FORSYS-Partner Project

Publications

Links to the publication lists

• Partner P1: Andreas Kremling (MPI, Magdeburg)
• Partner P2: Knut Jahreis (Uni Osnabrück)
• Partner P3: Ursula Rinas (Helmholtz HZI, )
• Partner P4: Stefan Schuster (FSU, Jena)
• Partner P5: Reinhard Guthke (HKI, Jena)
• Partner P6: BioControl Jena

Publications

• Kaleta C, de Figueiredo LF, Schuster S (2009) Can the Whole Be Less Than the Sum of its Parts? Pathway Analysis in Genome-Scale Metabolic Networks Using Elementary Flux Patterns, Genome Research, 19(10), 1872-83.

• Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010) Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis, BMC Systems Biology, 4:116.

• Jahreis K (2010): cAMP Signaling in Prokaryotes. In Krämer, R. and Jung, K. (Eds.) Bacterial Signaling. Wiley-VCH, Weinheim, pp 357-375.

• Li Z, Kessler W, van den Heuvel J, Rinas U (2011) Simple defined autoinduction medium for high-level recombinant protein production for T7-based Escherichia coli expression systems. Appl. Microbiol. Biotechnol., 91, 1203-1213.

• Li Z,, Nimtz M, Rinas U (2011) Optimized procedure to generate heavy isotope and selenomethionine-labeled proteins for structure determination using Escherichia coli-based expression systems. Appl. Microbiol. Biotechnol., 92, 823-833.

• Jain G, Jayaraman G, Kökpinar Ö, Rinas U, Hitzmann B (2011) On-line monitoring of recombinant bacterial cultures using multi-wavelength fluorescence spectroscopy. Biochem. Eng. J., 58-59, 133-139.

• Wessely F, Bartl M, Guthke R, P. Li, Schuster S, Kaleta C (2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Molecular Systems Biology, 7:515.

• Göhler AK, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2011): More than just a metabolic regulator - elucidation and validation of new targets of the regulator PdhR in Escherichia coli, BMC Systems Biology, accepted

• Gabor E, Göhler AK, Kosfeld A, Staab A, Kremling A, Jahreis K (2011): The phosphoenolpyruvate-dependent glucose-phosphotransferase system from Escherichia coli K-12 as the center of a network regulating carbohydrate flux in the cell. Eur J Cell Biol 90(9):711-20.

• Schuster S, de Figueiredo LF, Schroeter A, Kaleta C(2011): Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach. BioSystems 105(2), 147-53.

• Kremling A (2012): Kompendium Systembiologie. Mathematische Modellierung und Modellanalyse. Lehrbuch. Vieweg+Teubner, 2012.

• Göhler AK, Staab A, Gabor E, Homann K, Klang E, Kosfeld A, Muus J-E, Wulftange JS, and Jahreis K (2012). Characterization of MtfA, a novel regulatory output signal protein of the glucose-phosphotransferase system in E. coli K-12. J. Bacteriol. 194:1024-1035

• Xu Q, Göhler AK, Kosfeld A, Carlton D, Chiu HJ, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Jahreis K, Wilson IA.(2012). Structure of Mlc Titration Factor A (MtfA/YeeI) Reveals a Prototypical Zinc Metallopeptidase Related to Anthrax Lethal Factor.J Bacteriol. 2012 Mar 30 .

Posters

• Wessely F, Kaleta C, Schuster S (2009):Flux coupling analysis meets gene expression, German Conference on Bioinformatics, Halle, 28.-30.09.2009

• Nikolajewa S, Friedel M, Guthke R (2009): Analysis of gene regulation in Escherichia coli. Proceedings on the International Moscow Conference on Computational Molecular Biology (MCCMB'09), Moskau, Russland, 20.-23.7.2009, pp.258.

• Bettenbrock K, Kremling A, Jahreis K, Rinas U, Schuster S, Pfaff M, Guthke R (2009): FORSYS-Partner-Project:Dynamics and regulation of the metabolic balance in Escherichia coli. German Symposium on Systems Biology, Heidelberg, 12.-15.5.2009.

• Nikolajewa S (Friedel S), Guthke R (2009): Comparison of information-theoretic algorithms for the inference of the gene regulatory network for Escherichia coli. German Symposium on Systems Biology, Heidelberg, 12.-15.5.2009.

• Schmidt-Heck W, Kökpinar Ö, Li Z, Geffers R, Rinas R, Guthke R (2010): Ensemble Learning of Gene Regulatory Networks in E. coli under recombinant protein production conditions. German Conference on Bioinformatics (GCB2010), Braunschweig, 20.-22.9.2010.

• Schmidt-Heck W, Kökpinar Ö, Li Z, Geffers R, Rinas R, Guthke R (2011): Regulatory motif discovery in gene expression time series of Escherichia coli under recombinant protein production conditions. International Conference on Systems Biology (ICSB2011), Heidelberg/Mannheim, 28.08.2011-01.09.2011.

• Kramer B, Bettenbrock K, Conradi C (2011): Integrated modelling and control of E. coli's central carbon metabolism. International Conference on Systems Biology (ICSB2011), Heidelberg/Mannheim, 28.08.2011-01.09.2011.

• Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C (2011): Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. International Conference on Systems Biology (ICSB2011), Heidelberg/Mannheim, 28.08.2011-01.09.2011.

Talks

• Bettenbrock K(2009): Model-based modification of cellular regulation in Saccharomyces cerevisiae and Escherichia coli. German Symposium on Systems Biology, Heidelberg, 12.-15.05.2009.

• Schuster S (University of Jena) Use of game-theoretical approaches in Systems Biology, German Symposium on Systems Biology, Heidelberg, 12.-15.05.2009.

• Kremling A(2009): Mathematical models for catabolite repression in E. coli: from the sensory system to the global transcriptional network. German Symposium on Systems Biology, Heidelberg, 12.-15.05.2009.

• Guthke R (2009): Modellierung der rekombinanten Produktbildung in E. coli. Sandoz GmbH, Kundl/Österreich, 26.02.2009.

• Friedel S, Kaleta C, Guthke R (2009): Comparison of Information - theoretical Algorithms for the Inference of Gene Regulatory Networks in Escherichia coli. International Workshop "Integrative Network Inference in Systems Biology", Jena, 08.-09.10.2009.

• Guthke, R. (2009): Data and Knowledge Integration in Systems Biological Dynamic Models. Systems Biology Workshop, Universität Skövde, Schweden, 9.-10.11.2009.

• Guthke R, Friedel S, Schmidt-Heck W, Dürrschmid K, Bayer K, Rinas U (2009): Inference of Gene Regulatory Networks in Escherichia coli by Transcriptome and Proteome Data Analysis. BioProScale Symposium "Inhomogenieties in large-scale bioreactors: Description – scaling – control", Berlin 24-27.11.2009.

• Guthke R (2010): Gene networks from high-throughput data – reverse engineering and analysis. Linköping University, Department of Science and Technology, Norrköping, Sweden, 26.3.2010.

• Guthke R (2010): Integration von Messdaten und Vorwissen in die dynamische systembiologische Modellierung. Kolloquium Universität Leipzig, Institut für Biochemie, 29.3.2010.

• Bettenbrock K (2010): Systemsteuerung: Biomolekulare Mess-, Steuer- und Regeltechnik-Vom Gen zum Produkt. Auftaktkongress zum Strategieprzess Nächste Generation biotechnoloigischer Verfahren , Berlin, 8.07.2010.

• Kremling A, Bettenbrock K, Nees M (2010): From Systems Biology to Systems Biotechnology – A Modeller’s Perspective. Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Rinas U, Kökpinar Ö, Li Z (2010): Protein Production Related Alterations of Central Carbon Metabolism in E. coli.Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Kaleta C, Wessely F (2010): Modelling Metabolic Processes during Recombinant Protein Production by E. coli. Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Schmidt-Heck W (2010): Modelling of Gene Expression during Recombinant Protein Production by E. coli. Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Driesch D, Pfaff M (2010): Integrative Analysis of Transcriptomic and Proteomic Data from E. coli. Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Jahreis K, Kosfeld A, Goehler A (2010): The Glucose-PTS of E. coli as a Key to Metabolic Balance. Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Schuster S, Schröter A (2010): Biotechnological Relevance of Cooperation and Competition in Exoproduct. Int. Workshop „Systembiologie für die Industrie: Dynamik und Regulation der metabolischen Balance in Escherichia coli“, Jena, 7./8.10.2010.

• Guthke R (2010): Zur Bedeutung der Bioinformatik im Kontext der „omics“-Technologien. JeTT – Jenaer Technologietag, Fachhochschule Jena. Jena, 8.11.2010.

• Kaleta C (2011): Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Workshop Integration of OMICs datasets into Metabolic Pathway Analysis (IOMPA), Heidelberg, 02.09.2011.

• Kaleta C (2011): Identification of global principles in the control of metabolic pathways in Escherichia coli. Workshop Biomolecular Circuit Design, München, 18.11.2011.