Publications of Steffen Klamt

Journal Article (111)

2017
Journal Article
Kamp von, A. & Klamt, S. (2017)Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms.Nature Communications, 8, 15926 doi: 10.1038/ncomms15956.
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Kamp von, A., Thiele, S., Hädicke, O., & Klamt, S. (2017)Use of CellNetAnalyzer in biotechnology and metabolic engineeringJournal of Biotechnology, 261, 221–228doi: 10.1016/j.jbiotec.2017.05.001.
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Journal Article
Klamt, S., Regensburger, G., Gerstl, P. M., Jungreuthmayer, C., Schuster, S., Mahadevan, R., Zanghellini, J., & Müller, S. (2017)From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraintsPLoS Computational Biology, 13 (4), e1005409doi: 10.1371/journal.pcbi.1005409.
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2016
Journal Article
Gerstl, M. P., Klamt, S., Jungreuthmayer, C., & Zanghellini, J. (2016)Exact quantification of cellular robustness in genome-scale metabolic networksBioinformatics, 32 (5), 730–737doi: 10.1093/bioinformatics/btv649.
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Harder, B.-J., Bettenbrock, K., & Klamt, S. (2016)Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coliMetabolic Engineering, 38, 29–37doi: 10.1016/j.ymben.2016.05.008.
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Koch, S., Benndorf, D., Fronk, K., Reichl, U., & Klamt, S. (2016)Predicting compositions of microbial communities from stoichiometric models with applications for the biogas processBiotechnology for Biofuels, 9, 17doi: 10.1186/s13068-016-0429-x.
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Ud-Dean, S. M., Heise, S., Klamt, S., & Gunawan, R. (2016)TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments.BMC Bioinformatics, 17 (17), 252doi: 10.1186/s12859-016-1137-z.
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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., 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. (2016)MUFINS: multi-formalism interaction network simulatornpj Systems Biology and Applications, 2, 16032doi: 10.1038/npjsba.2016.32.
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2015
Journal Article
Bastiaens, P. I. H., Birtwistle, M. R., Blüthgen, N., Bruggeman, F. J., Cho, K.-H., de la Fuente, A., Hoek, J. B., Kiyatkin, A., Klamt, S., Kolch, W., Legewie, S., Mendes, P., Naka, T., Santra, T., Sontag, E., Westerhoff, H. V., & Kholodenko, B. N. (2015)Silence on the relevant literature and errors in implementationNature Biotechnology, 33 (4), 336–339doi: 10.1038/nbt.3185.
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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., Schilling, M., Timmer, J., Klamt, S., & Klingmüller, U. (2015)Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative ModelingPLoS Computational Biology, 11 (4), e1004192doi: 10.1371/journal.pcbi.1004192.
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Erdrich, P., Steuer, R., & Klamt, S. (2015)An algorithm for the reduction of genome-scale metabolic network models to meaningful core modelsBMC Systems Biology, 9, 48doi: 10.1186/s12918-015-0191-x.
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Hädicke, O., Bettenbrock, K., & Klamt, S. (2015)Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coliBiotechnology and Bioengineering, 112 (10), 2195–2199doi: 10.1002/bit.25623.
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post-print
Journal Article
Hädicke, O. & Klamt, S. (2015)Manipulation of the ATP pool as a tool for metabolic engineeringBiochemical Society Transactions (London), 43 (6), 1140–1145doi: 10.1042/BST20150141.
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Journal Article
Klamt, S. & Mahadevan, R. (2015)On the feasibility of growth-coupled product synthesis in microbial strainsMetabolic Engineering, 30, 166–178doi: 10.1016/j.ymben.2015.05.006.
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Mahadevan, R., Kamp von, A., & Klamt, S. (2015)Genome-scale strain designs based on regulatory minimal cut setsBioinformatics, 31 (17), 2844–2851doi: 10.1093/bioinformatics/btv217.
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Michailidou, M., Melas, I. N., Messinis, D. E., Klamt, S., Alexopoulos, L. G., Kolisis, F. N., & Loutrari, H. (2015)Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive ActionCPT: Pharmacometrics & Systems Pharmacology, 4 (6), 350–361doi: 10.1002/psp4.40.
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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., & Schilling, M. (2015)T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytesMolecular Systems Biology, 11, 795doi: 10.15252/msb.20156032.
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Thiele, S., Cerone, L., Saez-Rodriguez, J., Siegel, A., Guciolowski, C., & Klamt, S. (2015)Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.BMC Bioinformatics, 16 (1), 345doi: 10.1186/s12859-015-0733-7.
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Wiechert, W. & Klamt, S. (2015)Computational Systems Biology — neues Fach in den LebenswissenschaftenBiospektrum, 21 (1), 46–48doi: 10.1007/s12268-015-0537-3.
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2014
Journal Article
Erdrich, P., Knoop, H., Steuer, R., & Klamt, S. (2014)Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modelingMicrobial Cell Factories, 13, 128–128doi: 10.1186/s12934-014-0128-x.
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