Alexandre Marand

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...

Figure of the paper.

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/...).

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...

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/

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...

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.

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 ...

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 !

Beautiful work, @jleebensmack.bsky.social and team!

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...

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 ⬇️

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.

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.

So cool! Congratulations 🎊🎉

Plant cells at the organ surface use mechanical cues to activate a specific growth control programme During morphogenesis of multicellular organs, cells acquire distinct identities that meet specific functional requirements. Epidermal identity is widely considered essential for plant morphogenesis du...

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 PRC2 regulates vascular patterning in hypocotyls by repressing cytokinin biosynthesis genes via H3K27me3 deposition, thereby modulating cytokinin signaling

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.