Charlie Hale
@charleshale.bsky.social
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📥 774
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PhD student in the Buckler Lab at Cornell. Evolution, genomics, climate change, agriculture.
pinned post!
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:
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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 ...
https://www.biorxiv.org/content/10.1101/2025.04.23.650228v1
5 months ago
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@prereview.bsky.social
is a great model for broadening participation in the review process!
add a skeleton here at some point
5 days ago
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Charlie Hale
Jeffrey Ross-Ibarra
about 1 month ago
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...
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Charlie Hale
bioRxiv Plant Bio
about 2 months ago
SPEECHLESS duplication in grasses expands potential for environmentalregulation of stomatal development
https://www.biorxiv.org/content/10.1101/2025.07.29.667563v1
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Chenxin Li, PhD
2 months ago
"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...
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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...
https://www.nature.com/articles/s41477-025-02047-0
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Charlie Hale
bioRxivpreprint
2 months ago
Conservation of chromatin states and their association with transcription factors in land plants
https://www.biorxiv.org/content/10.1101/2025.07.12.664529v1
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Charlie Hale
Erin Morrow
3 months ago
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
add a skeleton here at some point
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Charlie Hale
Deva Woodly
3 months ago
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.
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Charlie Hale
MaizeGDB
4 months ago
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!
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Charlie Hale
Mark A. Hanson
4 months ago
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.
add a skeleton here at some point
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Charlie Hale
Carl Zimmer
4 months ago
“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
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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...
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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...
https://www.biorxiv.org/content/10.1101/2025.05.15.654294v1
4 months ago
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Charlie Hale
Isako Di Tomassi
4 months ago
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
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Charlie Hale
Daniel Bolnick
5 months ago
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.
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Charlie Hale
bioRxiv Plant Bio
5 months ago
Replicated repurposing of an ancestral transcriptional complex in land plants
https://www.biorxiv.org/content/10.1101/2025.04.25.650595v1
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Charlie Hale
Dr. Lucky Tran
5 months ago
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.
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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:
loading . . .
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 ...
https://www.biorxiv.org/content/10.1101/2025.04.23.650228v1
5 months ago
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Charlie Hale
Julian Sanchez
6 months ago
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.
add a skeleton here at some point
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Cedric Feschotte
6 months ago
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-...
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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.
https://www.reuters.com/world/us/us-freezes-funding-cornell-northwestern-university-latest-crackdown-2025-04-09/
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Charlie Hale
Andrew Mercer
6 months ago
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
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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.
https://www.pewresearch.org/internet/2025/04/03/how-the-us-public-and-ai-experts-view-artificial-intelligence/
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Charlie Hale
Zeke Hausfather
6 months ago
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....
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Charlie Hale
maura quint
7 months ago
I keep seeing people just do something they think maybe would be helpful and watching that snowball and it's just amazing. Don't wait for permission, don't wait to be invited. Pick something you think needs to happen and that you can do, and do that thing.
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Rebecca Solnit
7 months ago
THE RESIST LIST IS HERE. Proud my team just started this
@resistlist.bsky.social
, which will list actions that happened and that are slated to happen.
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Charlie Hale
Liz Haswell
7 months ago
US plant science peeps: this is a *very* informative summary of the current state of plant science funding, and a call for your stories to help
@aspbofficial.bsky.social
make their case with public officials. Please re-skeet! 🧪
#PlantScience
blog.aspb.org/research-imp...
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Research Impacts of Recent Executive Orders and Memos – and a Call to Action to the ASPB Community | Plant Science Today
Since President Donald Trump took office on January 20,4a series of executive actions have shaken the research community. Several executive orders were released that targeted diversity, equity, and in...
https://blog.aspb.org/research-impacts-of-recent-executive-orders-and-memos-and-a-call-to-action-to-the-aspb-community/?fbclid=IwY2xjawIeMuJleHRuA2FlbQIxMAABHRzSSZsNQnOAao2RjR5m1VpM5Vx5bQ9WBa8ybKxNl0Wh5RwkBdlrk0t8Rg_aem_zEC4JZZW48uUxL2VUa5o6g
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Charlie Hale
PlantEvolution 🌱🌾
7 months ago
To US colleagues who have lost or are in imminent danger of losing their jobs: please DM whether we can accommodate your research.
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Charlie Hale
Katie Mack
8 months ago
If you’re in the US and you’d like to know what projects and vital services federal grants currently fund in your state, you can search here:
www.usaspending.gov
And you can find the contact information for your elected representatives here:
www.usa.gov/elected-offi...
They need to hear from you.
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USAspending.gov
https://www.usaspending.gov/
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Charlie Hale
Robert Yaman
9 months ago
New post responding to
@mikegrunwald.bsky.social
's oped in
@nytimes.com
Grunwald may be right that industrial farming is necessary. But his clear-eyed realism about environmental challenges should extend to animal welfare too - both need pragmatic solutions consistent with food abundance.
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Charlie Hale
Matt Hufford
9 months ago
New preprint from
@sjsnodgrass.bsky.social
and our colleagues showing variable fractionation in Zea and Tripsacum post-polyploidy. We welcome your thoughts as we work toward submission to a journal.
www.biorxiv.org/content/10.1...
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Maize and wild relatives show distinct patterns of genome downsizing following polyploidy
Plant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, unt...
https://www.biorxiv.org/content/10.1101/2024.12.24.630189v1
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If you're a graduate student working on crop wild relatives, consider applying to give a talk at our grad student-led symposium at Cornell April 11, 2025! More info and application form here:
lnkd.in/gZuwbq4s
9 months ago
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Charlie Hale
Dan Gibbs 🌱🧬
9 months ago
The New Phytologist “next generation scientists 2025” meeting will be held at the University of Birmingham, 4th-7th August 🌱🌳 This is a free event aimed at early career plant scientists. For details of the meeting, eligibility, and how to apply, click here :
www.newphytologist.org/nextgenevent...
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Next generation scientists 2025
https://www.newphytologist.org/nextgenevents/2025
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Our lab has been dissecting the genomes of hundreds of wild grass species to figure out how to increase nutrient circularity in corn and reduce GHG emissions. Check out this piece on CERCA, our collaborative project with groups across the country!
foundationfar.org/news/ffar-gr...
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FFAR Grant Seeks to Decrease Corn Inputs, Increases Climate Resiliency
Grain production, including corn production, in the United States is highly efficient in terms of labor, cost and land, yet generates massive nitrogen losses that end up in our waterways and greenhous...
https://foundationfar.org/news/ffar-grant-seeks-to-decrease-corn-inputs-increases-climate-resiliency/
9 months ago
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Charlie Hale
Bill McKibben
10 months ago
This is an important initiative to get more clean power in the world's tenth biggest economy! Please take a minute to add a comment, especially if you're a New Yorker
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Charlie Hale
Hannah Ritchie
10 months ago
What's the deal with vertical farming? *Can* potentially work for a small group of crops: mostly greens and possibly some fruits. But far too expensive for cereals or other staple crops. My latest Substack which digs into the numbers:
www.sustainabilitybynumbers.com/p/vertical-f...
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Vertical farming: a local solution for greens, but not feeding the world any time soon
While it has lots of benefits, the economics just don't work.
https://www.sustainabilitybynumbers.com/p/vertical-farming
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Charlie Hale
Jeffrey Ross-Ibarra
10 months ago
new preprint from the lab! Elli Cryan, coadvised but the inimitable
@spicybotrytis.bsky.social
, does a deep dive into the GA incompatibility loci in maize, finding complex haplotypes, overturning evolutionary origins, and discovering a paramutation system! A 🧵
www.biorxiv.org/content/10.1...
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Molecular evolution of a reproductive barrier in maize and related species
Three cross-incompatibility loci each control a distinct reproductive barrier in domesticated maize ( Zea mays ssp. mays ) and its wild teosinte relatives. These three loci, Teosinte crossing barrier ...
https://www.biorxiv.org/content/10.1101/2024.12.02.626474v1
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Important: This is what DALL-E thinks I'd look like as a prairie grass
10 months ago
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Hello out there! 🌱 I study cis-regulatory evolution in grasses using big comparative genomics. Big-picture, I want to harness the amazing diversity of wild plants to help breed the next generation of crops 🌽 🌾 Here to connect and learn from folks passionate about ag/climate/evolution/genomics!
10 months ago
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