Journal Article (134)

2016
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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)
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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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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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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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Kolczyk, K.; Conradi, C.: Challenges in horizontal model integration. BMC Systems Biology (10), 28 (2016)
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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)
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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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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)
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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)
2015
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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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Conradi, C.; Shiu, A.: A Global Convergence Result for Processive Multisite Phosphorylation Systems. Bulletin of mathematical biology 77 (1), pp. 126 - 155 (2015)
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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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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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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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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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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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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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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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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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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)
Journal Article
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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