We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
doi.org
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 agoThink 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]
I am excited to share my first first-author preprint (co-led by Srivi Balaji) with @becca-young.bsky.social and @arbelharpak.bsky.social. We ask if AI can be used for good; specifically, whether we can use AI to grab species trait data from primary literature. (1/11) www.biorxiv.org/content/10.6...
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
(1/9) Our work (with @xliaoyi.bsky.social @arbelharpak.bsky.social) exploring the role of genes that escape X-chromosome inactivation in shaping the genetic architecture of sex-specific traits is now officially out in Molecular Biology and Evolution! academic.oup.com/mbe/article/...
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
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...
Representation in genetic studies affects inference about genetic architecture
Knowledge of a trait's "genetic architecture," namely the joint distribution of allele frequencies of causal variants and the direction and magnitude of their effects, is essential to understanding it...
biorxiv.org
1/13 In a new preprint, we (with @xliaoyi.bsky.social in the @arbelharpak.bsky.social lab) find that expression from the “inactivated” X (Xi) is consequential for both female-male differences in gene expression and variation among females in disease and physiology: www.biorxiv.org/content/10.1...
Escape from X inactivation drives sex differences and female trait variation
X chromosome inactivation (XCI) partially balances gene dosage between sexes, yet expression from the inactive X (Xi) is variable across genes. In this study, we investigate whether gene-level Xi expr...
biorxiv.org
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]
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. ...
biorxiv.org
I am excited to share the first first-author paper of my PhD describing work with Changde Cheng, Mark Kirkpatrick and @arbelharpak.bsky.social has been published at AJHG! We ask if sex-differential gene expression drives sex-differential selection in humans. (1/14) www.cell.com/ajhg/fulltex...
No evidence for sex-differential transcriptomes driving genome-wide sex-differential natural selection
We assess the evidence for a genome-wide relationship between sex differences in gene expression and sex differences in natural selection. We develop an improved model for testing this association but...
cell.com
