Charlie Hale @charleshale.bsky.social · 18/07/2026Anyone at #PlantBio2026 want to get out for a run during the conference? 000
Charlie Hale @charleshale.bsky.social · 16/06/2026We used genomic LLMs to find 330 genes with repeated functional shifts as grasses adapted and diversified. Great work by Sheng-Kai Hsu to make cross-species trait mapping tractable across 700+ complex genomes. www.biorxiv.org/content/10.6...biorxiv.orgConvergent genome- and gene-level constraints shape repeated environmental adaptation in grassesGrasses (Poaceae) dominate terrestrial ecosystems and sustain global food security, yet the genomic principles enabling their repeated adaptation to extreme environments remain unresolved. Combining d... 0116
Reposted by Charlie HaleJacquelyn Gill @jacquelyngill.bsky.social · 12/05/2026I'm hiring a postdoc to lead sedimentary aDNA reconstructions of alpine plant biodiversity as part of a broader project exploring the mechanisms of alpine plant resilience. Come join a collaborative team working in beautiful places! Bonus: postdocs at UMaine are unionized!fa-ewca-saasfaprod1.fa.ocs.oraclecloud.comPostdoctoral Research AssociateThe University of Maine is a community of more than 11,900 undergraduate and graduate students, and 2,500 employees located on the Orono campus, the regional campus in Machias, and throughout the stat... 19786
Reposted by Charlie HaleJeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/03/2026Postdoc in evolutionary genetics with @mbhufford.bsky.social isu.wd1.myworkdayjobs.com/IowaStateJob...isu.wd1.myworkdayjobs.comPostdoctoral Researcher - Evolutionary Genomics and Population GeneticsPosition Title: Postdoctoral Researcher - Evolutionary Genomics and Population Genetics Appointment Type: Post Doc/Trainee Job Description: Summary of Duties and Responsibilities: We are seeking a Pos... 01618
Charlie Hale @charleshale.bsky.social · 16/02/2026www.biorxiv.org/content/10.6... "TSS-proximal TFBSs are implicated in rapid, tissue-wide transcriptional stress responses....distal upstream regions contain conserved TF clusters that overlap rare cell type-specific accessible chromatin"biorxiv.org 054
Reposted by Charlie HaleProject Drawdown @projectdrawdown.bsky.social · 12/02/2026American climate science is losing federal support right when we need it most. Project Drawdown is stepping up: launching the Climate Science Serving America Fellowship for early/mid-career PhD scientists to do good science that does good. 🗓️ Apply by April 17 👉 bit.ly/4kx2J1Q 16634
Reposted by Charlie HaleMolecular Biology and Evolution @molbioevol.bsky.social · 23/01/2026Hale et al. analysed >500 grass genomes to support a “stable motifs, variable binding sites” model of cis-regulatory evolution that involves turnover of thousands of individual binding sites while preserving TF binding preferences. 🔗 doi.org/10.1093/molbev/msaf324 #evobio #molbio #PlantSkydoi.orgWidespread turnover of a conserved cis-regulatory code across 589 grass speciesAbstract. The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation thro 094
Reposted by Charlie HalePatrick McKenzie @patrickmckenzie.bsky.social · 09/01/2026I wrote in the most recent issue of Arnoldia about using @inaturalist.bsky.social and, more generally, about the continuing role of natural history in motivating questions in evo bio + my excitement about community science for unlocking new scales of analysis: arboretum.harvard.edu/arnoldia-sto... 1116
Reposted by Charlie HaleMark D. Levine @marklevinenyc.bsky.social · 23/12/2025Year 1 data on congestion pricing in Manhattan… * Vehicle traffic: -11% * Foot traffic: +3.4% * Storefront vacancy: -0.9% * Pollution: -22% * Revenue for mass transit: $548M So YES this has been a huge success. 9187812341
Charlie Hale @charleshale.bsky.social · 16/12/2025Our paper is out in MBE! doi.org/10.1093/molb... We tracked TF binding site evolution across 589 grass species, and found that while binding preferences are pretty stable over 80 million years of evolution, individual binding sites have turned over a lot. Thread here: bsky.app/profile/char... 12416
Reposted by Charlie HaleChenxin Li, PhD @chenxinli2.bsky.social · 16/12/2025"cis-regulatory evolution involves turnover of thousands of individual binding site instances while largely preserving transcription factors’ binding preferences." From: academic.oup.com/mbe/advance-...academic.oup.comWidespread turnover of a conserved cis-regulatory code across 589 grass speciesAbstract. The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation thro 0168
Reposted by Charlie HalebioRxiv Genomics @biorxiv-genomic.bsky.social · 13/12/2025Identification of Freezing Tolerance QTLs in Tripsacum dactyloides Using Open-Pollinated Bulk Segregant Analysis www.biorxiv.org/content/10.64898/20… 021
Reposted by Charlie HaleNeal Agarwal @neal.fun · 10/12/2025Made a site comparing the sizes of living things :) The great Julius Csotonyi spent 5 months painting over 60 illustrations for the site, no ai used > neal.fun/size-of-life/ 772654909
Reposted by Charlie HaleJosh Felton @botanyballer.bsky.social · 08/01/2025Are you planning to attend Botany 2025? Consider applying to be a PLANTS mentor! You'll be paired with another mentor to help your mentee network, comprehend talks, and discuss grad school and careers, all while making them feel welcome in the botany community. (1/2) 11916
Reposted by Charlie HalebioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 05/12/2025Lineage-specific evolution of regulatory landscapes in polyploid plant and its diploid progenitors www.biorxiv.org/content/10.64898/20… 032
Reposted by Charlie HaleJeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/11/2025Super proud of @alyssa-phillips.bsky.social 's paper, now out on biorxiv! She resolves the origin(s) of polyploid big blue-stem, a dominant species in the midwest tall-grass prairie. Her common garden analysis also informs on environmental adaptation and hints at the impacts of polyploidy.biorxiv.orgThe origins and adaptive consequences of polyploidy in a dominant prairie grassPolyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hy... 2368
Reposted by Charlie HalePatrick McKenzie @patrickmckenzie.bsky.social · 14/11/2025Available 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/10.1086/739413doi.orgHigh-throughput iNaturalist image analysis reveals flower color divergence in Monarda fistulosa | The American Naturalist: Vol 0, No ja 13419
Reposted by Charlie HaleZeke Hausfather @zekehausfather.com · 28/10/2025To 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! 28636144
Reposted by Charlie HaleJill Wegrzyn @jillwegrzyn.bsky.social · 16/10/2025We 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! 🧬 🦜 🌱 🐛 🐢 086
Reposted by Charlie HaleEmily Pontecorvo @emilypont.bsky.social · 20/10/2025Most 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... 1626355
Reposted by Charlie HaleMolecular Biology and Evolution @molbioevol.bsky.social · 21/10/2025Yun 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 021
Charlie Hale @charleshale.bsky.social · 18/09/2025@prereview.bsky.social is a great model for broadening participation in the review process! 211
Reposted by Charlie HaleJeffrey Ross-Ibarra @jrossibarra.bsky.social · 11/08/2025Our 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... 625173
Reposted by Charlie HalebioRxiv Plant Bio @biorxiv-plants.bsky.social · 31/07/2025SPEECHLESS duplication in grasses expands potential for environmentalregulation of stomatal development www.biorxiv.org/content/10.1101/202… 053
Reposted by Charlie HaleChenxin Li, PhD @chenxinli2.bsky.social · 21/07/2025"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...nature.comRecruitment, rewiring and deep conservation in flowering plant gene regulation - Nature PlantsA 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... 14812
Reposted by Charlie HalebioRxivpreprint @biorxivpreprint.bsky.social · 18/07/2025Conservation of chromatin states and their association with transcription factors in land plants www.biorxiv.org/content/10.1101/202… 054
Reposted by Charlie HaleErin Morrow @erinmorrow.bsky.social · 16/06/2025So 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/3HXlfB4bit.lyGraduate Students Push Back Against Science Funding CutsHundreds of graduate students are writing to their hometown newspapers to defend their research, as the Trump administration drastically reduces science funding. 24223
Reposted by Charlie HaleDeva Woodly @devawo.bsky.social · 14/06/2025I 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. 5248041767
Reposted by Charlie HaleMaizeGDB @maizegdb.bsky.social · 06/06/2025We'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! 1127
Reposted by Charlie HaleMark A. Hanson @hansonmark.bsky.social · 03/06/2025URGENT: 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. 4225253
Reposted by Charlie HaleCarl Zimmer @carlzimmer.com · 04/06/2025“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 171155572
Charlie Hale @charleshale.bsky.social · 26/05/2025New 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...biorxiv.orgGrass Rhizome Proteomics Reveals Convergent Freezing-Tolerance StrategiesEarly 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... 087
Reposted by Charlie HaleIsako Di Tomassi @isakoditomassi.bsky.social · 15/05/2025Holy 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 052
Reposted by Charlie HaleDaniel Bolnick @danielbolnick.bsky.social · 05/05/2025Thread 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. 4182159
Reposted by Charlie HalebioRxiv Plant Bio @biorxiv-plants.bsky.social · 29/04/2025Replicated repurposing of an ancestral transcriptional complex in land plants www.biorxiv.org/content/10.1101/202… 086
Reposted by Charlie HaleDr. Lucky Tran @luckytran.com · 28/04/2025Deaths 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. 5650332379
Charlie Hale @charleshale.bsky.social · 27/04/2025New 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:biorxiv.orgExtensive modulation of a conserved cis-regulatory code across 589 grass speciesThe 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 ... 44220
Reposted by Charlie HaleJulian Sanchez @normative.bsky.social · 09/04/2025The 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. 6746771326
Reposted by Charlie HaleCedric Feschotte @cedricfeschotte.bsky.social · 09/04/2025Predictably, 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-...reuters.comUS freezes funding for Cornell, Northwestern University in latest crackdownThe 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. 3293
Reposted by Charlie HaleAndrew Mercer @awmercer.bsky.social · 03/04/2025This 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. /1pewresearch.orgHow the U.S. Public and AI Experts View Artificial IntelligenceThese groups are far apart in their enthusiasm and predictions for AI, but both want more personal control and worry about too little regulation. 55032
Reposted by Charlie HaleZeke Hausfather @zekehausfather.com · 24/03/2025Whenever 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.... 491032342
Reposted by Charlie Halemaura quint @mauraquint.bsky.social · 20/02/2025I 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. 7877253
Reposted by Charlie HaleRebecca Solnit @rebeccasolnit.bsky.social · 20/02/2025THE 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. 241190478
Reposted by Charlie HaleLiz Haswell @ehaswell.bsky.social · 16/02/2025US 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...blog.aspb.orgResearch Impacts of Recent Executive Orders and Memos – and a Call to Action to the ASPB Community | Plant Science TodaySince 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... 14737
Reposted by Charlie HalePlantEvolution 🌱🌾 @plantevolution.bsky.social · 15/02/2025To US colleagues who have lost or are in imminent danger of losing their jobs: please DM whether we can accommodate your research. 3307134
Reposted by Charlie HaleKatie Mack @astrokatie.com · 28/01/2025If 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.usaspending.govUSAspending.gov 14356313375
Reposted by Charlie HaleRobert Yaman @robertyaman.bsky.social · 07/01/2025New 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. 2113
Reposted by Charlie HaleMatt Hufford @mbhufford.bsky.social · 26/12/2024New 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...biorxiv.orgMaize and wild relatives show distinct patterns of genome downsizing following polyploidyPlant 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... 084
Charlie Hale @charleshale.bsky.social · 21/12/2024If 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 063
Reposted by Charlie HaleDan Gibbs 🌱🧬 @djgibbs.bsky.social · 19/12/2024The 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...newphytologist.orgNext generation scientists 2025 13127
