Steffen Klamt

2.

Zeitschriftenartikel

Bauer, J.; Klamt, S.: OptMSP: A Toolbox for Designing Optimal Multi-Stage (Bio)Processes. Journal of Biotechnology 383, S. 94 - 102 (2024)

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3.

Zeitschriftenartikel

Dietz, K.; Sagstetter, C.; Speck, M.; Roth, A.; Klamt, S.; Fabarius, J. T.: A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid. Microbial Cell Factories 23, 344 (2024)

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4.

Zeitschriftenartikel

Espinel-Rios, S.; Behrendt, G.; Bauer, J.; Morabito, B.; Pohlodek, J.; Schütze, A.; Findeisen, R.; Bettenbrock, K.; Klamt, S.: Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. Process Biochemistry (143), S. 174 - 185 (2024)

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5.

Zeitschriftenartikel

Espinel-Rios, S.; Morabito, B.; Pohlodek, J.; Bettenbrock, K.; Klamt, S.; Findeisen, R.: Toward a modeling, optimization, and predictive control framework for fed-batch metabolic cybergenetics. Biotechnology and Bioengineering 121 (1), S. 366 - 379 (2024)

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6.

Zeitschriftenartikel

Frohwitter, J.; Behrendt, G.; Klamt, S.; Bettenbrock, K.: A new Zymomonas mobilis platform strain for the efficient production of chemicals. Microbial Cell Factories 23, 143 (2024)

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7.

Zeitschriftenartikel

Huber, N.; Alcalá Orozco, E. A.; Rexer, T.; Reichl, U.; Klamt, S.: Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metabolic Engineering 81, S. 10 - 25 (2024)

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8.

Zeitschriftenartikel

Kutscha, R.; Tomin, T.; Birner-Gruenberger, R.; Bekiaris, P. S.; Klamt, S.; Pflügl, S.: Efficiency of acetate-based isopropanol synthesis in Escherichia coli W is controlled by ATP demand. Biotechnology for Biofuels and Bioproducts 17, 110 (2024)

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9.

Zeitschriftenartikel

Schulz-Mirbach, H.; Krüsemann, J. L.; Andreadaki, T.; Nerlich, J. N.; Mavrothalassiti, E.; Boecker, S.; Schneider, P.; Weresow, M.; Abdelwahab, O.; Paczia, N. et al.; Dronsella, B.; Erb, T. J.; Bar-Even, A.; Klamt, S.; Lindner, S. N.: Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules. Nature Communications 15 (1), 6725 (2024)

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10.

Zeitschriftenartikel

Alcalá Orozco, E. A.; Grote, V.; Fiebig, T.; Klamt, S.; Reichl, U.; Rexer, T.: A Cell‐Free Multi‐enzyme Cascade Reaction for the Synthesis of CDP‐Glycerol. ChemBioChem: A European Journal of Chemical Biology 24 (21), e202300463 (2023)

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11.

Zeitschriftenartikel

Bekiaris, P. S.; Klamt, S.: Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions. Nature Communications 14, 4660 (2023)

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12.

Zeitschriftenartikel

Boecker, S.; Schulze, P.; Klamt, S.: Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. Biotechnology for Biofuels and Bioproducts 16, 148 (2023)

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13.

Zeitschriftenartikel

Kamp von, A.; Klamt, S.: Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. Bioinformatics 39 (10), btad600 (2023)

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14.

Zeitschriftenartikel

Wichmann, J.; Behrendt, G.; Boecker, S.; Klamt, S.: Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering. Metabolic Engineering 77, S. 199 - 207 (2023)

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15.

Zeitschriftenartikel

Behrendt, G.; Frohwitter, J.; Vlachonikolou, M.; Klamt, S.; Bettenbrock, K.: Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. ACS Synthetic Biology 11 (11), S. 3855 - 3864 (2022)

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16.

Zeitschriftenartikel

Boecker, S.; Espinel-Rios, S.; Bettenbrock, K.; Klamt, S.: Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering 73, S. 50 - 57 (2022)

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17.

Zeitschriftenartikel

Espinel-Rios, S.; Bettenbrock, K.; Klamt, S.; Findeisen, R.: Maximizing batch fermentation efficiency by constrained model-based optimization and predictive control of adenosine triphosphate turnover. AIChE-Journal 68 (4), e17555 (2022)

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18.

Zeitschriftenartikel

Klamt, S.; Kamp von, A.: Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks. Metabolites 12 (7), 585 (2022)

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19.

Zeitschriftenartikel

Mahour, R.; Lee, J. W.; Grimpe, P.; Boecker, S.; Grote, V.; Klamt, S.; Seidel-Morgenstern, A.; Rexer, T.; Reichl, U.: Cell‐free multi‐enzyme synthesis and purification of uridine diphosphate galactose. ChemBioChem 23 (2), e202100361 (2022)

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20.

Zeitschriftenartikel

Schneider, P.; Bekiaris, P. S.; Kamp von, A.; Klamt, S.: StrainDesign: a Comprehensive Python Package for Computational Design of Metabolic Networks. Bioinformatics 38 (21), S. 4981 - 4983 (2022)

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21.

Zeitschriftenartikel

Thiele, S.; Kamp von, A.; Bekiaris, P. S.; Schneider, P.; Klamt, S.: CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks. Bioinformatics 38 (5), S. 1467 - 1469 (2022)

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22.

Zeitschriftenartikel

Bekiaris, P. S.; Klamt, S.: Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Computational Biology 17 (6), e1009093 (2021)

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23.

Zeitschriftenartikel

Boecker, S.; Harder, B.-J.; Kutscha, R.; Pflügl, S.; Klamt, S.: Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli. Microbial Cell Factories 20, 63 (2021)

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24.

Zeitschriftenartikel

Boecker, S.; Slaviero, G.; Schramm, T.; Szymanski, W.; Steuer , R.; Link, H.; Klamt, S.: Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology 17, e10504 (2021)

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25.

Zeitschriftenartikel

Novak, K.; Neuendorf, C. S.; Kofler, I.; Kieberger, N.; Klamt, S.; Pflügl, S.: Blending industrial blast furnace gas with H 2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2. Bioresource Technology 323, 124573 (2021)

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26.

Zeitschriftenartikel

Schneider, P.; Radhakrishnan, M.; Klamt, S.: Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs. Biotechnology Journal 16, 2100236 (2021)

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27.

Zeitschriftenartikel

Bekiaris, P. S.; Klamt, S.: Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 21, 19 (2020)

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28.

Zeitschriftenartikel

Kamp von, A.; Klamt, S.: MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems. ACS Synthetic Biology 9 (3), S. 556 - 566 (2020)

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29.

Zeitschriftenartikel

Klamt, S.; Mahadevan, R.; Kamp von, A.: Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinformatics (21), 510 (2020)

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30.

Zeitschriftenartikel

Lieven, C.; Beber, M. E.; Olivier, B. G.; Bergmann, F. T.; Ataman, M.; Babaei, P.; Bartell, J. A.; Blank, L. M.; Chauhan, S.; Correia, K. et al.; Diener, C.; Dräger, A.; Ebert, B. E.; Edirisinghe, J. N.; Faria, J. P.; Feist, A. M.; Fengos, G.; Fleming, R. M. T.; García-Jiménez, B.; Hatzimanikatis, V.; van Helvoirt, W.; Henry, C. S.; Hermjakob, H.; Herrgård, M. J.; Kaafarani, A.; Kim, H. U.; King, Z.; Klamt, S.; Klipp, E.; Koehorst, J. J.; König, M.; Lakshmanan, M.; Lee, D.-Y.; Lee, S. Y.; Lee, S.; Lewis, N. E.; Liu, F.; Ma, H.; Machado, D.; Mahadevan, R.; Maia, P.; Mardinoglu, A.; Medlock, G. L.; Monk, J. M.; Nielsen, J.; Nielsen, L. K.; Nogales, J.; Nookaew, I.; Palsson, B. O.; Papin, J. A.; Patil, K. R.; Poolman, M.; Price, N. D.; Resendis-Antonio, O.; Richelle, A.; Rocha, I.; Sánchez, B. J.; Schaap, P. J.; Malik Sheriff, R. S.; Shoaie, S.; Sonnenschein, N.; Teusink, B.; Vilaça, P.; Vik, J. O.; Wodke, J. A. H.; Xavier, J. C.; Yuan, Q.; Zakhartsev, M.; Zhang, C.: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology 38, S. 272 - 276 (2020)

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supplementary-material

31.

Zeitschriftenartikel

Schneider, P.; Kamp von, A.; Klamt, S.: An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. PLoS Computational Biology 16 (7), e1008110 (2020)

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32.

Zeitschriftenartikel

Zahoor, A.; Messerschmidt, K.; Boecker, S.; Klamt, S.: ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. Biotechnology for Biofuels and Bioproducts (13), 185 (2020)

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33.

Zeitschriftenartikel

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 14 (9), 1800438 (2019)

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34.

Zeitschriftenartikel

Klamt, S.; Kamp von, A.; Harder, B.-J.: Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 25 (2), S. 156 - 158 (2019)

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35.

Zeitschriftenartikel

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)

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36.

Zeitschriftenartikel

Schneider, P.; Klamt, S.: Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics 35 (17), S. 3063 - 3072 (2019)

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37.

Zeitschriftenartikel

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 16 (3), S. 925 - 935 (2019)

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38.

Zeitschriftenartikel

Weinrich, S.; Koch, S.; Bonk, F.; Popp, D.; Benndorf, D.; Klamt, S.; Centler, F.: Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. Frontiers in Microbiology 10, 1095 (2019)

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39.

Zeitschriftenartikel

Bosch, J.; Klamt, S.; Stoll, M.: Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 78 (3), S. 1350 - 1377 (2018)

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40.

Zeitschriftenartikel

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)

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41.

Zeitschriftenartikel

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), S. 156 - 164 (2018)

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42.

Zeitschriftenartikel

Klamt, S.; Mahadevan, R.; Hädicke, O.: When do two-stage processes outperform one-stage processes? Biotechnology Journal 13 (2), 1700539 (2018)

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43.

Zeitschriftenartikel

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, S. 153 - 169 (2018)

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44.

Zeitschriftenartikel

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, S. 120 - 129 (2018)

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post-print

45.

Zeitschriftenartikel

Venayak, N.; Kamp von, A.; Klamt, S.; Mahadevan, R.: MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 9, 5332 (2018)

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46.

Zeitschriftenartikel

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)

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47.

Zeitschriftenartikel

Kamp von, A.; Klamt, S.: Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 8, 15926 (2017)

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48.

Zeitschriftenartikel

Kamp von, A.; Thiele, S.; Hädicke, O.; Klamt, S.: Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 261, S. 221 - 228 (2017)

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49.

Zeitschriftenartikel

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)

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50.

Zeitschriftenartikel

Gerstl, M. P.; Klamt, S.; Jungreuthmayer, C.; Zanghellini, J.: Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 32 (5), S. 730 - 737 (2016)

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51.

Zeitschriftenartikel

Harder, B.-J.; Bettenbrock, K.; Klamt, S.: Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 38, S. 29 - 37 (2016)

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52.

Zeitschriftenartikel

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)

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53.

Zeitschriftenartikel

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)

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54.

Zeitschriftenartikel

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)

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55.

Zeitschriftenartikel

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), S. 336 - 339 (2015)

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56.

Zeitschriftenartikel

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)

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57.

Zeitschriftenartikel

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)

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58.

Zeitschriftenartikel

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), S. 2195 - 2199 (2015)

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post-print

59.

Zeitschriftenartikel

Hädicke, O.; Klamt, S.: Manipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions (London) 43 (6), S. 1140 - 1145 (2015)

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post-print

60.

Zeitschriftenartikel

Klamt, S.; Mahadevan, R.: On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 30, S. 166 - 178 (2015)

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61.

Zeitschriftenartikel

Mahadevan, R.; Kamp von, A.; Klamt, S.: Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 31 (17), S. 2844 - 2851 (2015)

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62.

Zeitschriftenartikel

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), S. 350 - 361 (2015)

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63.

Zeitschriftenartikel

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)

MPG.PuRe

64.

Zeitschriftenartikel

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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65.

Zeitschriftenartikel

Wiechert, W.; Klamt, S.: Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 21 (1), S. 46 - 48 (2015)

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66.

Zeitschriftenartikel

Erdrich, P.; Knoop, H.; Steuer, R.; Klamt, S.: Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 13, 128 (2014)

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67.

Zeitschriftenartikel

Kamp von, A.; Klamt, S.: Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Computational Biology 10 (1), e1003378 (2014)

MPG.PuRe

68.

Zeitschriftenartikel

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, 72 (2014)

MPG.PuRe

69.

Zeitschriftenartikel

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, S. 26 - 38 (2014)

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70.

Zeitschriftenartikel

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)

MPG.PuRe

71.

Zeitschriftenartikel

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

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72.

Zeitschriftenartikel

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), S. 1576 - 1583 (2013)

MPG.PuRe

73.

Zeitschriftenartikel

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)

MPG.PuRe

74.

Zeitschriftenartikel

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), S. 2633 - 2642 (2013)

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75.

Zeitschriftenartikel

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

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76.

Zeitschriftenartikel

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)

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77.

Zeitschriftenartikel

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)

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78.

Zeitschriftenartikel

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

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79.

Zeitschriftenartikel

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), S. 381 - 387 (2012)

MPG.PuRe

80.

Zeitschriftenartikel

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), S. 3290 - 3313 (2012)

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81.

Zeitschriftenartikel

Hädicke, O.; Grammel, H.; Klamt, S.: Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5, 150 (2011)

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82.

Zeitschriftenartikel

Hädicke, O.; Klamt, S.: Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13 (2), S. 204 - 213 (2011)

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83.

Zeitschriftenartikel

Klamt, S.; Kamp von, A.: An application programming interface for CellNetAnalyzer. Biosystems 105 (2), S. 162 - 168 (2011)

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84.

Zeitschriftenartikel

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), S. 3253 - 3270 (2011)

MPG.PuRe

85.

Zeitschriftenartikel

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), 151 (2010)

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86.

Zeitschriftenartikel

Hädicke, O.; Klamt, S.: CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147 (2), S. 88 - 101 (2010)

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87.

Zeitschriftenartikel

Klamt, S.; Flassig, R.; Sundmacher, K.: TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26 (17), S. 2160 - 2168 (2010)

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88.

Zeitschriftenartikel

Samaga, R.; von Kamp, A.; Klamt, S.: Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. Journal of Computational Biology 17 (1), S. 39 - 53 (2010)

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89.

Zeitschriftenartikel

Klamt, S.; Haus, U.-U.; Theis, F.: Hypergraphs and cellular networks. PLoS Computational Biology 5 (5), S. e1000385 (2009)

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90.

Zeitschriftenartikel

Klamt, S.; von Kamp, A.: Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 10, S. 181 (2009)

MPG.PuRe

91.

Zeitschriftenartikel

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, S. 125 - 138 (2009)

MPG.PuRe

92.

Zeitschriftenartikel

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, S. 331 (2009)

MPG.PuRe

93.

Zeitschriftenartikel

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)

MPG.PuRe

94.

Zeitschriftenartikel

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)

MPG.PuRe

95.

Zeitschriftenartikel

Franke, R.; Mueller, M.; Wundrack, N.; Gilles, E. D.; Klamt, S.; Kaehne, T.; Naumann, M.: Host-pathogen systems biology: Logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Systems Biology 2, 4 (2008)

MPG.PuRe

96.

Zeitschriftenartikel

Haus, U.-U.; Klamt, S.; Stephen, T.: Computing knock-out strategies in metabolic networks. Journal of Computational Biology 15 (3), S. 259 - 268 (2008)

MPG.PuRe

97.

Zeitschriftenartikel

Klamt, S.; Grammel, H.; Straube, R.; Ghosh, R.; Gilles, E. D.: Modeling the electron transport chain of purple non-sulfur bacteria. Molecular Systems Biology 4, 156 (2008)

MPG.PuRe

98.

Zeitschriftenartikel

Saez-Rodriguez, J.; Hammerle-Fickinger, A.; Dalal, O.; Klamt, S.; Gilles, E. D.; Conradi, C.: Multistability of signal transduction motifs. IET Systems Biology 2 (2), S. 80 - 93 (2008)

MPG.PuRe

99.

Zeitschriftenartikel

Beste, D. J.; Hooper, T.; Stewart, G.; Bonde, B.; Avignone-Rossa, C.; Bushell, M. E.; Wheeler, P.; Klamt, S.; Kierzek, A. M.; McFadden, J.: GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biology 8, R89 (2007)

MPG.PuRe