Publications of Steffen Klamt

Journal Article (117)

2015
Journal Article
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, 128doi: 10.1186/s12934-014-0128-x.
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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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publisher-version
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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Journal Article
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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