PhD theses

Improving Reproducibility and Reuse of Modelling Results in the Life Sciences

Scharm M

Research results are complex and include a variety of heterogeneous data. This entails major computational challenges to (i) to manage simulation studies, (ii) to ensure model exchangeability, stability and validity, and (iii) to foster communication between partners. I describe techniques to improve the reproducibility and reuse of modelling results. First, I introduce a method to characterise differences in computational models. Second, I present approaches to obtain shareable and reproducible research results. Altogether, my methods and tools foster exchange and reuse of modelling results.

Defense: 30 August 2018

An investigation of microRNA target regulation mechanisms using an integrative approach

Schmitz U


Transcriptional Responses to Radiation Exposure Facilitate the Discovery of Biomarkers Functioning as Radiation Biodosimeters

Strunz S

The development of new methods for a retrospective quantification of the radiation dose of exposed individuals is of widespread interest. To this end, I developed a computational framework for biomarker discovery and radiation dose prediction and successfully identified gene signatures with which low and medium to high radiation doses can be accurately quantified. To enhance our understanding of the radiation-induced transcriptional response, I additionally analyzed microarray data of human PBLs after ex vivo gamma-irradiation and characterized affected functional processes and pathways.

Defense: 13 May 2014

Compartmental Modelling of the Wnt pathway

Schmitz Y

The Wnt pathway plays a critical role in development and disease. The key player of the pathway is b-cat. In the nucleus, the complex formation of b-cat and TCF initiates target gene expression. Its activity is mainly regulated by retention and degradation by its antagonists APC, Axin and GSK3. Based on experimental findings, I develop and investigate compartmental models in order to analyse of the role of nucleo-cytoplasmic shuttling of these proteins in Wnt signalling. I show that the compartmental separation of b-cat and its antagonists yields an increase of the b-cat/TCF concentration.

Defense: 19 December 2013

Characterisation of Signalling Pathways of pancreatic epithelial and cancer tissue using systems biology

Lange F


A Systems Biology Approach to Understand the Influence of SORLA on Amyloidogenic Processing in Alzheimer's Disease

Lao A

In this dissertation APP processing is modelled and the influence of SORLA in Alzheimer’s disease is evaluated. A model with both monomeric and dimeric APP in a single compartment best fitted the experimental data suggesting that SORLA prevents APP oligomerization and affects β-secretase indirectly. Including compartmental details into the combined model, the multi-compartmental model determines the relative contribution of SORLA to each APP-cleavage step showing that SORLA specifically impairs the processing of APP dimer and alters the dynamical behavior of beta-secretase.

Defense: 29 January 2013

Regulation of the general stress response of Bacillus subtilis

Liebal U

The bacterium Bacillus subtilis lives in the environmentally diverse soil habitat. Various environmental signals are sensed by the stressosome protein complex. Stimulation of the stressosome modifies its phosphorylation patterns and activates a signalling cascade that lead to protein expression changes. The thesis introduces models to study structural processes and signalling principles of the stressosome. Overall, the thesis enhances our understanding of the SigmaB-mediated general stress response and raises our awareness of the environmental integration of B. subtilis.

Defense: 4 February 2013

A systems biology approach to unravel the cellular function of microRNAs

Lai X


A systems biology approach to dynamic modelling of the AMP-activated kinase pathway

Frey S


Stochastic Modelling of Subcellular Biochemical Systems

Ullah M


Random set theory applied to the forecasting of stochastic point processes

Nuñez J


Master theses

A Machine Learning approach to identify White Blood Cells

Mariam Nassar


Design of the TriplexRNA: a database of cooperating microRNAs and their mutual targets

Andrea Bagnacani

MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Single miRNAs can repress the expression of many genes, however, experimental evidence suggest that their repressive effect alone is rather mild compared with that carried out by cooperating miRNAs. Although synergistic target regulation has been confirmed as a prevalent pattern in gene regulation, the mechanism behind this phenomena are little known, and it is unclear which miRNA pairs and gene targets are involved in the formation of RNA triplexes. The growing amount of data on miRNA-mediated gene expression is motivated by the role they play in cellular functions, where their presence can be correlated with cancers, and cardiovascular diseases, making them good biomarkers for diagnostic and prognostic purposes. However, existing databases relate disease associations with the duplex model: one miRNA inhibiting the expression of one or many genes, while none of them provide an exploration of the more effective regulation operated by synergistic pairs. To overcome this gap, the present work describes the design and implementation of the TriplexRNA: a database of cooperating miRNAs and their mutual targets, which we realised to enable researchers explore novel patterns in gene regulation. The database can be accessed at

Next Generation Sequencing Data Analysis of Stem Cell Derived Cardiomyocyte Cell Types

Markus Wolfien


M.Sc. within the study degree of Medical Biotechnology

Analysis of the carbon flow in response to iron supply in Clostridium acetobutylicum

Berger C


Effect of enzyme-complexes on the efficiency of metabolic pathways

Krey T


Cloud based analysis of Health Data with RESTful Web Services

Daniar R


Computational identification of ADAR editing sites in microRNA precursors

Blitti A


Adaptation in networks of heterogeneous mitochondrial populations

Arumugam U


Detection of potential drug targets in cancer signaling by mathematical modelling and optimization

Khan FM


Investigation of mammalian microRNA biogenesis by use of mathematical modeling

Freiesleben S


Stochastic Modelling and Simulations: An Extended Crossover method for modelling noise in stiff/bistable biochemical systems.

Asim Anees

Electrical Engineering, 2011

Data Mining and Clustering in Model Calibration for Systems Biology

Shah AF


Mathematical modelling and mathematical optimisation of biochemical systems: a method of analysis in biotechnology and biomedicine

Lai X


Development of a SBToolbox module to analyse Power-Law Models

Sun C


Significance Analysis for Microarray Data

Kutalik Z



Network analysis of cardic stem cell...

Matti Hoch


Bachelor thesis within the study degree of Medical Biotechnology

Visualising sub-networks in SBML models

Tom Gebhardt

further information at the SEMS Webpage.

Classifying reactions of computational models

Lambusch F

Further information at the SEMS webpage.

Downloads & more:

The thesis is available online (PDF).

Bestimmung von Distanzen zwischen Versionen XML - kodierter biologischer Modelle

Alm R


The impact of iron limitation on growth and product spectrum of Clostridium acetobutylicum

Berger C


Ansäuerungsleistung und Sauerstoffverbrauch von Säugetierzellen im extrazellulären Medium

Pauleweit S


Bifurkation analysis of the Hes1 oscillator

Oertel Y


Molecular Dynamics Simulation

Raasch P


Konzipierung und Erstellung eines Interfaces zum Export von Matlab SBmodel Modellen nach SBML

Drews G


Detektion charakteristischer Muster in Proteininteraktionsnetzwerken

Bittig A



Versioning Concepts and Technologies for Biochemical Simulation Models

Hälke R


Biological Aging, Negligible Senescence and the Concept of Renewal: A Complex Systems Approach by Memory Evolutive Systems

Haufschild M


Optimierung von Stimulusprofilen zellbiologischer Experimente durch mathematische Modellierung

Krause M


Simulation der Messung eines Cell Monitoring Systems (Modellbildung und Parameterschätzung)

Pauleweit S


A JAVA framework to integrate ncRNA detection methods

Raasch P


Erstellung eines Parameter Estimation Frameworks für die Systems Biology Toolbox for Matlab

Drews G


Combined Visualisation of Pathway and Protein-Protein Interaction Data

Bittig A


Zur Bestimmung sequenzabhängiger Zusammenhänge zwischen Transkriptom und Proteom

Weber I