Yoav Gilad
@ygilad.bsky.social
Associate Dean for data science, and Professor of Medicine and Human Genetics at the University of Chicago.
Pinned
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
It’s available on Amazon: tinyurl.com/mx2hewen
So what was the point of all this...? Why am I utterly not surprised
November 10, 2025 at 8:27 PM
So what was the point of all this...? Why am I utterly not surprised
Reposted by Yoav Gilad
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
It’s available on Amazon: tinyurl.com/mx2hewen
January 17, 2025 at 2:30 PM
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
It’s available on Amazon: tinyurl.com/mx2hewen
Reposted by Yoav Gilad
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.
I've never met anyone in real life who holds this position with whom I can have an actual discussion. Always anonymous peer review.
![Screenshot of text reading: "The original review had noted that "Mechanistic basis of how cells differentiate between [XXX and YYY] will be needed." However, rather than identifying a mechanism, the authors argue that "the mechanisms of both [XXX and YYY] are of great interest, and of little consequence to the claims—causal and otherwise—that we make". The mechanistic basis of cellular phenomena is the ethos of [ZZZ] as a journal as far as I understand, and it is disappointing that the authors regard the mechanisms to be inconsequential."](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:deufzypwwulzfvbgycug33dw/bafkreih45yxirmr2ga75usbt35ujkk7lcs6vz3hzzw5uy754jpya266j3m@jpeg)
October 28, 2025 at 7:15 PM
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.
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.
October 22, 2025 at 12:46 PM
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.
Reposted by Yoav Gilad
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
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
October 16, 2025 at 3:49 AM
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
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!
🔍 New on @elixirestonia.bsky.social website: a review of @ygilad.bsky.social An Intuitive Primer on Effective Functional Genomics Study Design. A clear, practical resource for students and researchers.
Read our review: elixir.ut.ee/news/2025/10...
Read our review: elixir.ut.ee/news/2025/10...
October 15, 2025 at 2:09 PM
Thank you for taking the time to review my book!
Reposted by Yoav Gilad
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
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
Interferon-sensitized hematopoietic progenitors dynamically alter organismal immunity
Abstract. Inflammation has enduring impacts on organismal immunity. However, the precise mechanisms by which tissue-restricted inflammation conditions syst
academic.oup.com
October 14, 2025 at 1:04 PM
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
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
Reposted by Yoav Gilad
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
September 30, 2025 at 2:29 PM
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
Reposted by Yoav Gilad
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 🧵]
September 24, 2025 at 8:33 PM
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 🧵]
Reposted by Yoav Gilad
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...
"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
August 30, 2025 at 8:58 PM
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...
"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...
Reposted by Yoav Gilad
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.
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.
July 8, 2025 at 5:46 PM
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.
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.
Reposted by Yoav Gilad
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
June 26, 2025 at 9:08 AM
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.
June 20, 2025 at 2:08 PM
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.
Reposted by Yoav Gilad
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...
www.biorxiv.org/content/10.1...
June 19, 2025 at 12:20 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Yoav Gilad
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.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
June 10, 2025 at 2:20 PM
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.
(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.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
June 10, 2025 at 2:20 PM
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.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
Reposted by Yoav Gilad
Our paper: ""Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids"
genome.cshlp.org/content/earl...
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
June 9, 2025 at 12:03 AM
Our paper: ""Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids"
genome.cshlp.org/content/earl...
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.
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.
June 9, 2025 at 12:03 AM
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.
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...
doi.org/10.1101/2025...
CrossFilt: A Cross-species Filtering Tool that Eliminates Alignment Bias in Comparative Genomics Studies
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We d...
doi.org
June 7, 2025 at 12:10 AM
Context in another thread. Just the preprint here:
doi.org/10.1101/2025...
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.
We were wrong.
June 7, 2025 at 12:07 AM
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.
We were wrong.
Reposted by Yoav Gilad
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...
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...
Distinguished professor proves effective mentorship is both art and science
For the inaugural recipient of the Genetics Society of America Mentorship Award Dr. Brandon Gaut, leading a lab is not only scientific but personal.
genestogenomes.org
May 17, 2025 at 10:09 PM
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...
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...
Reposted by Yoav Gilad
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
Also grateful for discussions and feedback from
@anshulkundaje.bsky.social @avsecz.bsky.social
May 13, 2025 at 5:45 PM
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
Also grateful for discussions and feedback from
@anshulkundaje.bsky.social @avsecz.bsky.social
Reposted by Yoav Gilad
🎉 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.
Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans https://www.biorxiv.org/content/10.1101/2025.05.04.652069v1
May 5, 2025 at 2:43 AM
🎉 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.