If you present a poster at a conference and don't get a bad pic of it from your lab mate, did it really happen? #PEQG26

#PEQG26: The Harpak Lab is coming in hot! 1/10

I am excited to share my first paper, our new preprint: www.biorxiv.org/content/10.6... with @arbelharpak.bsky.social and @docedge.bsky.social. Family GWAS provides direct genetic effect estimates and is increasingly important. But how much can we trust these estimates? (1/15)

"I did not say that it is a matter of ethics that genes have nothing to do with behavioral differences, because of course they do. I said that it matters HOW genes are involved in behavior, and it has only become clearer and clearer that the answer to that HOW is: non-deterministically."

First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics

Our work on the generalizability of polygenic scores (PGS) from the @arbelharpak.bsky.social Lab is now officially out! We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.” rdcu.be/e0LAr (1/27)

New preprint (led by Jared!) where we show that measures of genetic architecture, often assumed to be intrinsic to traits, in fact vary across biobanks. In my favorite figure, we show that sign bias (bias in the direction of GWAS effects) is closely linked to skewness in trait distribution.

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...

We're excited to share the final version of our paper, where we demonstrate how confounding remains a thorny problem for claims about causal genetic influences on human behavioral and socioeconomic outcomes. (w/ @jedidiahcarlson.com @oliviarxiv.bsky.social Ruth Shaw @arbelharpak.bsky.social) 🧵👇

The only snapshot of me presenting at ASHG last week. All press is good press, right? Right?

These embryo-selection startups are clearly feeding into an alt-right ecosystem that revels in techno-futurism much as such movements have in the past. GWAS participants & parents navigating IVF deserve better than being used as tools to attract the attention of edge lords.

So when next we tell you that it's a terrible idea to fire your writers and editors and either a) hire some of them back as "assistants" to clean up LLM generated "AI" slop or b) just wholly rely on content mills which do the same, i want you to remember what's happening to the Chicago Sun-Times.

So exciting to see this out -- Michael has hugely accelerated my statistical training over the last few years and is incredible at explaining and teaching complex ideas in stats 👏🏻👏🏻👏🏻

1. LLM-generated code tries to run code from online software packages. Which is normal but 2. The packages don’t exist. Which would normally cause an error but 3. Nefarious people have made malware under the package names that LLMs make up most often. So 4. Now the LLM code points to malware.

The New York Times recently had an article on IVF and embryo selection which I think buries a few important ledes about these products ...

Wow. "NIH" canceled my co-mentored (with Dave Sulzer) PhD student's F31 funding. His work is on understanding the genetics and neuroscience of language learning disorders. F31 provides no indirect $ to Columbia, just pays his salary. Not that it should matter, but he's an American citizen. W.T.F.

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

A quote from NYT "just the facts" news piece on eliminating Dept of Ed, describing conservative opposition in 1980: "They argued that education should be primarily managed at the state and local levels rather than through federal mandates." Imho accepts bad faith reasoning 1/

A Direct Hit, by @holdenthorp.bsky.social @science.org www.science.org/doi/full/10.... "This is a moment to unite."

Representatives from Elon Musk’s U.S. DOGE Service have fed sensitive data from across the Education Department into artificial intelligence software to probe the agency’s programs and spending, according to two people with knowledge of the DOGE team’s actions.

Think of a polygenic score you care about. Are direct genetic effects driving variation among people in this predictor? Or perhaps other, confounding factors? We at the @arbelharpak.bsky.social & @docedge.bsky.social Labs developed a method to tackle this question. [1/n]

Censor CDC scientists and ask them to withdraw papers from medical journals? This is not how it works, Mr President. Our response @bmj.com on the Trump Executive Order and his "forbidden words" www.bmj.com/content/388/...

"grants are being reviewed independently by two staff members instructed to indicate any potential violations of Trump’s orders" As the article says, these orders will likely be found illegal. Why is the NSF expediting this and why is anyone agreeing to reviewed already reviewed grants?

The success of LLMs has inspired their extension to genomics data. A preprints reports that such models lack understanding of genomics and provide minimal utility, even for basic tasks such as sequence classification. www.biorxiv.org/content/10.1...

CDC censors papers submitted to journals. "Researchers instructed to remove references to forbidden terms [including] transgender, LGBT, non-binary, assigned [fe]male at birth" insidemedicine.substack.com/p/breaking-n...