Saez-Rodriguez Group

Systems Biomedicine

Katharina Zirngibl

In 2014 I graduated from my master’s degree in Molecular Biology with a focus on cancer research at the Heidelberg University in conjunction with the German Cancer Research Center (DKFZ). During the course of these studies I discovered my affinity for computational biology and data analysis, which culminated in a thesis project in which I developed and employed an image analysis pipeline for high-throughput RNAi screenings of synthetic lethality.

Later that year I joined Dr. Kiran Patil’s group at EMBL Heidelberg for my PhD where I studied metabolic network adaptation in minimal residual disease in breast cancer using multi-omics data analysis and integration with metabolic modeling, statistical analysis and regulatory network analysis. After my graduation in December 2018, I joined the MRC Toxicology Unit in Cambridge for a bridging Postdoc to develop a human metabolic model capable of identifying metabolic pathways of interference from metabolomics drug library screens. Additionally, I worked on a methodology to predict metabolic interactions from single-cell transcriptomics data.

I joined the group of Julio Saez-Rodriguez in January 2021 where I will work on novel approaches to integrate multi-omics data joining statistical and network based approaches deployed in the group. My particular focus lies on bridging the gap between epigenetic gene regulation and its manifestation on the transcriptome.

Research Interests

I am interested in the question of integrating large comprehensive biological data sets to discover new functional mechanisms and to drive our understanding of biology. To tackle this question I explore the idea of enriching methods of statistical correlation with the use of existing knowledge to build mechanistic data driven models precisely predicting the phenotypic outcome of a cell in health and disease.

Having a classical molecular biology background, I have always been interested in studying biology from different angles (leading to excursions to biophysics, structural biology, image analysis, single cell analysis). I envision a modeling approach eventually extending to the integration of various dimensions of a cell’s biology, e.g. bridging different layers (epigenetics –proteomics), functionalities (regulation – enzymatic activity) and molecules (RNA – metabolites) at different scales (atoms – organelles) and resolutions (single cells – tissues).

Professional Career

2019 – 2020 Postdoctoral Fellow, Medical Research Council (MRC), Cambridge, UK
2019 Bridging Postdoctoral Fellow, European Molecular Biology Laboratory (EMBL) Heidelberg, Germany


2014 – 2018 PhD in Computational Biology, European Molecular Biology Laboratory (EMBL) Heidelberg and Heidelberg University, Germany
2011 – 2014 MSc in Molecular Biosciences with Major in Cancer Research, Heidelberg University and German Cancer Research Center (DKFZ), Germany
2008 – 2011 BSc in Biology, Ruhr-Universität Bochum, Germany
2006 – 2011 BA in Social Psychology and Educational Sciences, Ruhr-Universität Bochum, Germany