Head of the Group

Dr.-Ing. Steffen Klamt
Dr.-Ing. Steffen Klamt
Phone: +49 391 6110 480
Fax: +49 391 6110 509
Room: S2.10

Contact Person

Susanne Hintsch
Phone:+49 391 6110-477Fax:+49 391 6110-452

Group page


Publications ARB group

Journal Article (98)

  1. 2013
    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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. Holstein, K.; Flockerzi, D.; Conradi, C.: Multistationarity in Sequential Distributed Multisite Phosphorylation Networks. Bulletin of mathematical biology 75 (11), pp. 2028 - 2058 (2013)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. Straube, R.: Sensitivity and Robustness in Covalent Modification Cycles with a Bifunctional Converter Enzyme. Biophysical Journal 105 (8), pp. 1925 - 1933 (2013)
  16. 2012
    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)
  17. 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)
  18. Conradi, C.; Flockerzi, D.: Multistationarity in Mass Action Networks with Applications to ERK Activation. Journal of Mathematical Biology 65 (1), pp. 107 - 156 (2012)
  19. 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)
  20. 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)
  21. 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)
  22. 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)
  23. 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)
  24. 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)
  25. 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)
  26. 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)
  27. 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)
  28. Straube, R.: Comment on "Load-induced modulation of signal transduction networks": Reconciling ultrasensitivity with bifunctionality? Science Signaling 5 (205), p. Ic1 (2012)
  29. 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)
  30. 2011
    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)
  31. 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)
  32. Hädicke, O.; Klamt, S.: Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13 (2), pp. 204 - 213 (2011)
  33. 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)
  34. Klamt, S.; Kamp von, A.: An application programming interface for CellNetAnalyzer. Biosystems 105 (2), pp. 162 - 168 (2011)
  35. Pandey, R.; Flockerzi, D.; Hauser, M.; Straube, R.: Modeling the Light- and Redox-Dependent Interaction of PpsR/AppA in Rhodobacter sphaeroides. Biophysical Journal 100 (10), pp. 2347 - 2355 (2011)
  36. Ryll, A.; Samaga, R.; Schaper, F.; Alexopoulos, L.G.; Klamt, S.: Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 7 (12), pp. 3253 - 3270 (2011)
  37. Steinsiek, S.; Frixel, S.; Stagge, S.; Bettenbrock, K.: Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels. Journal of Biotechnology 154 (1), pp. 35 - 45 (2011)
  38. Wei, F.; Yang, D.; Straube, R.; Shuai, J.: Brownian diffusion of ion channels in different membrane patch geometries. Physical review E 83 (2), p. 021919 (2011)
  39. 2010
    Franke, R.; Theis, F.J.; Klamt, S.: From Binary to Multivalued to Continuous Models: The Iac Operon as a Case Study. Journal of Integrative Bioinformatics 7 (1), p. 151 (2010)
  40. Hädicke, O.; Klamt, S.: CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147 (2), pp. 88 - 101 (2010)
  41. Klamt, S.; Flassig, R.; Sundmacher, K.: TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26 (17), pp. 2160 - 2168 (2010)
  42. Samaga, R.; von Kamp, A.; Klamt, S.: Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 17 (1), pp. 39 - 53 (2010)
  43. 2009
    Klamt, S.; von Kamp, A.: Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 10, p. 181 (2009)
  44. Klamt, S.; Haus, U.-U.; Theis, F.: Hypergraphs and cellular networks. PLoS Computational Biology 5 (5), p. e1000385 (2009)
  45. Poltz, R.; Franke, R.; Schweitzer, K.; Klamt, S.; Gilles, E. D.; Naumann, M.: Logical network of genotoxic stress-induced NF-kB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and Applications in Bioinformatics and Chemistry 2, pp. 125 - 138 (2009)
  46. Saez-Rodriguez, J.; Alexopoulos, L. G.; Epperlein, J.; Samaga, R.; Lauffenburger, D. A.; Klamt, S.; Sorger, P. K.: Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5, p. 331 (2009)
  47. Samaga, R.; Saez-Rodriguez, J.; Alexopoulos, L. G.; Sorger, P. K.; Klamt, S.: The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 5 (8), e1000438 (2009)
  48. Wittmann, D. M.; Krumsiek, J.; Saez, J.; Lauffenburger, D. A.; Klamt, S.; Theis, F.: Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 3, 98 (2009)

Book Chapter (4)

  1. 2014
    Bettenbrock, K.; Bai, H.; Ederer, M.; Green, J.; Hellingwerf, K.J.; Holcombe, M.; Kunz, S.; Rolfe, M.D.; Sanguinetti, G.; Sawodny, O. et al.; Sharma, P.; Steinsiek, S.; Poole, R.K.: Towards a Systems Level Understanding of the Oxygen Response of Escherichia coli. In: Advances in Microbial Physiology, Vol. 64, pp. 65 - 114 (Ed. Poole, R. K.). Elsevier/Academic Press, Amsterdam (2014)
  2. Klamt, S.; Haedicke, O.; von Kamp, A.: Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. In: Large-Scale Networks in Engineering and Life Sciences, pp. 263 - 316. Springer International Publishing, Cham (2014)
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