Melanie Schirmer studied mathematics at the University of Bonn. She obtained her PhD in 2014 from the University of Glasgow (Scotland), where she worked on the analysis of next-generation sequencing data to distinguish biological variation (i.e. single-nucleotide polymorphisms) from errors and biases. 

She started her postdoc in 2015 at the Broad Institute of MIT and Harvard & Harvard T.H. Chan School of Public Health (USA) and became a computational scientist at the Broad in 2018. Her research there focused on the human microbiome and the identification of microbial factors involved in the pathogenesis of inflammatory bowel disease and immune responses. She then returned to Germany in 2020 to establish her own independent research group at the Technical University of Munich (TUM) with an Emmy Noether Award (2020) and an ERC Starting Grant (2022). Since 2023 she is a Rudolf Mößbauer Tenure Track Professor for Translational Microbiome Data Integration at TUM.