Leonardo Jo
@leonardojo.bsky.social
Postdoc fellow at Wageningen University
Gene regulatory mechanisms & plant development.
@ucdavis Alumni
First Gen. He/Him.
Gene regulatory mechanisms & plant development.
@ucdavis Alumni
First Gen. He/Him.
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
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
September 17, 2024 at 4:23 PM
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
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!!!!
August 28, 2024 at 3:45 PM
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
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…
www.sciencedirect.com
August 5, 2024 at 3:20 PM
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
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
Reposted by Leonardo Jo
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
I love the enthusiastic 🤩 students & the excellent teachers 🙏@daanweits @leonardojo.bsky.social @andruromanowski.bsky.social @dkawa.bsky.social @rsasidharan.bsky.social @viktoriiavoloboeva.bsky.social
June 5, 2024 at 7:23 AM
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
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.
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.
April 16, 2024 at 4:23 PM
[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.
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!
April 11, 2024 at 9:31 PM
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!!! 🤣
April 10, 2024 at 6:41 PM
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!
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
March 4, 2024 at 8:47 PM
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!
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!
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!
@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!
March 4, 2024 at 3:57 PM
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!
@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!
March 1, 2024 at 5:45 PM
Reposted by Leonardo Jo
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-...
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-...
February 13, 2024 at 4:05 AM
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-...
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-...
February 7, 2024 at 11:23 AM
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
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
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
Understanding the regulatory mechanisms controlling seed lipid accumulation provides opportunities f
www.biorxiv.org
January 28, 2024 at 2:01 PM
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.
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.
January 17, 2024 at 10:16 PM
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.
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.
Reposted by Leonardo Jo
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.
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
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
Plants growing at high densities can detect competitors through changes in the composition of light
www.biorxiv.org
December 23, 2023 at 9:31 AM
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.
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
December 19, 2023 at 3:42 PM
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.
December 15, 2023 at 9:08 AM
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
December 6, 2023 at 4:43 PM
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!
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!
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
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
As plant research generates an ever-growing volume of spatial quantitative data, the need for decent
www.biorxiv.org
December 4, 2023 at 10:08 AM
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!
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!
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
#plantbiology #protoplasts #GFP
November 10, 2023 at 1:18 PM
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
#plantbiology #protoplasts #GFP
Reposted by Leonardo Jo
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
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...
November 10, 2023 at 11:38 AM
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
October 27, 2023 at 1:10 PM
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...
@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.
www.youtube.com
October 13, 2023 at 2:44 PM
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...
@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...