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...
It’s that magical time of the year again! This has been a very good year for fall colors here in Chicago.
This view never gets old
(Hutchinson quad at uchicago - grateful to pass by this place every morning I go to work)
That’s so cool! I almost thought they were mountains
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:
Another fun year for the #mwpg, this year at the University of Minnesota! Great to see all the trainees participating with their cool work.
ugh that sucks - hope you find something fun to do in the meantime (if you’re not already exhausted!)
A windy sunset on Lake Michigan:
Morning sunlight pouring down through the canopy above the Twin Falls
Snowqualmie Falls in early morning - Albert Bierstadt in real life!
Bloedel reserve, one of the most well and meticulously curated natural reserves in the country, imho
Beginning of the Twin Falls trail
A morning hike through the woods is like a refill for the soul.
A very lucky morning in the Snoqualmie Falls (before hiking up the mountains)!
My favorite part of the journey, morning of day 3: Mt Baker Snoqualmie National Forest. Misty forest, endless spruce, redwood, cedar, and brightly colored wildflowers.
Into the Glacier Park - clouds were heavy but still got to see some of the ice capped peaks
Golden sunset over the Mississippi River
Fresh air stop at Whitefish in the evening of day 2 - maybe next vacation…
Days and nights on the empire builder train from Chicago to Seattle:
Beautiful strawberry moon tonight! That sliver of reflection over Lake Michigan adds even more to the moment’s tranquility.
Jennifer Blanc and @jeremyjberg.bsky.social use theory and simulations to study the process of testing for an association between polygenic scores and axes of ancestry variation when confounding factors are present.
Learn more about their findings in #GENETICS: buff.ly/EmKpXyP
Excited for our publication on how the geographic scale of a sample affects the discovery of rare, deleterious variants to be out this week. With a mix of theory, simulation, and data analysis, we show when samples are narrow vs broad, the number of variants discovered and their frequencies change
Congrats!!
The impact of background selection in mutation-selection-drift balance models of complex trait evolution www.biorxiv.org/content/10.1101/2025.05....
Mutation-selection-drift balance models of complex diseases www.biorxiv.org/content/10.1101/2025.05....
Beautiful shell(s)!
If you’d like a zoom recording, please dm me!
Thank you to everyone for coming in person (on a Monday morning) and on zoom! Much appreciated
Friends baked delicious dark chocolate brown butter black sugar sea salt cookies and brought a spread of cupcakes and chips to celebrate!
Defended my thesis proposal this week and am now a PhD candidate! Incredibly grateful for the support from my mentors, friends, and everyone who came to the talk in person and on zoom. I’m so lucky to be around such amazing people and can’t wait to continue this journey!
Congrats! loved your NAPC talk on the project :)
After a weekend that truly felt like summer (thunderstorms, sunshine, shorts and t-shirts), I just cannot believe that it’s going to dip below freezing again next week
(So says the weather app, which I wholeheartedly hope is wrong)
I wrote about how population stratification in genetic analyses led to a decade of false findings and almost certainly continues to bias emerging results. But we are starting to have statistical tools to sniff it out. A 🧵:
Now that’s some true love!
There’s no better getaway than the Oregon spring, and arguably no better therapy (at least for me!) than a few moist, crystal hours alone in the rain washed forest
Congrats Davey!!
My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.
It’s available on Amazon: tinyurl.com/mx2hewen
Congrats Paul!! Very well deserved!