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Topics for master theses

Here is a listing of possible topics for projects. Please come and see us to learn more about the topics. Further suggestions are welcome. 


  • Visualization and analysis of autocatalytic networks (implementation using JavaFX) - Mariette Hamberger - co-advisor: Prof. Mike Steel (University of Canterbury, NZ)
  •  Improved metagenomic contig binning using haplotagging data - Ersoy Kocak - co-advisor - Dr. Frank Chan
  • Performance of DIAMOND+MEGAN on CAMI data - Thorsten Rohling
  • Inclusion of Environmental Data in Machine Learning Models for Genomic Prediction in Rice - Mirjam Fröschl
  • Interpretability of Machine Learning Models for Genomic Selection in Maize - Lisa Marie Dussling
  • Assessment of Assembly Strategies for Bioreactor Metagenomes - Steffen Kienzler - Co-supervisor: Prof. Lars Angenent
  • Computational analysis of metagenome data from caprylate producing bioirectors - Timo Lucas - Co-supervisor: Prof. Lars Angenent


  • Analysis of twin study microbiome samples - Minyue Qi, co-advisor: Prof. Ruth Ley, MPI for Developmental Biology
  • Protein k-mer methods for microbiome analysis - Joachim Fritscher, co-advisor: Prof. Ruth Ley, MPI for Developmental Biology
  • Performance of DIAMOND+MEGAN on CAMI data - Thorsten Rohling, co-advisor: Prof. Alex Sczyrba
  • Machine learning algorithms applied to protein sequences - Jona Kübler - Advisor: Dr. Vikram Alva, MPI for Developmental Biology
  • Database analysis of function - Sylvia Siegel - Co-advisor: Prof. Lars Angenent, Dept. of Biological and Environmental Engineering


  • 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

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