The scientific drive of Simon Rasmussen is his curiosity and interest in transforming large and complex datasets from biological experiments into knowledge and biological understanding. He is established as a strong initiator of analysis efforts within large scale genomics data including areas such human genomics, metagenomics, bacterial genomics and evolution. This is emphasized by the publication of more than 20 papers in the most prestigious journals (Nature, Science and Cell) such as analyses of thousands of human genomes as well as the discovery of plague epidemics during the Bronze Age. The achievement of the latter was emphasized by it being selected as a scientific breakthrough by the European Research Council. Currently, he is building an infrastructure around human proteome variation as genome graph representations which will be used to store and analyse 100,000s of genomes. Here an important challenge is to translate individual genome variation to functional proteome variation. He aims to study this through differential prediction of protein features such as secondary structure, cleavage events and post-translational modifications. Furthermore, he develops methods for unsupervised deep learning of massive omics data and has shown the ability of this approach to integrate data from different fields.