Sonnhammer Master projects
Potential master thesis (exjobb) projects in the Sonnhammer group:
Projects are offered in the area of protein function prediction and analysis, mainly in three projects:
Specific project descriptions are listed here:
- Gene network reconstruction and analysis
- Orthology identification and analysis
- Protein domain architecture evolution and analysis
- A tool for analysing protein domain architecture evolution.
- Large-scale application of Hieranoid.
Hieranoid is a new algorithm for inferring orthologs. It has not yet been tested on a large scale yet, hence the goal of this project is to apply the method to at least 100 species and analyse the results. It will involve script writing to deploy Hieranoid on a compute cluster and analysis of the results.
- Network-based identification of new disease genes.
The goal is to use the FunCoup network to identify genes not previously associated with a disease but with an enrichment of network links to known disease genes. Furthermore, conservation of the relevant subnetwork in model organisms will be analysed in order to identify particularly interesting new candidates. The project will involve script writing and analysis of results.
- Testing the ortholog conjecture.
- Domain orthology
- Interactive website to explore protein networks
- Protein domain architecture evolution
- Benchmarking the next generation of homology inference tools
- Adaptive evolution in birds