Sign in

Olivia Smith

@oliviarxiv.bsky.social
74 followers 209 following 20 posts

Genomic Microdata Refinement @ UT Austin

PostsRepliesMedia
Olivia Smith @oliviarxiv.bsky.social · 09/09/2026
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).
biorxiv.org
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. ...
31812
Olivia Smith @oliviarxiv.bsky.social · 15/06/2026
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
Three people at a scientific poster presentation. The presenter is holding a notebook in one hand and is holding her other hand like a claw.A close up of a presenter at a scientific poster. She is holding a notebook in one hand and the other hand is forming a claw.
140
Reposted by Olivia Smith
Arbel Harpak @arbelharpak.bsky.social · 09/06/2026
#PEQG26: The Harpak Lab is coming in hot! 1/10
191
Reposted by Olivia Smith
xinyimiao.bsky.social @xinyimiao.bsky.social · 15/05/2026
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)
biorxiv.org
22514
Olivia Smith @oliviarxiv.bsky.social · 15/04/2026
"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."
010
Reposted by Olivia Smith
Jonathan Jacobs @bioinformer.bsky.social · 27/01/2026
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
academic.oup.com
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
057
Reposted by Olivia Smith
Joyce Wang @joyce-yiyi-wang.bsky.social · 26/01/2026
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)
rdcu.be
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...
34119
Olivia Smith @oliviarxiv.bsky.social · 14/01/2026
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.
A figure showing an exponential relationship between skewness of trait distribution and sign bias across three biobanks (UK Biobank, All of Us, and FinnGen). The adjusted R2 is 0.81 and p-value is less than 0.001 for this relationship.
020
Reposted by Olivia Smith
Jeff Spence @jeffspence.github.io · 07/11/2025
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...
nature.com
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
517274
Reposted by Olivia Smith
John Benning @jbenning.bsky.social · 07/11/2025
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) 🧵👇
14019
Olivia Smith @oliviarxiv.bsky.social · 20/10/2025
The only snapshot of me presenting at ASHG last week. All press is good press, right? Right?
040
Reposted by Olivia Smith
Graham Coop @gcbias.bsky.social · 02/08/2025
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.
17214
Reposted by Olivia Smith
Dr. Damien P. Williams, dread portent down from a mountain cave @wolven.blacksky.app · 21/05/2025
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.
4407135
Olivia Smith @oliviarxiv.bsky.social · 18/04/2025
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 👏🏻👏🏻👏🏻
051
Reposted by Olivia Smith
Janelle Shane @janelleshane.com · 13/04/2025
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.
11978743580
Reposted by Olivia Smith
Sasha Gusev @sashagusevposts.bsky.social · 03/04/2025
The New York Times recently had an article on IVF and embryo selection which I think buries a few important ledes about these products ...
nytimes.com
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?
24923
Reposted by Olivia Smith
Richard Sever @richardsever.bsky.social · 11/03/2025
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
openrxiv.org
Homepage - openRxiv
openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
552558846
Reposted by Olivia Smith
Cedar Riener @criener.bsky.social · 07/03/2025
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/
23511
Reposted by Olivia Smith
Eric Topol @erictopol.bsky.social · 11/02/2025
A Direct Hit, by @holdenthorp.bsky.social @science.org www.science.org/doi/full/10.... "This is a moment to unite."
24899375
Reposted by Olivia Smith
The Washington Post @washingtonpost.com · 06/02/2025
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.
washingtonpost.com
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.
107432248
Reposted by Olivia Smith
Samuel Pattillo Smith @sampatsmith.bsky.social · 04/02/2025
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]
biorxiv.org
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 their phenotype. ...
27638
Reposted by Olivia Smith
Jocalyn Clark @jocalynclark.bsky.social · 04/02/2025
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/...
651301521
Reposted by Olivia Smith
Rebekah Higgitt @rhiggitt.bsky.social · 04/02/2025
"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?
02215
Reposted by Olivia Smith
Nikolai Slavov @slavov-n.bsky.social · 01/02/2025
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...
biorxiv.org
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 ...
45521
Reposted by Olivia Smith
Richard Sever @richardsever.bsky.social · 02/02/2025
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...
insidemedicine.substack.com
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.
32414