Potential master thesis (exjobb) projects in the Sonnhammer group:

• Gene network reconstruction and analysis

• Orthology identification and analysis

• Protein domain architecture evolution and analysis

• A tool for analysing protein domain architecture evolution.
  The goal is to develop a web-based tool that can display evolutionary trees of proteins and their domain architecture. This is very useful for understanding how domains have been shuffled during evolution. The tool should either be written in Java and integrated in PfamAlyzer or be implemented using JavaScript.
• 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