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Leonardo Jo@leonardojo.bsky.social · 4mo ago

I'm very excited to announce that the Jo Lab is hiring our FIRST EVER PhD candidate! f you're eager to drive discovery in plants, join us at UU Plants! More info: www.uu.nl/en/organisat... Lab website: thejolab.org #Plantbiology #Phd #Job

I'm very excited to announce that the Jo Lab is hiring our FIRST EVER PhD candidate! f you're eager to drive discovery in plants, join us at UU Plants! More info: www.uu.nl/en/organisat... Lab website: thejolab.org #Plantbiology #Phd #Job

It's been a while, but I've finally found the time to included additional maps to ggPlantmap (github.com/leonardojo/ggplantmap), thanks to the contribution of the community.

The Jo Lab website is up! thejolab.org I expect to announce 1 PhD position and 1 Postdoc position in the spring of 2026 (April-May). Stay tuned!

I'm very happy to announce that starting February 2026, I'm joining Utrecht University as an Assistant Professor!!!

Today we celebrated the "graduation" of our UU_plants Rclub 2024! We hope to keep empowering young researchers to improve their R skills! Special highlight for the great cake made by PhD candidate Dani (bottom left)! #Rstudio #tidyverse

It took me SEVEN years to figure out that you can save a ggplot as a vectorized .svg file ggsave("file.svg"). The svg file can be opened on pptx/ai/inkspace and it will be completely vectorized, even text are still recognized as text boxes! No more recreating plots on illustrator!!!!

Very happy to share this review with @mnodine1 www.sciencedirect.com/science/arti... Here, we describe what is known (or unknown) about the mechanisms of chromatin reprogramming during the early embryogenesis in plants. A lot of exciting questions that still need to be explored. #plantbiology

“To remember or forget: Insights into the mechanisms of epigenetic reprogramming and priming in early plant embryos”

Chromatin is dynamically modified throughout the plant life cycle to regulate gene expression in response to environmental and developmental cues. Alt…

sciencedirect.com

Our course Plant Development & Environment 🌱 was the highest rated level 3 in BSc Biology! I love the enthusiastic 🤩 students & the excellent teachers 🙏@daanweits @leonardojo.bsky.social @andruromanowski.bsky.social @dkawa.bsky.social @rsasidharan.bsky.social @viktoriiavoloboeva.bsky.social

[Beta test] ggPlantmap + shinyapp. Seeking help from the community: I created a function that allows users to create interactive shiny apps to navigate through multiple values (ex: genes) on top of their #ggPlantmap.

OMG! My great mentor John Harada is the recipient of the @aspbofficial.bsky.social Stephen Hales award 2024! This is HUUUGE! He just entered the plant biology hall of fame! Im so happy for him!

The EPS best mentor award goes tooooo.. @kaisakajala.bsky.social !! I'm a bit biased but I believe it was really well deserved!!! 🤣

The final version of the ggPlantmap is out at @jxbotany.bsky.social academic.oup.com/jxb/advance-... Come for the information, stay for the beautiful figures! We hope it can encourage people to create their own eFP-viewer!

ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images

ggPlantmap, a new addition to the plant data visualization toolbox, allows users to create graphical maps from plant images for the representation of spatial qu

academic.oup.com

The final version of the ggPlantmap is out at @JXBot academic.oup.com/jxb/advance-... Come for the information, stay for the beautiful figures! We hope it can encourage people to create their own eFP-viewer!

Everything makes sense now... #chickpea #plantbio

ggPlantmap github.com/leonardojo/g... Convert Icy-traced Plant images into ggPlot Integrable with bulk or sc-RNAseq data Generate .svg for Plant eFP viewer @jxbotany.bsky.social 2024 academic.oup.com/jxb/advance-...

aRt: Building a root barrier. Built using: ggPlantmap and rayshader #plantbio #bioart

I’m happy to finally submit the final chapter of my PhD dissertation. Here we studied a very known TF in the field of seed lipid content - WRINKLED1. To our surprise, this was the first comprehensive study of genome-wide binding pattern of WRI1. #plantbio #seeds #lipids

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3y ago

Genome-Wide Profiling of Soybean WRINKLED1 Transcription Factor Binding Sites Provides Insight into the Regulation of Fatty Acid and Triacylglycerol Biosynthesis Program in Seeds https://www.biorxiv.org/content/10.1101/2024.01.23.576967v1

Note: ggPlantmap small update (v1.1). ggPlantmap.to.SVG() converts your ggPlantmap into a SVG file that is compatible with an ePlant EFP pipeline or any graphic software (like powerpoint). The polygons will be grouped based on an assigned column.

Our latest preprint: postdoc Pierre Gautrat devoted his EMBO fellowship to resolving how nutrient and light cues interact to control shade avoidance. With @andruromanowski.bsky.social. The answer is PIF-dependent regulation of cytokinin response regulators. Read all about it in this preprint.

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3y ago

Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues. https://www.biorxiv.org/content/10.1101/2023.12.22.572814v1

If you use the background_image() function from ggpubr (rpkgs.datanovia.com/ggpubr/refer...), you can display your ggPlantmap on top of a image. There is a small y-axis offset, but it can do the trick. I will work on implementing this function whenever I have some free time. #ggPlantmap

You are welcome chatgpt.

Contrary to my previous belief, root size doesn't seem to determine the number of xylem poles. Legume roots of different "thickness" can display 3 or 4 xylem poles. What could be the genetic basis (evo-devo) of different xylem pole numbers? #rootbiology #plantbiology

Our ggPlantmap manuscript is out at biorxiv. A bit awkward writing it honestly, but we made it! At the same time, I've seen some people using it and creating nice maps! I hope it empowers people to find new ways to explore their data!

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3y ago

ggPlantmap: an R package for creation of informative and quantitative ggplot maps derived from plant images. https://www.biorxiv.org/content/10.1101/2023.11.30.569429v1

Great work by bachelor student Martijn Posthumus during his 10-week internship. He built tagged versions of GFP that are transported to different cellular compartments. We will use it to study protein sub-cellular localization in plants. #plantbiology #protoplasts #GFP

Are you excited about molecular biology of plant-light interactions? We have good news! We have extended the deadline for application to our tenure track position @WUR to 27 November. #plantscijobs

Ronald Pierik@ronaldpierik.bsky.social · 3y ago

We are hiring! Tenure track in plant-light interactions in our newly established Plant Photobiology team at Wageningen University, the Netherlands. Please share! www.wur.nl/en/vacancy/a...

Root protoplasts (+ fluorescein diacetate) #ROOTS #protoplasts #plantbio

Minas Tirith - root cells version #aRt

We recorded the ggPlantmap seminar given at the @UU_Plants seminar series. I give a brief overview of the package and I speak a bit about how Rclubs can help students learn R more effectively. www.youtube.com/watch?v=TD5m...

ggPlantmap: an R package for the graphic mapping of plant images

Seminar given at the Utrecht University (UU) Plants seminar series.Oct 12th, 2023.

youtube.com