Master Theses

Here is a listing of possible topics for projects. Further suggestions are welcome.

2024

Simulation of ancient cave microbiome data - Available - co-advisor Prof. Cosimo Posth
Acceleration of phylogenetic context calculations by performing them directly in SQL - Available - co-adivsor Prof. Torsten Grust
Interactive exploration tool to analyze data hosted at MGnify - Available
Interaction exploration tool to analyze data hosted at MG-Rast - Available
Extending Sankoff's and Felsenstein's algorithms to rooted networks - Available
Application of protein language-models in microbiome analysis - Available
Comparison of read-based and contig-based analysis of metagenomic RNA sequencing data - Available
Analysis of Nano-sequencing data in the context of biotechnology - Available - co-advisor: Prof. Lars Angenent

Comparative visualization of multiple metagenome datasets - done - co-advisor: Prof Kay Nieselt
Visualization of gene trees - done - co-advisor
Mobile app for viewing MeganServer data -done - co-advisor
Mobile app for viewing everything Newick - done - co-advisor
Adapting microbiome health index to 16S rRNA data - done

Comparison of Whole Genome Shotgun and 16S Amplicon Metagenomic Sequencing - done
Taxonomic Segmentation - done
Machine learning based codon prediction for recombinant gene design - done
Benchmarking and Comparative Analysis of a Graph-based Tool for CRISPR Array Detection in Metagenomic Datasets - done
Generation and validation of pangenome graphs to explore genetic diversity in Cannabis sativa - done
Bioinformatic Discovery and Analysis of Fusion Enzymes in the Shikimate Pathway - done
Adapting the MEGAN long-read LCA algorithm to Kraken-style data - done
Using IsoSeq to reveal NLR-diversity in Arabidopsis thaliana - done

Multiple other theses

Sex biased gene expression in red algae - done
Evaluation & Comparison Of Metagenomic Plant Growth-Promoting Traits Annotation Strategies - done
Interoperability of Microbiome Analysis Tools - done
Investigating AnnoTree for its potential to improve the analysis of metagenomic sequencing data - done
Improved consistency of taxonomic binning of microbiomes based on assembly graph analysis - done
Prediction of Genes in Genomes with Frequent Ribosomal Frameshifting - done
RNAseq and Iso-seq data analysis - done
Prediction of genes in genomes with frequent (~10%) translational frameshifting - done

Comparison of Machine Learning and Deep Learning Methods for Multi-environment Genomic Predition - done
Impact of Repeats, Conserved Genes, Strains Richness and Chimeric Contigs on Metagenomic Assembly - done
Visualization and Analysis of Autocatalytic Networks - done
Improved Metagenomic Contig Binning using Haplotagging Data - done
Genome Mining of the Natural Product Potential and Diversity within the bacterial kingdom - done
Targeted functional annotation of bacterial genomes using DIAMOND and MEGAN in a phylogenomics approach - done
Use assembly graphs in contig binning - develop methods and implement in Java - done
Use of GTDB and AnnoTree for protein-alignment-based microbiome analysis - done
Prediction of genes in genomes with ambiguous genetic codes (where “stop” codons can be sense or stop, depending on the context): (https://www.sciencedirect.com/science/article/pii/S0092867416307887) - done

Visualization and analysis of autocatalytic networks (implementation using JavaFX) - done
Protein k-mer methods for microbiome analysis - done
Identifying the Role of ALPs in Methanobacteriaceae - done
Inclusion of Environmental Data in Machine Learning Models for Genomic Prediction in Rice - done
Database analysis of function - done
Computational analysis of metagenome data from caprylate producing bioreactors” -done
Interpretability of Machine Learning Models for Genomic Selection in Maize” - done
Effect of reference genome choice on variant calling”- done
Assessment of assembly strategies for bioreactor metagenomics” - done
Improved metagenomic contig binning using haplotagging data - done

JavaFX implementation of haplotype networks (SplitsTree5 - part II) - done
Evolution and horizontal gene transfer of regulatory elements in bacterial secondary metabolite gene clusters - done
Exploring the use of TPR "Trough to Peak Ratio" analysis to determine which bacteria are growing and which are stagnant in the human gut during a course of antibiotics - done
Design and implementation of a full-featured Time Series Analysis tool - done

JavaFX implementation of Phylogenetic network drawing and GUI (SplitsTree5 - part I) - done
Pathogen identification - done
Correspondence between KEGG and InterPro in metagenome analysis - done