Alexandre Marand
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marand-lab.bsky.social
Alexandre Marand
@marand-lab.bsky.social
Assistant Professor at the University of Michigan. Chromatin biology, transcription regulation, plant genomes.

https://marand-lab.github.io/
Reposted by Alexandre Marand
🚀 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
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...
biorxiv.org
October 29, 2025 at 4:47 PM
Reposted by Alexandre Marand
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
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.
www.nature.com
November 18, 2025 at 12:00 PM
Reposted by Alexandre Marand
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/...
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...
www.pnas.org
November 14, 2025 at 9:30 AM
Reposted by Alexandre Marand
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.
November 5, 2025 at 5:20 PM
Reposted by Alexandre Marand
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!
2026 Salt and Water Stress in Plants Conference GRC
The 2026 Gordon Research Conference on Salt and Water Stress in Plants will be held in Les Diablerets, Vaud (fr) Switzerland. Apply today to reserve your spot.
www.grc.org
November 6, 2025 at 1:06 AM
Reposted by Alexandre Marand
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
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
August 27, 2025 at 8:50 PM
Reposted by Alexandre Marand
Thrilled to share our work on transcription initiation and termination being spatially coordinated out today in Science! www.science.org/doi/10.1126/...
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...
www.science.org
October 10, 2025 at 6:14 PM
Reposted by Alexandre Marand
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!
October 16, 2025 at 7:53 PM
Reposted by Alexandre Marand
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
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...
www.biorxiv.org
October 16, 2025 at 2:22 PM
Reposted by Alexandre Marand
Hybrids reveal accessible chromatin trans genetic associations https://www.biorxiv.org/content/10.1101/2025.10.09.681407v1
October 11, 2025 at 12:32 AM
Reposted by Alexandre Marand
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:
October 7, 2025 at 2:08 AM
Reposted by Alexandre Marand
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...
October 6, 2025 at 7:30 PM
Reposted by Alexandre Marand
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/...).
October 5, 2025 at 2:44 PM
Reposted by Alexandre Marand
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...
Engineering Spatial Control of Bacterial Organelles
Bacteria were once thought to lack organelles, but it is now clear they confine cellular reactions using an array of membrane- and protein-based compartments. A central question, however, is how bacte...
www.biorxiv.org
September 23, 2025 at 5:38 PM
Reposted by Alexandre Marand
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/
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
Reposted by Alexandre Marand
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...
AI Isn't A Ticket to an A — Jessica Calarco
I teach a freshman seminar on kids and society. For their first project, my students create an infographic that aims to clarify a common misconception about “kids these days.” For reasons I’ll outline...
www.jessicacalarco.com
September 25, 2025 at 10:53 AM
Reposted by Alexandre Marand
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
Cornell University, Molecular Biology & Genetics
Job #AJO30607, WDR-00055221 Assistant Professor, Molecular Biology & Genetics, Cornell University, Ithaca, New York, US
academicjobsonline.org
September 22, 2025 at 3:25 PM
Reposted by Alexandre Marand
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.
September 19, 2025 at 8:51 AM
Reposted by Alexandre Marand
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....
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci | Molecular Systems Biology
imageimageVascular sites have distinct susceptibility to disease. Here, through single cell epigenomic profiling and predictive machine learning modeling, this study revealed that regulatory enhancers are vascular site specific, providing insight ...
www.embopress.org
September 10, 2025 at 3:54 PM
Reposted by Alexandre Marand
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 !
September 12, 2025 at 10:41 AM
Reposted by Alexandre Marand
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... .
Two independent origins of XY sex chromosomes in Asparagus
The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evol...
www.biorxiv.org
September 11, 2025 at 2:26 PM
Reposted by Alexandre Marand
@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...
We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data.
(Zoom registration link and more information in thread!)
🧵
September 11, 2025 at 2:34 PM
Reposted by Alexandre Marand
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 ⬇️
August 26, 2025 at 12:31 PM
Reposted by Alexandre Marand
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 👇
Drought recovery in plants triggers a cell-state-specific immune activation - Nature Communications
Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.
doi.org
August 31, 2025 at 2:17 AM