Charlie Hale
@charleshale.bsky.social
PhD student in the Buckler Lab at Cornell. Genomics, evolution, agriculture.
Pinned
Charlie Hale
@charleshale.bsky.social
· Apr 27
Extensive modulation of a conserved cis-regulatory code across 589 grass species
The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation through comparative genomics. While cis-regulatory regions ...
www.biorxiv.org
New preprint from my PhD! How cis-regulatory evolution shaped grass diversification worldwide
www.biorxiv.org/content/10.1...
We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?
Here’s what we found:
www.biorxiv.org/content/10.1...
We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?
Here’s what we found:
Reposted by Charlie Hale
Available now in @asn-amnat.bsky.social ! Taking on some big-scale natural history: processed >40k @inaturalist.bsky.social images of Monarda fistulosa using computer vision to query for flower presence and phenotype flower color: doi.org/10.1086/739413
November 14, 2025 at 6:29 PM
Available now in @asn-amnat.bsky.social ! Taking on some big-scale natural history: processed >40k @inaturalist.bsky.social images of Monarda fistulosa using computer vision to query for flower presence and phenotype flower color: doi.org/10.1086/739413
Reposted by Charlie Hale
To quote my friend @drkatemarvel.bsky.social, climate change won't make humanity extinct but we can do better than "not extinct". Raise your standards people!
October 28, 2025 at 8:46 PM
To quote my friend @drkatemarvel.bsky.social, climate change won't make humanity extinct but we can do better than "not extinct". Raise your standards people!
Reposted by Charlie Hale
We are seeking speakers for #pag33 hosted in San Diego: Jan 9th at 10:30am. Talk to us about your current/planned efforts to develop genomic resources for threatened/endangered species! @ebpgenome.bsky.social - hosted by @uconneeb.bsky.social @nanoporetech.com Abstracts by Oct 27th! 🧬 🦜 🌱 🐛 🐢
October 16, 2025 at 4:57 PM
We are seeking speakers for #pag33 hosted in San Diego: Jan 9th at 10:30am. Talk to us about your current/planned efforts to develop genomic resources for threatened/endangered species! @ebpgenome.bsky.social - hosted by @uconneeb.bsky.social @nanoporetech.com Abstracts by Oct 27th! 🧬 🦜 🌱 🐛 🐢
Reposted by Charlie Hale
Most public transit systems depend largely on fare revenue to fund basic operations, but ridership never recovered after the pandemic. I wrote about 3 major transit systems that are facing a fiscal cliff, and the somewhat lackadaisical political response to the crisis. heatmap.news/politics/chi...
October 20, 2025 at 9:30 PM
Most public transit systems depend largely on fare revenue to fund basic operations, but ridership never recovered after the pandemic. I wrote about 3 major transit systems that are facing a fiscal cliff, and the somewhat lackadaisical political response to the crisis. heatmap.news/politics/chi...
Reposted by Charlie Hale
Yun et al. leveraged RNA-seq data to model gene expression variation in the grass Brachypodium distachyon and its response to soil drying, identifying genotypic, environmental, and G×E effects on physiological, metabolic, and gene expression traits.
🔗 doi.org/10.1093/molbev/msaf218
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf218
#evobio #molbio
October 21, 2025 at 9:19 AM
Yun et al. leveraged RNA-seq data to model gene expression variation in the grass Brachypodium distachyon and its response to soil drying, identifying genotypic, environmental, and G×E effects on physiological, metabolic, and gene expression traits.
🔗 doi.org/10.1093/molbev/msaf218
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf218
#evobio #molbio
@prereview.bsky.social is a great model for broadening participation in the review process!
Community Reviews are science in real time!
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
September 18, 2025 at 5:21 PM
@prereview.bsky.social is a great model for broadening participation in the review process!
Reposted by Charlie Hale
Our paper showing that variation in transcription factor binding sites underlies the majority of additive genetic variance for phenotypic variation in maize is finally out!
Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).
www.nature.com/articles/s41...
Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).
www.nature.com/articles/s41...
August 11, 2025 at 2:29 PM
Our paper showing that variation in transcription factor binding sites underlies the majority of additive genetic variance for phenotypic variation in maize is finally out!
Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).
www.nature.com/articles/s41...
Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).
www.nature.com/articles/s41...
Reposted by Charlie Hale
SPEECHLESS duplication in grasses expands potential for environmentalregulation of stomatal development https://www.biorxiv.org/content/10.1101/2025.07.29.667563v1
July 30, 2025 at 11:02 PM
SPEECHLESS duplication in grasses expands potential for environmentalregulation of stomatal development https://www.biorxiv.org/content/10.1101/2025.07.29.667563v1
Reposted by Charlie Hale
"We found that TF orthologues from distant species retain
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
Recruitment, rewiring and deep conservation in flowering plant gene regulation - Nature Plants
A highly scalable approach is used to generate 3,000 genome-wide maps of transcription factor binding in ten flowering plants, along with multi-species single-nucleus RNA-seq atlases. Together, the re...
www.nature.com
July 21, 2025 at 12:09 PM
"We found that TF orthologues from distant species retain
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
Reposted by Charlie Hale
Conservation of chromatin states and their association with transcription factors in land plants https://www.biorxiv.org/content/10.1101/2025.07.12.664529v1
July 18, 2025 at 5:33 AM
Conservation of chromatin states and their association with transcription factors in land plants https://www.biorxiv.org/content/10.1101/2025.07.12.664529v1
Reposted by Charlie Hale
So grateful to be one of the 500+ early-career scientists returning to their roots this month. The SNAP team behind this campaign has been such a blast to work with! @snapcoalition.bsky.social
Check out my piece in the Marietta Daily Journal, as well as other national coverage: bit.ly/3HXlfB4
Check out my piece in the Marietta Daily Journal, as well as other national coverage: bit.ly/3HXlfB4
June 16, 2025 at 8:09 PM
So grateful to be one of the 500+ early-career scientists returning to their roots this month. The SNAP team behind this campaign has been such a blast to work with! @snapcoalition.bsky.social
Check out my piece in the Marietta Daily Journal, as well as other national coverage: bit.ly/3HXlfB4
Check out my piece in the Marietta Daily Journal, as well as other national coverage: bit.ly/3HXlfB4
Reposted by Charlie Hale
I just like to post these data from time to time to puncture the mythological aura of mid 20th c protests. They were less popular than pretty much any 21st c mass action & people criticizing them used the same lines. Protest is about people coming together, shaping narratives, & building power.
June 14, 2025 at 7:02 PM
I just like to post these data from time to time to puncture the mythological aura of mid 20th c protests. They were less popular than pretty much any 21st c mass action & people criticizing them used the same lines. Protest is about people coming together, shaping narratives, & building power.
Reposted by Charlie Hale
We're excited to share PlantCAD browser tracks: a new, unpublished dataset integrating AI techniques for plant genome analysis. Explore it here: github.com/andorfc/Plan...
We welcome the community's feedback and innovative use cases for this data!
We welcome the community's feedback and innovative use cases for this data!
June 6, 2025 at 2:48 PM
We're excited to share PlantCAD browser tracks: a new, unpublished dataset integrating AI techniques for plant genome analysis. Explore it here: github.com/andorfc/Plan...
We welcome the community's feedback and innovative use cases for this data!
We welcome the community's feedback and innovative use cases for this data!
Reposted by Charlie Hale
URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯
Any lab using @flybase.bsky.social please donate using the link in post below.
This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
Any lab using @flybase.bsky.social please donate using the link in post below.
This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate.
www.philanthropy.cam.ac.uk/give-to-camb...
www.philanthropy.cam.ac.uk/give-to-camb...
Drosophila Genetic Database
The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...
www.philanthropy.cam.ac.uk
June 3, 2025 at 5:20 PM
URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯
Any lab using @flybase.bsky.social please donate using the link in post below.
This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
Any lab using @flybase.bsky.social please donate using the link in post below.
This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
Reposted by Charlie Hale
“I would like to cure brain cancer. I think that's not particularly controversial.” Be that as it may, the NIH terminated that scientist's grant. Here's a huge survey of the 2,500 grants that NIH has killed or delayed...so far. Gift link: nyti.ms/43Jz1yJ
June 4, 2025 at 2:30 PM
“I would like to cure brain cancer. I think that's not particularly controversial.” Be that as it may, the NIH terminated that scientist's grant. Here's a huge survey of the 2,500 grants that NIH has killed or delayed...so far. Gift link: nyti.ms/43Jz1yJ
New comparative proteomics study from our lab, led by Elad Oren! Contrasting summer and winter protein expression in five perennial grass species, we identified three proteins consistently linked to freezing tolerance across independent adaptations.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Grass Rhizome Proteomics Reveals Convergent Freezing-Tolerance Strategies
Early maize planting requires cold tolerance in temperate regions, which elite maize lacks. Extending the growing season could boost productivity along with more efficient nutrient use. Wild PACMAD gr...
www.biorxiv.org
May 26, 2025 at 8:22 PM
New comparative proteomics study from our lab, led by Elad Oren! Contrasting summer and winter protein expression in five perennial grass species, we identified three proteins consistently linked to freezing tolerance across independent adaptations.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Charlie Hale
Holy shit. We have to move the needle on public perception of science. Scientists, share your story in a LOCAL HOMETOWN PAPER op-ed, published June 16! #McClintockLetters #SciComm
Share how we serve the public with fed dollars, & insights into fed funded research. tinyurl.com/McClintockLetters
Share how we serve the public with fed dollars, & insights into fed funded research. tinyurl.com/McClintockLetters
May 15, 2025 at 9:09 PM
Holy shit. We have to move the needle on public perception of science. Scientists, share your story in a LOCAL HOMETOWN PAPER op-ed, published June 16! #McClintockLetters #SciComm
Share how we serve the public with fed dollars, & insights into fed funded research. tinyurl.com/McClintockLetters
Share how we serve the public with fed dollars, & insights into fed funded research. tinyurl.com/McClintockLetters
Reposted by Charlie Hale
Thread with an email being sent to @asn-amnat.bsky.social @sse-evolution.bsky.social @systbiol.bsky.social members today calling for a Tri-society week of action for NSF:
Dear members:
The tri-societies (ASN, SSE,SSB) are running a ‘Week of Action for NSF’. Your engagement is crucial.
Dear members:
The tri-societies (ASN, SSE,SSB) are running a ‘Week of Action for NSF’. Your engagement is crucial.
May 5, 2025 at 11:59 AM
Thread with an email being sent to @asn-amnat.bsky.social @sse-evolution.bsky.social @systbiol.bsky.social members today calling for a Tri-society week of action for NSF:
Dear members:
The tri-societies (ASN, SSE,SSB) are running a ‘Week of Action for NSF’. Your engagement is crucial.
Dear members:
The tri-societies (ASN, SSE,SSB) are running a ‘Week of Action for NSF’. Your engagement is crucial.
Reposted by Charlie Hale
Replicated repurposing of an ancestral transcriptional complex in land plants https://www.biorxiv.org/content/10.1101/2025.04.25.650595v1
April 29, 2025 at 2:15 PM
Replicated repurposing of an ancestral transcriptional complex in land plants https://www.biorxiv.org/content/10.1101/2025.04.25.650595v1
Reposted by Charlie Hale
Deaths from heart disease down 75%, that’s NIH.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
April 28, 2025 at 5:20 PM
Deaths from heart disease down 75%, that’s NIH.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
New preprint from my PhD! How cis-regulatory evolution shaped grass diversification worldwide
www.biorxiv.org/content/10.1...
We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?
Here’s what we found:
www.biorxiv.org/content/10.1...
We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?
Here’s what we found:
Extensive modulation of a conserved cis-regulatory code across 589 grass species
The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation through comparative genomics. While cis-regulatory regions ...
www.biorxiv.org
April 27, 2025 at 1:44 PM
New preprint from my PhD! How cis-regulatory evolution shaped grass diversification worldwide
www.biorxiv.org/content/10.1...
We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?
Here’s what we found:
www.biorxiv.org/content/10.1...
We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?
Here’s what we found:
Reposted by Charlie Hale
The lesson for universities is you may as well fight back. You'll lose the money either way. The only question is whether you keep your dignity.
Exclusive: Weeks after President Donald Trump’s administration ordered NIH to pull $250 million in biomedical research grants to Columbia University, the agency is freezing all remaining grant money owed to the university until further notice. scim.ag/4if5Rg1
NIH freezes all research grants to Columbia University
Amid negotiations with Trump, the university could risk losing nearly $700 million
scim.ag
April 9, 2025 at 10:25 PM
The lesson for universities is you may as well fight back. You'll lose the money either way. The only question is whether you keep your dignity.
Reposted by Charlie Hale
Predictably, it’s our turn to be viciously targeted by this ruthless, short-sighted and spiteful administration. We will RESIST and I have trust in Cornell leadership to mount a potent defense to protect our community and values and ultimately prevail over this evil.
www.reuters.com/world/us/us-...
www.reuters.com/world/us/us-...
US freezes funding for Cornell, Northwestern University in latest crackdown
The Trump administration has frozen over $1 billion in funding for Cornell University and $790 million for Northwestern University while it investigates both schools over civil rights violations, a U.S. official said on Tuesday.
www.reuters.com
April 9, 2025 at 1:53 AM
Predictably, it’s our turn to be viciously targeted by this ruthless, short-sighted and spiteful administration. We will RESIST and I have trust in Cornell leadership to mount a potent defense to protect our community and values and ultimately prevail over this evil.
www.reuters.com/world/us/us-...
www.reuters.com/world/us/us-...
Reposted by Charlie Hale
This morning, my @pewresearch.org colleagues published a fantastic report comparing the U.S. general public's attitudes about AI with those of AI experts. Perhaps not surprisingly, there are big differences in positivity towards AI, but there are also fascinating points of agreement. /1
How the U.S. Public and AI Experts View Artificial Intelligence
These groups are far apart in their enthusiasm and predictions for AI, but both want more personal control and worry about too little regulation.
www.pewresearch.org
April 3, 2025 at 3:06 PM
This morning, my @pewresearch.org colleagues published a fantastic report comparing the U.S. general public's attitudes about AI with those of AI experts. Perhaps not surprisingly, there are big differences in positivity towards AI, but there are also fascinating points of agreement. /1
Reposted by Charlie Hale
Whenever I post about climate, skeptical folks inevitable respond with this graph. So I decided to do something radical: actually read the underling scientific paper and ask the authors.
As it turns out, it actually says the opposite of what skeptics claim: www.theclimatebrink....
As it turns out, it actually says the opposite of what skeptics claim: www.theclimatebrink....
March 24, 2025 at 7:24 PM
Whenever I post about climate, skeptical folks inevitable respond with this graph. So I decided to do something radical: actually read the underling scientific paper and ask the authors.
As it turns out, it actually says the opposite of what skeptics claim: www.theclimatebrink....
As it turns out, it actually says the opposite of what skeptics claim: www.theclimatebrink....