Team

Prof. Dr. Melanie Schirmer is a professor at the Technical University of Munich. The research of her lab focuses on computational microbiome research to investigate mechanisms of host-microbial interactions in human diseases. After studying mathematics at the University of Bonn (Germany), she obtained her PhD from the University of Glasgow (Scotland) looking at fine-scale variation in next-generation sequencing data to distinguish natural variation (i.e. single-nucleotide polymorphisms) from errors and biases in the sequencing data. In 2016 she started as a postdoctoral research associate in the Xavier and Huttenhower Groups at the Broad Institute of MIT and Harvard & Harvard T.H. Chan School of Public Health (USA). Her research focused on the human microbiome and the identification of microbial factors involved in the pathogenesis of inflammatory bowel disease and immune responses in healthy individuals. She continued her work at the Broad Institute as a Computational Scientist until she returned to Germany at the start of 2020 to establish her own independent research group and became a TUM professor in 2023.

Dr. Tingting Zheng is a postdoc in the Schirmer lab. She obtained her bachelor’s degree in Biotechnology in 2011 at the University of Jinan (China). Afterwards, she worked on a project in cancer genomics for her master’s at the University of Electronic Science and Technology of China. In 2015, she started her doctoral degree at the University of Hong Kong in the field of computational biology to study the impact of the human microflora on host physiology. From Feb 2020 to July 2021, she continued her work in microbiome research as a postdoctoral researcher at the City University of Hong Kong where she was involved in several projects, such as employing multi-omics data to identify age-associated signatures in the human microbiome and to explore the effects of probiotics on the gut microbiota. In the Schirmer Lab, she is performing comparative genomic analyses of clinical and gut bacterial strains to identify their role in cancer and gastrointestinal diseases.

Shen Jin is a PhD student in the Schirmer Lab. His research project focuses on understanding the influence of oral microbes on intestinal diseases. Shen obtained his Bachelor's degree in Computer Science at Beihang University, in China. Afterwards, he went to Carnegie Mellon University for his Master's in Computational Biology. Shen is interested in applying computational methods to address biological questions. He has been involved in several research projects, such as developing a deep learning model to identify sequential motifs in DNA and RNA sequences and applying statistical models to understand the sub-cellular organisation of mitochondria.

Agnieszka Gąska is a PhD student in the Schirmer Lab. She obtained her Bachelor's and Master’s degree in Biotechnology at the University of Silesia (Poland). Her Master’s thesis focused on comparing the composition of the gastrointestial microbiome of Apis mellifera (honeybee) from urban and agricultural areas. Afterwards, she worked on a project related to aging at the University of Virginia (USA), where she optimized a protocol (MALBAC) for single Saccharomyces cerevisiae cell sequencing to look for changes in the genome (aneuploidy and copy number variation) caused by aging in yeast cells. In her PhD project she is investigating interkingdom signalling as a target for next-generation drug design.

Svenja Schorlemmer is a PhD student in the Schirmer lab working on micobial hormone metabolism and its role in female health. She obtained her Bachelor's and Master's degree in Integrated Life Sciences at the Friedrich-Alexander-University Erlangen-Nürnberg (Germany). During her studies, she specialised in bioinformatics and computational biology. In her bachelor thesis she worked with proteomic data from Corynebacteria and her master thesis focused on molecular dynamic simulations. She is particularly interested in the clinical relevance of studying host-microbial interactions in health and disease.

Emilio García is a PhD student working on integrated multi-omics to elucidate hormone-microbiome interactions in female health. After completing his Bachelor of Engineering in Systems Engineering, he obtained a Master's degree in Computer Science from the Pontifical Catholic University of Peru, where he worked on Computer Vision methods to identify and count tumour-infiltrating lymphocytes in gastric cancer micrographs. Prior to joining the Schirmer lab, he worked at EMBL’s EBI as a software engineer and bioinformatician, analysing structural variation in whole-genomes of classical and wild-derived mouse strains.

Aurelie Cenier is a research scientist in the Schirmer Lab working on the validation of host-microbial interaction with a focus on human cell lines and organoids. She completed her BSc and MSc degree in microbiology at the University of Caen-Normandy in France. After that, she worked for two years in industry focusing on the development of insect-based fermented meals for animals using Lactobacillus. Prior to her current position she was at the University of Cambridge where she established pediatric and adult human gut organoid cultures as a model to investigate inflammation in patients with inflammatory bowel disease (IBD).

Jagadrupa Sahoo is a PhD student working on elucidating the role of Desulfovibrio in chronic intestinal inflammation and colitis-associated cancer using multi-omics data analysis. She obtained her Bachelor’s degree in Biotechnology from Amity University, Noida (India). During her Bachelor’s, she worked on the gut-brain axis, with a focus on molecular docking approaches to identify suitable drugs and their respective drug targets. She subsequently obtained her Master’s in Bioinformatics and Systems Biology from the University of Manchester (UK), where she worked with multi-omics data from IBD cohorts.