Today, we at the @arbelharpak.bsky.social & @docedge.bsky.social labs are excited to share our updated manuscript for PGSUS, a tool for diagnosing confounding in polygenic scores (PGSs).

A Litmus Test for Confounding in Polygenic Scores

Polygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one's genotype on one's phenotype. ...

biorxiv.org

Samuel Pattillo Smith@sampatsmith.bsky.social · 2y ago

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]

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

Olivia Smith@oliviarxiv.bsky.social · 11mo ago

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

#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."

Eric Turkheimer@ent3c.bsky.social · 5mo ago

I wrote a reply to @nathancofnas.bsky.social on Substack. Nathan has been dragging me over his tendentious interpretation of a blog post I wrote 20 years ago, which I already explained many times. Nathan's contention is that I am lying about what I really think, but fortunately he knows better.

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

Complete Diploid Genome of the Type Strain Yarrowia lipolytica YB-423 (ATCC 18942™)

Abstract. Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a co

academic.oup.com

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)

Three open questions in polygenic score portability

Nature Communications - Genetic predictors of health outcomes often drop in accuracy when applied to people dissimilar to participants of large genetic studies. Here, the authors investigate the...

rdcu.be

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.

Jared M. Cole@jmillercole.bsky.social · 8mo ago

Excited to share our new preprint from the @arbelharpak.bsky.social Lab! How do recruitment into genetic studies and study characteristics impact what we infer about the genetic bases of traits, and what are the consequences? (1/21) www.biorxiv.org/content/10.6...

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...

Specificity, length and luck drive gene rankings in association studies - Nature

Genetic association tests prioritize candidate genes based on different criteria.

nature.com

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.

Chicago Sun-Times@chicago.suntimes.com · last yr.

On Sunday, May 18, the print and e-paper editions of the Chicago Sun-Times included a special section titled the Heat Index: Your Guide to the Best of Summer, featuring a summer reading list that our circulation department licensed from a national content partner. 🧵

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 👏🏻👏🏻👏🏻

Michael Schwob@michaelschwob.bsky.social · last yr.

My first textbook is officially available for pre-order today. Grab a copy if you're interested in developing a (statistical) research-oriented mindset. The book is designed as a stepping stone from statistical coursework to novel statistical research. www.routledge.com/Exercises-in...

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.

David D. Levine@daviddlevine.com · last yr.

LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."

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

Opinion | Should Human Life Be Optimized?

Advances in genetic testing and artificial intelligence are changing what’s possible for those undergoing I.V.F. Are we ready for the future of fertility?

nytimes.com

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.

Elon Musk’s DOGE is feeding sensitive federal data into AI to target cuts

Department of Government Efficiency workers embedded in the Education Department have been processing sensitive agency data using artificial intelligence.

washingtonpost.com

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?

Richard Van Noorden@richvn.bsky.social · 2y ago

www.nature.com/articles/d41...

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...

Genomic Foundationless Models: Pretraining Does Not Promise Performance

The success of Large Language Models has inspired the development of Genomic Foundation Models (GFMs) through similar pretraining techniques. However, the relationship between pretraining performance ...

biorxiv.org

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...

BREAKING NEWS: CDC orders mass retraction and revision of submitted research across all science and medicine journals. Banned terms must be scrubbed.

Any unpublished manuscript mentioning certain topics, including gender and "LGBT," must be pulled or revised.

insidemedicine.substack.com