SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
+49 381 498-7571
olaf.wolkenhauer@uni-rostock.de
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
2015

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
2013

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
2012

A systems biology approach to dynamic modelling of the AMP-activated kinase pathway
Frey S
2011

Stochastic Modelling of Subcellular Biochemical Systems
Ullah M
2009

Random set theory applied to the forecasting of stochastic point processes
Nuñez J
2002
Master theses

A Machine Learning approach to identify White Blood Cells
Mariam Nassar
2018

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 https://triplexrna.org.

Next Generation Sequencing Data Analysis of Stem Cell Derived Cardiomyocyte Cell Types
Markus Wolfien
2014
M.Sc. within the study degree of Medical Biotechnology

Analysis of the carbon flow in response to iron supply in Clostridium acetobutylicum
Berger C
2012

Effect of enzyme-complexes on the efficiency of metabolic pathways
Krey T
2012

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
2012

Detection of potential drug targets in cancer signaling by mathematical modelling and optimization
Khan FM
2012

Investigation of mammalian microRNA biogenesis by use of mathematical modeling
Freiesleben S
2011

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
2009

Mathematical modelling and mathematical optimisation of biochemical systems: a method of analysis in biotechnology and biomedicine
Lai X
2007

Development of a SBToolbox module to analyse Power-Law Models
Sun C
2006

Significance Analysis for Microarray Data
Kutalik Z
2003
Studienarbeiten

Network analysis of cardic stem cell...
Matti Hoch
2017
Bachelor thesis within the study degree of Medical Biotechnology

Visualising sub-networks in SBML models
Tom Gebhardt
2015
further information at the SEMS Webpage.

Classifying reactions of computational models
Lambusch F
2015
Further information at the SEMS webpage.
The thesis is available online (PDF).

Bestimmung von Distanzen zwischen Versionen XML - kodierter biologischer Modelle
Alm R
2012

The impact of iron limitation on growth and product spectrum of Clostridium acetobutylicum
Berger C
2012

Ansäuerungsleistung und Sauerstoffverbrauch von Säugetierzellen im extrazellulären Medium
Pauleweit S
2007

Bifurkation analysis of the Hes1 oscillator
Oertel Y
2007

Molecular Dynamics Simulation
Raasch P
2007

Konzipierung und Erstellung eines Interfaces zum Export von Matlab SBmodel Modellen nach SBML
Drews G
2006

Detektion charakteristischer Muster in Proteininteraktionsnetzwerken
Bittig A
2005
Diplomarbeiten

Versioning Concepts and Technologies for Biochemical Simulation Models
Hälke R
2010

Biological Aging, Negligible Senescence and the Concept of Renewal: A Complex Systems Approach by Memory Evolutive Systems
Haufschild M
2010

Optimierung von Stimulusprofilen zellbiologischer Experimente durch mathematische Modellierung
Krause M
2010

Simulation der Messung eines Cell Monitoring Systems (Modellbildung und Parameterschätzung)
Pauleweit S
2008

A JAVA framework to integrate ncRNA detection methods
Raasch P
2008

Erstellung eines Parameter Estimation Frameworks für die Systems Biology Toolbox for Matlab
Drews G
2007

Combined Visualisation of Pathway and Protein-Protein Interaction Data
Bittig A
2006

Zur Bestimmung sequenzabhängiger Zusammenhänge zwischen Transkriptom und Proteom
Weber I
2004