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--- thesistopics [2021/02/17 09:20]
jstoye
+++ thesistopics [2025/03/31 17:32] (current)
arempel [<TITLE> (Bachelor/Master)]
@@ Line 5: / Line 5: @@
 </WRAP>
-===== Alignment-free Phylogenomics with Copy Number Variations (Bachelor) =====
-[[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=108064501|Andreas Rempel]], [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=3721521|Roland Wittler]] //(Please also refer to the project page: [[https://gitlab.ub.uni-bielefeld.de/gi/sans|SANS serif]])//
-SANS serif is a software that allows the reconstruction of a phylogenetic network from a set of input genomes. For this purpose, the current implementation explores the presence/absence of //k//-mers in the DNA sequences. However, this method is not capable of detecting copy number variations, which would require counting and comparing the number of occurrences of each //k//-mer in each input sequence. The aim of this project is an efficient implementation of this extended method, but also an evaluation as to whether it improves the quality of the resulting phylogenetic network.\\ Good knowledge of C++ is highly recommended.
+===== SAT solutions for rearrangement problems (Bachelor/Master) =====
+Genomic rearrangements play a critical role in evolution and adaptation, altering genome structure and organization, thereby influencing phenotypic traits. Understanding these rearrangements helps identify the mechanisms underlying many genetic diseases and evolutionary processes.
+However, even quantifying rearrangements for most genomes that occur in practice is NP-hard under realistic models.
+While Integer Linear Programming (ILP) is commonly used to address this challenge, it has been recently observed that SAT formulations of the same problems may offer a faster alternative. The project involves converting an existing ILP solution for genomic rearrangement quantification into a SAT-based solution, leveraging SAT solvers' computational efficiency.
-===== Improvement of Sequence-to-Graph Alignment (Bachelor) =====
+Contact [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=129443261 |Leonard]] for details.
-[[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]])//
+===== Plasmid recovery/assembly from long reads (Bachelor/Master) =====
+Despite advances in long-read sequencing technologies, plasmid assembly remains a significant challenge. Current state-of-the-art assemblers often fail to recover plasmids, especially those smaller than 10‎kb. This limitation is concerning because small plasmids often harbor important virulence and antimicrobial resistance genes. Popular assemblers such as Flye, Miniasm, Raven, and Canu show variable success, with recovery rates dropping dramatically for smaller plasmids. Furthermore, when plasmids are recovered, they often appear as multiple copies or are misassembled into the chromosome, highlighting fundamental limitations of current assembly algorithms. We are developing a novel pangenomic approach that uses gene identification within long reads and //k//-mers over the gene alphabet to improve the quality of the assembly graph. The main tasks for the students will be to analyze the performance of this method and to potentially improve it. ‎ Contact [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=108064501|Andreas]] for details.
-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.
+===== <TITLE> (Bachelor/Master) =====
+<Project description>
-===== Medical Bioinformatics Projects in Australia (Master) =====
-[[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=65864|Jens Stoye]], [[https://genomics.uq.edu.au/profile/263/lutz-krause|Lutz Krause]] //(University of Queensland Diamantina Institute, Brisbane, Australia)//
-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).

Genome Informatics

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