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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. 


  • Analysis of twin study microbiome samples - Minyue Qi, co-advisor: Prof. Ruth Ley, MPI-DB, Tübingen
  • Analysis of microbiomes in bioreactors -AVAILABLE Co-advisor: Prof. Lars Angenent, Center for for Applied GeoSciences, Tübingen
  • In silico analysis of the evolution and function of ABC transporters in bacterial secondary metabolite gene clusters  - AVAILABLE - Co-advisor: Prof. Nadine Ziemert (Biology Tübingen)
  • Protein k-mer methods for microbiome analysis - Joachim Fritscher
  • Functional annotation of long reads and contigs - AVAILABLE
  • Performance of DIAMOND+MEGAN on CAMI data - Thorsten Rohling


  • JavaFX implementation of haplotype networks  (SplitsTree5 - part II) - Nicolai Wahn , Co-reviewer: Prof David Bryant (Otago)
  • Evolution and horizontal gene transfer of regulatory elements in bacterial secondary metabolite gene clusters  - Frauke Adam - Co-advisor: Prof. Nadine Ziemert (Biology Tübingen)
  • 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 - Dennis Pohl - Co-advisor: Prof. Matthias Willmann (UKT)
  • Design and implementation of a full-featured Time Series Analysis tool - Patrick Grupp, Alexander Stoppel and Arne Weitbrecht - Co-advisors: Prof. Julia Frick, Prof. Silke Peter and Prof. Matthias Willmann


  • JavaFX implementation of Phylogenetic network drawing and GUI (SplitsTree5 - part I) -  Christopher Juerges,  supervisor: Dr. Benjamin Albrecht, co-reviewer: Prof David Bryant (Otago)
  • Pathogen identification - Jakob Matthes, co-reviewer: Prof. Matthias Willmann (UKT)
  • Correspondence between KEGG and InterPro in metagenome analysis -  Baiyu Lin 


  • Assembly of ancient mtDNA genomes - Robert Remy - Co-advisor: Prof Alan Cooper, Australian Center for Ancient DNA 
  • Real-time monitoring of resistance evolution - Bianca Regenbogen - Co-advisor: Dr. Richard Neher
  • SamSifter - A toolbox for metagenomic analysis - Florian Aldehoff - Co-advisor: Prof. Johannes Krause
  • Fingerprinting of microbial genomes - Qiunan Shen  - Co-advisor: Prof. Detlef Weigel, MPI for Developmental Biology 


  • Haplotype profile sharing in Arabidopsis thaliana - Wei Ding - Co-reviewer: Prof. Detlef Weigel, MPI for Developmental Biology 
  • Visualization of very large numbers metagenome samples - Jens Rauch - Co-reviewer: Prof. Ingo Autenrieth (UKT)


  • Functional analysis of trinucleotide repeats in plants - Björn Petri - co-advisor: Prof. Detlef Weigel, MPI for Developmental Biology - in cooperation with Computomics
  • Sequencing and assembly strategies for a new plant genome - Monitha Harilkumar - Uni Bonn and Computomics 


  • Annotation of bacterial genomes - Sina Beier - Co-advisor, PD Dr. Julia Frick, UKT
  • Reference-guided protein assembly - Phillip Kirstahler  - Co-advisor: Prof. Stephan Schuster, Penn State
  • Naive Bayesian classifier for metagenomics - Julian Gutekunst - Co-advisor: Gail Rosen (Drexel University)


  • Pathway evaluation in (meta) transcriptomics - Tim Scheuernbrand - Co-advisor: Dr. Kay Nieselt
  • Analysis of 16S data - Andreas Schätzle - Co-advisor: Dr. Suparna Mitra  and Prof. Stephan Bischoff (Uni Hohenheim)
  • Finding confidence interval for multiple metagenome comparison networks - Max Schubach - Co-advisor: Dr. Suparna Mitra 
  • Assembly and annotation of the Guppy transcriptome - Gideon ZIpperich - Co-advisor: Prof. Christine Dreyer (MPI-DB)
  • Correlating taxonomy and gene function with environmental parameters - Alexander Gitter
  • Short-Read aligners in Metagenomics - Zhiqin Huang


  • Faster BLAST analysis of metagenomic data - Dominik Damerow - Co-advisor: Prof. Pete Lockhart (Massey University)
  • New methods for the comparison of phylogenetic trees and networks - Franziska Zickmann - Co-advisors: Dr. Celine Scornavacca and Assist. Prof. Andreas Spillner (Greifswald)
  • Hybridization networks - Benjamin Albrecht- Co-advisor: Dr. Celine Scornavacca and Prof. Charles Semple (Christchurch)
  • TE Discovery by Next Gen Sequencing - Sebastian Bender - Co-advisor: Korbinian Schneeberger and Prof. Detlef Weigel MPI-DB),

  • Simulation of 3rd generation sequencing technologies - Julian Zipperer - Co-advisor: Prof. Stephan Schuster (PennState)

  • Analysis of human gut data - Hannelore Clement - Co-advisor: Dr. Suparna Mitra, Dr. Saskia Biskup
  • Analysis of 16 S rRNA - Mario Staerk - Co-advisor: Dr. Suparna Mitra, Prof. Christa Schleper (Vienna)
  • Datenbankgestützte Analyse von Metagenomikdaten - Hans-Joachim Ruscheweyh - Co-advisor: Prof. Thorsten Grust 
  • Functional and pathway analysis of metagenomic data -  Paul Rupek - Co-advisor: Prof. Stephan Schuster (Penn State)

  • Efficient data mining techniques for two-locus association mapping - Karin Klotzbücher - Co-advisor: Karsten Borgwardt (MPI-K)
  • Finding Patterns in Intervals - Christina Schmiedl - Co-advisor: Dr. Johannes Fischer, Prof. Volker Heun (LMU München)

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