Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Research Projects

Our group deals with wide range of research topics wherein the nonlinear dynamic nature of interactions and behaviors are being observed. Members of our team have diverse backgrounds spanning biology, biochemistry, engineering, physics and mathematics. But in general, the focus of our projects is about the universal principles by which cells function (growth, apoptosis, proliferation, differentiation).

Research Projects

A systems methodology to assess the risk of tumor relapse in melanoma by the profiling of plasma extracellular vesicles - MelEVIR
Cancer
The aim of the project is to develop, test and prepare for translation into clinical practice a systems-biology-based diagnostic tool for assessing the probability of tumor relapse in melanoma patients, based on the profiling of pEVs. In the methodology proposed, in vitro and clinical data are integrated using data-driven mathematical modeling. The insights obtained from patient data analysis, reconstruction of biochemical networks, and model simulations are used to a) select a set of microRNAs, long non-coding RNAs, and proteins present in pEVs of patients to be measured in a blood test as surrogates of immune system activity against MRD and b) assess the probability of tumor relapse in the close future.
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Systematic Rebuilding of Actinomycetes for Natural Product Formation - SYSTERACT
Microorganisms
The main objective of the SYSTERACT project is through an integrated and interdisciplinary approach to develop the model actinomycete Streptomyces coelicolor into a 'Superhost' for the efficient heterologous production of bioactive compounds, enabling a faster discovery of new antibiotics from environmental microbial resources (microbial strains and metagenomes). Central to this approach will be an iterative Systems Biology process, combining microbiology, genetics, biochemistry, and fermentation technology with modelling.
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Summer School on The Integration of Data and Models in Medicine (IDaMo)
The School brings together PhD students, postdocs and senior scientists, coming from medicine, biostatistics, bioinformatics, medical informatics, molecular/cell biology, epidemiology, and systems biology. The four day workshop will be structured into six parts, covering these six areas.
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Helmholtz Virtual Institute of Complex Molecular Systems in Environmental Health - HICE
System Theory
Helmholtz Virtual Institute in Aerosol & Health Research is funded by the Helmholtz Association led by the Helmholtz Zentrum München and the University of Rostock in European cooperation with 8 academic partners and 6 associated partners. The project started in January 2012 as a five-year project.
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Complex DNA lesions and their impact on cellular radiation response (Collar)
Radiation
The investigations will deepen our knowledge on the impact of radiation-induced complex DNA lesions with spinoffs for radiation protection and the development of new, advanced tumor therapy strategies.
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Coordinating Systems Medicine across Europe (CASyM)
The Coordinating Action Systems Medicine (CASyM) is a multidisciplinary European consortium that joined forces to develop an implementation strategy (road map) for Systems Medicine. The CASyM road map is driven by clinical needs: It aims to identify areas where a systems approach will address clinical questions and solve clinical problems.
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SBGN-ED
An extended editor for the Systems Biology Graphical Notation.
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de.NBI:SYSBIO
Data Management node in the German Network for Bioinformatics Infrastructure
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Systems Biology of E2F Signaling in Tumor Progression and Metastasis (SysMet)
Cancer
This project is to generate and analyze a computational multilevel model of a signaling network that has a key role in tumor progression and metastasis. The project brings together an experienced group of modelers with an internationally renowned group in cancer research with a leading role on E2F1 signaling, investigating for the first time the impact of E2F1 on cancer aggressiveness using a systems approach.
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Models, Mechanisms, Complexity. To a Philosophy of Systems Biology.
System Theory
The emergence of systems biology signaled a shift of focus, away from the molecular characterization of individual components, towards an understanding of functional activity. The field is however also too focused on pathway-centric approaches, mechanistic models and subcellular processes. It is increasingly evident that the behavior of cells is largely dependent upon influences from the environment. New approaches are thus required to integrate processes at the molecular and cell level with those at higher levels of structural and functional organization (e.g. tissues and tissue physiology). We argue that this calls for a rethinking of what systems biology should be about (the search for organizing principles) and that new approaches are required to tackle biological complexity. To this end we promote Mathematical General Systems Theory, multilevel modeling, and theorem proving as a way forward. In this project we are going to discuss the role of mathematical models, the notion of mechanisms and biological complexity in systems biology.
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Reactive Oxygen Species and the Dynamics of Ageing. A Mitochondrial Multi-gene, Multi-organ Approach (ROSAge)
Aging
It is widely assumed that mitochondrial dysfunction and subsequent ROS (Reactive Oxygen Species) production are crucial players in ageing. However, the specific role of mitochondrial pathways in the onset and progression of degeneration and ageing is still unclear, as is the degree of interplay among organs in the ageing process. We hypothesise that impairing mitochondrial respiratory function leads to oxidative stress and ROS production. This induces DNA damage, inflammation and, ultimately, cell senescence and ageing.
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Quantitative Modelling of Stem Cell Dynamics
Stem Cells
The adult tissue of an organism includes stem cells, which through cell division cycles maintain and regenerate the functional tissue through differentiation and maturation. With regard to stem cell dynamics our research focus is on multilevel systems. Multilevelness is a defining characteristic of complex systems. The behavior of the system "as a whole" is considered to emerge from the functioning and interactions of its parts. What we are seeking is a conceptual (mathematical) framework to analyse how the "fate" of the tissue is an emergent property that inherently arises from the complex yet robust underlying biology of stem cells. Without specifying how the emergence takes place, the concept has almost a mystical character; it is an observation rather than a contribution to understanding the phenomenon. For understanding it is necessary to identify how the behavior of the whole changes when the parts and/or interactions between them change. Understanding cross-level relations in complex systems is key to "demystifying" the concept of emergence.
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Analysis and simulation of electrical interactions of implants with bio-systems (WELISA).
An important aspect of the development of biofunctional implant surfaces is a better understanding of the influence of micro- and nanastructured materials on cells growing on surfaces. The theoretical analysis of the adhesion is limited to adult cells. But it is known that the accretion of the cells happens in two phases. One is the passive phase containing the adhesion and migration of the cell depending to the properties of the surface.
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Identification and functional analysis of microRNAs involved in malignant melanoma progression (MicroRna)
Cancer
MicroRNAs (miRNAs) are endogenous, small, non-coding ~22 nt RNA molecules that have emerged as a major class of regulatory genes for diverse range of biological functions. In our preliminary studies, we were able to demonstrate that primary melanoma show a distinct miRNA expression pattern compared with benign melanocytic nevi. The aim of the present project is to identify and functionally characterize miRNAs that might play a role during further melanoma progression (metastasis).
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Mathematical modeling of transport process at the blood brain barrier
Alzheimer
Aβ aggregation inside the brain is one major aspect of Alzheimer's disease. The appearance of Aβ plaques is highly correlated with the decline of brain activity. It is therefore necessary to understand the mechanisms regulating Aβ production, Aβ degradation and removal from the brain. The aim of the project is to develop an integrated model to understand the dynamics of Aβ aggregation and its transport through the blood brain barrier.
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Transformation of scientific knowledge in the life sciences - changes in the understanding of the living cell (ExCell)
ExCell is a joint project investigating the changed understanding of the living cell in science. The task for the project partners is to investigate the transformation of scientific knowledge in the life sciences in a comprehensive and interdisciplinary way. For the first time, the shift in paradigm, concerning the understanding of cellular processes in the context of the digital revolution in light microscopy and systems biology, is scrutinized.
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BMBF Junior Research Groups

The junior research groups focus on cancer and aging related research.

Simulation Experiment Management for Systems Biology (SEMS)
Systems biology is a scientific approach characterised by an iterative cycle of data-driven modelling and model-driven experimentation. The present project is to provide support for this iterative cycle through techniques and tools that improve and ease the working with simulation setups, using standard formats and ensuring result reproducibility.
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Nonlinear dynamics of biochemical networks in pancreatic cancer: From experimental data to mathematical models (FORSYS)
Cancer
This project combines theoretical and experimental systems biology to challenge pancreatic cancer (PC), a tumour disease with a very poor prognosis. It is focused on mathematical modelling of chemical kinetics and transport processes in biochemical reaction networks of PC cells. The model properties are analysed with methods of dynamical systems theory and methods of experimental design to understand, predict and improve the cellular response to chemotherapy. This effort is supported by quantitative cell biology, and the development of experimental techniques for systems biology.
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Completed Projects

Research projects we take part in producing research outputs by maintaining close collaborations.

Combining standards for today's models -- Volkswagen summer school 2015
The goal of this summer school is to encode the whole-cell model -- a popular model of the whole cell -- in standard formats. The summer school will take place in March 2015 in Rostock, Germany.
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Systems Biology of Clostridium acetobutylicum (COSMIC)
Microorganisms
Clostridium are bacteria which evolved before the earth had an oxygen atmosphere. To them the air we breathe is a poison. To survive they produce a spore resting stage, resistant to physical and chemical agents. Some species cause devastating diseases, such as the superbug Clostridium difficile. On the other hand, most are totally harmless, and make a wide range of chemicals useful to man. The best example is Clostridium acetobutylicum which makes butanol.
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Influence of micro- and nanostructered titanium surfaces on surrounding bio-systems (CeMaTif)
It is well known that cells react on chemical or topographical alterations of the surfaces they are attached to. Despite that, the underlying mechanisms causing these interactions are most widely unknown. Thus, the DFG funded project CeMaTif, consisting of four research groups from Rostock and Tübingen, aims at a better understanding of the influences which micro- and nanostructured titanium surfaces exert on adjoining biosystems.
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Photorespiration: Origins and metabolic integration in interacting compartments (PROMICS)
Plant Physiology
The PROMICS project addresses the cellular biology and metabolic integration of photorespiratory processes in the context of carbon metabolism (C3, C4 and cyanobacteria), stress response and productivity. The photorespiration is the result of the oxygenase pathway, see the picture below, of the rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) which leads to the reduced rates of photosynthetic CO2 assimilation, making photorespiration a wasteful process. However, it is just this inefficiency which can significantly decrease the photoinhibition or high temperature stress. The question arises where is the balance between the protection and crop yield or if the photorespiration is essential process at all.
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System Biology approaches to radiation biodosimetry and the analysis of individual radiosensitivity
Radiation
Protection of humans from the adverse effects of ionizing radiation is a major goal of the Radiation Protection field. In the case of accidental exposures to radiation the development of effective counter measures requires information on the actual exposure dose as well as knowledge on the individual radiosensitivity of the exposed group of individuals. The major scientific goal of this project is to identify suitable sub-sets of genes which correspond to the expression patterns and correlate this information with radiation dose and radiation quality. In addition, it will investigate the effects of single nucleotide polymorphisms on the individual radiation susceptibility and their influence on the proposed biodosimetry system.
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Mathematical modeling of Neurodegenerative Processes in Alzheimer's Disease (MSBN)
Alzheimer
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by amyloid plaques in the brain of affected individuals. This project aims at modelling of neurodegenerative processes in AD. Our study focuses on the interactome of neuronal factors central to the proteolytic processing of amyloid precursor protein (APP) into Aβ, the main constituent of senile plaques. Factors considered in this model include proteases, trafficking adaptors, as well as a novel sorting receptor SORLA.
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Integrative development of modeling and simulation methods for regenerative systems (dIEM oSIRIS)
Parkinson
The ability of regeneration characterizes cell biological systems and is increasingly required for computer science systems as well. The Graduate School "dIEM oSiRiS" is a DFG-funded research training group. It brings together researchers from Medicine, Biology and Computer Science and contributes towards achieving new insights into the functioning of biological cell systems, establishing modelling and simulation as an experimental methodology in Biology, and developing innovative modelling and simulation methods and tools from which the understanding and the design of regenerative systems in general will benefit.
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Modelling carbon core metabolism in Bacillus subtilis - Exploring the contribution of protein complexes in core carbon and nitrogen metabolism (BaCell-SysMo2)
Microorganisms
The BaCell project is part of the SysMo transnational network, an initiative focusing on approaches on the application of Systems Biology to microorganisms. In the BaCell project, our interest is to gain a better understanding of the dynamics of the transition from exponential to stationary growth phase in Bacillus subtilis. Obtaining knowledge in this model organism provides twofold advances: First, elucidating the fundamental processes in bacterial growth and stress response. Second, Bacillus subtilis is used in many biotechnological applications, thus our research improves production of medical drugs and consumer goods.
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Investigating the Cancer and Aging Link through Systems Biology (CALSYS)
Cancer
Recent experimental evidences suggest that cancer progression and aging could be linked at the cellular level by the abnormal function of some signalling pathways, cellular systems in charge of identifying and processing the external signals received by the cell. Those mechanisms protect our cells against external or internal insults that damage their genetic material. Leaded by the protein p53, the so-called DNA damage master controller, these processes repair the inflicted DNA damage but also take additional measures to avoid these genetic errors to be transferred to new cells. Depending on the severity of the damage, p53 can trigger a transient/permanent stop of cell replication or the programmed cellular death (apoptosis) in a strategy to kill some damaged cells but save the whole organism. Imbalance between these processes is very often present in different phases of cancer progression, but also is one of the sources of aging in the organism.
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SYSBIOMED - Systems biology for medical applications
System Theory
Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves (COSMIC-SysMo)
Microorganisms
The transition from growing to non-growing Bacillus subtilis cells - A systems biology approach (BaCell-SysMo)
Microorganisms
Systems biology of the AMP-activated protein kinase pathway (AMPKIN)
Diabetes
Computational Systems Biology of cell signalling (COSBICS)
Cancer
Microorganisms
Exploring coordination and control in cell signalling (ECCCS)
Parkinson
Modelling and simulation in cell signalling (MOSAICS)
Chorea Huntington
Dynamic behaviour in cell signalling
Cancer
Pathway identification from a given stimulus-response behaviour
Tuberculosis
Micro-array research, innovation, and exploitation (MARIE) consortium
Microorganisms

Aging
Aging
Stem Cells
Stem Cells
Plant Physiology
Plant Physiology
System Theory
System Theory
Alzheimer
Alzheimer
Cancer
Cancer
Diabetes
Diabetes
Parkinson
Parkinson
Chorea Huntington
Chorea Huntington
Microorganisms
Microorganisms
Radiation
Radiation
Tuberculosis
Tuberculosis