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Yoav Gilad @ygilad.bsky.social · 8d

but do you still need an R01 from NIGMS to be eligible for a new MIRA, or was that requirement dropped?

Reposted by Yoav Gilad

Craig Kaplan @triggerloop.bsky.social · 8d

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

Graph showing total R35+R01 awards issued by NIGMS from 2020 to 2025. R01 in black showing a steep decline. R35 showing an increase. Total awards in 2025 slightly up from 2024 but these years are lower than 2020-2023

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Reposted by Yoav Gilad

Yoav Gilad @ygilad.bsky.social · Jan 17

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

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Reposted by Yoav Gilad

Matt Rockman @wormsrock.bsky.social · 14d

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 🧵]

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Reposted by Yoav Gilad

Ran Blekhman @blekhman.bsky.social · Aug 30

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federal funding (e.g., from the NIH, CDC, NSF) for their health equity research, but have since had their funding rescinded due to federal administrative actions"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...

Rapid Response: Reinvesting in Racial and Indigenous Health Equity Research

The purpose of this call for proposals is to meet the current moment by supporting timely, actionable health equity research that has been interrupted by shifts in federal funding.

www.rwjf.org

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Yoav Gilad @ygilad.bsky.social · Jul 19

The enrichment results are a bit more nuanced. I am hoping the paper is doing a decent job explaining it.

No need for 'nearest gene' because we map the eQTLs...

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Yoav Gilad @ygilad.bsky.social · Jul 19

In both cases you can estimate variance (2nd central moment) instead of mean, but it tells you different things -- convergence of response on the bulk case, and fidelity of response in the single cell case. Makes sense?

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Yoav Gilad @ygilad.bsky.social · Jul 19

Single-cell RNA-seq can capture variation in expression between cells within the same individual. This tells you how noisy or tightly regulated a gene is in a given context, but it is less about person-to-person differences.

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Yoav Gilad @ygilad.bsky.social · Jul 19

Good question. Bulk RNA-seq captures variation in gene expression between individuals. That includes genetic effects, environmental differences, and other factors that vary from person to person.

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Yoav Gilad @ygilad.bsky.social · Jul 8

So, since 2005, your work resulted in both mine and your promotions! 😀

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Reposted by Yoav Gilad

Ran Blekhman @blekhman.bsky.social · Jul 8

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.

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Yoav Gilad @ygilad.bsky.social · Jul 2

Congratulations! I'm just going to politely point out that neither have applied to work with us... 😉

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Reposted by Yoav Gilad

Genevieve Housman @gahousman.bsky.social · Jun 26

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

Addressing missing context in regulatory variation across primate evolution

In primates, loci associated with adaptive trait variation often fall in noncoding regions. Understanding the mechanisms linking these regulatory vari…

www.sciencedirect.com

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Yoav Gilad @ygilad.bsky.social · Jun 20

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.

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Reposted by Yoav Gilad

Michelle Ward @michelle-c-ward.bsky.social · Jun 19

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...

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Reposted by Yoav Gilad

Yoav Gilad @ygilad.bsky.social · Jun 10

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.

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Yoav Gilad @ygilad.bsky.social · Jun 10

Thank you!

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Yoav Gilad @ygilad.bsky.social · Jun 10

If we want to connect genetic variation to disease, we need to move beyond baseline conditions. Our study shows that dynamic, context-specific regulation holds the key to understanding many unexplained GWAS signals. The preprint again:

www.biorxiv.org/content/10.1...

Disease-associated loci share properties with response eQTLs under common environmental exposures

Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To un...

www.biorxiv.org

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Yoav Gilad @ygilad.bsky.social · Jun 10

And response eQTLs are not random:

They affect constrained genes.
They are enriched in distal enhancers.
They occur in regions with complex regulatory architecture.

In other words, they look a lot like disease-associated loci.

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Yoav Gilad @ygilad.bsky.social · Jun 10

and profiled 1.4 million cells by single-cell RNA-seq. This let us identify response eQTLs, which are genetic effects that only appear in certain cell states, in this case, in response to different exposures.

These effects are missed in steady-state datasets.

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Yoav Gilad @ygilad.bsky.social · Jun 10

But mapping gene-by-environment interactions is slow. Most studies test one treatment in one cell type. We needed a faster way to scan across cellular contexts.

Together with Alexis Battle and her team, we treated heterogeneous differentiating cultures (HDCs) with ethanol, caffeine, and nicotine -

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Yoav Gilad @ygilad.bsky.social · Jun 10

Genetic effects on gene regulation depend on context.
That includes cell type, developmental stage, and environmental exposures. To understand complex traits, we need to know not just where genetic effects occur, but when and under what conditions.

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Yoav Gilad @ygilad.bsky.social · Jun 10

I'll say a few word in this thread, but if you want to go the preprint quickly, here it is:

www.biorxiv.org/content/10.1...

Disease-associated loci share properties with response eQTLs under common environmental exposures

Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To un...

www.biorxiv.org

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Yoav Gilad @ygilad.bsky.social · Jun 10

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.

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Reposted by Yoav Gilad

Yoav Gilad @ygilad.bsky.social · Jun 9

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

Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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