs but those who are now overseas. (Note—our academic year starts Monday.) "If you have an H-1B visa & are outside the U.S., you must return immediately"

OH NO! "The White House issued a proclamation today, Sept. 19, 2025, around 4:36 PM PDT imposing a $100,000 fee for each H-1B visa holder who enters the U.S. after Sept. 21, 2025, 12:01 AM EDT. In CA, this will take effect tomorrow, Sept. 20, 2025, at 9:01 PM PDT." Emergency notice at Stanford.

My team has a postdoc position available now, join us! careers.gene.com/us/en/job/20...

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

New faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT

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...

SINGER is a fantastic method for ARG Inference and based on some of the analyses I've seen definitely the best trade off between accuracy and sample size

We invite you to join our seminar at UCSF Mission Bay campus with Brieuc Lehmann from @ucl.ac.uk humangenetics.ucsf.edu/ihg-seminar-...

Delighted to see this paper with @anaignatieva.bsky.social now published in Genetics! academic.oup.com/genetics/adv... We tackle a thorny issue arising in statistical tests for genetic interactions (epistasis) using ancestral recombination graphs (ARGs)... 🧵

Here is a word cloud of the words that were missing from the noncompetitive renewal awards but had been present in the parent award. 3/4

New Preprint! This one led by Sam Gibbon, an outstanding undergrad I've worked with for the past year. We take a look at whether segregation patterns in tetraploids (disomic v polysomic) affects mut-sel dynamics. We found some surprising results, and some subtleties: www.biorxiv.org/content/10.1...

In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...

🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉 We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025! Details in thread! 🧵 1/3

scVerse conference is at Stanford this year! Encourage folks (especially Bay Area/West coast folks) to sign up and attend. Cool workshops/talks and other events + great community of developers for one of the most widely used open source software for single cell data analysis!

Why do males and females often differ in traits? The expected answer: selection. But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same

Delighted to share some wonderful work by our recent grad Matthew Aguirre on theoretical models of GRNs, and what eQTL data can teach us about these!

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...