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

Publications ARB group

Journal Article (107)

  1. Journal Article
    Boecker, S.; Zahoor, A.; Schramm, T.; Link, H.; Klamt, S.: Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli. Biotechnology Journal (accepted)
  2. Journal Article
    Klamt, S.; Kamp von, A.; Harder, B.-J.: Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 25 (2) (2019)
  3. Journal Article
    Koch, S.; Kohrs, F.; Lahmann, P.; Bissinger, T.; Wendschuh, S.; Benndorf, D.; Reichl, U.; Klamt, S.: RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PLoS Computational Biology 15 (2), e1006759 (2019)
  4. Journal Article
    Schneider, P.; Klamt, S.: Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics (accepted)
  5. Journal Article
    Thiele, S.; Heise, S.; Hessenkemper, W.; Bongartz, H.; Fensky, M.; Schaper, F.; Klamt, S.: Designing optimal experiments to discriminate interaction graph models. IEEE ACM Transactions on Computational Biology and Bioinformatics (accepted)
  6. Journal Article
    Bosch, J.; Klamt, S.; Stoll, M.: Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 78 (3), pp. 1350 - 1377 (2018)
  7. Journal Article
    Hädicke, O.; Kamp von, A.; Aydogan, T.; Klamt, S.: OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PLoS Computational Biology 14 (9), e1006492 (2018)
  8. Journal Article
    Harder, B.-J.; Bettenbrock, K.; Klamt, S.: Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 115 (1), pp. 156 - 164 (2018)
  9. Journal Article
    Klamt, S.; Mahadevan, R.; Hädicke, O.: When do two-stage processes outperform one-stage processes? Biotechnology Journal 13 (2), 1700539 (2018)
  10. Journal Article
    Klamt, S.; Müller, S.; Regensburger, G.; Zanghellini, J.: A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 47, pp. 153 - 169 (2018)
  11. Journal Article
    Kyselova, L.; Kreitmayer, D.; Kremling, A.; Bettenbrock, K.: Type and capacity of glucose transport influences succinate yield in two-stage cultivations. Microbial Cell Factories 17, 132 (2018)
  12. Journal Article
    Liu, X.; Reitsma, J. M.; Mamrosh, J. L.; Zhang, Y.; Straube, R.; Deshaies, R. J.: Cand1-Mediated Adaptive Exchange Mechanism Enables Variation in F-Box Protein Expression. Molecular Cell 69 (5), pp. 773 - 786 (2018)
  13. Journal Article
    Mahour, R.; Klapproth, J.; Rexer, T.; Schildbach, A.; Klamt, S.; Pietzsch, M.; Rapp, E.; Reichl, U.: Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 283, pp. 120 - 129 (2018)
  14. Journal Article
    Nitzschke, A.; Bettenbrock, K.: All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K 12. PLoS One 13 (4), 20194699 (2018)
  15. Journal Article
    Venayak, N.; Kamp von, A.; Klamt, S.; Mahadevan, R.: MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 9, 5332 (2018)
  16. Journal Article
    Hädicke, O.; Klamt, S.: EColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent model. Scientific Reports 7, 39647 (2017)
  17. Journal Article
    Kamp von, A.; Thiele, S.; Hädicke, O.; Klamt, S.: Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 261, pp. 221 - 228 (2017)
  18. Journal Article
    Kamp von, A.; Klamt, S.: Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 8, 15926 (2017)
  19. Journal Article
    Klamt, S.; Regensburger, G.; Gerstl, P.M.; Jungreuthmayer, C.; Schuster, S.; Mahadevan, R.; Zanghellini, J.; Müller, S.: From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology 13 (4), e1005409 (2017)
  20. Journal Article
    Prigent, S.; Frioux, C.; Dittami, S. M.; Thiele, S.; Larhlimi, A.; Collet, G.; Gutknecht, F.; Got, J.; Eveillard, D.; Bourdon, J. et al.; Plewniak, F.; Tonon, T.; Siegel, A.: Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Computational Biology 13, e1005276 (2017)
  21. Journal Article
    Straube, R.: Analysis of network motifs in cellular regulation: Structural similarities, input–output relations and signal integration. Biosystems 162, pp. 2015 - 232 (2017)
  22. Journal Article
    Straube, R.; Shah, M.; Flockerzi, D.; Wolf, D.A.: Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire. PLoS Computational Biology 13 (11), e1005869 (2017)
  23. Journal Article
    Zander, D.; Samaga, D.; Straube, R.; Bettenbrock, K.: Bistability and Nonmonotonic Induction of the lac Operon in the Natural Lactose Uptake System. Biophysical Journal 112 (9), pp. 1984 - 1996 (2017)
  24. Journal Article
    Bordron, P.; Latorre, M.; Cortés, M.-P.; González, M.; Thiele, S.; Siegel, A.; Maass, A.; Eveillard, D.: Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. MicrobiologyOpen 5 (1), pp. 106 - 117 (2016)
  25. Journal Article
    Gerstl, M. P.; Klamt, S.; Jungreuthmayer, C.; Zanghellini, J.: Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 32 (5), pp. 730 - 737 (2016)
  26. Journal Article
    Harder, B.-J.; Bettenbrock, K.; Klamt, S.: Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 38, pp. 29 - 37 (2016)
  27. Journal Article
    Koch, S.; Benndorf, D.; Fronk, K.; Reichl, U.; Klamt, S.: Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnology for Biofuels 9, 17 (2016)
  28. Journal Article
    Kolczyk, K.; Conradi, C.: Challenges in horizontal model integration. BMC Systems Biology (10), 28 (2016)
  29. Journal Article
    Müller, S.; Feliu, E.; Regensburger, G.; Conradi, C.; Shiu, A.; Dickenstein, A.: Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry. Foundations of Computational Mathematics 16 (1), pp. 69 - 97 (2016)
  30. Journal Article
    Ud-Dean, S.; Heise, S.; Klamt, S.; Gunawan, R.: TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics 17 (17), 252 (2016)
  31. Journal Article
    Wrzosek, K.; García Rivera, M. A.; Bettenbrock, K.; Seidel-Morgenstern, A.: Racemization of undesired enantiomers: Immobilization of mandelate racemase and application in a fixed bed reactor. Biotechnology Journal 11 (4), pp. 453 - 463 (2016)
  32. Journal Article
    Wu, H.; Kamp von, A.; Leoncikas, V.; Mori, W.; Sahin, M.; Gevorgyan, A.; Linley, C.; Grabowski, M.; Mannan, A. A.; Stoy, N. et al.; Steward, G. R.; Ward, L. T.; Lewis, D.J.M.; Sroca, J.; Matsuno, H.; Klamt, S.; Westerhoff, H.V.; McFadden, J.; Plant, N.J.; Kierzek, A.M.: MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 2, 16032 (2016)
  33. Journal Article
    Bastiaens, P. I.H.; Birtwistle, M.; Blüthgen, N.; Bruggeman, F.; Cho, K.-H.; de la Fuente, A.; Hoek, J.; Kiyatkin, A.; Klamt, S.; Kolch, W. et al.; Legewie, S.; Mendes, P.; Naka, T.; Santra, T.; Sontag, E.; Westerhoff, H.; Kholodenko, B.: Silence on the relevant literature and errors in implementation. Nature Biotechnology 33 (4), pp. 336 - 339 (2015)
  34. Journal Article
    Conradi, C.; Shiu, A.: A Global Convergence Result for Processive Multisite Phosphorylation Systems. Bulletin of mathematical biology 77 (1), pp. 126 - 155 (2015)
  35. Journal Article
    D`Allessandro, L. A.; Samaga, R.; Maiwald, T.; Rho, S.-H.; Bonefas, S.; Raue, A.; Iwamoto, N.; Kienast, A.; Waldow, K.; Meyer, R. et al.; Schilling, M.; Timmer, J.; Klamt, S.; Klingmüller, U.: Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Computational Biology 11 (4), e1004192 (2015)
  36. Journal Article
    Erdrich, P.; Steuer, R.; Klamt, S.: An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Systems Biology 9, 48 (2015)
  37. Journal Article
    Hädicke, O.; Bettenbrock, K.; Klamt, S.: Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnology and Bioengineering 112 (10), pp. 2195 - 2199 (2015)
  38. Journal Article
    Hädicke, O.; Klamt, S.: Manipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions (London) 43 (6), pp. 1140 - 1145 (2015)
  39. Journal Article
    Klamt, S.; Mahadevan, R.: On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 30, pp. 166 - 178 (2015)
  40. Journal Article
    Mahadevan, R.; Kamp von, A.; Klamt, S.: Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 31 (17), pp. 2844 - 2851 (2015)
  41. Journal Article
    Michailidou, M.; Melas, I.; Messinis, D.; Klamt, S.; Alexopoulos, L.; Kolisis, F.; Loutrari, H.: Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action. CPT: Pharmacometrics & Systems Pharmacology 4 (6), pp. 350 - 361 (2015)
  42. Journal Article
    Mueller, S.; Huard, J.; Waldow, K.; Huang, X.; D'Alessandro, L.; Bohl, S.; Börner, K.; Grimm, D.; Klamt, S.; Klingmüller, U. et al.; Schilling, M.: T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes. Molecular Systems Biology 11, 795 (2015)
  43. 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)
  44. Journal Article
    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)
  45. Journal Article
    Wiechert, W.; Klamt, S.: Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 21 (1), pp. 46 - 48 (2015)
  46. Journal Article
    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)
  47. Journal Article
    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)
  48. Journal Article
    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)
  49. Journal Article
    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)
  50. Journal Article
    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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