My postdoc preprint is now online @biorxiv-plants.bsky.social. We established HYDRA, a shoot regeneration assay in Arabidopsis without exogenous hormones, and show that photosynthesis-derived carbon drives regeneration via RBR1 pathway–mediated cell cycle activation. www.biorxiv.org/content/10.6...

Photosynthesis-derived carbon gates cell cycle activation to enable hormone-autonomous shoot regeneration

Shoot regeneration is a powerful model for cell fate reprogramming but how it occurs in nature remains poorly understood because studies in Arabidopsis thaliana conventionally rely on in vitro assays ...

biorxiv.org

New review out in Current Biology with colleagues in the Plant Cell Atlas (@plantcellatlas.bsky.social)! We discuss how single-cell genomics is reshaping our understanding of plant cell-type identity and evolution across the Green Lineage. bit.ly/4eAip2Q

Genes for genetic painting in flowers now available on Addgene!: addgene.org/browse/artic...

New preprint out 🌱 We present a new T-DNA vector system for Arabidopsis that supports clean, genomically mapped, single-copy T-DNA insertion with predictable cell-type/conditional gene expression. @mokhalil.bsky.social + Gehring labs biorxiv.org/content/10.6... 🧵1/16

Rational design of T-DNA vectors enables predictable, single-copy integration in Arabidopsis thaliana

Agrobacterium-mediated transformation is the dominant method for plant transgenesis, yet it frequently produces multi-copy, structurally complex T-DNA insertions associated with transgene silencing, u...

biorxiv.org

Check out this cool new preprint by @willshaw.bsky.social from the Gehring and Khalil labs about the optimization of T-DNA vector backbones to achieve predictable and stable (over)expression in Arabidopsis

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 2mo ago

Rational design of T-DNA vectors enables predictable, single-copy integration in Arabidopsis thaliana https://www.biorxiv.org/content/10.64898/2026.06.08.730999v1

Plants are our most scalable technology for managing atmospheric CO₂. Can we CRISPR them to capture it faster? 🌱 Our review: “𝘎𝘦𝘯𝘰𝘮𝘦 𝘦𝘯𝘨𝘪𝘯𝘦𝘦𝘳𝘪𝘯𝘨 𝘰𝘧 𝘱𝘭𝘢𝘯𝘵 𝘱𝘩𝘰𝘵𝘰𝘴𝘺𝘯𝘵𝘩𝘦𝘴𝘪𝘴 𝘧𝘰𝘳 𝘤𝘢𝘳𝘣𝘰𝘯 𝘴𝘦𝘲𝘶𝘦𝘴𝘵𝘳𝘢𝘵𝘪𝘰𝘯” is out now. With co-first author Flora Wang + the Niyogi, Savage, and Lemaux Labs at UC Berkeley + IGI.

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 ago

Transient cell states encode positional information to direct asymmetric growth https://www.biorxiv.org/content/10.64898/2026.05.21.726925v1

Big congrats to my former lab bench neighbor Carly whose PhD work on building a snRNA-seq atlas of young Arabidopsis seed development was just published @natplants.nature.com

Nature Plants@natplants.nature.com · 3mo ago

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

Not sure which scRNA-seq platform to use for 🪴 plant samples? How well do doublet detection algorithms really work in 🌱? How can I optimise sample prep ? Find out in our benchmark study! Led by @carogro.bsky.social and @thomaseekhout.bsky.social. Open access at EMBO Journal: doi.org/10.1038/s443...

Benchmarking plant single cell RNA-sequencing sample processing strategies - The EMBO Journal

The isolation of single plant cells from complex tissues is prone to selective enrichment and sampling biases, which complicates accurate profiling of the large diversity in cell types. Optimizing methodologies for cell enrichment and single-cell transcriptomics is therefore critical for single-cell studies addressing plant cell heterogeneity. Here, we systematically compared protoplast enrichment technologies (including conventional and image-based flow cytometry, as well as magnetic cell sorting) and single-cell RNA sequencing (scRNA-seq) platforms (10X Genomics Chromium, BD Rhapsody) using Arabidopsis roots. Image-based flow cytometry offered increased precision due to customizable gating strategies, while magnetic sorting provided faster processing and enhanced representation of cell size heterogeneity. Both scRNA-seq platforms captured root cell heterogeneity and yielded reproducible gene expression profiles, but showed platform-associated differences in cell type composition. Notably, single-nucleotide polymorphism analysis of a mixed ecotype sample revealed that, among cells identified as doublets by computational algorithms, two-thirds were likely to have been misclassified. These insights identify key biases in plant cell purification and scRNA-seq workflows and provide practical guidance for improving data quality across plant species.

doi.org

The last paper of my PhD work in Argentina. We dig deeper into the Marchantia MpC1HDZ transcription factor. Many experiments, but my favourite: in addition to its role in oil body cell differentiation, it is also important for another cell type! #PlantScience academic.oup.com/plphys/advan...

Our new preprint! Winter-like extended cold primes plants for regeneration🌱❄️! Work by Fu-Yu Hung, now a new PI in Taiwan!

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 4mo ago

Prolonged cold exposure enhances regeneration potential in Arabidopsis https://www.biorxiv.org/content/10.64898/2026.04.20.719581v1

Our work on UV-B perception and signaling in #Marchantia is now out in @plantphys.bsky.social. doi.org/10.1093/plph... Thanks to all authors @yuankeliang.bsky.social @romanulm.bsky.social @grandpahiro.bsky.social #PlantScience

Excited to see the major chapter of my PhD in print! We present a massively-parallel approach for screening CRISPR edits in plants to speed up agricultural test cycles + benchmark genomic LMs. Thanks to my fantastic co-authors and advisors. Link below!

Savage Lab@savagecatsonly.bsky.social · 4mo ago

Can CRISPR edits enable precise tuning of plant gene expression? We think: yes. In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.

We have been cooking up this story for a while and we are excited to finally be able to share! Read on if you're interested in whole plant regeneration WITHOUT the application of hormones!

please share! 🌱Application deadline is March 27 to apply for the Cold Spring Harbor Frontiers and Techniques in Plant Science 3 week summer course! 🌱 It's a great time- you learn a lot and really bond with others in the course. 🌱 I was in the class of 2000! 😀 meetings.cshl.edu/alumni.aspx?...

Course Alumni

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

Highly recommended EMBO Workshop on Plant Photobiology (ISPP2026) in Les Diablerets, Switzerland! (even if I may be slightly biased...) Registration open. We are very much looking forward to seeing you there! ⬇️

Please consider attending this conference in the Swiss Alps meetings.embo.org/event/26-pla... . Exciting science & great venue, lots of opportunities for selected talks from abstracts. Join the conversation on Bluesky with #EMBOispp2026

New preprint out! Zhoubo Hu et al "A redox-regulated RCC1-like protein controls catalase activity in Arabidopsis". We identify CAIR1, a UVR8-interacting protein, as a redox-responsive regulator of catalase localization and activity, maintaining cellular ROS balance. 🌱 www.biorxiv.org/content/10.6...

A redox-regulated RCC1-like protein controls catalase activity in Arabidopsis https://www.biorxiv.org/content/10.64898/2026.01.30.702735v1

This is a very special paper for me. I had the idea of combining transcription factor binding with chromatin in 2016/8. It took some time, but thanks to Fred and Vikas, we can finally share the story in @plos.org Genetics looking at chromatin states in Arabidopsis and Marchantia. #PlantScience

Chromatin state architecture governs transcription factor accessibility across plant genomes

Author summary In eukaryotes, DNA is tightly associated with histone proteins. Histone covalent modifications and histones isoforms, also called histone variants provide most of the complexity of chro...

journals.plos.org

Our new year starts of course with new preprint on brassinosteroid signaling tinyurl.com/nhzcfkxd. We re-analyzed the function of Kelch phosphatases, which were previously characterized as protein tyrosine phosphatases that dephosphorylate the critical pTyr200 in the GSK3 kinase BIN2. (1/6)

Plant Kelch phosphatases are Ser/Thr phosphatases involved in cell cycle regulation

Brassinosteroids (BRs) are plant steroid hormones sensed at the cell surface by the membrane receptor kinase BRI1. Activation of BRI1 leads to the dephosphorylation of BZR1/BES1 transcription factors ...

tinyurl.com

We are very much looking forward to welcoming you in Les Diablerets 🇨🇭 for the International Symposium on Plant Photobiology (ISPP2026), Sept. 8-11, 2026! @martinalegris.bsky.social @emiliedemarsy.bsky.social @chfankhauser.bsky.social @plantphotobiology.bsky.social ➡️ See the links below.

ISPP2026@ispphotobiology.bsky.social · 9mo ago

🌿🌈 Less than a year for ISPP 2026 in Switzerland! 🇨🇭 Check our website ispp2026.unine.ch for more details.

New preprint! 😁 We uncover how early land plants evolved UV-B tolerance by dissecting the UVR8 pathway in Marchantia polymorpha. Conserved yet rewired—evolutionary plasticity revealed. 👉 www.biorxiv.org/content/10.1... #PlantScience #UVB #Evolution

Conservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorpha

Ultraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia polymorpha (Marchantia) serves as a key model organism to study signaling pathways and to in...

biorxiv.org

Conservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorpha https://www.biorxiv.org/content/10.1101/2025.07.16.665153v1

Happy to share this work we did together with @yuankeliang.bsky.social in @romanulm.bsky.social lab. We looked in detail at UVR8-mediated UV-B signaling in Marchantia and found some conserved functions but also a few surprises! #plantscience #marchantia #UVR8

Conservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorpha

Ultraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia polymorpha (Marchantia) serves as a key model organism to study signaling pathways and to in...

biorxiv.org

New from the Gehring lab

A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of ferti...

biorxiv.org

POSTDOC POSITION AVAILABLE, Geneva, Switzerland - Applications are invited for a postdoc position to study UV-B perception and signalling in plants. Please apply, forward to suitable candidates, and/or repost; many thanks! Deadline February 24, 2025. See www.ulm-lab.ch for more information.

Do you want an EMS-like drug that you can easily use in your lab or your garden shed to generate structural variation in your favorite plant? We show here that the topo2 inhibitor & common chemotherapy drug etoposide works really well to generate structural variation .

A simple method to efficiently generate structural variation in plants

Phenotypic variation is essential for the selection of new traits of interest. Structural variants, consisting of deletions, duplications, inversions, and translocations, have greater potential for ph...

biorxiv.org