Completed Master Theses


Topic: Uncertainty estimation of ancient genomic data and their low-dimensional representations
Supervisor: Kay Nieselt / Cosimo Posth/Susanne Zabel
Author: Samira Breitling

Topic: CLINT: Clinical integrative genomics and transcriptomics analyses with application to breast cancer data from blood
Supervisor: Kay Nieselt / Olaf Riess
Author: Daniel Giesel

Topic: CLINT: Clinical integrative genomics and transcriptomics analyses with application to COVID-19 data
Supervisor: Kay Nieselt / Olaf Riess
Author: Sebastian Meyer 


Topic: Improving the reconstruction of very ancient mitochondrial genomes from non-human organisms
Supervisors: Kay Nieselt/Cosimo Posth/Mathias Witte Paz
Author: Meret Häusler

Topic: Interpretation of Neural Network Classifiers using Rule-based Models
Supervisors: Kay Nieselt/Jan Komorowski
Author: Mark Melzer

Topic: Applied Machine Learning for predicting metal binding sites in proteins
Supervisor: Kay Nieselt/Tjeerd Dijkstra/Wolfgang Fuhl/Caroline Jachmann
Author: Gizem Alsahan

Topic: Applying Shneiderman’s mantra to Evidente: Enhance zooming and aggregation for large taxonomic data
Supervisors: Kay Nieselt/Daniel Huson/Mathias Witte Paz
Author: Dolores Varga


Topic: A pipeline for the computational prediction of antibody targets
Supervisors: Kay Nieselt/Samuel Wagner/Simon Hackl
Author: Majd Hammour

Topic: Comparative modeling of Treponema pallidum variable protein regions
Supervisor: K. Nieselt/S. Hackl
Author: Jascha Henseler

Topic: Computational prediction of the 3' end of bacterial transcripts
Supervisor: K. Nieselt/C. Wolz
Author: Camill Kaipf

Topic: The OMPeome of Treponema pallidum
Supervisor: K. Nieselt
Author: Simon Hackl


Topic: Liver - adipose tissue cross-talk in obesity and Non-alcoholic Fatty Liver Disease (NAFLD) inferred by RNA-Seq data
Supervisor: K. Nieselt/M. Claassen
Author: Marvin Döbel

Topic: The manifold insights gained from TSS sequencing data analysed with TSSpredator and other computational methods
Supervisor: K. Nieselt/H. Groß
Author: Dilek Tuncbilek-Dere

Topic: From TSS prediction to transcriptome characterization
Supervisor: K. Nieselt/H. Groß
Author: Mathias Witte Paz

Topic: PhyloBlast
Supervisor: K. Nieselt/F. Götz
Author: Jennifer Müller

Topic: Comparison of expression conservation of orthologs and paralogs
Supervisor: K. Nieselt/N. Ziemert
Author: Huang Chin-Hua

Topic: Integrative Transcriptomics- and Proteomics Visualization
Supervisor: K. Nieselt/M. Krone
Author: Julian Fratte

Topic: Identification and distribution of Siderophore receptor genes in the bacterial kingdom
Supervisor: K. Nieselt/S. Heilbronner
Author: Gordon Armstrong


Topic: Using dRNA-seq to identify a non-clustered glycosyltransferase, essential for the production of brasilicardin A in Nocardia terpenica
Supervisor: K. Nieselt/Prof. H. Groß
Author: Tobias Schwarz



Topic: How bitter is Lactococcus lactus? An integrative genomic approach to identify genes of bitterness
Supervisor: K. Nieselt/Prof. H. Schmidt (Stuttgart)
Author: Robin Harmening

Topic: Genome architecture-aware mapping using the SuperGenome
Supervisor: K. Nieselt/N. Ziemert
Author: Friederike Hanssen


Topic: Visualization approaches for tumor evolution in liquid biopsy data
Supervisor: N. Gehlenborg (extern, Medical Harvard)/K. Nieselt
Author: Theresa Harbig

Topic: Representation of ME-models in SBML
Supervisor: O. Kohlbacher/K. Nieselt
Author: Marc Alexander Voigt

Topic: Single Cell RNA-seq for Plant Protoplasts
Supervisor: M. Timmermans/K. Nieselt
Author: Chong Lu

Topic: Application of NGS to the identification of antibiotic resistant bacteria
Supervisor: Prof. K. Musser (Wadsworth Center, Albany, USA)/K. Nieselt
Author: Wolfgang Haas

Topic: Large-scale Pangenomics
Supervisor: M. Pop, UMD (extern)/K. Nieselt
Author: Nils Oliver Schliebs


Topic: Integrative characterization of the house dust mite murine asthma model
Supervisor: K. Nieselt/Boehringer (extern)
Author: Kevin Menden

Topic: Studying Parasite-Host interaction
Supervisor: K. Nieselt/T. Dijkstra
Author: Fabian Mörtter

Topic: Phylogenetic reconstruction of genomes from ancient DNA and modern DNA
Supervisor: K. Nieselt/Prof. Fischer (Greifswald)
Author: Veronika Böttcher


Topic: Methods for time-series differential gene expression analysis
Supervisor: K. Nieselt/R. Neher
Author: Adrian Geißler

Topic: Metabarcoding workflows for Biodiversity assessment of belowground fungal communities
Supervisor: K. Nieselt/N. Ziemert
Author: Max Emil Schön

Topic: TSSpredator 2.0: Improved and enhanced transcription start site prediction
Supervisor: K. Nieselt/A. Herbig (J. Krause)
Author: Sven Fillinger

Topic: Evaluation and Extension of PASSAGE – Parallel Sequencing Systems for the Analysis of Gene Expression
Supervisor: K. Nieselt/H. Köhler
Author: Lucia Vedder


Topic: Testing framework and improved algorithms for ancient genome reconstruction
Supervisor: K.Nieselt/J. Krause
Author: Judith Neukamm



Topic: StreptoExpress – genomewide expression analyses of Streptomyces coelicolor
Supervisor: K. Nieselt
Author: Natalya Sabirova

Topic: From the SuperGenome to the Pangenome of Bacteria
Supervisor: K. Nieselt/F. Götz
Author: André Hennig


Topic: Bioprocess Data Modelling of Chinese Hamster Ovary Cells
Supervisor: K. Nieselt/O. Kohlbacher
Author: Julia Söllner

Topic: Efficient algorithms for Ancient Human Genome Reconstruction
Supervisor: K. Nieselt/J. Krause
Author: Alexander Peltzer

Topic: The SuperGenome of Staphylococcus aureus   
Supervisor: A. Herbig/K. Nieselt
Author: Linus Backert

Topic: Algorithms for the assembly of ancient genomes
Supervisor: K. Nieselt/J. Krause
Author: Volodymyr Piven

Topic: A new very fast mapping algorithm based on sorting
Supervisor: K. Nieselt/A. Herbig
Author: Jörg Peter


Topic: Prediction and Systematic Comparison of Non-Coding RNAs in the Bacteria Kingdom
Supervisor: A. Herbig/K. Nieselt
Author: Andreas Friedrich

Topic: The history and evolution of SNPs in Yersinia pestis
Supervisor: K. Nieselt/J. Krause
Author: Philip Stevens

Topic: Statistics with confidence in comparative metagenomics
Supervisor: K. Nieselt/D. Huson
Author: Max Schubach

Topic: Metagenomic Pathway Analysis
Supervisor: K. Nieselt/D. Huson
Author: Tim Scheurenbrand


Topic: A dynamic model of metabolism in Enterococcus faecalis
Supervisor: K. Nieselt/Prof. P. Wills (NZ)
Author: Markus List



Topic: 3D-Visualization Analytics for Transcriptomic Data
Supervisor: K. Nieselt/Prof. G. Scheuermann
Author: Günter Jäger



Topic: Automated Extraction of Variation Mentionas from Literature Sources and Mapping to a unique Database Identifier
Supervisor: K. Nieselt/Prof. P. M. Hofmann-Apitius
Author: Philippe Thomas



Topic: Predition of tissue specific enhancers in Caenorhabditis elegans
Supervisor: K. Nieselt/R. Sommer/C. Dieterich
Author: Philipp Drewe