Justin J.J. van der Hooft

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0 Abstract. Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable compara

Have you ever used a #bioinformatics #database and were frustrated by its lack of coverage? Did you ever think about starting your own resource? We just published a new strategy for community-driven #biocuration, based on our experiences with the #MIBiG database (1/8)! doi.org/10.1093/bib/...

Using cross-species co-expression to predict metabolic interactions in microbiomes | mSystems An improved mechanistic understanding of microbial interactions can guide targeted interventions or inform the rational design of microbial communities to optimize them for applications such as pathog...

Using cross-species co-expression to predict metabolic interactions in microbiomes

#mSystems by Robert Koetsier et al from @marnixmedema.bsky.social and @jjjvanderhooft.bsky.social

with @wildtypemc.bsky.social, Jo Handelsman, Clara Belzer, Yijun Zhu ...

journals.asm.org/doi/10.1128/...

#ProudPI - see also: www.linkedin.com/posts/jjjvan...

Good morning from #Wageningen 😎

Historical Dutch Site with modern art in (kasteel) #Ruurlo 😎

Do you also wonder what happened here? 😎 Enjoy your weekend!

Seen today in the Forum building at #Wageningen #campus @w-u-r.bsky.social

Great bonus lecture for Data Analysis & Visualization on graph and network visualization including many different examples of displaying and conveying information from graphs by our own @skepteis.bsky.social! It combined the Swiss train network with a molecule 😎 @w-u-r.bsky.social #teaching #course

#Wageningen 😎 @w-u-r.bsky.social

Natural stadia from green to colour 😎 - this weekend in #Amersfoort #autumn #colours #flowers

#Amersfoort today 😎

Good morning from #Wageningen 😎

🚨 New Resource & Preprint Alert 🚨

This resource collected by the mFam consortiun led by Gerd Balcke and Steffen Neumann contributes >7000 mass spectra of 2,126 unique metabolites to the public domain through MassBank.
Preprint: lnkd.in/eYcJMqYn
Interactive plot: lnkd.in/egBaTTNH

#CompMetabolomics

From Mass to Class: Classification of Amphetamines MS/MS Spectra via Graph Neural Networks Identifying emerging novel psychoactive substances (NPS), using liquid chromatography high-resolution tandem mass spectrometry (LC-HR-MS/MS), is often hindered by their frequent absence from mass spec...

From Mass to Class: Classification of Amphetamines MS/MS Spectra via Graph Neural Networks #JCIM pubs.acs.org/doi/10.1021/...

A cartoon/ digital drawing summarising the findings of the paper "Defensive fungal symbiosis on insect hindlegs" by T. Nishino et al published in 2025. On the top left, a female Megymenum gracilicorne bug shows off symbiotic organs on the hind legs where she carries Ascomycota fungi. These were previously assumed to be Tympanal organs in these bugs but only females had them?; that didnt make a whole lot of sense to the authors...To the right of the bug is a row of eggs lying side by side. The paper shows that the bugs deposit the symbiotic fungi on the egg surface after egg-laying. Next on the image, fungal conidia grow on the egg surface. The eggs are pinkish in colour. A few fungi wear sunglasses like they are body guards. The paper shows that they protect the eggs from Trissolcus brevinotaulus, a parasitoid wasp, that likes to lay its eggs inside the developing bug's eggs. There are two wasps in this cartoon "eyeing" the fungi and looking frustrated. Eggs turn from whitish to pinkish within 10-days because they are reflecting the body colour of the nymph within the eggs.

Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky

Nature is so creative, diverse, and colorful! 🍄 🍄‍🟫 🪵 All observed today during a walk in the Bennekom forest near #Wageningen with several colleagues including fungi enthousiasts 😎 (despite the autumn weather!) @w-u-r.bsky.social

🎉 A flyer for the 2026 workshop on #phylogenomics and #genome evolution

We have #instructors and #organizers from top-tier universities around the globe who will share their experiences in a two-week intensive course.

Register here while there are still seats available! evomics.org/apply-worksh...

The W-index: a novel tool to evaluate gender equity in STEM research https://www.biorxiv.org/content/10.1101/2025.10.29.685415v1

Great contribution by @w-u-r.bsky.social colleague Josep Rubert during the Metabolomics & Microbiome symposium at @dsmfirmpostnl.bsky.social this Wednesday! The interaction between host, microbes, and nutrition is fascinating!

#metabolomics #microbiome #CompMetabolomics

Available to read now via Open Access:
pubs.rsc.org/en/content/a...
Fast, general-purpose metabolome analysis by mixed-mode liquid chromatography–mass spectrometry
Nicola Zamboni et al @nzamboni.bsky.social @alaaothman.bsky.social @ethz.ch
#MassSpec

Great experience for our team members attending and presenting their projects during the Metabolomics & Microbiome 2025 meeting at @dsmfirmpostnl.bsky.social in Delft, NL! 👏 😎 #ProudPI
#microbiology #fungi #UTIr #metabolomics #CompMetabolomics

Autumn 🍂 at @w-u-r.bsky.social Wageningen University & Research #campus #Wageningen 😎

🚨 New Preprint Alert 🚨

Proud of @elenadelpup.bsky.social for posting her preprint on plantiSMASH 2.0 👏 Find out all about it and links to give it a try in her thread 👇

#genomemining #plants #geneclusters #naturalproducts #discovery
#ProudPI
@w-u-r.bsky.social

Opinie | AI zou een politieke topprioriteit moeten zijn Digitalisering en AI veranderen de samenleving ingrijpend. Nederland heeft dringend een strategisch AI-beleid nodig voor autonomie en veiligheid.

"Waar blijft het Ministerie voor Digitale Zaken om de regie over tech in de samenleving terug te pakken?" vragen @marleenstikker.bsky.social en ik in NRC. #AI raakt zo ongeveer alle facetten van de samenleving. Uitermate slecht idee dus om het aan Big Tech over te laten.

www.nrc.nl/nieuws/2025/...

Are you building applications using docker? In my recent blog post, I am investigating git's curious behavior when used as a subprocess inside a containerized Flask application. You can read more here: mmzdouc.github.io/posts/2025/1...

Interested in Python programming and good software engineering practices? Check out my newest blog post where I introduce a "modern Python" GitHub repository template and talk about my motivation for its creation! mmzdouc.github.io/posts/2025/1...

MITE training session registration form Registration form for mailing list

Working on tailoring enzymes and want to learn more about the MITE database? We are organizing a hands-on training session on how use the DB and create new entries: October 30th and November 4th 10-11 am Amsterdam time. Sign up here: forms.gle/KHPqe9XV1RRg... See you there! #secmet #natprod

We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵

#naturalproducts #cheminformatics #biosynthesis #machinelearning #molecularrepresentation #research #biosynformatics #biosynfoni | Lucina-May Nollen Through what lens should our models view molecules? In cheminformatics, we mostly train our tools using molecular descriptors developed for property and bioactivity prediction. But within Natural Pro...

#Biosynfoni #molecular #fingerprint
#naturalproducts #discovery

Congrats 👏 🙌 🎉 to Lucina-May Nollen for publishing her MSc Thesis in the Journal of Cheminformatics! 😎

Find out more about our fingerprint in the link here below 👇, and consider using it!

www.linkedin.com/posts/lucina...