New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

FYI: New online! Gene regulatory networks: from correlative models to causal explanations

Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens! Read it in Science dx.doi.org/10.1126/scie... @ucberkeleyofficial.bsky.social @hhmi-science.bsky.social

Our first study on how the leaf succulent Kalanchoë laxiflora makes stomatal subsidiary cells is finally peer-reviewed & out - and it made the cover! 🌵 🧬 🔬 doi.org/10.1126/scia... Despite 150 years of evolution, grasses and Crassulacean succulents use the SAME gene to make subsidiary cells! 🤯

🌱💚🎉 Sharing (again 😁) my review on regulation of chloroplast biogenesis. First work of my emerging research group at @cbgpmadrid.bsky.social

🔥Fantastic paper!🔥 TE with a role in vegetative phase change and gametogenesis, mediated by 24-nt siRNAs acting in trans to a wide range of genes. Found by GWAS in A. thaliana 🌱. Congratulations to the authors! 👏🏻👏🏻👏🏻 #epigenetics #plantscience www.pnas.org/doi/10.1073/...

#TansleyInsight: Masters of perception: phosphorylation-dependent signaling in plants Mark Roosjen, Justin W. Walley & Dolf Weijers 👇 📖 nph.onlinelibrary.wiley.com/doi/10.1111/... #LatestIssue #PlantScience

Faculty position in Plant Molecular Biology (Associate Professor or Tenure-Track Assistant Professor) at Aarhus University, Denmark mbg.au.dk/aktuelt/ledi...

🪴Postdoc position - UT Austin, TX, USA - Developmental Mechanisms of Adaptation to Underwater Environment/Genome Editing🪴 Do you love amphibious/aquatic plants? Then consider applying to the position! See the attached ads. utaustin.wd1.myworkdayjobs.com/UTstaff/job/...

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...

DNA replication globally disrupts the epigenome. But does this create a chromatin-access opportunity for TF binding to facilitate cell identity change? Now 𝐫𝐞𝐩𝐥𝐢-𝐀𝐓𝐀𝐂-𝐬𝐞𝐪 shows 𝘥𝘦 𝘯𝘰𝘷𝘰 chromatin opening & TF binding occurs specifically post-replication, in cellular differentiation & reprogramming!

Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.

🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI! Thank you all the volunteer researchers whose hard work has made this possible! #plantscience #plantbiology 🧪 bit.ly/3ZHtneT

Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain https://www.biorxiv.org/content/10.64898/2026.02.07.704075v1

New paper! From Sam Snodgrass and @genomeofforrest.bsky.social, w/ @druncie.bsky.social, @gcbias.bsky.social, and a collaboration with Andres Moreno and @santiagogmm.bsky.social. Can we quantify the impact of humans on maize dispersal? Plant yourself in a comfy chair and lend me your ear: 1/10

🧵 Just out in Cell after more than 10 years in the making! 🎓 www.cell.com/cell/fulltex... Plants and animals evolve radically different body plans. Do they also operate under fundamentally different molecular evolutionary constraints during organ formation? @cellpress.bsky.social

The plant ontology of cell types #comment #MolecularPlant cell.com/molecular-pl...

Well done, Akie! Identification of a peptide hormone-receptor module bypassing the ABA signaling to close stomata upon drought. A big breakthrough🍃😊 -Local peptide signalling induces stomatal closure under drought stress @natcomms.nature.com www.nature.com/articles/s41...

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway. And found a hidden RNA-decay axis from Piwi to the RNA exosome.

Bob was incredible. I spoke with him a week before he passed and all he wanted to talk about was his plans for teaching in the Spring. He was an amazing scientist and pushed for teaching excellence in the department at every meeting. He will be sorely missed. newsroom.ucla.edu/stories/in-m...

Our 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...

NSF policy changes - some updates that PIs should be aware of. www.nsf.gov/policies/doc...

The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at [email protected] if you have questions. www.nsf.gov/funding/oppo...

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 👇