Human genetics and applied mathematics - genetic architecture and genealogical algorithms - Assistant Professor @HarvardDBMI
Cambridge, MA
Joined April 2016
- Tweets884
- Following303
- Followers1.9K
- Likes3.6K
Pinned Tweet
Now published @CellGenomics
cell.com/cell-genomics/fullt…
New preprint on a surprising question - with a pangenome reference, *what is a genetic variant?*
biorxiv.org/content/10.1101/…
With Pouria Salehi Nowbandani, Shenghan Zhang, Haoyang Hu, and Heng Li @lh3lh3
Luke O'Connor retweeted
🧬New today from Lu et al!
📄Effect heterogeneity reveals complex pleiotropic effects of rare coding variants
cell.com/ajhg/abstract/S0002…
🖥️github.com/atgu/ALLSPICER
Luke O'Connor retweeted
Mathematics has now fully morphed into biology:
Project costs millions $ ✅
Put out paper that nobody has read ✅
Massive paper supplement nobody will read ✅
Advertise with pretty art ✅
Vicious authorship fight ✅
Say you're curing cancer ✅
Luke O'Connor retweeted
On biorxiv this week: "Integrated map of somatic mosaicism across human tissues in 25 individuals" from the Somatic Mosaicism across Human Tissues Network (biorxiv.org/content/10.64898…)
Excited to share our preprint: what is the penetrance spectrum of coding mutations in autism?
Very excited to share a powerful new method, graphREML, for common-variant heritability partitioning and enrichment from GWAS sumstats, now published in @NatureGenet
Led by 1st author Hui Li, co-supervised with @XihongLin
graphREML should run in 10-60 minutes per trait depending on hardware
If you only need enrichment p-values for some new annotations, you can perform a score test using precomputed derivatives (graphREML-ST), which should be <1 minute for 20 traits
We've worked hard to make our software convenient to use, including for agents: github.com/oclb/graphld
Paper: nature.com/articles/s41588-0…
Now published @AJHGNews
cell.com/ajhg/abstract/S0002…
New preprint with Guy Sella on the question: what is polygenicity?
biorxiv.org/content/10.1101/…
Luke O'Connor retweeted
Kodama CLI is very AI-agent-friendly!
> Command-line interface
> The package provides a command-line tool kodama for constructing linear ARGs, running GWAS, estimating heritability, and computing polygenic risk scores.
It should be easy for you to develop your own methods leveraging linear ARGs for speed - if you do try our software, I'd love to hear from you!
github.com/quattro/linear-da…
So excited to share our latest preprint, introducing a powerful genealogical compression algorithm for biobank-scale genetic data
With Amber Shen, Xinran Wang, and Nick Mancuso @nmancuso_
biorxiv.org/content/10.64898…
Of this we get about 100x from compressed matrix operations and 40x due to statistical tricks which are seemingly new (we reuse covariate-related computations across traits while accounting for differences in missingness)
It should be easy for you to develop your own methods leveraging linear ARGs for speed - if you do try our software, I'd love to hear from you!
github.com/quattro/linear-da…