PhD Supervisors

Tilmann Weber is Professor and associate Scientific Director at DTU Biosustain and head of the Natural Products Genome Mining group. He is coordinator of the MAGic-MOLFUN doctoral network. Tilmann and his group are working on the interface of natural products discovery, bioinformatics and metabolic engineering. He is highly interested in using generating and mining genomic data to find interesting secondary/specialized metabolite biosynthetic pathways using bioinformatics approaches, such as antiSMASH, which his lab is co-developing with the group of K. Blin (DTU) and Marnix Medema (WUR). These information then build the basis to use metabolic engineering techniques, such as CRISPR technology, to functionally characterize the BGCs and improve their production. Tilmann is author of >100 scientific publications and patents. He is Associate Editor of Synthetic and Systems Biotechnology and in the Editorial Board of Metabolic Engineering.

Tilmann Weber lab

TOL’s research group focus on microbial natural products chemistry based on advanced chemical analysis in order to discover and characterize the structures of e.g. new pigments, antibiotics, and microalgal fish killing toxins. This includes investigations into understanding their natural ecological role as well as characterization of their biosynthetic pathways based on the linking of chemical and bioinformatics analysis.

TOL’s group 

In the Van der Hooft Computational Metabolomics Group, we develop approaches and tools to support structural and functional annotation in untargeted metabolomics workflows. To do this together in a responsible and respective way, we held the following shared team values in high regard: open-mindedness, pragmatism, and collegiality. Inspired by natural language processing and principles used in genomics workflows, we aim to create tools that will enable biochemical interpretation of spectral data and allow for effective prioritisation of relevant (i.e., novel and bioactive) molecules. We use the plant root microbiome and human food metabolome as prime applications since they represent complex metabolite mixtures full of yet unknown metabolic matter that once elucidated will boost our insights in molecular mechanisms underpinning the regulation of growth, development, and health. Together with the group of Dr Marnix Medema, we work on developing the foundations for integrative omics mining workflows that build on our computational genomics and computational metabolomics workflows.

Van der Hooft Computational Metabolomics Group

Bioinformatics Group in Wageningen

Wageningen University

The Medema group at WUR develops and applies algorithms for the (meta)genomic identification and functional prediction of microbial biosynthetic pathways and their products, with the aim to unravel the chemical language of microbiomes and accelerate drug discovery. The group is also involved in the development of the antiSMASH software for identification of biosynthetic gene clusters, and develops a range of additional tools and databases to chart their diversity and identify their functional roles in microbiomes (e.g., MIBiG, BiG-SCAPE, BiG-SLiCE, BiG-MAP, PIKAChU, etc.).

Bioinformatics WUR

The Ziemert lab is interested in the evolution and distribution of bacterial secondary metabolites. These bioactive compounds are especially important in human medicine as the chemical scaffolds are the main templates for new drugs such as antibiotics and anticancer agents. We are a highly interdisciplinary at the interface of bioinformatics, molecular and environmental microbiology, and phylogenetics. We are currently developing bioinformatic tools for the discovery of natural products from microbial genomes, elucidating the evolutionary history of their biosynthetic gene clusters and tracing their distribution in the environment.

Ziemert Lab

Our research is focused on the discovery and investigation of interesting secondary metabolites. By employing “Genome Mining” we identify biosynthetic gene clusters of compounds with particular bioactive properties and unusual chemical features. Using genetics, biochemistry and chemical methods we elucidate the stepwise biosynthesis of the molecules. This enables us to engineer the respective pathways in order to optimize the production and to generate novel derivatives with better properties (e.g., by mutasynthesis experiments).

Evi Stegmann Lab

Stefano Donadio is Founder and CEO at Naicons Srl. Over 30-year industrial experience in large, medium-size and startup companies involved in antibiotic discovery and development. His experience spans from drug discovery and development to company creation and management. He has contributed to developing the production processes for dalbavancin (marketed in 2014) and ramoplanin (in phase III clinical studies). He is the author of over 140 publications and patent applications in the fields of antibiotics and antibiotic-producing bacteria. He holds a degree in Chemistry from The University of Naples, Italy, with post-doctoral experience at Johns Hopkins University and The University of Wisconsin-Madison.

Naicons Srl

Naicons Srl 

Duncan Lab

c-LEcta