We like to introduce map3C, developed by Joseph Galasso, that drastically improves the mapping and contact calling performance of snm3C-seq and now enables accurate 3D genome modeling. map3C was developed in collaboration with Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...

New pre-print from the team! The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses. Have a read! #PlantScience @johninnescentre.bsky.social

Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades www.salk.edu/news-release...

Coming to you live from #ISPLORE2025JP Fresh preprint from my lab showing that leaves progressively oxygenate and how this is important for their morphogenesis.Thanks to our collaborators from @Fra_LicO2si lab. #plantscience www.biorxiv.org/content/10.1...

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.

A timely article as several recent conference discussions have led to similar thoughts www.nature.com/articles/s41...

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 👇

Our new Nature Plants paper is out (and we’re on the cover 😁)!👉 bit.ly/4lS8sOB By combining scRNA-seq with conserved TF binding (multiDAP) we define gene regulatory networks for 65 cell types across 4 tissues in a wide range of flowering plants!

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...

Happy to see our latest #plantscience review by @aidamaric.bsky.social, @advaitagashe.bsky.social and Johanna onlinr! We describe how epigenetic mechanisms control ethylene signal generation and progression, and how ethylene in turn modulates chromatin. www.sciencedirect.com/science/arti...

Plz share! (I am a co-author from NAASC) “An unwelcoming climate & culture at scientific conferences is an obstacle to retaining scientists w/marginalized identities. Here we describe..a professional plant science societies..collaboration to make conferences more inclusive.” doi.org/10.7554/eLif...

Thanks for the enthusiasm in using our online web browser! Due to the high traffic, we have allocated additional resources for user access, so if anyone encountered a bug with accessing the data, please give it a try again and reach out if additional errors are encountered!

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

Tremendous work by the extremely talented postdocs @TrALEE_Sci @NatanellaE @nobolly .Thank you for putting in a major effort on this “side project” to develop a powerful community resource arabidopsisdevatlas.salk.edu

From a gene’s single cell expression–through spatial localization–to novel function, and beyond! Now out @natplants.nature.com We built a comprehensive spatial-transcriptomic atlas of Arabidopsis, revealing cell-type identities across organs in unprecedented detail 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.

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...

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab. Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes. #plantscience www.biorxiv.org/content/10.1...

Next up, a satellite meeting of #PlantBio2025, a celebration of the late great scientist, Joanne Chory share.google/xfOr0g8QkZ4A... Led off by Joe Ecker, and a list of her awards. She also trained a lot of people, see academictree.org/plantbio/tre...

How plants sense injury in their barrier tissue, periderm? Painstakingly detailed and amazing work by post doc Hiroyuki Iida shows that wounding is sensed by the diffusion of two gases: ethylene and oxygen. @treebiocoe.bsky.social‬ @erc.europa.eu‬ 1/x 🧵 www.nature.com/articles/s41...

Plants "bleed" too, but through gases! When wounded, ethylene leaks out and oxygen seeps in. This gas shift acts as an alarm, triggering self-repair to seal the breach. Excited to share our new collaborative work uncovering this clever plant mechanism! Excellent summary here, indulge! #plantscience

Preprint alert: single-cell methylation signature of autism in collaboration with Dan Geschwind. Autism-mC signal is enriched in promoters and cell-type enhancers but uncorrelated with gene expression. Led by @GeschwindLab Postdoc Katie Eyring and grad student Cuining Liu.

I am humbled and honored to receive the Arabidopsis dissemination award. Thank you @naascarabidopsis.bsky.social for this recognition and I wish I could be there with you all! #ICAR2025 Thank you @joeecker.bsky.social for welcoming me into the Arabidopsis world! 🙏🏻🌱📖📕

Graphical abstract of the year award goes to www.sciencedirect.com/science/arti...

Super excited to release a huge evolution project on the works for many years: Evolution experiments synchronized across climates to understand rapid adaptation Preprint: doi.org/10.1101/2025... All data available: www.grene-net.org/data #MOILAB @ucberkeleyofficial.bsky.social @hhmi.org 🧵👇

We have a unique opportunity for a junior researcher, PhD student or postdoc, to use a revolutionary technique for mineral nutrient imaging and tracing in plants. Please re-post! Interested candidates should apply through the portal at the link below: career5.successfactors.eu/career?compa...

Excited to share my new Tansley Review @newphyt.bsky.social on emerging single-cell and spatial omics technologies, many of which are just beginning to be applied in plant biology! Big opportunities lie ahead for the field. [1/n]  nph.onlinelibrary.wiley.com/doi/10.1111/...

Two publications this month showcasing our efforts to understand multi stress resilience in plants www.nature.com/articles/s42... academic.oup.com/plphys/artic...

Grateful to share that our study on "The genetic architecture of cell type–specific cis regulation in maize" is now published in @science.org! Huge thank you to all co-authors and the 4 tough, but fair, reviewers who all helped to improve the study 🌽🧬 www.science.org/doi/10.1126/...

I'm thrilled to share that our study is now published in Cell: Extensive N4 cytosine methylation is essential for Marchantia sperm function. www.cell.com/cell/fulltex... This paper confirms our 4mC discovery in Marchantia sperm and takes it much further. A thread: 0/13

Our lab's first review article written with @yadhusankar.bsky.social and @vijayalakshmi.bsky.social is out now in The Plant Journal! 🎉🌱 We discuss temporal regulation of (plant) development. When and how do plants control organ and cell identity progression? onlinelibrary.wiley.com/doi/10.1111/...

Happy to see our latest paper by @drosborneplantsci.bsky.social et al out today in Developmental Cell @cellpress.bsky.social! We identify a role for VRN2-PRC2 in regulating light-responsive growth in Arabidopsis through the conditional epigenetic repression of PIF signalling. tinyurl.com/swbyff24

Something we have been working on. Built off the work of the unforgettable Dr. Joanne Chory. doi.org/10.1101/2025...

The next frontier in #autophagy is understanding how it functions across cell types to maintain organismal homeostasis. w/ @moritznowack.bsky.social lab, we present TWO #preprint on cell type spec. autophagy in root hairs‼️ #plantscience www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

The first paper from my lab is now online in @ThePlantCell 🌱 doi.org/10.1093/plce... This work is dedicated to the late Prof. Joanne Chory, who profoundly shaped my journey in science and beyond. Thank you to everyone involved: Srinivas Kunta, Yardena Dahan, Shai Torgeman, @Volacninstitute.

🌱 Thrilled to see our latest collaborative work with @jennyrussinova.bsky.social @nvukas.bsky.social published in Cell! By combining single-cell RNA-seq and live imaging, we uncovered previously hidden brassinosteroid signaling states and their role in optimizing root growth. doi.org/10.1016/j.ce...

Some of my postdoc work has been "exposed" today in @theplantjournal.bsky.social! 😁🎉🔬 We developed ExPOSE - a method to perform expansion microscopy in plant protoplast systems. Here's a quick🧵of the details: @meter76.bsky.social @lily-oconnor.bsky.social onlinelibrary.wiley.com/doi/10.1111/...

🚨 We’re hiring–please spread the word! 🚨 Our lab at @thesainsburylab.bsky.social is looking for a pre-doc intern to join our research on plant immunity. If you’re a current undergrad/master’s or recent graduate interested in gaining research experience, please apply! tatsuyanobori.com

Finally some truth about what the impact of institutional silence is as DEI is mothballed. "I see the University for what it is: a place of incredible power and prestige more concerned with public image than the well-being of affected faculty, staff, postdocs and students..." disq.us/t/4tb43sv

How do leaf cell types respond to drought, and how does this vary among leaves of a rosette? Single-nucleus RNA seq of 600+ individual leaves along a drought time course

Stress drives plasticity in leaf maturation transcriptional dynamics https://www.biorxiv.org/content/10.1101/2025.02.24.639183v1

Alright so to brighten the mood... Who's ready for another iteration of 28 Days, 28 Black Plant Scientists/Botanists? 💪🏾🌱 For those that want more background here's a link from last yr. While I search through names myself, I'm happy to hear any nominations via DM/email! plantae.org/2024-black-h...

Happy to share our latest @biorxiv-plants.bsky.social led by @manuelgonzalezfuen.bsky.social “Effector-triggered processing body formation attenuates host translation via ER stress responses and autophagy upon bacterial infection” #proteostasis #plantimmunity 🧵(1/16) www.biorxiv.org/content/10.1...

Food production matters www.theguardian.com/global-devel...

[Please repost] Re-upping this in the new year. Please let us know if you want to contribute to the 1001 Genomes Plus Project, which revolves around a curated collection of almost 600 long-read assemblies of #Arabidopsis thaliana. #plantscience

It was a pleasure contributing to this work. It was stunning to observe the spatial results after each experiment!

Announcing a curated collection of long-read genomes for Arabidopsis thaliana: The 1001 Genomes Plus Project. Currently 453 unique accessions/almost 600 assemblies. Interested in contributing? Please contact us! #plantscience www.biorxiv.org/content/10.1...

Preprint alert, please share!! With our new study, we engineered an orthogonal hypoxia-responsive system in plants inspired by mammalian HIF protein degradation. We demonstrated that this system could control protein stability and activity, enabling modulation of Oxygen sensing outputs. Here's how:

AtSDR4L and paralog promote seed-to-seedling transition in multiple seed compartments https://www.biorxiv.org/content/10.1101/2024.11.29.626136v1

I am looking for a speaker for the "Plant Gene Expression Analysis" workshop at the PAG32 conference in January. There are no funds to support speakers unfortunately. Other confirmed speakers are @tralee-sci.bsky.social, Colleen Doherty and Ronan O'Malley. Please message me if you are interested!