Master Theses
Here is a listing of possible topics for projects. Further suggestions are welcome.
2024
No theses in Summer Semester 2024 (Prof Huson is on sabbatical).
2023
- Comparative visualization of multiple metagenome datasets - Jonas Fischer - co-advisor: Prof Kay Nieselt
- Visualization of gene trees - Julia Leimeister - co-advisor: Prof Kay Nieselt
- Mobile app for viewing MeganServer data - Florian Riedl - co-advisor: Prof Jonathan Brachthäuser
- Mobile app for viewing everything Newick - Philipp Jüngling - co-advisor
- Adapting microbiome health index to 16S rRNA data - Yimeng You - co-advisor: Prof Ruth Ley
- Investigating the potential of UniRef databases and clustered NCBI-nr databases in the DIAMOND+MEGAN approach for microbiome analysis - done
- Applying Shneiderman's mantra to Evidente: Enhance zooming and aggregation for large taxonomic data - done
2022
- 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 - Thersa Störiko - Co-advisor: Prof. Detlef Weigel
- Using IsoSeq to reveal NLR-diversity in Arabidopsis thaliana - Leon van Ess - advisor: Prof. Detlef Weigel
Multiple other theses
2021
- 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 - Co-advisor: Dr. Susana Coelho, Director MPI for Developmental Biology -done
- Prediction of genes in genomes with frequent (~10%) translational frameshifting (i.e. Euplotes - https://www.nature.com/articles/srep21139#t1 - with a fragmented genome like Oxytricha) Co-advisor: Dr. Estienne Swart, MPI for Developmental Biology - done
2020
- 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
- qiime2megan- develop a set of tools that allows one to import qiime2 data into MEGAN and vice versa, export MEGAN analyses into qiime2 (Python or Java) -doneDirector MPI for Developmental Biology
- 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
2019
- 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
2018
- Analysis of twin study microbiome samples - done
- Performance of DIAMOND+MEGAN on CAMI data - done
- Machine learning algorithms applied to protein sequences - done
2017
- 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
2016
- JavaFX implementation of Phylogenetic network drawing and GUI (SplitsTree5 - part I) - done
- Pathogen identification - done
- Correspondence between KEGG and InterPro in metagenome analysis - done
2015
- Assembly of ancient mtDNA genomes - done
- Real-time monitoring of resistance evolution - done
- SamSifter - A toolbox for metagenomic analysis - done
- Fingerprinting of microbial genomes - done
2014
- Haplotype profile sharing in Arabidopsis thaliana - done
- Visualization of very large numbers metagenome samples - done
2013
- Functional analysis of trinucleotide repeats in plants - done
- Sequencing and assembly strategies for a new plant genome - done
2012
- Annotation of bacterial genomes - done
- Reference-guided protein assembly - done
- Naive Bayesian classifier for metagenomics - done
2011
- Pathway evaluation in (meta) transcriptomics - done
- Analysis of 16S data - done
- Finding confidence interval for multiple metagenome comparison networks - done
- Assembly and annotation of the Guppy transcriptome- done
- Correlating taxonomy and gene function with environmental parameters - done
- Short-Read aligners in Metagenomics -- done
2010
- Faster BLAST analysis of metagenomic data - done
- New methods for the comparison of phylogenetic trees and networks- done
- Hybridization networks - done
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TE Discovery by Next Gen Sequencing - done
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Simulation of 3rd generation sequencing technologies - done
- Analysis of human gut data - done
- Analysis of 16 S rRNA - done
- Datenbankgestützte Analyse von Metagenomikdaten - done
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Functional and pathway analysis of metagenomic data - done
- Efficient data mining techniques for two-locus association mapping- done
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Finding Patterns in Intervals - done