Algorithmen der Bioinformatik

Master Theses

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


No theses in Summer Semester 2024 (Prof Huson is on sabbatical).


  • 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


  • 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


  • 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 - - with a fragmented genome like Oxytricha)  Co-advisor: Dr. Estienne Swart, MPI for Developmental Biology - 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
  • 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): (  - 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


  • Analysis of twin study microbiome samples - done
  • Performance of DIAMOND+MEGAN on CAMI data - done
  • Machine learning algorithms applied to protein sequences - 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


  • 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


  • Haplotype profile sharing in Arabidopsis thaliana - done
  • Visualization of very large numbers metagenome samples - done



  • Functional analysis of trinucleotide repeats in plants - done
  • Sequencing and assembly strategies for a new plant genome - done



  • Annotation of bacterial genomes - done
  • Reference-guided protein assembly - done
  • Naive Bayesian classifier for metagenomics - done


  • 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



  • Faster BLAST analysis of metagenomic data - done
  • New methods for the comparison of phylogenetic trees and networks- done
  • Hybridization networks - done
  • TE Discovery by Next Gen Sequencing - done

  • Simulation of 3rd generation sequencing technologies - done

  • Analysis of human gut data - done
  • Analysis of 16 S rRNA - done
  • Datenbankgestützte Analyse von Metagenomikdaten - done
  • Functional and pathway analysis of metagenomic data - done

  • Efficient data mining techniques for two-locus association mapping- done
  • Finding Patterns in Intervals - done