Systems Biology

The ISYS Systems Biology team is engaged in the application and development of methods of Systems Theory in Biology. Our focus lies on mechanism-based modeling, model reduction and model analysis of metabolic and signal transduction networks. For this purpose, we perform both experimental and theoretical work. The ISYS is part of the Stuttgart Research Center Systems Biology (SRCSB) at the University of Stuttgart.

Systems biology requires a tight integration of experimental and theoretical expertise. We collaborate with several experimental and theoretical groups. Details are given in the project descriptions.

 

Research Projects
EnzCaps: Development of encapsulated multi-enzyme complexes
  • Cell-free synthesis of complex products in organic solvents using synthetic microcapsules.
  • Modeling and optimization of coupled enzyme reactions in dependency of various solvents.
  • Metabolic control analysis and population dynamics.
RecogNice: Modeling regulation of carbon, oxygen and nitrogen in large-scale processes
  • Avoidance of production yield losses at scale-up.
  • Simulation in a Plug-Flow-Reactor with metabolite and transcriptome measurements (next generation sequencing).
  • Influence of cyclic oxygen limitation on the growth rate.
  • Combination of metabolic and regulatory models.
Virtual Liver: Modeling the LPS-induced inflammatory reaction
  • Modeling the bacterial (LPS-induced) inflammatory response of the liver as well as the crosstalk to apoptotic signaling
  • Model analysis and discrimination for the improved understanding of the underlying biochemical processes
  • Identification of biomarkers which control the inflammatory response
ZeBiCa2: Cell-free biomineralization
  • Modelling and analysis of the central metabolism of Emiliana huxleyi.
  • Flux balance analysis for organisms with circadian rhythms.
  • In vitro synthesis of highly structured calcium carbonate particles for uses in medical technology, optics and material sciences.
 
Z-Fuels: Optimization of acetaldehyde production
  • Stoichiometric and kinetic modeling of the metabolism of Zymomonas mobilis.
  • Model-based prediction of genetic interventions for optimal culture condition for improved yields of acetaldehyde.
  • Model predictive control of the bioreactor with integrated micro-bubble destillation.
 
Completed Projects
 

 

Student's Theses

We are always looking for students who want to contribute to one of our research projects through bachelor's or master's thesis. If you are interested please do not hesitate to contact us.

 

Publications of the Sytems Biology Team
Journal Papers
  • J. Rex, U. Albrecht, C. Ehlting, M. Thomas, U. M. Zanger, O. Sawodny, D. Häussinger, M. Ederer, R. Feuer & J. G. Bode, “Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages”, PLoS Computational Biology, 2016, doi:10.1371/journal.pcbi.1005018
  • J. von Wulffen, O. Sawodny & R. Feuer, “Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis”, PLoS One, 11, pp. e0158711, 2016, doi:10.1371/journal.pone.0158711
  • R. Feuer, S. Vlaic, J. Arlt, O. Sawodny, U. Dahmen, U. M. Zanger & M. Thomas, “LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods”, PLoS One, 10, 2015, doi:10.1371/journal.pone.0135852
  • D. Knies, P. Wittmuess, S. Appel, O. Sawodny, M. Ederer & R. Feuer, “Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach”, Metabolites, 5, pp. 659-676, 2015, doi:10.3390/metabo5040659
  • M. Ederer, S. Steinsiek, S. Stagge, M. D. Rolfe, A. T. Beek, D. Knies, M. J. T. de Mattos, T. Sauter, J. Green, R. K. Poole, K. Bettenbrock & O. Sawodny, “A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen”, Frontiers in Microbiology, 5, pp. 124, 2014, doi:10.3389/fmicb.2014.00124
  • S. Henkel, B. A. Ter, S. Steinsiek, S. Stagge, K. Bettenbrock, de Mattos J. Teixera, T. Sauter, O. Sawodny & M. Ederer, “Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions”, PLoS One, 9, 2014, doi:10.1371/journal.pone.0107640
  • A. Lutz, J. Sanwald, M. Thomas, R. Feuer, O. Sawodny, M. Ederer, C. Borner, M. Humar & I. Merfort, “Interleukin-1beta Enhances FasL-Induced Caspase-3/-7 Activity without Increasing Apoptosis in Primary Mouse Hepatocytes”, PLoS One, 9, pp. 1-27, 2014, doi:10.1371/journal.pone.0115603
  • J. Bona-Lovasz, A. Bona, M. Ederer, O. Sawodny & R. Ghosh, “A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria”, Metabolites, pp. 912-930, 2013, doi:10.3390/metabo3040912
  • J. Klotz, R. Feuer, O. Sawodny, M. Bossert, M. Ederer & S. Schober, “Properties of Boolean Networks and Methods for Their Tests”, EURASIP Journal on Bioinformatics and Systems Biology, 2013, doi:10.1186/1687-4153-2013-1
  • R. Feuer, K. Gottlieb, G. Viertel, J. Klotz, S. Schober, M. Bossert, O. Sawodny, G. A. Sprenger & M. Ederer, “Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol”, EURASIP Journal of Bioinformatics and Systems Biology, 14, 2012, doi:10.1186/1687-4153-2012-14
  • J. Witt, F. Konrath, O. Sawodny, M. Ederer, D. Kulms & T. Sauter, “Analyising the role of UVB-induced Translational Inhibition and PP2Ac Deactivation in NF-kB Singanlling Using Minimal Mathematical Model”, PLoS Computational Biology, 2012, doi:10.1371/journal.pone.0040274
  • M. Ederer, E. Gilles & O. Sawodny, “The Glansdorff-Prigogine stability criteria for biochemical reaction networks”, Automatica, 47, pp. 1097-1104, 2011, doi:10.1016/j.automatica.2011.01.072
  • R. Schlatter, N. Philippi, G. Wangorsch, R. Pick, O. Sawodny, C. Borner, J. Timmer, M. Ederer & T. Dandekar, “Integration of Boolean models exemplified on hepatocyte signal transduction”, Briefings in Bioinformatics, 13, pp. 365-376, 2011, doi:10.1093/bib/bbr065
  • R. Schlatter, K. Schmich, A. Lutz, J. Trefzger, O. Sawodny, M. Ederer & I. Merfort, “Modeling the TNFa-Induced Apoptosis Pathway in Hepatocytes”, PLoS One, 6, 2011, doi:10.1371/journal.pone.0018646
  • H. Sebastian, T. Nägele, I. Hörmiller, T. Sauter, O. Sawodny, M. Ederer & A. G. Heyer, “A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana”, EURASIP Journal on Bioinformatics and Systems Biology, 2011, doi:10.1186/1687-4153-2011-2
  • J. Witt, S. Barisic, O. Sawodny, M. Ederer, D. Kulms & T. Sauter, “Modeling Time Delay in the NFkappaB Signaling Pathway following Low Dose IL-1 Stimulation”, EURASIP Journal on Bioinformatics and Systems Biology, 2011, doi:10.1186/1687-4153-2011-3
  • R. Schlatter, H. Conzelmann, E. Gilles, O. Sawodny & T. Sauter, “Analysis of an apoptotic core model focused on experimental design using artifical data”, IET Systems Biology, 3, pp. 255-265, 2009, doi:10.1049/iet-syb.2008.0138
  • R. Schlatter, K. Schmich, I. A. Vizcarra, P. Scheurich, T. Sauter, C. Borner, M. Ederer, I. Merfort & O. Sawodny, “ON/OFF and Beyond - A Boolean Model of Apoptosis”, PLoS Computational Biology, 5, pp. e1000595, 2009, doi:10.1371/journal.pcbi.1000595
  • J. Witt, S. Barisic, E. Schumann, F. Allgöwer, O. Sawodny, T. Sauter & D. Kulms, “Mechanism of PP2A-mediated IKK dephosphorylation: a systems biological approach”, BMC Systems Biology, 2009, doi:10.1186/1752-0509-3-71
  • R. Feuer, M. Ederer, E. Gilles, G. Sprenger, O. Sawodny & T. Sauter, “Analyse der evolutiven Adaptation am Beispiel einer pyruvat-auxotrophen Escherichia coli-Mutante”, at - Automatisierungstechnik, pp. 257-268, 2008
Conference Papers
  • J. Sanwald, U. Albrecht, J. Wagenpfeil, M. Thomas, O. Sawodny, J. G. Bode & R. Feuer, “Modeling the LPS-induced Effects on Transcription Factor Activation and Gene Expression in Murine Macrophages”, International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Milano, Italy, 2015, pp. 3989-3992, doi:10.1109/EMBC.2015.7319268
  • J. G. Klotz, S. Schober, M. Ederer, G. Sprenger, M. Bossert & O. Sawodny, “Prediction of Regulatory Impact under Defined Environmental Conditions Based on a Combination of Metabolic and Transcriptional Networks”, International Workshop on Computational Systems Biology (WCSB), 2012
  • R. Feuer, K. Gottlieb, J. G. Klotz, S. Schober, M. Bossert, O. Sawodny, G. A. Sprenger & M. Ederer, “Model-based analysis of adaptive evolution”, International Workshop on Computational Systems Biology (WCSB), Zurich, Switzerland, 2011
  • J. G. Klotz, R. Feuer, K. Gottlieb, O. Sawodny, G. A. Sprenger, M. Bossert, M. Ederer & S. Schober, “Properties of a Boolean network model of Escherichia coli”, International Workshop on Computational Systems Biology (WCSB), Zurich, Switzerland, 2011
  • M. Ederer, R. Schlatter, J. Witt, R. Feuer, J. Bona-Lovasz, S. Henkel & O. Sawodny, “An Introduction to Kinetic, Constraint-Based and Boolean Modeling in Systems Biology”, IEEE Conference on Control Applications (CCA), Yokohama, Japan, 2010, pp. 129-134, doi:10.1109/CCA.2010.5611136
  • S. Henkel, T. Nägele, I. Hörmiller, T. Sauter, O. Sawodny, M. Ederer & A. G. Heyer, “A systems biology approach to analyze diurnal dynamics of carbohydrate metabolism in a plant leaf”, International Workshop on Computational Systems Biology (WCSB), 2010, pp. 47-50
  • F. Ronny, J. Bona-Lovasz, O. Sawodny, R. Ghosh & M. Ederer, “The impact of the intracellular membrane formation on the central metabolism of Rhodospirillum rubrum”, International Workshop on Computational Systems Biology (WCSB), Luxembourg, 2010
  • R. Schlatter, D. Knies, M. Ederer & O. Sawodny, “Analysis of Boolean Models using Quality Assurance Methods from Software Engineering”, IEEE Conference on Control Applications (CCA), Yokohama, Japan, 2010, pp. 518-523, doi:10.1109/CCA.2010.5611070
  • R. Feuer, M. Ederer, N. Trachtmann, T. Sauter, E.-D. Gilles, G. Sprenger & O. Sawodny, “Methods for analysis of evolutive adaptation of E.coli”, SICE Conference, Kagawa, Japan, 2007, pp. 1359-1365, doi:10.1109/SICE.2007.4421194
  • J. Witt, S. Husser, D. Kulmns, S. Barisic, O. Sawodny & T. Sauter, “Modeling of IL-1 induced NF-kB signaling and analysis of additional UVB influence”, SICE Conference, Kagawa, Japan, 2007, pp. 1353-1358, doi:10.1109/SICE.2007.4421193
  • J. Witt, S. Husser, D. Kulms, S. Barisic, O. Sawodny & T. Sauter, “Modeling and Analysis on IL-1 induced NF-kB signaling”, FOSBE Conference, Stuttgart, Germany, 2007
  • T. Eissing, S. Waldherr, C. Gondro, E. Bullinger, O. Sawodny, F. Allgöwer, P. Scheurich & T. Sauter, “Sensitivity Analysis of Programmed Cell Death and Implications for Crosstalk Phenomena during Tumor Necrosis Factor Stimulation”, IEEE Conference on Control Applications (CCA), Munich, Germany, 2006, pp. 1746-1752, doi:10.1109/CACSD-CCA-ISIC.2006.4776905

 

Members of the Systems Biology Team
Dipl.-Biol. (t.o.) Julia Rex mailto icon julia.rex
Dipl.-Biol. (t.o.) Julia Lischke mailto icon julia.lischke
M. Sc. David Knies mailto icon david.knies
Dipl.-Biol. (t.o.) Joachim von Wulffen mailto icon joachim.von-wulffen