Advancing Large-Scale Leveraging of Omics Profiles for Specialized Metabolite Discovery and Characterization

webinaire IBMP - 9h15

Dr Justin van der HOOFT, Bioinformatics Group, Department of Plant Sciences, Wageningen University, The Netherlands, invité par E. Gaquerel et D. Elser


Specialized metabolites play key roles in regulating physiological processes in organisms related to growth and development and serve as communicators between organisms Their encoded messages include cries for help, embrace yourself, as well as deadly kisses. However, only a few percent of specialized metabolites is structurally characterized, and even less are connected to their genetic machinery in the organisms producing them. In this seminar, I will introduce the Van der Hooft Computational Metabolomics Group and our research agenda, in which I recognise three paths to better understand complex metabolite mixtures: i) increased metabolite annotation power, ii) chemically-informed comparative metabolomics, and iii) linked metabolomics profiles to function and genotype/genomic information. I will highlight recent advances in metabolomics mining and annotation tools to better understand the complex metabolite mixtures that specialized metabolites are typically part of as well as recent advances in combined analysis of genomics and metabolomics data. In this seminar, I will present the tandem of MS2LDA and MotifDB (www.ms2lda.org) for substructure discovery and annotation in metabolomics data and Spec2Vec, a novel machine learning based mass spectral similarity score that improves library matching and analogue searching. I will then highlight a number of GNPS tools that improve structural and functional annotation including MASST and ReDU. Furthermore, I will introduce the Paired Omics Data Platform as a resource and NPLinker as a tool that both facilitate the integrated analysis of genomics and metabolomics data. I will finish off with my perspective on integrating  genome and metabolome mining workflows to accelerate specialized metabolite discovery and their structural and functional characterization. I expect that the presented methodological developments will advance our understanding of the role of metabolites and their complex molecular interactions that underpin growth, development, and health.