Alexandre Marand

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/...

Post-replicative chromatin accessibility predicts cell fate change Knudsen and colleagues use repli-ATAC-seq to compare replicated and unreplicated chromatin in two models of cell identity change. They find that lineage-specific elements are accessible earlier in rep...

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.

Announcing the publication of TAIR12: Consult the fully reannotated genome on the European Nucleotide Archive - Phoenix Bioinformatics TAIR (The Arabidopsis Information Resource), together with our nonprofit host Phoenix Bioinformatics, is pleased to announce the public release of TAIR12

🎉📣 #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...

Policy Notice: Implementation of Policy Changes to Proposal and Award Policies and Procedures Guide (PAPPG) 24-1, Supplement 1 This notice implements several revisions to NSF's Proposal and Award Policies and Procedures Guide (PAPPG) 24-1.

NSF policy changes - some updates that PIs should be aware of.

www.nsf.gov/policies/doc...

Enabling Discovery Through Genomics (EDGE)

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

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...

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

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes Understanding the genetic code of cis-regulatory elements (CREs) is essential for engineering gene expression and modulating agronomic traits in crops. In plants, CREs underlying rapid evolution of ge...

🚀 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

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.

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

Auxin transport positions stem cells in the vascular cambium during normal development and regeneration | PNAS The vascular cambium contains bifacial stem cells producing secondary phloem in one and secondary xylem to the opposite direction. In Arabidopsis r...

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 Recent advances in plant spatial omics, including transcriptomics and metabolomics, have enabled fine-scale cellular insights by registering spatial information. Combining spatial approaches with droplet-based single-cell technologies has further enhanced our understanding of many complex biological processes. However, the unique features of plants, such as rigid cell walls and size variability, require adaptation of mammalian-derived analytical methods. This review summarizes current strategies for acquiring plant spatial multi-omics data, with a focus on widely accessible commercial platforms. We also outline analysis workflows, from preprocessing to downstream interpretation, and provide a practical tutorial using demonstration datasets. This resource offers researchers a concise guide to experimental and computational approaches for plant spatial multi-omics.

Advances in plant spatial multi-omics data analysis #plantscience

mRNA initiation and termination are spatially coordinated Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage o...

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!

Hybrids reveal accessible chromatin trans genetic associations Crosses between genetically distant Zea mays (Maize) inbreds cause hybrid vigour (heterosis): an over-dominant increase in vegetative growth and grain yield. Although the contributing loci are unknown...

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: