Publications of Steffen Klamt

Journal Article (111)

2014
Journal Article
Kamp von, A. & Klamt, S. (2014)Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic NetworksPLoS Computational Biology, 10 (1), e1003378doi: 10.1371/journal.pcbi.1003378.
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Lohr, V., Hädicke, O., Genzel, Y., Jordan, I., Buentemeyer, H., Klamt, S., & Reichl, U. (2014)The avian cell line AGE1.CR.pIX characterized by metabolic flux analysisBMC Biotechnology, 14, 72doi: 10.1186/1472-6750-14-72.
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Ryll, A., Bucher, J., Bonin, A., Bongard, S., Gonçalves , E., Saez- Roidriguez, J., Niklas, J., & Klamt, S. (2014)A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic modelsBiosystems, 124, 26–38doi: 10.1016/j.biosystems.2014.07.002.
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2013
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., 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. (2013)SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and toolsBMC Systems Biology, 7, 135doi: 10.1186/1752-0509-7-135.
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Flassig, R., Heise, S., Sundmacher, K., & Klamt, S. (2013)An effective framework for reconstructing gene regulatory networks from genetical genomics data.Bioinformatics, 29 (2), 246–254doi: 10.1093/bioinformatics/bts679.
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Gonçalves, E., Bucher, J., Ryll, A., Niklas, J., Mauch, K., Klamt, S., Rocha, M., & Saez-Rodriguez, J. (2013)Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical modelsMolecular BioSystems, 9 (7), 1576–1583doi: 10.1039/c3mb25489e.
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Gruchattka, E., Hädicke, O., Klamt, S., Schuetz, V., & Kayser , O. (2013)In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factoriesMicrobial Cell Factories, 12, 84doi: 10.1186/1475-2859-12-84.
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Hädicke, O., Lohr, V., Genzel, Y., Reichl, U., & Klamt, S. (2013)Evaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivationsBiotechnology and Bioengineering, 110 (10), 2633–2642doi: 10.1002/bit.24926.
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Jungreuthmeyer, C., Nair, G., Klamt, S., & Zanghellini, J. (2013)Comparison and improvement of algorithms for computing minimal cut setsBMC Bioinformatics, 14 (1), 318doi: 10.1186/1471-2105-14-318.
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Melas, I. N., Samaga, R., Alexopoulos, L. G., & Klamt, S. (2013)Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction GraphsPLoS Computational Biology, 9 (9), e1003204doi: 10.1371/journal.pcbi.1003204.
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Pinna, A., Heise, S., Flassig, R., de la Fuente, A., & Klamt, S. (2013)Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluationBMC Systems Biology, 7, 73doi: 10.1186/1752-0509-7-73.
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Samaga, R. & Klamt, S. (2013)Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networksCell Communication and Signaling, 11 (1), 43doi: 10.1186/1478-811X-11-43.
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2012
Journal Article
Ballerstein, K., von Kamp, A., Klamt, S., & Haus, U.-U. (2012)Minimal cut sets in metabolic networks are elementary modes in a dual networkBioinformatics, 28 (3), 381–387doi: 10.1093/bioinformatics/btr674.
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Huard, J., Mueller, S., Gilles, E. D., Klingmüller, U., & Klamt, S. (2012)An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytesFEBS Journal, 279 (18), 3290–3313doi: 10.1111/j.1742-4658.2012.08572.x.
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2011
Journal Article
Hädicke, O., Grammel, H., & Klamt, S. (2011)Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteriaBMC Systems Biology, 5, 150doi: 10.1186/1752-0509-5-150.
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Hädicke, O. & Klamt, S. (2011)Computing complex metabolic intervention strategies using constrained minimal cut setsMetabolic Engineering, 13 (2), 204–213doi: 10.1016/j.ymben.2010.12.004.
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Journal Article
Klamt, S. & Kamp von, A. (2011)An application programming interface for CellNetAnalyzerBiosystems, 105 (2), 162–168doi: 10.1016/j.biosystems.2011.02.002.
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Ryll, A., Samaga, R., Schaper, F., Alexopoulos, L. G., & Klamt, S. (2011)Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specificationMolecular BioSystems, 7 (12), 3253–3270doi: 10.1039/c1mb05261f.
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2010
Journal Article
Franke, R., Theis, F. J., & Klamt, S. (2010)From Binary to Multivalued to Continuous Models: The Iac Operon as a Case StudyJournal of Integrative Bioinformatics, 7 (1), 151doi: 10.2390/biecoll-jib-2010-151.
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Hädicke, O. & Klamt, S. (2010)CASOP: a computational approach for strain optimization aiming at high productivityJournal of Biotechnology, 147 (2), 88–101doi: 10.1016/j.jbiotec.2010.03.006.
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