Glad to see the interest of so many communities working across different crops & pangenomes. If your genome-of-interest is not in our database, run plantiSMASH on webserver or CLI (see documentation ). You can upload your results on the #plantiSMASH Zenodo community here: zenodo.org/communities/...
🚨 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
Awesome! Good luck with your analysis
#FAIRData #bioinformatics #naturalproducts #plantmetabolism #computationalbiology #genomics #plantiSMASH #OpenScience #biorxiv #antiSMASH
#plantscience #specializedmetabolism #biosyntheticgeneclusters #transcriptionfactors #webserver #compbio @antismash.bsky.social
📖 Comprehensive documentation, for web server and CLI users and developers, and Zenodo-linked, versioned releases. 📘 Docs: lnkd.in/dc6YBpgU
Thank you to all plantiSMASH 2.0 coauthors! @marnixmedema.bsky.social @jjjvanderhooft.bsky.social @anneosbourn.bsky.social et al.
plantiSMASH 2.0 features:
🧬 Expanded detection rules for new BGC types
🔍 Substrate prediction and Regulatory analysis to prioritize BGCs
📚 Updated plantiSMASH 2.0 database covering 30k+ putative BGCs across 430 plant genomes ➡️ lnkd.in/dNQ54KFK
💡 plantiSMASH is a computational tool and web server for the identification of biosynthetic gene clusters (BGCs) in plant genomes.
🖥️ Webserver: lnkd.in/dh5Ckrp3
🐙 GitHub: lnkd.in/diMHJGCD
🎓 Zenodo plantiSMASH community: lnkd.in/dQs4j_vc
🌱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? ⬇️
Hi @chenxinli2.bsky.social ! We were undergoing development of the new plantiSMASH 2.0 codebase. Is the issue persisting? Please contact us or submit an issue on GitHub if that's the case :) Thanks for spotting this!
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
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
Kicking off with the teaching for the #machinelearning course at @w-u-r.bsky.social ! My colleague #BenNordijk had the idea of drawing us on the whiteboard so that students won't confuse us.
Thank you to my supervisors @jjjvanderhooft.bsky.social and @marnixmedema.bsky.social for supporting this and other opportunities throughout my PhD!
#FAIRDataFund #FAIRdata #knowledgegraphs #plantsciences #naturalproducts
Or also our review on Effective Visualisation Strategies, section 4.4 on multi-omics data integration and the use of knowledge graphs: pubs.rsc.org/en/content/a...
Check out our opinion paper with Felicia Wolters for more insights on how we are planning to attain this! lnkd.in/dFPfmUTN (source of the Fig. 2 below)
If any of these opportunities sounds interesting to you, please DM me here!
More about the FAIR data fund: community.data.4tu.nl/the-fair-dat...
The grant will support two small projects with student assistants and organising a Mini-Symposium on knowledge graphs for natural product discovery 💡 “Powering a Unified Knowledge Base for Plant Natural Product Discovery” 💡
➡️ In a 🌰nutshell🐚:
I will connect 🌿 plant 🌿 multi-omics data via knowledge graphs to generate useful visualisations and predictions for discovering useful plant chemistry 🧪🧪!
The computational strategies, standards, and tools developed will support a continuous communal effort to explore plant metabolic diversity and discover natural products.
In my project, I will build a linked knowledge base and a flexible and standardized analysis workflow to integrate paired omics data for plant pathway and metabolite prioritization.
The #4TUResearchData FAIR Data Fund offers researchers an opportunity to apply for financial aid to cover the costs of making their datasets FAIR: Findable, Accessible, Interoperable and Reusable (the FAIR principles: lnkd.in/dCuf5QzJ).
I am glad to announce that I am one of the 8 winners of the 4th Edition of the #FAIR Data Fund!
#4TU.ResearchData is an international data repository for science, engineering and design. They offer research dataset curation, sharing, long-term access and preservation services.
📢 Symposium: Bioinformatics in Food Science. Registrations are now open! Please repost to spread the word.
📅 The symposium is free of charge and will take place at February 24, 2025, at Omnia Auditorium, Wageningen Campus.
💻 Exciting speakers lined up - visit the link for details! lnkd.in/dkzfurdY
