====== Bachelor and Master Thesis Topics within the AG Genome Informatics ======
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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 [[http://www.techfak.uni-bielefeld.de/~stoye|Prof. Jens Stoye]].
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===== Duplication Reconstruction In Natural Genomes (Bachelor/Master) =====
[[ https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=129443261 | Leonard Bohnenkämper]] (Also refer to the [[ https://github.com/gi-bielefeld/spp_dcj_exact | github]])


SPP-DCJ-exact ([[ https://doi.org/10.4230/LIPIcs.WABI.2026.15 |publication]]) is an exact ILP solution for reconstructing ancestral genome structures under the DCJ-indel model. While the DCJ-indel model captures losses of material well, gains are not connected with //where// in the phylogeny a gain came from and similarly, duplications are handled as arbitrary gains without regard for duplication structure. An interesting problem is therefore to examine whether the model can be enhanced through such more specific operations.