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--- thesistopics [2022/11/10 13:35] – [Heuristic for the Fast Comparison of Genomes (Bachelor)] leonard
+++ thesistopics [2026/09/28 16:06] (current) – [Duplication Reconstruction In Natural Genomes (Bachelor/Master)] leonard
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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]])
-===== Improvement of Sequence-to-Graph Alignment (Bachelor) =====
-[[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=70863414|Tizian Schulz]] //(Please also refer to the project page: [[https://gitlab.ub.uni-bielefeld.de/gi/plast|PLAST]])//
-PLAST is a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. The first method has been published [[https://doi.org/10.1093/bioinformatics/btab077|here]], but there exist various ideas how to improve the method. Some are well suited for a Bachelor thesis. Contact Tizian for details.
+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.
-===== Heuristic for the Fast Comparison of Genomes (Bachelor) =====
-[[ https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=129443261 | Leonard Bohnenkämper]] (Also refer to the [[ https://gitlab.ub.uni-bielefeld.de/gi/ding | gitlab1]]/ [[ https://gitlab.ub.uni-bielefeld.de/lbohnenkaemper/dingiiofficial | 2]])
-DING ([[ https://doi.org/10.1089/cmb.2020.0434 |publication]]) is an exact ILP solution for an NP-hard problem, comparing arbitrary genomes on a high level under the DCJ-Indel model. It is already very fast for small to medium size genomes. However, for some large or very complex genomes that occur in practice, DING is not able to calculate solutions. There are some ideas how to circumvent this problem using approximate or heuristic methods, which could be developed as a Bachelor thesis or as a Master project module. Contact [[ https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=129443261 | Leonard ]] for details.

Genome Informatics

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