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Posts by Alexandre Marand

Postdoctoral Scholar position in the Coaker group
University of California, Davis
We are seeking a Postdoctoral Scholar to join our research program focused on immune receptor engineering and spatial analyses of plant pathogens interactions using computational and imaging approaches. The position will involve integration of molecular, imaging, and computational approaches. Relevant publications from the laboratory include Nature Plants (2025, PMID: 40721669), Proceedings of the National Academy of Sciences (2024, PMID: 38814867), and Cell Reports (2023, PMID: 37342910). https://www.coakerlab.org/
Qualifications:
•	Ph.D. in plant biology, molecular biology, genetics, computational biology, or a related field
•	Strong background in genomics and/or computational biology 
•	First author publications in peer-reviewed journals
•	Ability to work both independently and collaboratively in a multidisciplinary environment
•	Experience in plant innate immunity is preferred

Application Instructions:
The position is initially available for two years, with the possibility of extension based on performance and funding. Salary is based on the University of California postdoctoral salary scale (https://www.ucop.edu/academic-personnel-programs/_files/2025-26/represented-oct-2025-scales/t23.pdf). The salary range for this position is $69,073-$82,836 US Dollars/year. 
Review of applications will begin June 1, 2026 and will continue until the position is filled.
Please submit a CV, a brief statement of research interests (~1 page), and contact information for three references to glcoaker@ucdavis.edu. The research statement should describe your previous work, how your expertise aligns with ongoing research in the lab, and potential future research directions.

Postdoctoral Scholar position in the Coaker group University of California, Davis We are seeking a Postdoctoral Scholar to join our research program focused on immune receptor engineering and spatial analyses of plant pathogens interactions using computational and imaging approaches. The position will involve integration of molecular, imaging, and computational approaches. Relevant publications from the laboratory include Nature Plants (2025, PMID: 40721669), Proceedings of the National Academy of Sciences (2024, PMID: 38814867), and Cell Reports (2023, PMID: 37342910). https://www.coakerlab.org/ Qualifications: • Ph.D. in plant biology, molecular biology, genetics, computational biology, or a related field • Strong background in genomics and/or computational biology • First author publications in peer-reviewed journals • Ability to work both independently and collaboratively in a multidisciplinary environment • Experience in plant innate immunity is preferred Application Instructions: The position is initially available for two years, with the possibility of extension based on performance and funding. Salary is based on the University of California postdoctoral salary scale (https://www.ucop.edu/academic-personnel-programs/_files/2025-26/represented-oct-2025-scales/t23.pdf). The salary range for this position is $69,073-$82,836 US Dollars/year. Review of applications will begin June 1, 2026 and will continue until the position is filled. Please submit a CV, a brief statement of research interests (~1 page), and contact information for three references to glcoaker@ucdavis.edu. The research statement should describe your previous work, how your expertise aligns with ongoing research in the lab, and potential future research directions.

We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...

4 days ago 61 71 1 3
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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...

1 week ago 49 26 1 2
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Gene regulatory networks: from correlative models to causal explanations Nature Reviews Genetics, Published online: 09 March 2026; doi:10.1038/s41576-026-00939-1In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without compromising explanatory power.

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

3 weeks ago 18 8 0 1
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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

3 weeks ago 177 104 1 8

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! 🤯

3 weeks ago 76 29 3 1

🌱💚🎉

Sharing (again 😁) my review on regulation of chloroplast biogenesis.

First work of my emerging research group at @cbgpmadrid.bsky.social

4 weeks ago 17 8 0 0
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🔥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/...

1 month ago 44 21 0 2
Fig. 2 Integrative proteomics approaches for data-driven reconstruction of kinase signaling.

Fig. 2 Integrative proteomics approaches for data-driven reconstruction of kinase signaling.

#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

1 month ago 16 8 0 0
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Faculty position in Plant Molecular Biology (Associate Professor or Tenure-Track Assistant Professor) at Aarhus University, Denmark
mbg.au.dk/aktuelt/ledi...

1 month ago 35 52 2 1
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🪴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/...

1 month ago 20 25 0 0

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/...

1 month ago 39 18 1 1
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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!

1 month ago 67 26 1 0

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.

2 months ago 78 33 0 6
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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

2 months ago 99 60 4 2

Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain www.biorxiv.org/content/10.64898/2026.02...

2 months ago 2 1 0 0

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

2 months ago 59 40 1 5
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🧵 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

3 months ago 97 51 5 2
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The plant ontology of cell types #comment #MolecularPlant cell.com/molecular-pl...

3 months ago 4 1 0 0
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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...

3 months ago 29 4 0 0
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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.

3 months ago 77 25 3 2

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.

3 months ago 98 42 3 5
In memoriam: Robert Goldberg, 82, renowned plant biologist and revered UCLA educator The pioneering genetic scientist, whose research transformed plant molecular biology and whose teaching enriched the lives of generations of UCLA students, died Nov. 21.

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...

4 months ago 14 5 1 1

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...

4 months ago 24 16 1 0
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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...

4 months ago 15 23 1 4
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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...

4 months ago 88 55 1 2
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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...

4 months ago 32 9 0 1
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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

5 months ago 35 18 2 0
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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

5 months ago 165 86 7 6
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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/...

5 months ago 72 28 1 2
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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.

5 months ago 209 79 6 11