Prof. Niko Beerenwinkel - ETH Zurich, D-BSSE - Computational Biology Group (CBG)
Field of research
We are active in the fields of computational biology, bioinformatics, biostatistics, and systems biology. Our activities include the development of mathematical and statistical models, their efficient implementation in computer programs, and application to biomedical problems.
We are interested in disease-associated biological networks and in pathogen evolution associated with disease progression. Our ultimate goal is to predict the effect and to support the design of medical interventions in complex, rapidly evolving, biological systems, such as virus populations, bacterial colonies, and tumors. We make use of high-throughput molecular profiling data and apply high-dimensional statistical modeling in order to study intracellular as well as intercellular biological networks and to predict the effect of genetic alterations.
We model the evolutionary dynamics of pathogen populations to investigate virulence, disease progression, immune escape, and drug resistance development. Our models aim at understanding evolutionary escape and improving diagnostics, prognostics, and rational treatment design.
Specific Contribution to Research in InfectX
In this project, we aim to understand the signaling cascades that are triggered in host cells upon infection. Our goal is to construct probabilistic models of the cellular network responsible for pathogen sensing and inflammation and to identify host proteins as new potential drug targets.
We analyse the RNAi infection screens performed by different groups involved in InfectX. These intervention experiments shed light on the set of host proteins involved in the signaling pathway and on epistatic interactions among them. Thus, RNAi screens offer indirect evidence of the structure of the underlying signaling network. We develop statistical methods for the analysis of RNAi data. This includes ranking of genes to identify primary hits, reconstruction of signaling pathways and comparison of entry mechanisms for different pathogens.
Lab Members Involved in InfectX
Dr Ewa Szczurek, Postdoctoral Researcher, ETH Fellow. Ewa also works closely with Prof. Bühlmann's group.
Fabian Schmich, Ph.D. Student
Juliane Siebourg, PhD Student