Daniel Mende

Microbiome evolution

The Mende Lab is a computational group studying the evolution and biology of microbial communities (e.g. the human microbiome) as well as pathogens. The main focus of the group is on the analysis of sequencing data. We focus on the analyses metagenomics and genomics data while integrating additional datasets to gain a better understanding of the biological principles behind microbial evolution and host/environment-microbe interactions. The group is further involved in the development of state-of-the-art methods for metagenomics data analysis such as the mOTUs tool. We work in close collaboration with the GGD Amsterdam as well as reference laboratories. In a world, where sequencing data has become ubiquitous, our vision is to combine local expertise with global data to understand the mechanisms and underlying evolutionary history of our relationship with our microbial companions and opponents.

Research team

Head of the team

Daniel Mende, PhD Assistent Professor

Daniel Mende (1985) studied bioinformatics at the University of Frankfurt (Germany) before moving to the European Molecular Biology Laboratory in Heidelberg (Germany) for his PhD studies with Peer Bork (2009-2013) with a focus on the human microbiome and the development of methods for its analysis. For his postdoctoral studies, Daniel moved to the University of Hawaii to work with Ed DeLong on microbial communities in the Oceans in 2014. In 2019, he started his own research group at the Amsterdam UMC studying the role, evolution and biology of the human microbiome as well as pathogens.

Team members
Nicholas Pucci; PhD student studying infant microbiome and its role in the development of childhood obesity.
News & Publications
Daniel Mende is part of the directorate of the University of Amsterdam Research Priority Area (RPA) Personal Microbiome. The RPA will support the establishment of microbiome infrastructure in Amsterdam with 2.25M Euro over 5 years. The mOTUs tool, co-developed by the Mende group was highly rated in the 2021 CAMI benchmark for metagenomics analysis methods (Meyer et al., Nature Protocols, 2021)
Drs. Daniel Mende
Email: d.r.mende@amsterdamumc.nl