We are so excited to see our work out in @nature.com! We present a multi-omic single-cell atlas of 12 organs in human fetal development, explore the enhancer landscape, use deep learning to infer rules of transcription factor activity, and interpret non-coding variants in complex traits: #GeneReg 🧬🖥️
This @anshulkundaje.bsky.social, Kyle Fahr and William Greenleaf paper is finally out, we've been following it for a while in its preprint form, phenomenal work.
www.nature.com/articles/s41...
PSA: Never-ever use @omnigroup.com OmniGraffle to assemble figures for scientifc manuscripts. OmniGraffle messes up fonts so that there is no way to edit these files later in Adobe Illustrator. I've just spent ~4 hours trying to convert Omni PDFs into something that Illustrator can open with no luck
Our review "Integrating genetic data with biological insight: A practical guide to cis-Mendelian randomization" is now published at @ajhgnews.bsky.social - led by @vkarhune.bsky.social and Benji Woolf with critical insight from Dipender Gill and Pallav Bhatnagar. Thread follows:
Cis-MR studies are not intrinsically superior to genome-wide MR studies, and algorithmically-performed cis-MR analyses will rarely be optimal. But when performed with care, cis-MR is a powerful tool to inform about putative causal effects.
I never made that connection!
We have both sülearvuti and läpakas, first is more formal. But desktops are becoming so rare these days that everything is just arvuti.
Great to see this out! It was a pleasure to be one of the reviewers. @vkarhune.bsky.social @stevesphd.bsky.social
Estonian arvuti and Finnish tietokone insist that that ordinateur is perfectly fine.
This is from SpliceAI lookup: spliceailookup.broadinstitute.org#variant=chr6...
The variant is in the first exon, very close to the promoter and the missense predictions are begning. In contrast, PromoterAI predicts effect on expression, which seems consistent with the eQTL effect direction.
Also, I am not 100% convinced that the missense is the mechanism. The same rs10305420 variant is also a fine mapped eQTL for GLP1R in GTEx thyroid tissue (PIP = 0.96 in our unpublished re-analysis).
The p-value for obesity is even smaller in the UKBB+FinnGen+MVP meta-analysis!
public-mvp-ukbb.finngen.fi/variant/6-39...
Delighted to share our latest research from the 23andMe Research Team, just published in @nature.com !
We looked at data from >27,000 participants to uncover how human genetics influences weight loss efficacy and side effects of GLP-1 medications like semaglutide. A short thread 🧵👇
Just praegu tuli pressiteade neilt.
Genetics is good indeed.
Our experience was:
Received: 27 May 2025
Accepted: 18 September 2025
And the reviews were very useful!
Congrats! So well deserved!
Happy and honored to receive the 2026 ESHG award! Many thanks to past and present lab members and collaborators; it’s our work together that is recognized here.
See you at the @eshg.bsky.social meeting in Gothenburg 🇸🇪 in June!
👀 Absolute banger paper. Leveraging cattle/pig GWAS/eQTL to help explain the missing regulatory gap in humans. Consistent with previous works, selection makes identifying relevant eQTLs in humans challenging.
www.biorxiv.org/content/10.6...
Junk RNA
I have the same one! Love it!
It is a pleasure to work with Maarja. Congratulations on this well-deserved MSCA Postdoctoral Fellowship!
Failure to understand that the fundamental principle of Mendelian randomization (MR) is of gene-environment equivalence contributes to the flood of nonsense MR papers that are appearing; Shah Ebrahim, Gib Hemani and I explain why in this short commentary. journals.plos.org/plosmedicine...
Dear friends, after many wonderful years in the U.S., it’s time for a new adventure. My lab and I are moving to the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge starting April 2026. If you’re in the UK, come say hi. If you’re not, come visit 🙂
Huge thanks to @kauralasoo.bsky.social who stepped up with baby in his arms to lead the discussion of a complex JC paper picked and co-prepared with Maris.
Brilliant science, collaboration, real kindness, stepping up for each other, and family first. We need more role models like this. 🫶
Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social!
Connecting to some recent threads here:
First, a couple of weeks ago:
www.biorxiv.org/content/10.6...
Single cell RNAseq on blood from 200 donors across 4 sites in Indonesia spanning regional axes of genetic and environmental diversity. This is one of very few scRNA data sets from the Global South, including urban and rural settings.
Finally, today's offering! www.biorxiv.org/content/10.6...
This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social
I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e...
This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...
✨ A new star allele was born! Excited to share our first in vivo pharmacokinetic recall study involving 114 participants from @ESTbiobank with previously uncharacterised variants in CYP2C19 and CYP2D6:
www.nature.com/articles/s41... #Pharmacogenomics @pharmvar.org @clinpgx.org