Statistical geneticist @UWMadison
Joined November 2014
- Tweets 1,992
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Pinned Tweet
27 May 2025
@Jiacheng_Miao's PIGEON paper on GxE methodology is now published @NatureHumBehav with a new title. In our view, this paper can reshape the study design for future complex trait GxE work.
Paper📰doi.org/10.1038/s41562-025-0…
Software🧑‍💻github.com/qlu-lab/GSUB
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Qiongshi Lu retweeted
Apr 11
We showed that polygenic components of treatment efficacy capture far more variation than individual variants, but it's hard to detect them from treatment samples alone (too small). Need transfer learning from large GWAS to pull it out.
medrxiv.org/content/10.1101/…
Apr 9
The 23&me GLP1 gwas paper is very well done (the most readable gwas paper ... ever?), but I think putting this supp table 22 result in the main text would have helped keep things in perspective
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Qiongshi Lu retweeted
Interested to pursue graduate studies (MS/PhD) at the intersection of biological, biomedical problems and data science? Join us for a virtual open house on Nov 13th to learn more about our Biomedical Data Science program at UW Madison @UWMadison!
biostat.wiscweb.wisc.edu/edu…
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27 May 2025
@Jiacheng_Miao's PIGEON paper on GxE methodology is now published @NatureHumBehav with a new title. In our view, this paper can reshape the study design for future complex trait GxE work.
Paper📰doi.org/10.1038/s41562-025-0…
Software🧑‍💻github.com/qlu-lab/GSUB
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27 May 2025
Based on this advance, we make two predictions:
1) The future success of complex trait GxE research resides in sharing and meta-analyzing GWIS summary statistics.
2) Future GxE method development should focus on techniques that rely only on summary-level data.
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27 May 2025
I had the wrong software link earlier in the thread. See below for the correct one. We've done three very different PIGEON GxE applications. Read the paper for more details. All sumstats produced in the paper are publicly available too.
Software🧑‍💻github.com/qlu-lab/PIGEON
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Qiongshi Lu retweeted
24 May 2025
In this Article, the authors introduce PIGEON, a statistical framework for estimating gene-environment interactions for complex traits. @Jiacheng_Miao @Q_StatGen
nature.com/articles/s41562-0…
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5 Feb 2025
Beyond excited to share this new paper with all of you . It's the most fun we've ever had. We figured out how to study a latent index driving partner choice without measuring it directly🥂
@qinwen_zzz
Preprint📰: biorxiv.org/content/10.1101/…
Sumstats⬇️: qlu-lab.org/data.html
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5 Feb 2025
The index GWAS also allows us to remove assortative-mating-driven biases in GWAS applications. For example, genetic correlation of education and height reduced to null after conditioning on the index. But rg of education and cognition remained unchanged
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5 Feb 2025
This is a big project with many more results in the paper. But overall, we are excited about being able to study genetic associations with something we cannot directly measure. Lead author @qinwen_zzz is an undergrad who's doing PhD interviews recently. Snatch him while you can!
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Qiongshi Lu retweeted
28 Jan 2025
Our first multi-national GWAS on income is out in @NatureHumBehav 🧬💰
- 162 loci (88 novel)
- significant heterogeneity between countries
- significant heterogeneity between men and women
- unique non-education income effects
Open Access Link: nature.com/articles/s41562-0…
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3 Dec 2024
Our new PRS paper is out! We introduce a method to create regularized ensemble PRS on GWAS sumstats. Individual-level data is no longer needed for sophisticated ensemble learning @ZijieZhao1996 @stphn_drn
Paper📰:biorxiv.org/content/10.1101/…
Software🧑‍💻:github.com/qlu-lab/PUMAS
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3 Dec 2024
One of the applications is ensemble learning. We've explored a vanilla version before through linear regression, and have done some cross-ancestry applications. Here, we realize its full potential and showcase much better ensemble learning models on sumstats
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3 Dec 2024
@stphn_drn has a detailed thread to show all our results. He also implemented these new ensemble features in our PUMAS software. Stephen is applying for PhD programs this year. Look out for his application. We want him in Wisconsin too!
Thread🧵:x.com/stphn_drn/status/18640…
3 Dec 2024
My first co-author paper is now preprinted! With
@ZijieZhao1996 and @Q_StatGen
we introduce PUMAS-ensemble, a regularized ensemble PRS requiring only GWAS summary statistics and LD reference data as input.
biorxiv.org/content/10.1101/…
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Qiongshi Lu retweeted
3 Dec 2024
My first co-author paper is now preprinted! With
@ZijieZhao1996 and @Q_StatGen
we introduce PUMAS-ensemble, a regularized ensemble PRS requiring only GWAS summary statistics and LD reference data as input.
biorxiv.org/content/10.1101/…
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