The pathogenic activity of viruses is to a large extent based on their ability to modulate protein activities in infected cells. In the course of an European Research Council (ERC)-funded (5 years perspective) project (ProDAP) we want to study the influence of viruses on the host proteome.
We use state-of-the-art mass spectrometry (MS) and deep sequencing techniques to obtain large-scale data and study how a particular immune stimulus transforms the landscape of protein interactions. To analyze the data and pinpoint interesting patterns we have developed comprehensive bioinformatic pipelines combining the leading approaches for Bayesian statistical modeling, biological data processing and visualization (R, Julia, Stan, Plotly, Sun Grid Engine).
For the ProDAP project we will generate novel large-scale MS-based datasets dissecting the cellular response to virus infections. We plan to complement MS data with automated lightmicroscopy experiments that will link molecular-level changes to the changes of host phenotype.
Your ultimate mission will be to use the power of bioinformatics and bring our understanding of host-pathogen interactions to the next level. You are expected to further develop our bioinformatic framework and deliver the tools that will analyze this new data and explain how and why the infection modulates protein expression and protein-protein interactions.
A critical part of our scientific mission is to make our data, acquired using mass spectrometry and sequencing-based approaches, available to the broad scientific community to serve as an important resource for further research. The unique nature of our experiments requires a dedicated user interface and data visualization methods, which are not readily provided by the existing platforms for scientific data sharing.
Your project will be to develop a web server for browsing and visualizing our data in an intuitive and efficient manner. The web server will use state-of-the-art frameworks:
This position will give you the opportunity to become familiar with modern web technologies as well as cutting-edge molecular biology and bioinformatics research.