Alexandre Marand
@marand-lab.bsky.social
Assistant Professor at the University of Michigan. Chromatin biology, transcription regulation, plant genomes. https://marand-lab.github.io/
CRISPR-mediated centromere fission generates neochromosomes with distorted meiotic inheritance in Arabidopsis biorxiv.org/content/10.6... new preprint from us - includes changing the Arabidopsis karyotype from 5 -> 6 chromosomes using Cas9 & outcomes of 5/6 chromosome hybrid meiosis
How do transcription factors bind DNA strongly, and in a switch like manner, while remaining sequence specific? Our new paper on a canonical plant TF suggests the answer is a previously underappreciated assembly state: transcription factor nanoclusters. www.science.org/doi/10.1126/...
Nanoclustering of a plant transcription factor enables strong yet specific DNA binding
Transcription factor nanoclusters balance the DNA binding trade-off between weakly binding oligomers and nonspecific condensates.
science.org
One of our recent papers describing techniques to identify root barriers to parasitic plant infection. Plus we show that lignin in the cortex can block branched broomrape infection of tomato.
Plant & Cell Physiology@plantcellphysiol.bsky.social · 2mo agoHairy link... Gouran et al. @bradylabs.bsky.social @plantdevo.bsky.social provide an integrated experimental framework that enables holistic analysis of broomrape parasitism, which may be applied at scale to accelerate resistance gene discovery in #tomato & other hosts 🔗 doi.org/10.1093/pcp/...
Ever stretch a plastic bag until it wrinkled? Keeping a thin sheet flat while it rapidly expands is surprisingly difficult. So how do growing plant leaves remain flat as they rapidly grow? Check out our new @currentbiology.bsky.social review, How to Grow a Flat Leaf www.cell.com/current-biol...
How to grow a flat leaf
Peng et al. review mechanisms driving lamina expansion, including gene expression, auxin-mediated proliferation, and microtubule-directed growth, linking disrupted coordination to morphological defect...
cell.com
🌾 Every grass leaf shares the same repeating short-long cell pattern in its epidermis. Our new #preprint identifies the protein that builds it. 🔬🧬 📄 preprint: www.biorxiv.org/content/10.6... 🧵⬇️ 1/11
🌾 Grass leaves are the photosynthetic powerhouses of human civilisation. @lbmountain.bsky.social's transcriptomic atlas of nearly 70,000 cells from shoot apex to mature leaf follows the genetic programs that form a grass leaf 🧬 paper doi.org/10.1093/plce... expression browser shiny.ips.unibe.ch
1/ Excited to share our new bioRxiv preprint! "4D spatial transcriptomics reveals nodule identity emerges through stacked parallel developmental programs" 📄 doi.org/10.64898/202... Using Xenium, we generated a 4D (3D space + time) atlas of nodule development in Medicago truncatula.
Excited to share that our work on single-nucleus RNA-seq of the shoot apical meristem — the shoot stem cell niche — has found a home. #Plantascience #scRNAseq #stemcells www.science.org/doi/10.1126/...
Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem
snRNA-seq reveals shoot stem cell heterogeneity and traces their differentiation into primary stem cell types.
science.org
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky
An active Helitron transposon family in wheat - Nature Plants
Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...
nature.com
So proud to share our latest publication @CellCellPress! Yue Rui reveals that the same enzyme that makes the wall, cellulose synthase complex (CESA), also tethers the plasma membrane to the wall during water-deficit stress, providing resilience. sciencedirect.com/science/articl…
Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers https://www.biorxiv.org/content/10.64898/2026.05.21.726779v1
New preprint from the Vecchiarelli Lab! 🧵 Congratulations to first author Dr. Claire Dudley! @claire-dudley.bsky.social Claire uncovered a critical player in the organization for the photosynthetic cytoplasm of cyanobacteria - polyphosphate! #polyP www.biorxiv.org/content/10.6...
biorxiv.org
Plants are unique in that single somatic cells have the remarkable potential to dedifferentiate and regenerate entirely new plants. However, the cell types and regulatory dynamics enabling dedifferentiation competence have not been fully explored... until now ⬇️ (1/12)
bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3mo agoCell-specific dedifferentiation in Arabidopsis thaliana https://www.biorxiv.org/content/10.64898/2026.05.21.726904v1
How do cells break symmetry to generate new shape and form? Using the apical hook as a model, we @joeecker.bsky.social applied spatial and single-cell multiomics, and identify a regulatory hotspot in a transient cell niche that drives this U-shaped structure 1/8 bsky.app/profile/bior...
bioRxivpreprint@biorxivpreprint.bsky.social · 3mo agoTransient cell states encode positional information to direct asymmetric growth https://www.biorxiv.org/content/10.64898/2026.05.21.726925v1
Thrilled to announce our newest preprint on #dedifferentiation in Arabidopsis 🧬🌱. We used scRNA-seq and hormone treatments to track transcriptional reprogramming in diverse somatic cell types and found what we think is some pretty cool biology. Feedback welcome! www.biorxiv.org/content/10.6...
biorxiv.org
New OA Resource: "A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination" rdcu.be/fj8H2 Single-nucleus RNAseq profiling of early Arabidopsis seed development. #PlantScience
Excited to share that I will be opening my lab this fall at the @weizmanninstitute.bsky.social in the Department of Plant & Environmental Sciences! I am looking for postdocs interested in plant biology, stress biology, and single-cell technologies. #PlantBiology #SingleCell #Epigenomics #Postdoc
I would encourage plant genomics folks to attend -- organizers are interested in more plant people, and while you have to listen to weird things like cancer, there's lot of technologies and ideas that plant folks could benefit from hearing.
Jeffrey Ross-Ibarra@jrossibarra.bsky.social · 3mo agoFinal session of Biology of Genomes. Has been a great conference (thanks @jennytung.bsky.social for the invite!). Mostly human genetics, and being the only plant weirdo presenting was odd, but I've learned a lot (and gee whiz technologies and data in humans are so much better) and had fun.
We are very happy and proud to present a study led by @jorgehg.bsky.social (now PI in Madrid – keep an eye on him!) in our team @bic-wur.bsky.social. In this work, we discover how auxin-regulated ARF transcription factors learned to activate transcription. A 🧵…(1/17) www.biorxiv.org/content/10.6...
biorxiv.org
A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organis...
cell.com
This a very important, and extremely well-executed study from Ralph Grand’s group @uniheidelberg.bsky.social. Congrats to all the authors! www.biorxiv.org/content/10.6...
📢Out now on bioRxiv: We used Plant STARR-seq to characterize the species- and condition-specific enhancer activity of over 350,000 sequences derived from four plant species. For more, see below and read the paper at: www.biorxiv.org/content/10.6...
The maize community is so privileged to have the amazing support of @maizegdb.bsky.social. I don’t think we could do most of what we do without them. Check out their most recent work including large dna model prediction of effects here academic.oup.com/genetics/art...
Delivering artificial intelligence–ready genomics with the Maize Genetics and Genomics Database
Abstract. The integration of artificial intelligence (AI) into computational biology is changing biological research, particularly in agriculture, where la
academic.oup.com
Thank you, Vanessa, Mike and all involved! So many cool findings described in this work, including parallel evolution of leaf shape and the rapid radiation of Scalesia after genome doubling and Galápagos arrival.
Mike Martin@museumevogen.bsky.social · 3mo agoTHANK YOU to Dr. Vanessa Bieker for her excellent work, and the ‘dream team’ including: @jleebensmack.bsky.social @pablovargas1111.bsky.social @pjaramillod.bsky.social @plantdevo.bsky.social @naturalselection.bsky.social @mfmazuecos.bsky.social @jazminrm.bsky.social www.nature.com/articles/s41...
Fantastic paper led by Matthew Davis from @grey-monroe.bsky.social, on genome degradation in long-term walnut tissue culture: Somatic embryogenesis increases mutation rates >30x, with aneuploidy, large deletions, somatic recombination, and elevated #TE activity. www.pnas.org/doi/10.1073/...
Latest paper from the lab with several collaborators: We've built a four-dimensional spatial transcriptome atlas of barley grain development and germination, allowing detailed interrogation of where and when genes are expressed academic.oup.com/plcell/artic...
A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination
A four-dimensional spatial gene expression transcriptome atlas of Hordeum vulgare (barley) grain development and germination revealed tissue, cell, cluster
academic.oup.com
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...
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...
