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--- thesistopics [2020/02/14 09:07]
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+====== Bachelor and Master Thesis Topics within the AG Genome Informatics ======
+\\
+<WRAP center round info 99%>
+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]].
+</WRAP>
-====== Bachelor and Master Thesis Topics within the AG Genome Informatics ======
+===== 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]])//
-<WRAP center round info 90%>
+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.
- 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]].
+===== (Runtime) Heuristic for the Fast Comparison of Genomes (Bachelor/Master) =====
+[[ 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 thesis or project module. Contact [[ https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=129443261 | Leonard ]] for details.
-</WRAP>
+===== DCJ-Indels of Natural Genes (Bachelor) =====
+[[http://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=65864 | Jens Stoye]]
-===== Medical Bioinformatics Projects in Australia =====
+We have developed the tool DING (DCJ-Indels of Natural Genomes), which could also be applied to protein sequences, resulting in a new tool DING (DCJ-Indels of Natural Genes).
-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).
+Necessary is basic knowledge in algorithms and sequence analysis, ideally also algorithms in comparative genomics.