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Marnix H. Medema

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Professor

Wageningen University & Research

Netherlands

Research Interests

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About

Professor Marnix H. Medema is a faculty member at Wageningen University & Research in the Netherlands. His research primarily focuses on the integration of multi-omics data, biosynthetic pathways, and the interaction of bacteria within the rhizosphere. Recent publications include work on catabolic gene clusters, AI in natural product science, and computational tools for genome analysis. His contributions significantly enhance the understanding of microbial interactions and natural product discovery.

Recent Grants

Grant: Open

Urinary tract infections – the sum is more than the parts

Open Date: 2023-03-01

Close Date: 2028-02-01

Grant: Open

Tapping the potential of plant specialized metabolic diversity through integrative omics

Open Date: 2023-01-01

Close Date: 2027-12-01

Grant: Close

DECIPHER

Open Date: 2020-12-01

Close Date: 2025-11-01

Grant: Close

Unwiring beneficial functions and regulatory networks in the plant endosphere

Open Date: 2020-06-01

Close Date: 2025-06-01

Grant: Close

In pursuit of next-generation lipopeptide antibiotics

Open Date: 2018-05-01

Close Date: 2022-04-01

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Collaborators (25)

Dennis Claessen

Professor of Molecular Microbiology

Leiden University

NETHERLANDS

Marnix H. Medema

Research Interests

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About

Recent Grants

Articles (30)

FERMO: A Dashboard for Biochemometric Prioritization of Molecular Features from Mass Spectral Data

Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae

plantiSMASH 2.0: Improvements to Detection, Annotation, and Prioritization of Plant Biosynthetic Gene Clusters

NPLinker 2: a modular and customizable framework for paired omics analyses

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

COMMBAT: a web platform for exploring expression control of biosynthetic gene clusters

The antiSMASH database version 5

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Regulatory Genes as Beacons for Discovery and Prioritization of Biosynthetic Gene Clusters in Streptomyces

Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH

MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways

Diverse rhizospheric Bacillus are required for protection against a leaf pathogen

Breaking into nature's secret medicine cabinet: lichens – a biochemical goldmine ready for discovery

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria

Pairing omics to decode the diversity of plant specialized metabolism

LogoMotif: a comprehensive database of transcription factor binding site profiles in Actinobacteria

Harnessing regulatory networks in Actinobacteria for natural product discovery

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

Convergent evolution for antibiotic biosynthesis in bacteria and animals

Metabolome-guided genome mining of RiPP natural products

Total Synthesis and Structure Assignment of the Relacidine Lipopeptide Antibiotics and Preparation of Analogues with Enhanced Stability

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota

PIKAChU: a Python-based informatics kit for analysing chemical units

Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome

The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol

Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification

Author Correction: Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

Collaborators (25)

Dennis Claessen

Silvia Ribeiro Monteiro

Dylan Dodd

Nadine Ziemert

Michael A. Fischbach

Detmer Sipkema

Koen Verhoeven

Gilles van Wezel

Omri Finkel

Jingyuan Fu

Wilfred van IJcken

Mihai G. Netea

Justin van der Hooft

Vincent Courdavault

Jo Handelsman

Francisco M. Cazorla

Tilmann Weber

Somayah Elsayed

Nicolas Papon

CAYO RAMOS

M. Eric Schranz

Mitja Maximilian Zdouc

Herman Spaink

Jos Raaijmakers

Robin van Velzen

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