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.
#Teamwork #ProudPI in #CompMetabolomics 😎 Doing untargeted mass spectrometry-based #metabolomics? Want to boost your chances in correctly matching your mass spectra to library spectra? Give our new #SpecReBoot resampling strategy a try! 🙂 www.linkedin.com/posts/jjjvan...
SpecReBoot Library Matching Preprint | Justin J.J. van der Hooft
🚨 New Preprint Alert 🚨 Congratulations 👏 🎉 to the CompMet team for presenting this preprint on boosting library matching for untargeted mass spectrometry-based metabolomics workflows 🙌 Metabolite a...
linkedin.com
Artistic views in #Arnhem 😎 - you can find them in Park Sonsbeek near the central station, but the actual art is only there until October....
A small reminder this morning that Nature always finds its ways.... 😎
Fwd: "Ten simple rules for scholarly blogging" https://doi.org/10.54900/xn57k-gyw73 "Similar to preprints, blogs enable researchers to communicate ideas, preliminary findings, and emerging debates without waiting for lengthy peer-review processes. At the same time, blogs provide more space than […]
Original post on mastodon.social
mastodon.social
Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies
antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00
biorxiv.org
Great to see the antiSMASH family grow!
Nadine Ziemert@nadineziemert.bsky.social · last wk.Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️
No living ones this time around, but I saw many flowers in Rotterdam this weekend 😎 #Kunsthal #Rotterdam
Artistic views during the @w-u-r.bsky.social #Bioinformatics Group #retreat near Putten a few days ago 😎
Historical places in the Netherlands: today in #Zutphen 😎 One of the places that has been inhabitated for centuries and that was attacked by the Vikings near the end of the 9th century 😯 The city was build on river dunes - and you can still see this elevation! #Dutchcities
www.linkedin.com/posts/jjjvan...
Characterizing the effect of short wavelengths on the floral flavonoid metabolome of medicinal cannabis using a comparative computational metabolomics workflow - Metabolomics | Justin J.J. van der Hoo...
Many congratulations 👏 🎉 to Laura Rosina Torres Ortega & Willy Contreras-Avilés, PhD for publishing this shared collaborative work on the application of computational Metabolomics workflows to assess ...
linkedin.com
I can clearly see where the "bloemkoolwolk" name comes from for the cumulus cloud....😎
Today at #MetSoc2026 I gave a keynote presentation on self-evolving, multi-agent AI for metabolomics — from @holobiomicslab.bsky.social. The headline outcome: we're releasing the first ASB Skill Collection — open, evidence-grounded metabolomics building blocks for any scientific AI agents. 🧵👇
Take a look at some of the speakers joining us at the #SBNP meeting this November! There’s still time to secure your space at the meeting. Register before the final deadline: 10th September 2026 Explore the full programme and find out more: bit.ly/4oDSSJy
Norway is banning generative AI for schoolchildren under 13 starting in September.
Norway says math, reading, and writing come first as it introduces AI restrictions for under-13s
Norway is taking steps to limit how generative AI can be used in schools from the start of the next school year.
techradar.com