Ideas for Thesis Projects

The following is an incomplete list of ideas for thesis topics in (Algorithmic) Bioinformatics that may be supervised by members of the group. You are encouraged to suggest your own ideas and follow your own interests as well.

Polishing circular assemblies from long reads

Most long-read assemblers are optimized to assemble linear, not circular, contigs. Some assemblers do support circular structures, but the resulting contigs may need polishing. The goal of this project is to investigate different strategies for refining contigs produced by different assemblers (like CANU) when we expect circular contigs.

In the long run, this project may be extended to write an optimized assembler for circular structures.

Contact: Sven Rahmann

Converting images of structural formulas of organic molecules to a formal representation (InChI)

In early 2021, kaggle presented a challenge that asks participants to derive a formal molecule description (InChI strings) from a scanned image of the structural formula of any organic molecule.

This project will look at the successful approaches in this challenge and extend them. This will involve AI methods like deep neural networks, but also methods for graph-to-string encoding.

Contact: Sven Rahmann

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