PhD student / PostDoc (f/m/x) in Cancer Systems Biology
The University of Bonn is an internationally operating research university with a broad spectrum of subjects. With 200 years of history, around 38,000 students, more than 6,000 employees and an excellent reputation: The University of Bonn is one of the most important universities in Germany. In the recent excellence initiative, the University of Bonn was the most successful university in Germany with six Clusters of Excellence.
In this excellent scientific environment, the Interdisciplinary Research Unit Mathematics and Life Sciences (https://www.mathematics-and-life-sciences.uni-bonn.de/en) develops and applies novel mathematical approaches and software tools for data analysis and modelling. Application areas include cancer and immunology, with an emphasis on high-throughput (single-cell) data. We are intensively collaborating with world leading experts in mathematics and immunology in the Hausdorff Center for Mathematics, ImmunoSensation2, and the German Center for Neurodegenerative Diseases. Currently, we are searching for individuals who strengthen our team.
Mechanistic models of biochemical reaction networks have substantially improved the understanding of biological processes. The application of mechanistic mathematical models is currently, however, limited to small- and medium-scale problems. In contrast, the abundance of high-dimensional datasets is rapidly increasing due to the advent of novel measurement devices, e.g., next-generation sequencing and next-generation proteomics. To interpret the resulting datasets, novel methods for mechanistic modeling are required which scale to large datasets. We recently introduced computational approaches which for the first time allowed the use of large-scale mechanistic models and demonstrated that these methods can facilitate personalized medicine (Fröhlich et al., Cell Systems, 2018).
The goal of this project is to develop and implement a model-based approach to predict the drug response of cancer cells. The research is part of the collaborative research project CanPathPro (http://www.canpathpro.eu/) in which large amounts of exome, transcriptome, proteome, phosphoproteome and histological data of cancer cell lines and cancer mouse models are collected. This unique dataset will be exploited to unravel the molecular mechanisms leading to outbreak and progression of cancer. Beyond the modelling of cancer signaling, we aim at the incorporation of the interaction of cancer cells with the surrounding tissue. In particular immune cells will be of special interest.
- Development of mathematical models
- Development of model-based analysis approaches for omics data
- Implementation of methods for high-performance computing (HPC) infrastructures
- Application of methods and interpretation of the results
- Collaboration with national and international partners
- Master / PhD degree in computer science, engineering, mathematics, physics or equivalent
- Background in mathematical modeling (e.g., ODE models), optimization or machine learning
- Programming experience (preferably Python and/or C++)
- Experience with large-scale databases and data visualization is an asset
- Being comfortable in interacting with colleagues in an interdisciplinary setting
- Proficiency in written and spoken English
- Passion for science and scientific work
- Working in an innovative, well-equipped and scientifically stimulating environment
- Further training opportunities
- Initial short-term employment contract for 2-3 years with a standard public service salary (TV-L EG 13, Phd: 75% / PostDoc: 100%)
The University of Bonn is committed to diversity and equal opportunity. It is certified as a family friendly university. It aims to increase the proportion of women in areas where women are under-represented and to promote their careers in particular. It therefore urges women with relevant qualifications to apply. Applications will be handled in accordance with the Landesgleichstellungsgesetz (State Equality Act). Applications from suitable individuals with a certified serious disability and those of equal status are particularly welcome.
The deadline for the application round is October 31, 2019. Application documents (cover letter, CV, certificates, and two reference letters or contact details of former advisors) should be submitted as soon as possible as a single PDF file via email.
Contact: Prof. Dr. Jan Hasenauer, firstname.lastname@example.org