!POSTPONED TO A LATER DATE  T.B.D. DUE TO CIRCUMSTANCES!

Time: 14:00–17:00 + borrel afterwards
Location: Room B9211, Aurora, Wageningen Campus
Instructors: David Meijer · Barbara Terlouw · Esteban Charria Girón (Bioinformatics Group, Wageningen University & Research)
Audience: Wageningen University & Research / Affiliated institutes (max. 50 participants)
Registration: closed
Contact: Esteban Charria Girón (esteban.charriagiron@wur.nl)

Learning goals

By the end of the workshop, participants will:

• Recognize the core logic of assembly-line biosynthesis for polyketide, nonribosomal peptide, RiPP, terpene, and hybrids.
• Interpret basic biosynthetic gene cluster (BGC) architectures and infer likely building blocks and tailoring steps.
• Formulate simple experimental set ups to test biosynthetic hypotheses.
• Identify bioinformatics tools for natural products discovery available at BIF (e.g. genome mining, biosynthesis-informed fingerprints, knowledge graphs).

Program (14:00–17:00)

14:00–14:10 – Welcome & framing: “From genes to molecules to data”: Short welcome, practical information, and introductions of the three instructors. Brief audience poll (wet-lab vs computational vs both), workshop expectations, and an overview of the storyline: from biosynthetic gene clusters to molecules, data & AI, and back.

14:10–14:30 – Lightning pitches: Selected lightning talks from participants (5 talks x 4 min each). Each pitch briefly answers:

1. What are you working on?
2. How does natural products biosynthesis play a role in your work?
3. One concrete question or challenge you have (one slide).

14:30–15:30 – Three perspectives, one pipeline

1) Chemical logic of biosynthesis: Going over the building blocks and substrates employed in different pathways (acetyl/malonyl units, amino acids, isoprene units, shikimate-derived intermediates, etc.). Typical reactions in natural product biosynthesis: C–C and C–N bond formation, redox chemistry, and tailoring reactions. Also explain how the “same” chemistry is wired differently in Bacteria, fungi, and plants.

2) Experimental hooks & what we actually see: How can we translate biosynthetic insights into real experiments:

• Screening and untargeted metabolomics (What is there?).
• What you expect to see in LC-MS/MS experiments for a PKS vs NRPS product.
• Typical follow-up experiments: feeding experiments, co-culture, mutants, overexpression.
• Heterologous expression of target BGCs and what can go wrong (e.g. shunt products or side pathways in host).

3) Anecdotes of NP discoveries – From bioinformatics to experimental data and back: How genome mining tools identify signatures of the chemistry just discussed (domain architectures, motifs, “biosynthetic fingerprints”) and how ML/fingerprints/knowledge graphs, together with core reference databases (e.g. MIBiG, MITE, NPAtlas, and others), can support discovery – illustrated via concrete stories:

• How genome mining + pathway logic guided biosynthetic pathway elucidation for tridecaptin and marushamycin.
• Collaborative biosynthesis / oligomerization, showing how BGC predictions, MS/MS data and context-dependent expression come together.
• Nocardichelin biosynthesis and lipopeptide discovery guided by Harvest.

15:20–15:35 – Mini panel Q&A: Joint Q&A with all three instructors

15:35–15:45 – Coffee / tea break

15:45–16:45 – Rotating mini-workshops (3 stations): Participants are divided into three groups (A, B, C). Each group visits all three stations in rotation (~20 minutes per station, plus short changeovers).

Station 1 — Reading BGCs like a map: Participants work with printed BGC cartoons (PKS, NRPS, hybrid) and:

• Identify the biosynthetic class and building blocks.
• Discuss the roles of key tailoring enzymes.

Station 2 — From phenotype to molecules: Using a case study (e.g. antibiotic discovery), groups see figures (inhibition data or FERMO output) and:

• Propose what biosynthetic class might be involved (based on MS/MS and BGC results).
• Suggest follow-up experiments to test their hypotheses.

Station 3 — Tools & AI: Demo or screenshots of BGC-to-compound prediction (RetroMol and Harvest), biosynthesis-informed fingerprints and knowledge graph concepts. Short exercise in which participants discuss how two example molecules might be represented and connected in such a system.

16:45–17:00 – Wrap-up: Final recap of key messages and practical information about slides/materials, tools, and any mailing list or follow-up activities.

Borrel & networking (from 17:00)

Informal borrel after the workshop, offering time for networking and follow-up discussions. Participants are encouraged to connect across groups and disciplines, and to explore potential collaborations within the WUR and friends ecosystem.

Fee
The fee for this workshop for all participants is € 50,-

Cancellation
You may cancel free of charge up to three weeks before the start of the course. After this date you will be charged the participation fee. In case of a no-show you will be charged the participation fee with an added € 50,- cancellation fee.