Ronnie de Jonge
@dejongepmi.bsky.social
Associate professor at the departments of Biology and Information and Computing Sciences of Utrecht University. In my lab we study the molecular mechanisms by which plants and microbes communicate at the soil-root interface.
Reposted by Ronnie de Jonge
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 11:26 AM
One more week to apply for an open PhD position in my team at Utrecht University. Interested in genetics, genomics, bioinformatics, microorganisms and plant-microbiota interactions, don't hesitate and apply! www.uu.nl/en/organisat...
PhD Position on Decoding Plant Microbiota–Host Specificity Using AI
Join us to generate data and build AI-driven models to decode plant–microbiota host specificity!
www.uu.nl
June 6, 2025 at 6:33 PM
One more week to apply for an open PhD position in my team at Utrecht University. Interested in genetics, genomics, bioinformatics, microorganisms and plant-microbiota interactions, don't hesitate and apply! www.uu.nl/en/organisat...
Reposted by Ronnie de Jonge
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
May 14, 2025 at 2:07 PM
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
Reposted by Ronnie de Jonge
Transposon activity eliminates a crucial fungal secondary metabolite cluster while preserving pathogenicity https://www.biorxiv.org/content/10.1101/2025.05.14.653967v1
May 15, 2025 at 3:18 AM
Transposon activity eliminates a crucial fungal secondary metabolite cluster while preserving pathogenicity https://www.biorxiv.org/content/10.1101/2025.05.14.653967v1
🌱 We're hiring! Join our team as a PhD candidate to explore plant–microbiota host specificity. Plant biology/microbiology background needed; bioinformatics skills a big plus💻! Apply by mid-June. www.uu.nl/en/organisat... #uubeta #plantmicrobiome #microbiota
PhD Position on Decoding Plant Microbiota–Host Specificity Using AI
Join us to generate data and build AI-driven models to decode plant–microbiota host specificity!
www.uu.nl
May 15, 2025 at 9:36 AM
🌱 We're hiring! Join our team as a PhD candidate to explore plant–microbiota host specificity. Plant biology/microbiology background needed; bioinformatics skills a big plus💻! Apply by mid-June. www.uu.nl/en/organisat... #uubeta #plantmicrobiome #microbiota
Reposted by Ronnie de Jonge
Not everyday we see phyllosphere microbiota in @cp-cellhostmicrobe.bsky.social🥬 Specific bacteria within the maize leaf microbiota seem to promote individual leaf growth by repressing defense genetic regulatory network & modulating leaf growth-defense tradeoff
🔗 www.sciencedirect.com/science/arti...
🔗 www.sciencedirect.com/science/arti...
Individual leaf microbiota tunes a genetic regulatory network to promote leaf growth
In natural ecosystems, microbes have the ability to stably colonize plant leaves, overcoming the fluctuating environmental conditions that the leaves …
www.sciencedirect.com
March 1, 2025 at 12:51 AM
Not everyday we see phyllosphere microbiota in @cp-cellhostmicrobe.bsky.social🥬 Specific bacteria within the maize leaf microbiota seem to promote individual leaf growth by repressing defense genetic regulatory network & modulating leaf growth-defense tradeoff
🔗 www.sciencedirect.com/science/arti...
🔗 www.sciencedirect.com/science/arti...
Reposted by Ronnie de Jonge
Great talk by Heribert Hert on microbiomes in relation to drought resistance, regreening strategies and the orphan crop Fonio microbiomejournal.biomedcentral.com/articles/10....
February 12, 2025 at 9:51 AM
Great talk by Heribert Hert on microbiomes in relation to drought resistance, regreening strategies and the orphan crop Fonio microbiomejournal.biomedcentral.com/articles/10....
Reposted by Ronnie de Jonge
Our first paper on natural variation in root exudate composition in wild #Arabidopsis. This represents a turning point in the way we characterize and understand phenotypic traits with implications beyond the plant itself @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary
January 24, 2025 at 5:25 PM
Our first paper on natural variation in root exudate composition in wild #Arabidopsis. This represents a turning point in the way we characterize and understand phenotypic traits with implications beyond the plant itself @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com/doi/10.1111/...
@rlberendsen.bsky.social kicks off a day of science starting with @jurriaanton.bsky.social on immune memory in plants.
January 8, 2025 at 8:36 AM
@rlberendsen.bsky.social kicks off a day of science starting with @jurriaanton.bsky.social on immune memory in plants.
Reposted by Ronnie de Jonge
www.nature.com/articles/s41... 🌱🚜 Excited to see our paper in @naturemicrobiol.bsky.social ! Amazing effort by @y-song.bsky.social in collaboration with TU Delft (Neil Budko, Elisa Atza) and the Dutch potato breeding industry to harness the power of the microbiome! 🥔🔬@utrechtpmi.bsky.social
Seed tuber microbiome can predict growth potential of potato varieties - Nature Microbiology
Time-resolved drone imaging of potato crop development and seed tuber microbiome data can be used to predict potato vigour, or growth potential, in next-season crops in trial fields.
www.nature.com
December 28, 2024 at 3:06 PM
www.nature.com/articles/s41... 🌱🚜 Excited to see our paper in @naturemicrobiol.bsky.social ! Amazing effort by @y-song.bsky.social in collaboration with TU Delft (Neil Budko, Elisa Atza) and the Dutch potato breeding industry to harness the power of the microbiome! 🥔🔬@utrechtpmi.bsky.social
Reposted by Ronnie de Jonge
Rhizobacteria cleaves flg22 through a type II secreted subtilase and suppresses plant immunity. #plantmicrobe #plantimmunity
www.cell.com/cell-reports...
www.cell.com/cell-reports...
A type II secreted subtilase from commensal rhizobacteria cleaves immune elicitor peptides and suppresses flg22-induced immune activation
Eastman, Jiang, and Ficco et al. screen 165 root-associated bacteria for suppression of plant immune activation and growth restriction induced by the peptide immune elicitor flg22. They show that Dyella japonica uses the type II secreted subtilase IssA to cleave the peptide immune elicitors flg22 and AtPEP1 and suppress plant immune activation.
www.cell.com
December 17, 2024 at 8:12 PM
Rhizobacteria cleaves flg22 through a type II secreted subtilase and suppresses plant immunity. #plantmicrobe #plantimmunity
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Reposted by Ronnie de Jonge
Super excited to share the news that our BarrierFates consortium got 3M€ funding from NWO XL to study maize root barrier cell types! 🌽🔬
Delighted to embark on this journey with
@dorotakawa.bsky.social , @hannahschneider.bsky.social , Victoria Mironova and Jian Xu!
www.nwo.nl/en/news/64-m...
Delighted to embark on this journey with
@dorotakawa.bsky.social , @hannahschneider.bsky.social , Victoria Mironova and Jian Xu!
www.nwo.nl/en/news/64-m...
64 million euros for groundbreaking fundamental research projects | NWO
21 research consortia have the chance to reach a breakthrough thanks to funding from the ENW-XL Open Competition. From fundamental research on the effects of certain materials on the methane cycle to ...
www.nwo.nl
December 16, 2024 at 10:48 AM
Super excited to share the news that our BarrierFates consortium got 3M€ funding from NWO XL to study maize root barrier cell types! 🌽🔬
Delighted to embark on this journey with
@dorotakawa.bsky.social , @hannahschneider.bsky.social , Victoria Mironova and Jian Xu!
www.nwo.nl/en/news/64-m...
Delighted to embark on this journey with
@dorotakawa.bsky.social , @hannahschneider.bsky.social , Victoria Mironova and Jian Xu!
www.nwo.nl/en/news/64-m...
Reposted by Ronnie de Jonge
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
December 11, 2024 at 2:30 AM
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
Reposted by Ronnie de Jonge
❗️The abstract submission and registration for Rhizosphere 6 is now open! 🌾🌿
www.rhizo6.org/home
please join us in Edinburgh next year for what should be an exciting meeting.
@hutton.ac.uk
#rhizosphere6
www.rhizo6.org/home
please join us in Edinburgh next year for what should be an exciting meeting.
@hutton.ac.uk
#rhizosphere6
Rhizosphere 6 - Rooting for Earth
Welcome to Rhizosphere 6
We are looking forward to welcoming the global rhizosphere research community to Edinburgh for Rhizosphere 6 in June 2025. The meeting will foster exchange, interaction and ...
www.rhizo6.org
December 9, 2024 at 4:03 PM
❗️The abstract submission and registration for Rhizosphere 6 is now open! 🌾🌿
www.rhizo6.org/home
please join us in Edinburgh next year for what should be an exciting meeting.
@hutton.ac.uk
#rhizosphere6
www.rhizo6.org/home
please join us in Edinburgh next year for what should be an exciting meeting.
@hutton.ac.uk
#rhizosphere6
Reposted by Ronnie de Jonge
We have a vacancy for a PhD position with our recently started PMI PI @arsheed-sheikh.bsky.social at Utrecht University. Please apply via: www.uu.nl/en/organisat...
December 5, 2024 at 9:48 AM
We have a vacancy for a PhD position with our recently started PMI PI @arsheed-sheikh.bsky.social at Utrecht University. Please apply via: www.uu.nl/en/organisat...
Reposted by Ronnie de Jonge
We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...
Bioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the Rhizosphere
Contribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!
www.uu.nl
December 4, 2024 at 4:09 PM
We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...
Reposted by Ronnie de Jonge
🚨 Tenure-track jobs at NYU Biology!!
We're going to hire two new assistant professors working in ecological and evolutionary genetics and genomics.
Live and work in Greenwich Village, with friendly colleagues invested in your success.
Apply!
apply.interfolio.com/155792
We're going to hire two new assistant professors working in ecological and evolutionary genetics and genomics.
Live and work in Greenwich Village, with friendly colleagues invested in your success.
Apply!
apply.interfolio.com/155792
September 30, 2024 at 4:30 PM
🚨 Tenure-track jobs at NYU Biology!!
We're going to hire two new assistant professors working in ecological and evolutionary genetics and genomics.
Live and work in Greenwich Village, with friendly colleagues invested in your success.
Apply!
apply.interfolio.com/155792
We're going to hire two new assistant professors working in ecological and evolutionary genetics and genomics.
Live and work in Greenwich Village, with friendly colleagues invested in your success.
Apply!
apply.interfolio.com/155792
Reposted by Ronnie de Jonge
Thrilled to have our recent review on giant #fungal #transposons, called Starships, featured on the cover of Trends in Genetics! Accompanied by some fantastic artwork! With @mycomile.bsky.social. www.cell.com/trends/genet...
December 3, 2024 at 10:02 AM
Thrilled to have our recent review on giant #fungal #transposons, called Starships, featured on the cover of Trends in Genetics! Accompanied by some fantastic artwork! With @mycomile.bsky.social. www.cell.com/trends/genet...
Reposted by Ronnie de Jonge
The Machine Learning for Molecules workshop 2024 will take place THIS FRIDAY, December 6.
Tickets for in-person participation are "SOLD" OUT.
We still have a few free tickets for online/virtual participation!
Registration link here: moleculediscovery.github.io/workshop2024/
Tickets for in-person participation are "SOLD" OUT.
We still have a few free tickets for online/virtual participation!
Registration link here: moleculediscovery.github.io/workshop2024/
ML for molecules and materials in the era of LLMs [ML4Molecules]
ELLIS workshop, HYBRID, December 6, 2024
moleculediscovery.github.io
December 3, 2024 at 12:35 PM
The Machine Learning for Molecules workshop 2024 will take place THIS FRIDAY, December 6.
Tickets for in-person participation are "SOLD" OUT.
We still have a few free tickets for online/virtual participation!
Registration link here: moleculediscovery.github.io/workshop2024/
Tickets for in-person participation are "SOLD" OUT.
We still have a few free tickets for online/virtual participation!
Registration link here: moleculediscovery.github.io/workshop2024/
Reposted by Ronnie de Jonge
Abstract Submission OPEN for #ICAR2025 International Conference on Arabidopsis Research!
Topics for Concurrent and Workshop sessions published!
📅 June 16-20 Ghent 🇧🇪
🕸️ icar2025.com
Topics for Concurrent and Workshop sessions published!
📅 June 16-20 Ghent 🇧🇪
🕸️ icar2025.com
Summary. - International Conference on Arabidopsis Research: ICAR2025
icar2025.com
December 1, 2024 at 7:39 PM
Abstract Submission OPEN for #ICAR2025 International Conference on Arabidopsis Research!
Topics for Concurrent and Workshop sessions published!
📅 June 16-20 Ghent 🇧🇪
🕸️ icar2025.com
Topics for Concurrent and Workshop sessions published!
📅 June 16-20 Ghent 🇧🇪
🕸️ icar2025.com
Reposted by Ronnie de Jonge
We're super proud of Doctor Sietske van Bentum! A more than outstanding defence of her thesis 'Disease-associated shifts in the rhizosphere microbiome: towards a soy-borne legacy'
November 27, 2024 at 10:38 AM
We're super proud of Doctor Sietske van Bentum! A more than outstanding defence of her thesis 'Disease-associated shifts in the rhizosphere microbiome: towards a soy-borne legacy'
I enjoyed Utrecht City Center yesterday evening. Those new lights really bring the Dom Tower to life 😍.
November 29, 2024 at 6:20 PM
I enjoyed Utrecht City Center yesterday evening. Those new lights really bring the Dom Tower to life 😍.
Reposted by Ronnie de Jonge
Yesterday, our dear colleague Saskia van Wees delivered her inaugural address, 'Plants are anything but defenceless creatures'. A fascinating exploration of plant resilience, hormones and innovation. 🌱 Read more: www.uu.nl/en/news/inau... #Science #uubeta #UtrechtUniversity #Plants
Inaugural lecture by Saskia van Wees: "Plants are anything but defenceless creatures"
Saskia van Wees investigates the intricacies of plant resistance and the role plant hormones play in these processes. Today, she delivers her inaugural lecture.
www.uu.nl
November 29, 2024 at 6:09 PM
Yesterday, our dear colleague Saskia van Wees delivered her inaugural address, 'Plants are anything but defenceless creatures'. A fascinating exploration of plant resilience, hormones and innovation. 🌱 Read more: www.uu.nl/en/news/inau... #Science #uubeta #UtrechtUniversity #Plants
Reposted by Ronnie de Jonge
2x professorships available in Manchester Institute of Biotechnology including in Microbial Engineering area (broadly defined to include microbiomes, environmental biotech etc) — join us!
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Chair Appointments within Manchester Institute of Biotechnology:Manchester Institute of Biotechnology
www.jobs.manchester.ac.uk
November 29, 2024 at 10:01 AM
2x professorships available in Manchester Institute of Biotechnology including in Microbial Engineering area (broadly defined to include microbiomes, environmental biotech etc) — join us!
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Reposted by Ronnie de Jonge
