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Ronnie de Jonge

@dejongepmi.bsky.social
1.4K followers 687 following 10 posts

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.

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Reposted by Ronnie de Jonge
Zamin Iqbal @zaminiqbal.bsky.social · 10/09/2025
#microsky
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Ronnie de Jonge @dejongepmi.bsky.social · 06/06/2025
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...
uu.nl
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!
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Daniel Tamarit @danieltamarit.bsky.social · 14/05/2025
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
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 15/05/2025
Transposon activity eliminates a crucial fungal secondary metabolite cluster while preserving pathogenicity www.biorxiv.org/content/10.1101/202…
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Ronnie de Jonge @dejongepmi.bsky.social · 15/05/2025
🌱 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
uu.nl
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!
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Guillaume Méric @gmeric.bsky.social · 01/03/2025
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...
sciencedirect.com
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 …
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Plant-Microbe Interactions @utrechtpmi.bsky.social · 12/02/2025
Great talk by Heribert Hert on microbiomes in relation to drought resistance, regreening strategies and the orphan crop Fonio microbiomejournal.biomedcentral.com/articles/10....
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Xavier Picó @xavierpico.bsky.social · 24/01/2025
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
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Ronnie de Jonge @dejongepmi.bsky.social · 08/01/2025
@rlberendsen.bsky.social kicks off a day of science starting with @jurriaanton.bsky.social on immune memory in plants.
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Roeland Berendsen @rlberendsen.bsky.social · 28/12/2024
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
nature.com
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.
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Gitta Coaker @gittacoaker.bsky.social · 17/12/2024
Rhizobacteria cleaves flg22 through a type II secreted subtilase and suppresses plant immunity. #plantmicrobe #plantimmunity www.cell.com/cell-reports...
cell.com
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.
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Kaisa Kajala @kaisakajala.bsky.social · 16/12/2024
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...
nwo.nl
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 ...
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Austin Wang @austintwang.bsky.social · 11/12/2024
(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
arxiv.org
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...
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PlantEcoHutton @plantecohutton.bsky.social · 09/12/2024
❗️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
rhizo6.org
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 ...
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Corné Pieterse @cornepieterse.bsky.social · 05/12/2024
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...
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Bas E. Dutilh @bedutilh.bsky.social · 04/12/2024
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...
uu.nl
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!
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Matt Rockman @wormsrock.bsky.social · 30/09/2024
🚨 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
Looking north at the Washington Square Arch, with 1 Fifth avenue behind it and a fountain in front of it. NYU Biology is a block to the right from this scene, on Washington Square East.
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Aaron Vogan @fungage-lab.bsky.social · 03/12/2024
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...
Concept of a Starship transposon jumping out of a fungal culture. Illustration by Oen Gregory.
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Günter Klambauer @gklambauer.bsky.social · 03/12/2024
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/
moleculediscovery.github.io
ML for molecules and materials in the era of LLMs [ML4Molecules]
ELLIS workshop, HYBRID, December 6, 2024
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Bert De Rybel @bertderybel.bsky.social · 01/12/2024
Abstract Submission OPEN for #ICAR2025 International Conference on Arabidopsis Research! Topics for Concurrent and Workshop sessions published! 📅 June 16-20 Ghent 🇧🇪 🕸️ icar2025.com
icar2025.com
Summary. - International Conference on Arabidopsis Research: ICAR2025
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Plant-Microbe Interactions @utrechtpmi.bsky.social · 27/11/2024
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'
Sietske van Bentum PhD defence
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Ronnie de Jonge @dejongepmi.bsky.social · 29/11/2024
I enjoyed Utrecht City Center yesterday evening. Those new lights really bring the Dom Tower to life 😍.
Dom Tower Utrecht.
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Plant-Microbe Interactions @utrechtpmi.bsky.social · 29/11/2024
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
uu.nl
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.
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Michael Brockhurst @brockhurstlab.bsky.social · 29/11/2024
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...
jobs.manchester.ac.uk
Chair Appointments within Manchester Institute of Biotechnology:Manchester Institute of Biotechnology
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Yves Van de Peer @yvdp.bsky.social · 24/11/2024
www.biorxiv.org/content/10.1...
biorxiv.org
The Rise of Polyploids During Environmental Catastrophes
Polyploidy, or whole-genome duplication (WGD), both a strong evolutionary and ecological force and a potential pitfall, occurs extensively across the tree of life, particularly in angiosperms. While p...
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Daniel Tamarit @danieltamarit.bsky.social · 25/11/2024
Large crowds mobilising today to protest (we could not even fit in 3 different trains) in The Hague. The Dutch government wants to cut 1 billion euros to science and education. This policy will damage the country profoundly. Stop the budget cuts. Protect the future. @woinactie.bsky.social
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Ronnie de Jonge @dejongepmi.bsky.social · 25/11/2024
Duizenden studenten en medewerkers protesteren in Den Haag tegen bezuinigingen - nos.nl/l/2545894
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Claes de Vreese @claesdevreese.bsky.social · 25/11/2024
Huge turnout at the anti budget cut demonstrations in the Hague. The cuts are shortsighted, disenfranchise students, stiffle innovation, hurt young scholars, create talent loss, undercut future growth. WHO really wants this? #DoeHetNiet Unhappy faces w @natalihelberger.bsky.social 🟥🟥🟥🟥🟥🟥🟥🟥🟥🟥
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thijsroovers.bsky.social @thijsroovers.bsky.social · 25/11/2024
Zo ziet een succesvolle actie er van bovenaf uit
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Tanja Slotte @tanjaslotte.bsky.social · 22/11/2024
Come be my colleague! Three tenure track positions open at Stockholm University. Great start-up packages & environment for evolution and biodiversity research!
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Ivan Radin @radinbio.bsky.social · 21/11/2024
My department, Plant and Microbial Biology at the University of Minnesota is looking for a new head and colleague in any area of Plant and/or Microbial Biology. Job ad: hr.myu.umn.edu/jobs/ext/365... So please spread the word to anyone who might be interested. Thank you 😁
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Vinay Shukla @vinayshukla.bsky.social · 21/11/2024
Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae www.nature.com/articles/s41... #plantscience
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Paul Carini @uncultured.carinilab.com · 20/11/2024
Let’s say you had several thousand bacterial genomes you’d like sequenced. How cheap can they be sequenced these days? What technology? Cost from DNA extraction onward.
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Jonathan Eisen @phylogenomics.bsky.social · 20/11/2024
Microbiome FacultyJob at UC Davis in the Department of Medical Microbiology and Immunology (one of the departments where I reside ...) See recruit.ucdavis.edu/JPF06847
recruit.ucdavis.edu
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Itai Yanai @itaiyanai.bsky.social · 20/11/2024
Out today in Nature: "The Human Cell Atlas"! In my News and Views, I compare the cell atlas to early naturalists creating an atlas of South America. Researchers mining this cell atlas can now make big discoveries, just as the next naturalists then discovered evolution. www.nature.com/articles/d41...
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Vaughn Cooper @vscooper.micropopbio.org · 19/11/2024
🚨Travel awards for Early Career Researchers to attend ASM Microbe🧫 1. Awarded through ASM Branches 2. $1650 per award, 3 per branch 3. Apps open now! 4. Named for Peggy Cotter, ASM past president & advocate 5. A proud accomplishment when I was COMS Chair 6. Apply / share! asm.org/Travel-Award...
asm.org
Peggy Cotter Travel Award
ASM is a nonprofit professional society that publishes scientific journals and advances microbiology through advocacy, global health and diversity in STEM programs.
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Tristan Caro @tacaro.bsky.social · 24/08/2024
Excited to share our new work in FEMSEC exploring single-cell SIP with Raman spectroscopy. This is a tool that I'm excited for more researchers/fields to apply! A quick thread: academic.oup.com/femsec/advan... with @rockymicrobe.bsky.social
academic.oup.com
Single-cell measurement of microbial growth rate with Raman microspectroscopy
Abstract. Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microb
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Leibniz IPK @leibnizipk.bsky.social · 15/11/2024
An international team led by IPK reports a #pangenome of #barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. Out now in Nature! #PlantScience 🗞️ www.ipk-gatersleben.de/pressemittei... 📃 www.nature.com/articles/s41...
nature.com
Structural variation in the pangenome of wild and domesticated barley - Nature
A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally complex loci ...
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Christoph Kaleta @kaletalab.bsky.social · 15/11/2024
1/3 🌍 We're hiring! The Medical Systems Biology Lab at Kiel University is looking for a passionate #PostDoc in #Metabolic #Microbiome #Modeling. Join us at one of Europe’s microbiome research hubs and push the boundaries of microbiome science! @kieluni @UKSH_KI_HL 🔗 jobs.uksh.de/job/Kiel-Pos...
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Stephen Turner @stephenturner.us · 14/11/2024
The Evo model made the cover of Science this month 🧬🖥️🧪 Perspective: Learning the language of DNA www.science.org/doi/10.1126/... Research paper: Sequence modeling and design from molecular to genome scale with Evo www.science.org/doi/10.1126/... Code (Apache) github.com/evo-design/e...
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Miriam @mirischreiber.bsky.social · 14/11/2024
The barley pangenome paper is finally out. 🎉 #genomics rdcu.be/d0ecz
rdcu.be
Structural variation in the pangenome of wild and domesticated barley
Nature - A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally...
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Plant-Microbe Interactions @utrechtpmi.bsky.social · 14/11/2024
Utrecht PMI is on Bluesky!
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Suguru Nishijima @suguru-nishijima.bsky.social · 14/11/2024
Pleased to announce that our latest paper is published in Cell! We developed a novel ML model that predicts fecal microbial load from relative species profiles, revealing it as a key factor shaping gut microbiome variation and disease-microbe associations www.sciencedirect.com/science/arti...
sciencedirect.com
Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative a…
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Corné Pieterse @cornepieterse.bsky.social · 13/11/2024
First steps on Bluesky.... Let's test how it works by re-sharing Klokhuis Dutch national kids TV broadcast on our Netherlands Plant Ecophenotyping Centre: hetklokhuis.nl/tv-uitzendin... #PlantScience
hetklokhuis.nl
Uitzending - Plantenlaboratorium
Om ervoor te zorgen dat iedereen op de aardbol genoeg te eten heeft zullen we heel slim met ons voedsel om moeten gaan. Tirsa gaat naar een hightech plantenlaboratorium in Utrecht. Daar wordt uitvoeri...
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 13/11/2024
The Salk Institute shared the sad news that Prof. Joanne Chory passed away yesterday due to complications from Parkinson’s disease. She was one of the most influential biologists of our time. And this is how I will remember Joanne, expertly guiding us on where to go. Joanne, we will miss you! ❤️
Two people on a punting boat
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Agathe Chaigne @agathechaigne.bsky.social · 14/11/2024
Science in the Netherlands. The new government is planning very strong cuts in the research and higher education budget. There was a national protest planned for today in Utrecht, which got cancelled yesterday by the organisers after advice from the mayor/police because of security threats. 1/3
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Angela Maas 🟥 @angelamaas.bsky.social · 14/11/2024
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Marc Somssich @somssich.bsky.social · 11/11/2024
There are even more here, btw: go.bsky.app/H3986W6
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Marc Somssich @somssich.bsky.social · 11/11/2024
Hello new Plant Scientists, 2 Things: 👉 To connect to 150 Plant Science Accounts and 3 relevent feeds, here's a #StarterPack for you: go.bsky.app/8Zfmwf7 👉 To get your #PlantScience posts into the Plant Science Research Feed (here: bsky.app/profile/did:...), always use the Hashtag #PlantScience
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 20/05/2024
Metabuli(분리), our metagenomic read classifier, is now published at Nature Methods. By combining DNA & AA information it recovers 99% and 98% assignments of DNA or AA classifiers. Great work by my student Jaebeom Kim. 📄 www.nature.com/articles/s41... 💾 github.com/steineggerla... Pdf: rdcu.be/dIrgm
nature.com
Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA - Nature Methods
Metabuli enhances metagenomic read classification by jointly analyzing DNA and amino acid sequences for specificity and sensitivity, respectively.
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