Publications of Steffen Klamt

At this page you find publications of Steffen Klamt. To see all publications of the group click here.

Klamt S and Stelling J (2006) Stoichiometric and constraint-based modelling. In: System Modeling in Cellular Biology: From Concepts to Nuts and Bolts. Edited by Szallasi Z, Stelling J and Periwal V. Cambridge, MIT Press, pp.73-96.

Klamt S (2005) Strukturelle Analyse von Stoffwechselnetzen illustriert am bakteriellen Redox- und Zentralstoffwechsel. Ph.D. thesis, Stuttgart University. Shaker Verlag, Aachen. (ISBN: 3-8322-3976-6)

Ballerstein K, von Kamp A, Klamt S and Haus UU. (2012) Minimal cut sets in a metabolic network are elementary modes in a dual network. Bioinformatics 28:381-387. PubMed

Ryll A, Samaga R, Schaper F, Alexopoulos LG and Klamt S. (2011) Large-scale network models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular Biosystems 7:3253-3270. PubMed
Hädicke O, Grammel H and Klamt S. (2011) Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5:150. open acess
Kaleta C, de Figueiredo LF, Heiland I Klamt S and Schuster S. (2011) Special issue: integration of OMICS datasets into metabolic pathway analysis. BioSystems 105:107-108. PubMed
Klamt S and von Kamp A. (2011) An application programming interface for CellNetAnalyzer. BioSystems 105:162-168. PubMed
Hädicke O and Klamt S (2011) Computing complex metabolic intervention strategies using constrained minimal cut sets. Metabolic Engineering 13:204-213. PubMed

Klamt S, Flassig RJ and Sundmacher K (2010) TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics 26:2160-2168. open access
Franke R, Theis FJ and Klamt S (2010) From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study. Journal of Integrative Bioinformatics 7:151. open access
Hädicke O and Klamt S (2010) CASOP: a computational approach for strain optimization aiming at high productivity. Journal of Biotechnology 147:88-101. PubMed
Samaga R, von Kamp A and Klamt S (2010) Computing combinatorial intervention strategies and failure modes in signaling networks. Journal of Computational Biology 17:39-53. open access

Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S and Sorger PK (2009) Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5:331. open access
Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S and Theis FJ (2009) Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Systems Biology 3:98. open access
Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK and Klamt S (2009) The logic of EGFR/ErbB signaling: Theoretical properties and analysis of high-throughput data. PLoS Computational Biology 5(8):e1000438. open access
Klamt S and von Kamp A (2009) Computing paths and cycles in biological interaction graphs. BMC Bioinformatics 10:181. open access
Klamt S, Haus U-U and Theis F (2009) Hypergraphs and Cellular Networks. PLoS Computational Biology 5:e1000385. open access

Klamt S, Grammel H, Straube R, Ghosh R and Gilles ED (2008) Modeling the electron transport chain of purple non-sulfur bacteria. Molecular Systems Biology 4:156. open access
Saez-Rodriguez J, Hammerle-Fickinger A, Dalal O, Klamt S, Gilles ED and Conradi C (2008) Multistability of signal transduction motifs. IET Systems Biology 2:80-93. PubMed
Haus UU, Klamt S and Stephen T (2008) Computing knock-out strategies in metabolic networks. Journal of Computational Biology 15:259-268. PubMed
Franke R, Mueller M, Wundrack N, Gilles ED, Klamt S, Kaehne T and Naumann M (2008) Host-pathogen systems biology: Logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Systems Biology 2:4. open access

Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU, Weismantel R, Gilles ED, Klamt S and Schraven B (2007) A logical model provides insights into T cell receptor signaling. PLoS Computational Biology 3:e163. open access
Beste DJ, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell ME, Wheeler P, Klamt S, Kierzek AM and McFadden J (2007) GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biology 8:R89. open access
Klamt S, Saez-Rodriguez J and Gilles ED (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1:2. open access

Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L and Gilles ED (2006) A methodology for the structural amd functional analysis of signaling and regulatory networks. BMC Bioinformatics 7:56. open access
Klamt S (2006) Generalized concept of minimal cut sets in biochemical networks. Biosystems 83:233-247. PubMed
Saez-Rodriguez J, Mirschel S, Hemenway R, Klamt S, Gilles ED and Ginkel M (2006) Visual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 7:506. open access

Klamt S, Gagneur J and von Kamp A (2005) Algorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Systems Biology 152:249-255. PubMed

Gagneur J and Klamt S (2004) Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5:175. open access
Papin JA, Stelling J, Price ND, Klamt S, Schuster S and Palsson BO (2004) Comparison of network-based pathway analysis methods. Trends in Biotechnology 22:400-405. PubMed
Klamt S and Gilles ED (2004) Minimal cut sets in biochemical reaction networks. Bioinformatics 20(2):226-234. open access
Kremling A, Klamt S, Ginkel M and Gilles ED (2004) Workbench for model set up, simulation, and analysis of cellular systems. IT-Information Technology 46:12-19. publisher page

Klamt S and Stelling J (2003) Two approaches for metabolic pathway analysis? Trends in Biotechnology 21(2):64-69. PubMed
Klamt S, Stelling J, Ginkel M and Gilles ED (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19(2): 261-269. open access

Stelling J, Klamt S, Bettenbrock K, Schuster S and Gilles ED (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420:190-193. PubMed
Klamt S and Stelling J (2002) Combinatorial complexity of pathway analysis in metabolic networks. Molecular Biology Reports 29(1-2):233-236. PubMed
Klamt S and Schuster S (2002) Calculating as many fluxes as possible in underdetermined metabolic networks. Molecular Biology Reports 29(1-2):243-248. PubMed
Schuster S and Klamt S (2002) Applying metabolic pathway analysis to make good use of methanol. Trends in Biotechnology 20(8):322. publisher page
Klamt S, Schuster S and Gilles ED (2002) Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnology & Bioengineering 77(7):734-751. PubMed
Schuster S, Klamt S, Weckwerth W, Moldenhauer F and Pfeiffer T (2002) Use of network analysis of metabolic systems in bioengineering. Bioprocess and Biosystems Engineering 24(6):363-372. publisher page

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