Melanie Schirmer

Short CV

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.

Professorship: Translational Microbiome Data Integration

Selected Awards

• 2021, 2022, 2023, Highly cited researcher (Clarivate)
• 2022, ERC Starting Grant
• 2022, Life Sciences Bridge Award (Aventis Foundation)
• 2020, Emmy-Noether Award (Deutsche Forschungsgemeinschaft)
• 2018, Career Development Award (Crohn's and Colitis Foundation)
• 2017, 2018, Certificate of recognition for scientific accomplishment as an early career investigator (The American Gastroenterological Association)

Research Interests

Host-microbial interactions, Microbiome, Multi-omics Data, Computational Biology, Microbiology, Organoids, Female health, Inflammatory bowel disease, Cirrhosis

Selected Publications

• D.F. Rojas-Tapias, E.M. Brown, E.R. Temple, M. Onyekaba, A.M.T. Mohamed, K. Duncan, M. Schirmer, …., R.J. Xavier, Inflammation-associated nitrate facilitates ectopic colonization of an oral microbe in the intestine, [Nature Microbiology, 2022]
• S. Jin, D. Wetzel, M. Schirmer, Deciphering mechanisms and implications of bacterial translocation in human health and disease [Current Opinion in Microbiology, 2022]
• J. Lloyd-Price, C. Arze, A.N. Ananthakrishnan, M. Schirmer, J. Avila-Pacheco, ..., C. Huttenhower, Multi-omics of the Gut Microbial Ecosystem in Inflammatory Bowel Disease [Nature, 2019]
• M. Schirmer, L. Denson, H. Vlamakis, E.A. Franzosa, S.M. Thomas, ..., R.J. Xavier, Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course [Cell Host & Microbe, 2018]
• M. Schirmer, E.A. Franzosa, J. Lloyd-Price, L.J. McIver, R. Schwager, ..., C. Huttenhower, Dynamics of metatranscription in the inflammatory bowel disease gut microbiome [Nature Microbiology, 2018]
• M. Schirmer, S.P. Smeekens, H. Vlamakis, M. Jaeger, M. Oosting, ... R.J. Xavier, Linking the human gut microbiome to inflammatory cytokine production capacity [Cell, 2016]
• A. Zhernakova, A. Kurilshikov, M.J. Bonder, E.F. Tigchelaar, M. Schirmer, ..., J. Fu, Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity [Science, 2016]
• M. Schirmer, R. D’Amore, U.Z. Ijaz, N. Hall and C. Quince, Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data [BMC Bioinformatics, 2016]
• M. Schirmer, U. Z. Ijaz, L. D’Amore, N. Hall and C. Quince, Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform [Nucleic Acid Research, 2015]
• M. Schirmer, W.T. Sloan and C. Quince, Benchmarking of viral haplotype reconstruction programs: an overview of the capacities and limitations of currently available programs [Briefings in Bioinformatics, 2014]

Complete List: scholar.google.com/citations