New PrePrint from the Vecchiarelli and Mosalaganti (@shyamalm.bsky.social) labs! 🧵 Collaboration with the Giessen and Pi labs Congratulations to co-first authors Y Hoang (@hoanghamyy.bsky.social) and Pankaj Jadhav! www.biorxiv.org/content/10.1...

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment. The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP jasonjwilliamsny.github.io/grfp2025/

You're welcome to use/share this with your students. Here's a quick write-up explaining how I use it in my class, along with a link to a PDF version for easy printing/sharing. www.jessicacalarco.com/teaching-res...

We have an open Assistant Professor position in Evolutionary Cell and Molecular Biology in the @weillinstitute.bsky.social at Cornell University. academicjobsonline.org/ajo/jobs/30607

New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3 Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.

I am tremendously excited to share our work revealing the epigenomic landscape of single vascular cells. We discover that enhancers are not only cell type but vascular site specific and regulate the genetic drivers of disease risk. Let's dive in! 🧬👇 #epigenetics www.embopress.org/doi/full/10....

Another tour-de-force from David Baker's lab : custom DNA-binding miniproteins to target specific DNA sequences for diverse applications in gene regulation and editing. With David, nothing is impossible !

Analyses of a new genomes for garden asparagus and a Mediterranean basin congener reveal independent origins of dioecy and XY sex chromosomes. The work led by Phil Bentz @pbentz.bsky.social finds no overlap in the two Y-linked sex-determination genes - www.biorxiv.org/content/10.1... .

@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting! CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...

Big news from the Demirer lab: first 4 research papers are preprinted! Check them out, feedback welcomed: eCIS for plant protein delivery: tinyurl.com/mrx4d878 R2 for targeted insertion: tinyurl.com/5n73za6h Transient expression: tinyurl.com/38p2ud6w Chemotaxis assay: tinyurl.com/3nw9haes More ⬇️

Our #research on #drought #recovery, now published with @springernature.com in @natcomms.nature.com: Drought recovery in plants triggers a cell-state-specific immune activation. doi.org/10.1038/s414... Read thread below 👇

delighted to share work from my postdoc @cshlnews.bsky.social - here, we use TurboID in maize meristems to be able to resolve CLV receptor interactions, unlocking its potential to resolve in vivo receptor interactions important for meristem signaling.

Thrilled to share our latest work: how plants control growth through activation of a surface-specific growth programme. Thanks @zoenv.bsky.social, @nathan-german.bsky.social and the other coauthors for all the hard work! www.biorxiv.org/content/10.1...

In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance. While undoubtedly important, how we *use* these models after training is potentially even more important. tangermeme v1.0.0 is out now. Hope you find it useful!

PRC2 regulates cytokinin and HD-ZIP III pathways to orchestrate vascular tissue pattern formation in Arabidopsis (Yufei Zhang , Runzhou Huang , Tingting Yang , An Li , Zihao Wang , Yuexin Wu , Yang Deng , Jing Zhang , Xin-Qiang He , Yue Zhou) doi.org/10.1093/plce... #PlantScience

Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes https://www.biorxiv.org/content/10.1101/2025.08.20.671329v1

Assistant/ Associate Professor of Mycology at UGA - Go be part of a Legendary Fungal Group fungi.franklinresearch.uga.edu and dept of plant pathology plantpath.caes.uga.edu www.ugajobsearch.com/postings/445...

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...

August’s Nature Plants cover story shows how we integrated large-scale multiDAP and snRNA data to reveal drivers of cell type identity and evolution in flowering plants. www.nature.com/nplants/volu... We packed a lot into this paper! Here’s a single-cell spin on what we found:

a little secret- the actual amount of data produced and filtered using the Drosophila cell atlas standards was >800k but we more stringently filtered it to ~430k for all downstream analyses. We plan to make this additional 400k data availability in NCBI GEO and here arabidopsisdevatlas.salk.edu

My Department (Biology) at @dartmouthartsci.bsky.social is hiring this year! We have an opening for a Tenure Track Cell and/or Molecular biologist (broadly defined). Please share with your trainees/labmates/friends and reach out if you have questions. apply.interfolio.com/171625

Amazing resource for the community. Fantastic work @tralee-sci.bsky.social and team!

Thrilled to have our spatial single-cell atlas of the Arabidopsis lifecycle in @NaturePlants. Turns out that its easy to make nice images when spatial expression of 1,000 genes is available! 1/n @natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social www.nature.com/articles/s41...

New OA Resource: "A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle" rdcu.be/eBmkU An extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents 10 developmental time points in 6 diverse organs.

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

And here’s my News & Views on the subject: www.nature.com/articles/s41...

We are excited to announce the PCA Imaging Workshop Webinar Series: FIJI Basics for Visualizing and Quantifying Plant Images! This workshop will be held on Wednesday, September 24, 2025 at 7:30am PT/9:30am CT/10:30am ET. Register Now! bit.ly/45zJE7V @radinbio.bsky.social @rheelab.bsky.social

After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41... with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1

Our new work uncovering how WIND1 promotes somatic embryogenesis as a bifunctional chromatic regulator!!!! We knew WIND1 promotes new fate acquisition and now we show WIND1 also helps repressing existing identity!

New newer. I think we’ve added four or five since I posted this in June.

MSA Pairformer efficiently extracts structure, protein-protein interactions, and mutation effects from MSAs by decomposing the effects of phylogeny and structural contacts. @yoakiyama.bsky.social Zhidian Zhang @milot.bsky.social @martinsteinegger.bsky.social @sokrypton.org

My first first author manuscript has posted! I’m very excited to share SWIF-TE with yall. It is a fast, memory efficient tool to identify novel TE insertions from short-read data. 🧬 #TEworldwide #transposons

Very proud to share our latest preprint: postdoc/LRSF fellow Yue Rui studies the mechanisms regulating attachment of the cell wall to the plasma membrane. The Cellulose Synthase Complex and REMORINs determine the extent of attachment and root osmotic stress tolerance. www.biorxiv.org/content/10.1...

#drought in #tress researchers find that Gymnosperms experienced larger growth deficits, especially during dry season, whereas wet-season droughts were more detrimental for angiosperms. Increasing drought frequency and severity may lead to stronger growth deficits. www.science.org/doi/10.1126/...

Happy to share our new paper out today in @cp-cellreports.bsky.social in collaboration with @tobiaswarnecke.bsky.social @akihisaosakabe.bsky.social about how evolution can do big things with small changes. www.sciencedirect.com/science/arti...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process. #plantscience link.springer.com/article/10.1...?

🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town. Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag. 🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41... 🧵Let’s break down what makes DynaTag so powerful (1/7)

This is one of the most exciting emerging fields in plant biology today and a great, welcoming, and collaborative community. Deadline for application and registration is next Monday! Apply here: lnkd.in/gvkMxuKR

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:

There are over 200 posters from 40+ institutes and 300 registrants already. This is promising to be an exciting meeting and networking of plant scientists, especially those in the midwest. Register and join the community!

Online now @ Cell is the yeast multicellular engineering paper from Fankang Meng - the fruits of his productive PhD in our group. He developed modular synthetic biology tools to bring multicellular behaviours to yeast - specific adhesion, juxtacrine signalling and more. www.cell.com/cell/fulltex...

A key Senate spending committee has joined its House of Representatives counterpart in rejecting deep cuts that President Donald Trump’s administration proposed for research at the USDA for the 2026 fiscal year that begins on 1 October. scim.ag/3InyWcQ

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

Our latest! K63-polyUb of the ERECTA receptor kinase by PUB30/31 is required for the ligand induced receptor endocytosis for stomatal patterning. Our results show that ERECTA signals at the PM. Congrats, Liangliang, Minh & the team🌱! www.biorxiv.org/content/10.1...

At long last, our paper on conservation and divergence of a nitrogen circuit upstream of NLP6/7 &NIR1 in Arabidopsis and tomato is published! It's an exciting combo of whole plant, in vitro, protoplast and systems bio approaches: tinyurl.com/nitrogencirc... @gozdedemirel.bsky.social

This opinion piece, just published in my hometown newspaper in GA, seeks to make a strong case for continued federal support for scientific research in the USA. It's one of many across the nation, part of the #McClintockLetters Initiative www.theclaytontribune.com/opinion-edit...

Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference! @tatsuyanobori.bsky.social To Apply to the GRC: lnkd.in/gvkMxuKR To Learn More About Dr. Nobori's Research: www.tatsuyanobori.com

Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference! To Apply to the GRC: lnkd.in/gvkMxuKR To Learn More About Dr. Shahan's Research: sites.lifesci.ucla.edu/mcdb-shahan/ @rachelmshahan.bsky.social

Over the last couple of years I have been writing individual chapters of what I call 𝗔 𝗦𝗵𝗼𝗿𝘁 𝗛𝗶𝘀𝘁𝗼𝗿𝘆 𝗼𝗳 𝗣𝗹𝗮𝗻𝘁 𝗦𝗰𝗶𝗲𝗻𝗰𝗲 Each chapter covers a specific, basic, but for some reason special and interesting aspect of #PlantScience research. Have a look here 👇🧵

Happy to see this out! @reginafairbanks.bsky.social analysis of perhaps the most famous maize domestication locus, teosinte glume architecture 1, which controls much of the change from the enclosed fruitcase (top) in teosinte to the "naked" grains of maize (bottom) www.pnas.org/doi/10.1073/... 1/2