Justin J.J. van der Hooft

Buzzing times 😎 #colourful #biodiversity

Detection of functional clusters (FCs) specific to the phenylalanine (PAL) and p-coumaroyltyramine (THT) pathways. Top left: Network depicting the relationship between transcripts and mass signatures within the PAL FC. Bottom left: Network illustrating the interplay between transcripts and mass signatures within the THT FC. Top right: Heatmap illustrating the expression levels of all transcripts within the PAL and THT FCs. Upper middle right: Heatmap displaying the abundance of all mass signatures present in the PAL and THT FCs. Lower middle right: Correlation matrix highlighting the correlations among transcripts and mass signatures within the PAL FC. Bottom right: Correlation matrix displaying the relationships between transcripts and mass signatures within the THT FC, including Mutual rank and transformed edge weights.

Elucidating #plant #Biosynthetic pathways: @jjjvanderhooft.bsky.social @marnixmedema.bsky.social &co develop #MEANtools, an unsupervised computational workflow that integrates #MultiOmics data to predict #metabolic pathways by linking transcripts to metabolites @plosbiology.org 🧪 plos.io/4odL94g

Three-step biosynthesis of salicylic acid from benzoyl-CoA in plants - Nature The salicylic acid (SA) biosynthesis pathway—involving ligation of benzoyl coenzyme A and benzyl alcohol to give benzyl benzoate; hydroxylation of benzyl benzoate to give benzyl salicylate; and cleavage of benzyl salicylate to give SA—is highly conserved in plants.

Nature research paper: Three-step biosynthesis of salicylic acid from benzoyl-CoA in plants

go.nature.com/4m406UO

Evolution of antifungal resistance in the environment - Nature Microbiology This Review discusses the evolution, emergence and expansion of environmental fungicide and antifungal drug resistance.

A little holiday news:

Evolution of antifungal resistance in the environment www.nature.com/articles/s41...

This started out as a little thought way back in early 2024 between @normanvanrhijn.bsky.social and I, and turned into a full on review! We hope it proves useful to the community.

A timely study shows how bus service reductions harm seniors:

"People could not reach their usual range of destinations, travelled less often, and felt a sense of entrapment in their homes...People experienced a loss of freedom, independence, and control over their lives."

doi.org/10.1016/j.jt...

Dinosaurs passing by tonight 😎 #Wageningen

The Rare Plasmid Biosphere: A Hidden Reservoir of Genetic Diversity Bacterial communities typically display highly uneven abundance patterns, with a few dominant taxa and many low-abundance ones contributing to extensive genetic diversity (1-4). Notably, this rare bio...

The Rare Plasmid Biosphere: A Hidden Reservoir of Genetic Diversity
by João Rebelo, Célia Domingues & Francisco Dionisio and co
www.biorxiv.org/content/10.1...

#cloudart #Wageningen #nofilters 😎

A map where only borders of countries are shown correctly while ignoring shape and size. This means that countries with many neighbours are shown to be rather big, irrespectinve there actual size

Country topology 😊

Investigation of an endophytic Streptomyces sp. from the liverwort Bazzania trilobata: A new source for abyssomicins Liverworts are the most ancient group of land plants and share intimate symbioses with microorganisms, yet their endophytes have remained unexplored a…

#secmet

Looking from above.... 😎 #Wageningen

Working with a #view #Prague 😎

Glad you had a good time! 😎

hanging out with strangers in a campus pub should be considered part of the serious process of thinking

As mentioned in my talk yesterday at #MetSoc2025,@schymane@mstdn.social and myself offered a bottle of wine to the winners of #CASMI 2016 contest.
Pleased to confirm eventual delivery of a fine Czech Merlot to www.linkedin.com/in/tobias-ki... for winningCategory 3: Full Information.

Thanks to Tomáš Pluskal for showing Elena Del Pup and myself, together with Kyo Bin Kang and his team around the IOCB Prague - Institute of Organic Chemistry and Biochemistry of the Czech Academy of… ... Thanks to Tomáš Pluskal for showing Elena Del Pup and myself, together with Kyo Bin Kang and his team around the IOCB Prague - Institute of Organic Chemistry and Biochemistry of the Czech Academy of S...

Thanks @pluskal-lab.org! 😎

www.linkedin.com/posts/jjjvan...

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome...

So cool, a novel archaeon with a super small genome and no metabolic genes!
"An unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses."
www.biorxiv.org/content/10.1...

Many congrats 👏🎉 🙌 to @elenadelpup.bsky.social for winning the best student oral talk #MetSoc2025 prize @emn-metsoc.bsky.social @metsoc.bsky.social in #Prague!
Elena highlighted #CompMetabolomics & #transcriptomics strategies for ☘️ NP discovery. #ProudPI
@marnixmedema.bsky.social & Eric Schranz!

#metabolomics #CompMetabolomics #Visualization #data #organization #annotation #prioritization

Effective data visualization strategies in untargeted metabolomics Covering: 2014 to 2023 for metabolomics, 2002 to 2023 for information visualization LC-MS/MS-based untargeted metabolomics is a rapidly developing research field spawning increasing numbers of…

🔓Read in our MS Metabolomics themed collection, a #OpenAccess review from Kevin Mildau, Henry Ehlers, @jjjvanderhooft.bsky.social et al. at @w-u-r.bsky.social‬ @tuwien.at‬ covering effective data visualization strategies in untargeted metabolomics #natprod

Find it here🔽

Zhixu Ni presenting LipidCXSMILES developed together with @egonw.mastodon.social.ap.brid.gy and #epilipidnet and #lipidmaps here at #MetSoc2025 bridging real lipid chemical structures, and the uncertainty because MS gives only so much structural hints.

@jorainer.bsky.social and @philouail.bsky.social gave a great overview of the ecosystem around #RforMassSpectrometry and #XCMS!

#MetSoc25
I am super glad they now also provide options to combine with #Python and #matchms (thanks🙏)

Scientific Community Building through Workshops: the NPLinker eScience experience A blog post by Wageningen University & Research Assistant Professor Justin van der Hooft

In this blog post, @jjjvanderhooft.bsky.social reflects on the challenges and lessons learned from organizing a computational omics workshop in @w-u-r.bsky.social

It was a great talk - well done all of you and especially @philouail.bsky.social 🙌👏😎

Philippine @philouail.bsky.social presenting #xcms , summary of 20 years development and recent extensions at the #MetSoc2025 conference!

#ProudPI 😎 #rstats @bioconductor.bsky.social #metabolomics #MassSpectrometry

And you can still join this great bunch if you are a member of the MetSoc!

The @emn-metsoc.bsky.social of the @metsoc.bsky.social rocks! Great to see how this initiative has developed into an essential part of the #metabolomics society and community! #MetSoc25 (and thanks for letting me be an "elderly career member" 😜)

Proud of @elenadelpup.bsky.social who presented her work on #plant paired omics mining for biosynthesis pathway discovery! 😎👏 She presented #plantiSMASH and a MEANtools case study combining #transcriptomics & #metabolomics data.
Work with @marnixmedema.bsky.social
#CompMetabolomics #MetSoc25 #Prague

#metabolomics #aroundtheglobe #community #teamwork 😎 together in #Prague #MetSoc25

Proud of Niek de Jonge who did a fantastic job in presenting his work on cross-ion mode spectral similarity scoring! 😎 👏
Work with Florian Huber @me-datapoint.bsky.social

#metabolomics #CompMetabolomics #MetSoc25 #MS2DeepScore