Bachelor and Master Thesis Topics within the AG Genome Informatics

The following is a (probably incomplete) list of thesis topics offered within the Genome Informatics group. If you are interested in working on one of these (or anything else in Genome Informatics), please contact the responsible group members or see Prof. Jens Stoye.

The ABCs of MLE with DCJ

Jens Stoye, Pedro Feijão (Simon Fraser University, Vancouver)
Master

For faster Maximum Likelihood Estimation (MLE) of the Double Cut and Join (DCJ) distance, we want to develop and test a closed formula for the exact number of DCJ sorting scenarios of length k = d+1 between two genomes A and B, where d is the DCJ distance between A and B. This could, for example, be done by studying the set of defective parking functions.

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Evolution of Cilia-building Proteins

Jens Stoye, Roland Wittler, Heymut Omran (Münster University Hospital)
Master

In collaboration with the Münster University Hospital we want to study the phylogeny of proteins involved in the structure of motile cilia, whose defect can cause a number of severe heritable diseases. The project involves the detection of homologs (and their differentiation into orthologos and paralogs) of the relevant proteins in various species, a prediction of their evolution using various tools for phylogenetic analysis, the study of their genomic context, and a consistency check based on phenotypic/morphological data. */

Improvement of Exome Analysis

Jens Stoye, Roland Wittler, Heymut Omran (Münster University Hospital)
Master

In collaboration with the Münster University Hospital we plan to improve and develop methods for exome sequencing support. This involves the study of existing and development of new analysis methods: quality control, annotation (including deletion and duplication prediction) and software engineering. Programming skills in Python or Java are necessary.

Medical Bioinformatics Projects in Australia

Jens Stoye, Lutz Krause (University of Queensland Diamantina Institute, Brisbane, Australia)
Master

In collaboration with the Computational Clinical Genomics Group at the University of Queensland Diamantina Institute, Brisbane, Australia, we develop and apply bioinformatics and data-mining methods in the context of biomedical research. Student projects are available in the context of biomarker discovery for cancer, genome-wide epigenetic association studies, analysis of next-generation sequencing data, mining and visualizing the human microbiota, evolutionary genomics of human parasites, calling structural variants from next-generation sequencing data and genome-wide association studies (GWAS).