Publications ARB group

Carius, L.; Carius, A. B.; McIntosh, M.; Grammel, H.: Quorum sensing influences growth and photosynthetic membrane production in high-cell-density cultivations of Rhodospirillum rubrum. BMC Microbiology 13, 189 (2013)

Carius, L.; Hädicke, O.; Grammel, H.: Stepwise reduction of the culture redox potential allows the analysis of microaerobic metabolism and photosynthetic membrane synthesis in Rhodospirillum rubrum. Biotechnology and Bioengineering 110 (2), pp. 573 - 585 (2013)

Chaoiya, C.; Berenguier, D.; Keating, S. M.; Naldi, A.; van Iersel, M. P.; Rodriguez, N.; Dräger, A.; Büchel, F.; Cokelaer, T.; Kowal, B. et al.; Wicks, B.; Gonçalves, E.; Dorier, J.; Page, M.; Monteiro, P. T.; Kamp von, A.; Xenarius , I.; de Jong, H.; Hucka, M.; Klamt, S.; Thieffrey, D.; Le Novère, N.; Saez-Rodriguez, J.; Helikar, T.: SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and tools. BMC Systems Biology 7, 135 (2013)

Flassig, R.; Heise, S.; Sundmacher, K.; Klamt, S.: An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinformatics 29 (2), pp. 246 - 254 (2013)

Gonçalves, E.; Bucher, J.; Ryll, A.; Niklas, J.; Mauch, K.; Klamt, S.; Rocha, M.; Saez-Rodriguez, J.: Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 9 (7), pp. 1576 - 1583 (2013)

Gruchattka, E.; Hädicke, O.; Klamt, S.; Schuetz, V.; Kayser , O.: In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 12, 84 (2013)

Hädicke, O.; Lohr, V.; Genzel, Y.; Reichl, U.; Klamt, S.: Evaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivations. Biotechnology and Bioengineering 110 (10), pp. 2633 - 2642 (2013)

Holstein, K.; Flockerzi, D.; Conradi, C.: Multistationarity in Sequential Distributed Multisite Phosphorylation Networks. Bulletin of mathematical biology 75 (11), pp. 2028 - 2058 (2013)

Jahn, S.; Haverkorn van Rijsevijk, B. R.; Sauer, U.; Bettenbrock, K.: A role for EIIANtr in controlling fluxes in the central metabolism of E. coli K12. Biochimica et Biophysica Acta-Molecular Cell Research 1833 (12), pp. 2879 - 2889 (2013)

Jungreuthmeyer, C.; Nair, G.; Klamt, S.; Zanghellini, J.: Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14 (1), 318 (2013)

Melas, I. N.; Samaga, R.; Alexopoulos, L. G.; Klamt, S.: Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology 9 (9), e1003204 (2013)

Pinna, A.; Heise, S.; Flassig, R.; de la Fuente, A.; Klamt, S.: Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 7, 73 (2013)

Samaga, R.; Klamt, S.: Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 11 (1), 43 (2013)

Sharma, P.; Stagge, S.; Bekker, M.; Bettenbrock, K.; Hellingwerf, K. J.: Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone. PLoS One 8 (10), e7541 (2013)

Straube, R.: Sensitivity and Robustness in Covalent Modification Cycles with a Bifunctional Converter Enzyme. Biophysical Journal 105 (8), pp. 1925 - 1933 (2013)

Straube, R.; Conradi, C.: Reciprocal Enzyme Regulation as a Source of Bistability in Covalent Modification Cycles. Journal of Theoretical Biology 330, pp. 56 - 74 (2013)

Heise, S.; Flassig, R.; Klamt, S.: Benchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Systems Genetic Data. In: Gene Network Inference: Verification of Methods for Systems Genetic Data., pp. 33 - 47. Springer, Heidelberg (2013)

Waddell, S. J.; Kamp von, A.; Klamt, S.; Neyrolles, O.: Host-pathogen interactions. In: Systems Biology of Tuberculosis, pp. 107 - 126. Springer, New York (2013)

Kramer, B.; Conradi, C.: On Bistability Causing Structures in Escherichia Coli’s Metabolism. In: Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, pp. 276 - 277. 11th International Conference, CMSB 2013, Klosterneuburg, Österreich, September 22, 2014 - September 24, 2014. (2013)

Ryll, A.; Bucher, J.; Niklas , J.; Klamt, S.: A fusion approach linking signaling logic and metabolic mass-flow kinetics in hepatocytes. In: Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, pp. 255 - 256. 11th International Conference on Computational Methods in Systems Biology CMSB 13, Klosterneuburg, Austria, September 22, 2013 - September 24, 2013. (2013)

Marbach, A.: Zellheterogenität am Beispiel der Expression des Escherichia coli lac Operona. Dissertation, Otto-von-Guericke-Universität, Magdeburg (2013)