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

And to make this more concrete, here is a re-review we just got. The editor overruled this negative reviewer, who here is *lecturing us on the ethos of the journal*. I've never met anyone in real life who holds this position with whom I can have an actual discussion. Always anonymous peer review.

You can explain to me the complexity and rules related to endowment all you want, but there is just no way Harvard can't afford to keep their graduate programs intact. It's a choice.

Happy to be at ASHG! 2 students in the lab will present posters on gene regulatory evolution in primates on Thurs: Emma focuses on responses to stimuli: 9109T John focuses on transposable elements: 6036T Please stop by if interested #ASHG25

Thank you for taking the time to review my book!

Your immune system remembers skin inflammation long after it resolves because of #interferon alpha! Check out our new paper describing these findings just published at @jimmunol.bsky.social 👇👇👇 It was amazing working on this with my role model @drshrutinaik.bsky.social

I think the R01 is basically a non-starter at NIGMS now. Data from NIH Reporter for new and competing awards, comparing number of R01s issued relative to R35s (MIRA). This has major ramifications for basic science and basic science investigators that are not yet in the MIRA pool

C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

More foundations should do this: "Funding is exclusively available to applicants who have already received federal funding (e.g., from the NIH, CDC, NSF) for their health equity research, but have since had their funding rescinded due to federal administrative actions" www.rwjf.org/en/grants/ac...

Some personal news: I was recently promoted to Full Professor at the University of Chicago. This milestone is deeply meaningful, and also feels quite surreal. When I started as a graduate student at UChicago in 2005 I never imagined my journey would lead me here 20 years later as a professor.

Check out our new review about addressing missing context in regulatory variation across primate evolution 🧬🐒 www.sciencedirect.com/science/arti...

I heard in the elevator a graduate student joking about destroying their lab and starting over, and I was just thinking that the lab I did my PhD. in was actually completely destroyed this week.

Happy to share our work led by Renee: ‘Anthracyclines induce global changes in cardiomyocyte chromatin accessibility that overlap with cardiovascular disease loci.’ www.biorxiv.org/content/10.1...

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?" (For the record, no one has ever asked me this, but it is a really good question!) I think we know where they are.

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?" (For the record, no one has ever asked me this, but it is a really good question!) I think we know where they are.

Our paper: ""Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids" genome.cshlp.org/content/earl...

Why do so many disease risk variants show no regulatory effects in GTEx and/or other standard eQTL studies? What do we mean when we say a regulatory effect is "context-specific" and how do we define the context? We explored these questions using brain organoids and oxygen stress.

Context in another thread. Just the preprint here: doi.org/10.1101/2025...

I’ve been studying gene regulation in primates for over 20 years, and using RNA-seq since 2008 to compare expression across species. We thought we were being careful. We used curated orthologous exons to minimize alignment bias and focused on biologically meaningful comparisons. We were wrong.

Absolutely thrilled to see Dr. Brandon Gaut receive the inaugural @genetics-gsa.bsky.social Mentorship Award! 🏆🎉 Brandon brings humanity back to science, supports inclusive training, and pushes back on the publish-or-perish culture. So well deserved—congrats! 👏🙌 genestogenomes.org/distinguishe...

It was fun to write this piece with such a great team of colleagues in the field! Also grateful for discussions and feedback from @anshulkundaje.bsky.social @avsecz.bsky.social

🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.

Nice! Environmentally responsive eQTLs are enriched for being more distal and for constrained genes relative to conventional QTLs.

This is such an exciting project! Huge thanks to Wenhe Lin, @jmpopp.bsky.social, @radster95.bsky.social, Olivia Allen, Jonathan Burnett, and to @alexisbattle.bsky.social, @ygilad.bsky.social, and Matthew Stephens for their mentorships! Check out our preprint for more! www.biorxiv.org/content/10.1...

Congratulations to my colleague, collaborator, and friend @jkpritch.bsky.social for his so well deserved election to the national academy of science! Only thing is... NAS: what took you so long..?!

It's his favorite movie. He recognizes the music and he'll come to watch. Flow

New interview in the University TImes at Pitt based on my interview. utimes.pitt.edu/news/jeremy-...

Posted this last week but then the biorxiv site promptly went down for maintenance! Check out our new work using spatial txn to study heart transplant rejection! doi.org/10.1101/2025...

I am a bit surprised to see many posts on the response to the selection during Black Death paper without also a link to the response to the response, as it has been out for a long while now: www.nature.com/articles/s41... www.biorxiv.org/content/10.1...

I tested many free 'AI detection' tools, and they all highlighted large parts of my older RO1s (2010-2015) as written by AIs...

Fortunately, they didn't yet discover the trans-gender regulatory elements.

🧪 First posting of NIH grant review panels to #FederalRegister since Jan 21. Very limited. Just NIH Directors Awards (New Innovator, DP2) and one NIDDK study section, meeting dates range from March 24-April 4 www.federalregister.gov/public-inspe...

This was fun.

How do you study gene-environment (GxE) interactions in humans? Well, there's probably no way to avoid studying each exposure individually, but what about the cellular context? If you choose directed differentiation, you have to study GxE one cell type at a time. If you choose an organoid system -

Incredible to see this project taking shape! Good luck Mara&co! In parallel we are continuing to build genomes and polymorphism data for all Drosophila species! The combined resources will be a dream for understanding forces driving evolution on micro &macroscales journals.plos.org/plosbiology/...

These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today. We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe www.cell.com/cell/current...

41/47 (87%) of NIH study sections are cancelled this week Frustrating to see all this good research stalled (& not funded) You can search for study sections that ‘did not meet as scheduled’ here with ones with * ⤵️ www.csr.nih.gov/RevPanelsAnd...

The court ordered that NIH grant funding be unfrozen, so The Regime found a way around it. For NIH grants to be funded, a review panel must rank them. In order for a review panel to meet, they must post it on the Federal Register. Submissions to the Federal Register are now on hold “indefinitely”.

Collaborators fired at USDA. Program officers fired at NSF. Study sections suspended indefinitely at NIH (also firings). It's impossible to just keep your head down and do the work, as the work and the people are vanishing in front of us. 🧪

It looks like 8/8 study sections that were scheduled to begin today have been cancelled: www.csr.nih.gov/RevPanelsAnd...

I can afford to recruit a postdoc or staff scientist.

Iterative improvement of deep learning models using synthetic regulatory genomics www.biorxiv.org/content/10.1...

One often overlooked aspect of university endowments is how much is leveraged against debt. I don’t know the details everywhere, but in the institutions I’m familiar with, that fraction is quite considerable, making endowment spending far less flexible than it might seem at first glance.

Press release by the appropriations subcommittee on NIH budget slashing by @delauro.house.gov 🙏