Interesting study suggesting that nucleus, cytoskeleton, and endomembranes preceded acquisition of mitochondria, during eukaryogenesis www.nature.com/articles/s41...

🚀 New preprint! We introduce K-PROB, a k-mer–based Bayesian framework that mines pangenomic promoter and expression diversity to predict cis-regulatory elements driving gene expression variation in crops 🌽🌱 🔗 biorxiv.org/content/10.1101/2025.10.27.684862v1 #Genomics #GeneRegulation #Maize #Soybean

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

By combining molecular genetics with cell-ablation experiments, we found that vascular cambium stem cells and xylem-identity cells form an interchangeable unit, a stem cell niche. Meticulous work by @xixizhang9001.bsky.social, Ondrej Smetana, Jing Zhang & Xiaoyu Wang 1/x www.pnas.org/doi/10.1073/...

Our latest paper has just been published in Cell! doi.org/10.1016/j.ce... We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

Interested in learning about the latest and greatest research in how plants respond to excess salt, too little or too much water? Come to the GRC in Salt and Water Stress in Switzerland. Lots of opportunities for all career levels. www.grc.org/salt-and-wat.... Please repost!

My department at Dartmouth Medical School is hiring a tenure-track Assistant Professor. We are looking broadly for a biochemist or cell biologist. Please share this add! apply.interfolio.com/171438 @dartmouthbcb.bsky.social @futurepislack.bsky.social

Advances in plant spatial multi-omics data analysis #plantscience

Thrilled to share our work on transcription initiation and termination being spatially coordinated out today in Science! www.science.org/doi/10.1126/...

The UGA Plant Biology Department is hiring! Please help spread the word. We have an opening for an Assistant Professor in Plant Synthetic Biology for Strategic Resources Research. See ad for details – and join us here in Athens, GA!

A pre-print I was working on was recently released! Our multiple discovery filtering (MDF) approach can be used in any model organism and makes it really easy to find trans-regulatory variants. Software coming soon! 🧪 www.biorxiv.org/content/10.1...

Hybrids reveal accessible chromatin trans genetic associations https://www.biorxiv.org/content/10.1101/2025.10.09.681407v1

The Department of Biology at the University of Massachusetts Amherst invites applications for a full-time, tenure-track Assistant Professor position in the area of Plant Physiology:

The @uncchapelhill.bsky.social Department of Biology is searching for tenure-track Assistant Professor in Plant Molecular Biology. Chapel Hill is a wonderful place and Biology is an amazing group of people. To apply, see: unc.peopleadmin.com/postings/307...

Our new short article is online at Plant Biotech J (onlinelibrary.wiley.com/doi/10.1111/...)! "Single Cell Multi-Omics Reveals Rare Biosynthetic Cell Types in the Medicinal Tree Camptotheca acuminata" Product of an NSF-EAGER award that I was co-PI from 2023-2025 (www.nsf.gov/awardsearch/...).

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...