I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...

Hey @genomeresearch.bsky.social, second time I decline a review assignment (sorry, just really busy this month), but your system still sends reminders of the request. Something seems to be wrong in recording the response. Promise to accept assignments as soon as have some bandwidth!

We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...

Single Cell Genomics Day: A (Virtual) Practical Workshop. June 12, 2026, organized by @nygenome.org's Rahul Satija Free, livestreamed, no registration.

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted at UChicago. Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia open.substack.com/pub/blekhman...

Had an amazing time at #BOG26 — and even got to give my first talk 🥳

Happy to share our new preprint on non-coding genetic variation in the human brain and Parkinson's disease. Great team effort with @alexanrna.bsky.social, @juliedeman.bsky.social, Koen Theunis, and all co-authors, supervised by @steinaerts.bsky.social and @jdemeul.bsky.social. Thread below:

New paper alert: Our latest shows how maternal diet impacts ribosome levels and early growth intergenerationally in #Celegans Led by Sigma Pradhan and in collab with @nstroustrup.bsky.social journals.plos.org/plosbiology/... @plosbiology.org @izb-unibern.bsky.social @unibe.ch

📣 New preprint 🧵: we profiled post-mortem human BA22 (speech cortex) in autism across 100 donors using single-nucleus multiomics (~500,000 nuclei), integrating RNA + chromatin accessibility. Shout-out to my co-first authors Varun Suresh and Yuhan Hao: www.biorxiv.org/content/10.6...

Our latest publication is now out at Genome Biology! link.springer.com/article/10.1... We uncover a unique association between a H3K27me3 reader complex and active transcription. A thread with our key findings: (1/8) #TEsky #Polycomb #transcription #smallRNAs

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

Beyond the mean: genetic control of gene expression fidelity and dispersion www.biorxiv.org/content/10.6...

@nygenome.org is hiring Genomic AI Fellows! (fancy postdoc positions) If you're interested in working at the interface of AI and genomics in a great environment please apply at: jobs.silkroad.com/NYGenome/Car...

"Beyond the baseline: mapping the context-specific regulatory landscape of disease" by Yoav Gilad and Alexis Battle authors.elsevier.com/sd/article/S...

New review on context-specificity and disease genetics from @ygilad.bsky.social and me: authors.elsevier.com/sd/article/S...

UAB is recruiting neuroscience faculty at two different levels - come join our vibrant neuroscience community!

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

Pre-print on cardiomyocyte response to novel anti-cancer drug CX-5461 now published! Includes new gene expression response data at higher CX doses. Response to micromolar CX doses starts to mimic DOX responses, suggesting that off-target effects on the heart should be considered for this drug.

I can hardly find science posts here. I don't know how to change that. Yes, I know a lot is going on (obviously), but I get all the other things everywhere... this was where I used to get the science 😞

Recommended

My daughter Maya, who had to wear a scoliosis brace for 2 years, wants to connect with other teens who live with invisible diseases. www.under-the-iceberg.com/about

This action could not be completed, please try again later. What a joke

We're hiring for multiple open rank positions in the broad areas of biochemistry, molecular biology, and computational biology. With the recruitment of a new chair our Departmental strengths now include nuclear architecture, genomics and ancient DNA. jobs.sciencecareers.org/job/676677/b...

Faculty position at the department of medicine, University of Chicago. Please share.

I’ve been wondering more and more if TADs are about limiting recombination search and less about gene expression?

My lab is recruiting postdocs in AI/ML for genetics & genomics through the Malone Postdoctoral Fellows program. Apply by Jan 30! Lots of other great labs across the Malone Center as well.

The 400th copy of my book was sold yesterday. Thank you to everyone who ordered a copy! Some of you shared with me comments and suggestions, and I invite more readers to do so. www.barnesandnoble.com/w/an-intuiti...

So what was the point of all this...? Why am I utterly not surprised

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.