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Daniel Tamarit @danieltamarit.bsky.social · 1d

Yesterday the @biosb.bsky.social and Netherlands Integrative Microbial Ecology initiative organised a symposium on #MicrobialEcology. We hosted 80+ researchers, with 10 talks and 10 posters at @utrechtuniversity.bsky.social. A beautiful chance to hear more about exciting research across the country!

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Jolien van Hooff @jvhooff.bsky.social · 5h

Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!

Tegenlicht @vprotegenlicht.bsky.social · 6h

Hoe is al het complexe leven op aarde eigenlijk ontstaan?

Wat DNA uit slootwater ons vertelt over jouw onbekende voorouders | VPRO Tegenlicht

YouTube video by VPRO Tegenlicht

youtu.be

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Sep 3

Using this methodology, they recovered both known and many novel QTLs for color and height, opening up new breeding targets.

This study represents a blueprint for high-throughput genetics studies, with the entire methodology as well as all the raw data fully and conveniently available.

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Sep 3

They used an innovative GWAS approach involving the construction of many traits as ratios of the imaging data and quantifying these traits using various summary statistics. They then optimized the GWAS for computational efficiency to facilitate mapping this large number of traits.

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Sep 3

Check out the latest paper by the Snoek lab in @theplantjournal.bsky.social, a genetics study involving a large field trial with 200 lettuce genotypes phenotyped by a drone.

Great work by Rens Dijkhuizen, Bram van Eijnatten, Sarah Mehrem, @guidopmi.bsky.social & others!
doi.org/10.1111/tpj....

From aerial drone to quantitative trait locus: leveraging next‐generation phenotyping to reveal the genetics of color and height in field‐grown Lactuca sativa

Understanding the genetic basis of lettuce color is important because these traits correlate with metabolites such as anthocyanins, which are known to have strong antioxidant properties. Furthermore,....

doi.org

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Josje Romeijn @jromeijn.bsky.social · Jun 20

The first paper of my PhD is now available as a preprint! 🎉

Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.

www.biorxiv.org

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Team Thomma @teamthomma.bsky.social · Jul 24

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution

Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

rdcu.be

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Monica L Garcia Gomez @moneralee.bsky.social · Jul 25

It's alive!! 🌱 Check out our combination of experimental approaches and computational modeling, showing how growth conflicts among neighboring cell files underlie the orientation of cell divisions in root regeneration. Such a rewarding experience to be part of this collaboration!

Kalika Prasad @kalikaprasad.bsky.social · Jul 25

Our new paper is out!
1/14 How does an organ rebuild its shape after injury? It's not just about making new cells, but aligning them in the right direction — like bricks shaping a structure. We show that it's all driven by Cell Geometry!

www.cell.com/current-biol...

Wound repair in plants guided by cell geometry

Mathew et al. show that growth conflicts reshape cells after injury, forming rhomboidal geometries that trigger diagonal divisions. This reorients cell files to restore tapered morphology. A two-step ...

www.cell.com

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Stephan Köstlbacher @stephkoe.bsky.social · Jul 20

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🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing

Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

www.biorxiv.org

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Daniel Tamarit @danieltamarit.bsky.social · Jul 28

Late due to vacation, but
📢 New preprint out, presenting a new approach to reduce compositional heterogeneity in alignments. A passion project led by the amazing @stephkoe.bsky.social

👀 Check out this great explanation thread below 👇

Stephan Köstlbacher @stephkoe.bsky.social · Jul 20

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🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing

Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

www.biorxiv.org

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Jun 17

🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨

www.uu.nl/en/organisat...

PhD Position in Multiscale Mechanistic Modelling of Animal Development

How do protein interactions at the subcellular scale regulate the morphology of an entire organ? Join us to explore this question with computer models!

www.uu.nl

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Jun 12

Paulien Hogeweg was Rob's supervisor during his MSc and PhD. She kicks off the meeting by reminiscing about Rob's beginnings:

"First students are special, especially those who become a lifelong colleague, successor, and now, fellow emeritus"

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Jun 12

Today we celebrate over 40 years of research of Rob de Boer, chair Professor of Theoretical Biology.

Rob complemented his tremendous scientific career with a deep impact in multiple roles, as a dedicated teacher, an inspiring mentor, and a kind and generous colleague. Thank you, Rob!

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Monica L Garcia Gomez @moneralee.bsky.social · May 12

PhD Position in Modelling Regulation of Plant Stress Responses across Species!! 🌱🌽🌾🥬🌡️🌡️

Apply before June 16 to join this exciting project with Kirsten ten Tusscher in the context of CropXR!! www.uu.nl/en/organisat...

PhD Position in Modelling Regulation of Plant Stress Responses across Species

Join us to model plant stress responses and help breed climate-resilient crops in a collaborative, interdisciplinary research environment!

www.uu.nl

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Bas E. Dutilh @bedutilh.bsky.social · May 15

Faster && more accurate virus sequence clustering with Vclust! Thanks to Andrzej, Sebastian, et al. for the great collaboration. The author list also includes @prozwalak.bsky.social from the VEO Group.

Sebastian Deorowicz @sdeorowicz.bsky.social · May 15

Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published:
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social

Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods

Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

www.nature.com

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Universität Jena @uni-jena.de · May 21

Researchers led by @bedutilh.bsky.social at the Cluster of Excellence @microverse.bsky.social investigate #phages, showing how viruses not only cause harm but also create the basis for diversity & balance. Read more in the #UniJena research magazine.

➡️ www.lichtgedanken.uni-jena.de/en/3157/smal...

Angela Muraya (centre) examines her plants with Natia Geliashvili (left) and Bas E. Dutilh (right).

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Michael Seidl @mfseidl.bsky.social · May 21

Are you interested in molecular plant microbe interactions and would like to study effector biology in Fusarium-lettuce patho-system? Consider this PhD position @uva.nl in the lab of Martijn Rep as part of our recently funded joint TKI project werkenbij.uva.nl/en/vacancies...

Vacancy — PhD Candidate Plant-pathogenic Fungus Interaction

Are you an early-career researcher with a passion for molecular plant or microbial science? Would you like to take on a highly relevant project in the field of plant-pathogen interactions? Then we hav...

werkenbij.uva.nl

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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · May 15

New paper by Arpit Swain, José Borghans and Rob de Boer, now in @plos.org Computational Biology. Using mathematical modeling, they show that estimating cell lifespans from deuterium labelling requires considering turnover rates of precursor cells.

Find it here:
journals.plos.org/ploscompbiol...

How are estimated cellular turnover rates influenced by the dynamics of a source population?

Author summary The expected lifespan of different types of cells is a fundamental biological quantity that is essential to know in order to advance translational medicine, for example, to improve immu...

journals.plos.org

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Gerben de Zwaan @gerbenz.bsky.social · May 15

Great Mentor, Exciting project, Fun city. What more could you wish for!?

Daniel Tamarit @danieltamarit.bsky.social · May 14

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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Ronnie de Jonge @dejongepmi.bsky.social · May 15

🌱 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

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Michael Seidl @mfseidl.bsky.social · May 14

Interested in microbial genome evolution? Consider applying for this exciting PhD project with a great mentor @danieltamarit.bsky.social embedded in a vibrant community @binfutrecht.bsky.social @utrechtuniversity.bsky.social

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Daniel Tamarit @danieltamarit.bsky.social · May 14

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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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · May 12

PhD position available at @binfutrecht.bsky.social. Join us if you are interested in modelling how plants respond to stress!

www.uu.nl/en/organisat...

PhD Position in Modelling Regulation of Plant Stress Responses across Species

Join us to model plant stress responses and help breed climate-resilient crops in a collaborative, interdisciplinary research environment!

www.uu.nl

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Michael Seidl @mfseidl.bsky.social · May 9

Come and join to work with @bramvandijk.bsky.social and others! Exciting PhD project between @rug.nl and @utrechtuniversity.bsky.social @binfutrecht.bsky.social with inspiring supervisors

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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · May 9

🧩 PhD Position – Origins of Darwinian Inheritance 🧩

This joint PhD project between the @rug.nl (Rampal Etienne & Martijn Egas) and @utrechtuniversity.bsky.social (Bram van Dijk) explores how simple prebiotic systems could evolve reliable information transfer.

Apply here: shorturl.at/WgYMF

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