Justin J.J. van der Hooft
@jjjvanderhooft.bsky.social
Assistant Professor in Computational Metabolomics. Fascinated by the diverse chemistry of nature. Strives for Community-based solutions and Open Science.
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Next generation of 1001 Genomes Plus browser and data download
Please indicate all features you would like to see in a browser that displays features of completely sequenced Arabidopsis thaliana genomes
docs.google.com
November 24, 2025 at 6:46 PM
Do you also wonder what happened here? 😎 Enjoy your weekend!
Seen today in the Forum building at #Wageningen #campus @w-u-r.bsky.social
Seen today in the Forum building at #Wageningen #campus @w-u-r.bsky.social
November 14, 2025 at 2:58 PM
Do you also wonder what happened here? 😎 Enjoy your weekend!
Seen today in the Forum building at #Wageningen #campus @w-u-r.bsky.social
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
November 14, 2025 at 1:18 PM
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
November 12, 2025 at 12:28 PM
November 9, 2025 at 7:49 PM
🚨 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
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
November 1, 2025 at 7:14 PM
🚨 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
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
Reposted by Justin J.J. van der Hooft
From Mass to Class: Classification of Amphetamines MS/MS Spectra via Graph Neural Networks #JCIM pubs.acs.org/doi/10.1021/...
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...
pubs.acs.org
November 1, 2025 at 7:02 PM
From Mass to Class: Classification of Amphetamines MS/MS Spectra via Graph Neural Networks #JCIM pubs.acs.org/doi/10.1021/...
Reposted by Justin J.J. van der Hooft
Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky
November 1, 2025 at 4:59 PM
Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky
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
November 1, 2025 at 5:12 PM
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
Reposted by Justin J.J. van der Hooft
🎉 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...
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...
November 1, 2025 at 5:01 PM
🎉 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...
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...
Reposted by Justin J.J. van der Hooft
The W-index: a novel tool to evaluate gender equity in STEM research https://www.biorxiv.org/content/10.1101/2025.10.29.685415v1
November 1, 2025 at 5:03 PM
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
#metabolomics #microbiome #CompMetabolomics
October 31, 2025 at 9:05 AM
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
#metabolomics #microbiome #CompMetabolomics
Reposted by Justin J.J. van der Hooft
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
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
October 30, 2025 at 9:28 AM
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
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
#microbiology #fungi #UTIr #metabolomics #CompMetabolomics
October 30, 2025 at 3:37 PM
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
#microbiology #fungi #UTIr #metabolomics #CompMetabolomics
October 30, 2025 at 3:29 PM
🚨 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
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
🌱plantiSMASH 2.0💥 is now live!
I’m very excited to share that the 2.0 version of plantiSMASH is now available online and as a preprint on bioRxiv 📄https://lnkd.in/dN4F56pf
🌱 What’s new in plantiSMASH 2.0? ⬇️
I’m very excited to share that the 2.0 version of plantiSMASH is now available online and as a preprint on bioRxiv 📄https://lnkd.in/dN4F56pf
🌱 What’s new in plantiSMASH 2.0? ⬇️
plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters https://www.biorxiv.org/content/10.1101/2025.10.28.683968v1
October 30, 2025 at 3:26 PM
🚨 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
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
Reposted by Justin J.J. van der Hooft
"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/...
www.nrc.nl/nieuws/2025/...
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.
www.nrc.nl
October 24, 2025 at 6:35 AM
"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/...
www.nrc.nl/nieuws/2025/...
Reposted by Justin J.J. van der Hooft
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...
Fixing Persistence Issues with Git Inside Docker Containers
TL;DR: Cloned Git directories inside Docker containers can persist across builds or runs, causing branching and committing issues. Explicitly removing the directory before cloning prevents these error...
mmzdouc.github.io
October 21, 2025 at 1:51 PM
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...
Reposted by Justin J.J. van der Hooft
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...
Modern Python Project GitHub Template
TL;DR: I created a freely available template to facilitate setting up “modern” Python projects.
mmzdouc.github.io
October 22, 2025 at 2:06 PM
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...
Reposted by Justin J.J. van der Hooft
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
MITE training session registration form
Registration form for mailing list
forms.gle
October 24, 2025 at 1:37 PM
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
Reposted by Justin J.J. van der Hooft
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/🧵
October 23, 2025 at 1:08 PM
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/🧵
#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...
#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...
#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...
www.linkedin.com
October 19, 2025 at 7:06 PM
#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...
#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...
October 18, 2025 at 1:05 PM