Steffen Klamt

Journal Article (103)

1.
Journal Article
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), pp. 3855 - 3864 (2022)
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2.
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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, pp. 50 - 57 (2022)
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3.
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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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4.
Journal Article
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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5.
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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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6.
Journal Article
Schneider, P.; Bekiaris, P. S.; Kamp von, A.; Klamt, S.: StrainDesign: a Comprehensive Python Package for Computational Design of Metabolic Networks. Bioinformatics 38 (21), pp. 4981 - 4983 (2022)
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7.
Journal Article
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), pp. 1467 - 1469 (2022)
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8.
Journal Article
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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9.
Journal Article
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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10.
Journal Article
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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11.
Journal Article
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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12.
Journal Article
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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13.
Journal Article
Bekiaris, P. S.; Klamt, S.: Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 21, 19 (2020)
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14.
Journal Article
Kamp von, A.; Klamt, S.: MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems. ACS Synthetic Biology 9 (3), pp. 556 - 566 (2020)
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15.
Journal Article
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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16.
Journal Article
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, pp. 272 - 276 (2020)
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supplementary-material
17.
Journal Article
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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18.
Journal Article
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 (13), 185 (2020)
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19.
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 14 (9), 1800438 (2019)
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20.
Journal Article
Klamt, S.; Kamp von, A.; Harder, B.-J.: Computergestütztes Design mikrobieller Zellfabriken. Biospektrum 25 (2), pp. 156 - 158 (2019)
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21.
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)
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22.
Journal Article
Schneider, P.; Klamt, S.: Characterizing and Ranking Computed Metabolic Engineering Strategies. Bioinformatics 35 (17), pp. 3063 - 3072 (2019)
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23.
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 16 (3), pp. 925 - 935 (2019)
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24.
Journal Article
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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25.
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)
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26.
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)
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27.
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)
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28.
Journal Article
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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29.
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)
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30.
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)
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31.
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)
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32.
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)
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33.
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)
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34.
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)
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35.
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)
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36.
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)
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37.
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)
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38.
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)
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39.
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)
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40.
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)
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41.
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)
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42.
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)
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43.
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)
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44.
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)
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45.
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)
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46.
Journal Article
Klamt, S.; Mahadevan, R.: On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 30, pp. 166 - 178 (2015)
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47.
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)
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48.
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)
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49.
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)
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50.
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)
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51.
Journal Article
Wiechert, W.; Klamt, S.: Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 21 (1), pp. 46 - 48 (2015)
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52.
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)
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53.
Journal Article
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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54.
Journal Article
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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55.
Journal Article
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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56.
Journal Article
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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57.
Journal Article
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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58.
Journal Article
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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59.
Journal Article
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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60.
Journal Article
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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61.
Journal Article
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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62.
Journal Article
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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63.
Journal Article
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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64.
Journal Article
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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65.
Journal Article
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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66.
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)
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67.
Journal Article
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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68.
Journal Article
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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69.
Journal Article
Klamt, S.; Kamp von, A.: An application programming interface for CellNetAnalyzer. Biosystems 105 (2), pp. 162 - 168 (2011)
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70.
Journal Article
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)
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71.
Journal Article
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)
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72.
Journal Article
Hädicke, O.; Klamt, S.: CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147 (2), pp. 88 - 101 (2010)
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73.
Journal Article
Klamt, S.; Flassig, R.; Sundmacher, K.: TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26 (17), pp. 2160 - 2168 (2010)
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74.
Journal Article
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)
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75.
Journal Article
Klamt, S.; Haus, U.-U.; Theis, F.: Hypergraphs and cellular networks. PLoS Computational Biology 5 (5), p. e1000385 (2009)
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76.
Journal Article
Klamt, S.; von Kamp, A.: Computing Paths and Cycles in Biological Interaction Graphs. BMC Bioinformatics 10, p. 181 (2009)
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77.
Journal Article
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)
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78.
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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)
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79.
Journal Article
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)
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80.
Journal Article
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)
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81.
Journal Article
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)
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82.
Journal Article
Haus, U.-U.; Klamt, S.; Stephen, T.: Computing knock-out strategies in metabolic networks. Journal of Computational Biology 15 (3), pp. 259 - 268 (2008)
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83.
Journal Article
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)
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84.
Journal Article
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), pp. 80 - 93 (2008)
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85.
Journal Article
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)
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86.
Journal Article
Klamt, S.; Saez-Rodriguez, J.; Gilles, E. D.: Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1, 2 (2007)
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87.
Journal Article
Saez-Rodriguez, J.; Simeoni, L.; Lindquist, J.; Hemenway, R.; Bommhardt, U.; Arndt, B.; Haus, U. U.; Weismantel, R.; Gilles, E. D.; Klamt, S. et al.; Schraven, B.: A logical model provides insights into T cell receptor signaling. PLoS Computational Biology 3, e163 (2007)
MPG.PuRe
DOI
publisher-version
88.
Journal Article
Klamt, S.: Generalized concept of minimal cut sets in biochmical networks. Biosystems 83 (2-3 ), pp. 233 - 247 (2006)
MPG.PuRe
DOI
89.
Journal Article
Klamt, S.; Saez-Rodriguez, J.; Lindquist, J.; Simeoni, L.; Gilles, E. D.: A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7, p. 56 (2006)
MPG.PuRe
DOI
publisher-version
90.
Journal Article
Saez-Rodriguez, J.; Mirschel, S.; Hemenway, R.; Klamt, S.; Gilles, E. D.; Ginkel, M.: Visual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 7, 506 (2006)
MPG.PuRe
DOI
publisher-version
91.
Journal Article
Klamt, S.; Gagneur, J.; von Kamp, A.: Algorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Proceedings - Systems Biology 152 (4), pp. 249 - 255 (2005)
MPG.PuRe
DOI
92.
Journal Article
Gagneur, J.; Klamt, S.: Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5, 175 (2004)
MPG.PuRe
DOI
publisher-version
93.
Journal Article
Klamt, S.; Gilles, E. D.: Minimal cut sets in biochemical reaction networks. Bioinformatics 20, pp. 226 - 234 (2004)
MPG.PuRe
DOI
94.
Journal Article
Kremling, A.; Ginkel, M.; Klamt, S.; Gilles, E. D.: Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme. it - Information Technology 46, pp. 12 - 19 (2004)
MPG.PuRe
DOI
95.
Journal Article
Papin, J. A.; Stelling, J.; Price, N. D.; Klamt, S.; Schuster, S.; Palsson, B. O.: Comparison of network-based pathway analysis methods. Trends in Biotechnology 22 (8), pp. 400 - 405 (2004)
MPG.PuRe
DOI
96.
Journal Article
Klamt, S.; Stelling, J.: Two approaches for metabolic pathway analysis? Trends in Biotechnology 21 (2), pp. 64 - 69 (2003)
MPG.PuRe
DOI
97.
Journal Article
Klamt, S.; Stelling, J.; Ginkel, M.; Gilles, E. D.: FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19 (2), pp. 261 - 269 (2003)
MPG.PuRe
DOI
98.
Journal Article
Klamt, S.; Schuster, S.: Calculating as many fluxes as possible in underdetermined metabolic networks. Molecular Biology Reports 29 (1-2), pp. 243 - 248 (2002)
MPG.PuRe
DOI
99.
Journal Article
Klamt, S.; Schuster, S.; Gilles, E. D.: Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnology and Bioengineering 77 (7), pp. 734 - 751 (2002)
MPG.PuRe
DOI
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