Journal Article (115)

2015
Journal Article
Straube, R.: Analysis of Substrate Competition in Regulatory Network Motifs: Stimulus-Response Curves, Thresholds and Ultrasensitivity. Journal of Theoretical Biology 380, pp. 74 - 82 (2015)
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Thiele, S.; Cerone, L.; Saez-Rodriguez, J.; Siegel, A.; Guciolowski, C.; Klamt, S.: Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 16 (1), 345 (2015)
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Wiechert, W.; Klamt, S.: Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 21 (1), pp. 46 - 48 (2015)
2014
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Carius, L.; Rumschinski, P.; Faulwasser, T.; Flockerzi, D.; Grammel, H.; Findeisen, R.: Model-based derivation, analysis and control of unstable microaerobic steady-states-Considering Rhodospirillum rubrum as an example. Biotechnology and Bioengineering 111 (4), pp. 734 - 747 (2014)
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Conradi, C.; Mincheva, M.: Catalytic constants enable the emergence of bistability in dual phosphorylation. Interface: Journal of the Royal Society 6 (11), 95, pp. 1742 - 5662 (2014)
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Ederer, M.; Steinsiek, S.; Stagge, S.; Rolfe, M. D.; TerBeek, A.; Knies, D.; Teixeira de Mattos, M. J.; Sauter , T.; Green , J.; Poole, R. K. et al.; Bettenbrock, K.; Sawodny, O.: A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Frontiers in Microbiology 5, 124, p. 124 (2014)
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Erdrich, P.; Knoop, H.; Steuer, R.; Klamt, S.: Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 13, p. 128 - 128 (2014)
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Flockerzi, D.; Holstein, K.; Conradi, C.: N-site Phosphorylation Systems with 2N-1 Steady States. Bulletin of Mathematical Biology 76 (8), pp. 1892 - 1916 (2014)
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Henkel, S.; Beek, A. T.; Steinsiek, S.; Stagge, S.; Bettenbrock, K.; M. Joost Teixeira de Mattos, M.; Sawodny, O.; Ederer, M.; Sauter, T.: Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions. PLoS One 9 (9), p. e107640 (2014)
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Kamp von, A.; Klamt, S.: Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Computational Biology 10 (1), e1003378 (2014)
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Lohr, V.; Hädicke, O.; Genzel, Y.; Jordan, I.; Buentemeyer, H.; Klamt, S.; Reichl, U.: The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnology 14, p. 72 (2014)
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Prigent, S.; Collet, G.; Dittami, S. M.; Delage, L.; Ethis de Corny, F.; Dameron, O.; Eveillard, D.; Thiele, S.; Cambefort, J.; Siegel, A. et al.; Tonon, T.: The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. The Plant Journal 80 (2), pp. 367 - 381 (2014)
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Ryll, A.; Bucher, J.; Bonin, A.; Bongard, S.; Gonçalves , E.; Saez- Roidriguez, J.; Niklas, J.; Klamt, S.: A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosystems 124, pp. 26 - 38 (2014)
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Steinsiek, S.; Stagge, S.; Bettenbrock, K.: Analysis of Escherichia coli Mutants with a Linear Respiratory Chain. PLoS One 9 (1), p. e87307 (2014)
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Straube, R.: Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase. PLoS Computational Biology 10 (5), p. e1003614 (2014)
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Varničić, M.; Bettenbrock, K.; Hermsdorf, D.; Vidaković-Koch, T.; Sundmacher, K.: Combined electrochemical and microscopic study of porous enzymatic electrodes with direct electron transfer mechanism. RSC Advances 4 (69), pp. 36471 - 36479 (2014)
2013
Journal Article
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, p. 189 (2013)
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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)
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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, p. 135 (2013)
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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)
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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)
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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)
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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)
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Holstein, K.; Flockerzi, D.; Conradi, C.: Multistationarity in Sequential Distributed Multisite Phosphorylation Networks. Bulletin of mathematical biology 75 (11), pp. 2028 - 2058 (2013)
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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)
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Jungreuthmeyer, C.; Nair, G.; Klamt, S.; Zanghellini, J.: Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14 (1), p. 318 (2013)
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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), p. e1003204 (2013)
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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, p. 73 (2013)
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Samaga, R.; Klamt, S.: Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 11 (1), p. 43 (2013)
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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), p. e7541 (2013)
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Straube, R.: Sensitivity and Robustness in Covalent Modification Cycles with a Bifunctional Converter Enzyme. Biophysical Journal 105 (8), pp. 1925 - 1933 (2013)
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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)
2012
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Ballerstein, K.; von Kamp, A.; Klamt, S.; Haus, U.-U.: Minimal cut sets in metabolic networks are elementary modes in a dual network. Bioinformatics 28 (3), pp. 381 - 387 (2012)
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Conradi, C.; Flockerzi, D.: Switching in mass action networks based on linear inequalities. SIAM Journal on Applied Dynamical Systems 11 (1), pp. 110 - 134 (2012)
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Conradi, C.; Flockerzi, D.: Multistationarity in Mass Action Networks with Applications to ERK Activation. Journal of Mathematical Biology 65 (1), pp. 107 - 156 (2012)
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Franz, A.; Rehner, R.; Kienle, A.; Grammel, H.: Rapid selection of glucose-utilizing variants of the polyhydroxyalkanoate producer Ralstonia eutropha H16 by incubation with high substrate levels. Letters in Applied Microbiology 54 (1), pp. 45 - 51 (2012)
Journal Article
Huard, J.; Mueller, S.; Gilles, E. D.; Klingmüller, U.; Klamt, S.: An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 279 (18), pp. 3290 - 3313 (2012)
Journal Article
Kolczyk, K.; Samaga, R.; Conzelmann, H.; Mirschel, S.; Conradi, C.: The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics 13, p. 251 (2012)
Journal Article
Kremling, A.; Goehler, A.; Jahreis, K.; Nees, M.; Auerbach, B.; Schmidt-Heck, W.; Kökpinar, Ö.; Geffers, R.; Rinas, U.; Bettenbrock, K.: Analysis and Design of Stimulus Response Curves of E. coli. Metabolites 2 (4), pp. 844 - 871 (2012)
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Marbach, A.; Bettenbrock, K.: Iac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. Journal of Biotechnology 157 (1), pp. 82 - 88 (2012)
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Pandey, R.; Flockerzi, D.; Hauser, M. J. B.; Straube, R.: An extended model for the repression of photosynthesis genes by the AppA/PpsR system in Rhodobacter sphaeroides. FEBS Journal 279 (18), pp. 3449 - 3461 (2012)
Journal Article
Pérez, M. M.; Dickenstein, A.; Shiu, A.; Conradi, C.: Chemical Reaction Systems with Toric Steady States. Bulletin of Mathematical Biology 74 (5), pp. 1027 - 1065 (2012)
Journal Article
Rudolf, C.; Grammel, H.: Fructose metabolism of the purple non-sulfur bacterium Rhodospirillum rubrum: Effect of carbon dioxide on growth, and production of bacteriochlorophyll and organic acids. Enzyme and Microbial Technology 50 (4-5), pp. 238 - 246 (2012)
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Steinsiek, S.; Bettenbrock, K.: Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems. Journal of Bacteriology 194 (21), pp. 5897 - 5908 (2012)
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Straube, R.: Comment on "Load-induced modulation of signal transduction networks": Reconciling ultrasensitivity with bifunctionality? Science Signaling 5 (205), p. Ic1 (2012)
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Wang, G.-S.; Grammel, H.; Abou-Aisha, K.; Sägesser, R.; Gosh, R.: High-Level Production of the Industrial Product Lycopene by the Photosynthetic Bacterium Rhodospirillum rubrum. Applied and Environmental Microbiology 78 (20), pp. 7205 - 7215 (2012)
2011
Journal Article
Carius, A. B.; Henkel, M.; Grammel, H.: Glutathione Redox Effect on Photosynthetic Membrane Expression in Rhodospirillum rubrum. Journal of Bacteriology 193 (8), pp. 1893 - 1900 (2011)
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García Palacios, J.; Kramer, B.; Kienle, A.; Kaspereit, M.: Experimental validation of a new integrated simulated moving bed process for the production of single enantiomers. Journal of Chromatography A 2218 (16), pp. 2232 - 2239 (2011)
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Hädicke, O.; Grammel, H.; Klamt, S.: Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5, p. 150 (2011)
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Hädicke, O.; Klamt, S.: Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13 (2), pp. 204 - 213 (2011)
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