Your studies in Bioinformatics will be in the project: “Title: Network-based protein function prediction”.
The goal of the project is to develop computational algorithms and methods that use high-throughput biological data to build comprehensive networks of how genes and their products interact with each other. We use systems biology approaches to build the FunCoup database of global association networks of functional coupling (http://FunCoup.sbc.su.se/). Networks can be used for statistical enrichment analysis of interactions between a query gene list and known pathways, which is much more sensitive than traditional gene overlap analysis. The project therefore also includes development and application of network-based pathway analysis methods.
Methods include regression models, Bayesian integration, various statistical analyses, and in-house developed modelling techniques. In FunCoup, heterogeneous publicly available high-throughput data sources are combined to predict functional coupling between proteins in order to build global networks that model pathways and interaction cascades. The project aims to expand FunCoup to also use physical regulatory evidence such as ChIP-Seq to infer regulatory links, and enzymatic activities to infer directed links. It further involves improved modelling and scoring of functional associations to make the networks more stable between releases. Structuring the networks into modules will be done to assign functions to network neighbourhoods. The project involves programming, data analysis, benchmarking, and application of the developed methods to genes of particular interest in order to discover new protein functions.
The successful candidate must be highly motivated and have a M.Sc. in bioinformatics or related field, and knowledge of molecular biology. Alternatively, a M.Sc. in molecular biology or related field and at least 1 year of documented practical experience in bioinformatics research and programming. Demonstrable familiarity with sequence and molecular data analysis techniques is essential. Computer programming with Java, Python, R, (Perl, C++), UNIX skills, and knowledge of biological database systems are necessary merits.
To apply, go to https://www.su.se/english/about-the-university/work-at-su/available-jobs, and PhD Student Positions, closing date 21 September 2021. For further information about the research project, contact Erik.Sonnhammer@scilifelab.se, http://sonnhammer.org.