Research Group

Analysis and Redesign of Biological Networks

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Publications

Below you find a complete list of publications of members of the group. Separate lists of the research team leaders can be found here: Steffen Klamt, Ronny Straube, Carsten Conradi.

Book chapters

• 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.

Monographs

• Conradi C (2008) Multistationarity in (bio)chemical reaction networks with mass action kinetics: model discrimination, robustness and beyond. Ph.D. thesis. Forschungsberichte aus dem Max-Planck-Institut Dynamik komplexer technischer Systeme. Shaker Verlag.
• Straube R (2006) Quasi integrals and the origin of bursting pH oscillations in an enzyme model system. Ph.D. thesis, Magdeburg University.
• 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)

Peer-reviewed articles

2013

• Carius L, Hädicke O, Grammel H (2013) Stepwise reduction of the culture redox potential allows the analysis of microaerobic metabolism and photosynthetic membrane synthesis in Rhodospirillum rubrum. Biotechnology and Bioengineering 10: 573-85. PubMed
• Flassig RJ, Heise S, Sundmacher K, Klamt S (2013) An effective framework for reconstructing gene regulatory networks from genetical genomics data. Bioinformatics 29: 246-254. PubMed

2012

• Huard J , Mueller S, Gilles ED, Klingmueller U and Klamt S (2012) An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 279:3290-3313. Open Access
• Kolczyk K , Samaga R, Conzelmann H, Mirschel S and Conradi C (2012) The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics 13:251. Open Access
• Pandey R , Flockerzi D, Hauser MJB, Straube R (2012) An extended model for the repression of photosynthesis genes by the AppA/PpsR system in Rhodobacter sphaeroides. FEBS Journal 279:3449-3i461. PubMed
• Conradi C and Flockerzi D (2012) Multistationarity in mass action networks with applications to ERK activation. Journal of Mathematical Biology 65:107-156. PubMed
• Perez-Millan M, Dickenstein A, Shiu A and Conradi C (2012) Chemical reaction systems with toric steady states. Bulletin of Mathematical Biology 74:1027-1065. PubMed
• Conradi C and Flockerzi D (2012) Switching in Mass Action Networks Based on Linear Inequalities . SIAM Journal on Applied Dynamical Systems 11:110-134. Link
• 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
• Straube R. (2012) Comment on 'Load-induced modulation of signal transduction networks': Reconciling ultrasensitivity with bifunctionality? Science Signaling 5:lc1. PubMed

2011

• 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 Access
• 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
• Pandey R, Flockerzi D, Hauser MJB and Straube R (2011) Modeling the Light and Redox Dependent Interaction of PpsR/AppA in Rhodobacter sphaeroides. Biophysical Journal 100(10):2347-2355. PubMed
• Wei F, Yang D, Straube R and Shuai J (2011) Brownian Diffusion of Ion Channels in Different Membrane Patch Geometries. Physical Review E 83:021919. PubMed

2010

• 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
• Straube R and Nicola EM (2010) Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system. BMC Systems Biology 4:165. Open Access
• Straube R, Vermeer S, Nicola EM and Mair T (2010) Inward Rotating Spiral Waves in Glycolysis. Biophysical Journal 99(1):L4-L6. PubMed
• Cheviakov AF, Ward MJ and Straube R (2010) An Asymptotic Analysis of the Mean First Passage Time for Narrow Escape Problems: Part II: The Sphere. SIAM Multiscale Modeling & Simulation 8(3):836-870. preprint DOI:10.1137/100782620

2009

• 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
• Straube R and Ridgway D (2009) Investigating the Effects of Molecular Crowding on Ca²⁺ Diffusion Using a Particle-Based Simulation Model. Chaos 19(3):037110. PubMed
• Coombs D, Straube R and Ward MJ (2009) Diffusion on a Sphere with Localized Traps: Mean First Passage Time, Eigenvalue Asymptotics, and Fekete Points. SIAM J. on Applied Mathematics 70(1):302-332. DOI:10.1137/080733280
• Straube R and Ward MJ (2009) An asymptotic analysis of intracellular signaling gradients arising from multiple small compartments. SIAM J. on Applied Mathematics 70:248-269. DOI:10.1137/080733401
• Uhr M, Kaltenbach HM, Conradi C and Stelling J (2009) Analysis of Degenerate Chemical Reaction Networks. Positive Systems. Lecture Notes in Control and Information Sciences 389:163-182. abstract DOI:10.1007/978-3-642-02894-6_16
• Mirschel S, Steinmetz K, Rempel M, Ginkel M and Gilles ED (2009) PROMOT: modular modeling for systems biology. Bioinformatics 25(5):687-689. Open Access

2008

• 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
• Bagyan S, Mair T, Suchorski Y, Hauser MJB and Straube R (2008) Spatial desynchronization of glycolytic waves as revealed by Karhunen-Loève analysis. Journal of Physical Chemistry B 112(45):14334-14341.
  preprint PubMed
• Conradi C, Flockerzi D and Raisch J (2008) Multistationarity in the activation of an MAPK: parametrizing the relevant region in parameter space. Mathematical Biosciences 211(1):105-131. abstract PubMed
• Flockerzi D and Conradi C (2008) Subnetwork analysis for multistationarity in mass action kinetics. Journal of Physics - Conference Series 138:012006. abstract DOI:10.1088/1742-6596/138/1/012006

2007

• 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
• Straube R and Falcke M (2007) Reversible clustering under the influence of a periodically modulated binding rate. Physical Review E 76:010402(R). preprint PubMed
• Straube R, Ward MJ and Falcke M (2007) Reaction rate of small diffusing molecules on a cylindrical membrane. Journal of Statistical Physics 129(2):377-405. preprint DOI:10.1007/s10955-007-9371-4
• Conradi C, Flockerzi D, Raisch J and Stelling J (2007) Subnetwork analysis reveals dynamic features of complex (bio)chemical networks. PNAS 104(49):19175-19180. Open Access

2006

• 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
• Straube R, Flockerzi D and Hauser MJB (2006) Sub-Hopf / fold-cycle bursting and its relation to (quasi-) periodic oscillations. Journal of Physics: Conference Series 55:214-231. Open Access

2005

• 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
• Straube R, Flockerzi D, Müller SC and Hauser MJB (2005) Origin of bursting pH oscillations in an enzyme model system. Physical Review E 72:066205. abstract PubMed
• Straube R, Flockerzi D, Müller SC and Hauser MJB (2005) Reduction of chemical reaction networks using quasi integrals. Journal of Physical Chemistry A 109:441-450. abstract PubMed
• Conradi C, Saez-Rodriguez J, Gilles ED and Raisch J (2005). Using Chemical Reaction Network Theory to discard a kinetic mechanism hypothesis. Systems Biology, IEE Proceedings (now IET Systems Biology) 152(4):243-248. abstract PubMed

2004

• 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

2003

• 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
• Straube R, Müller SC and Hauser MJB (2003) Bursting oscillations in the revised mechanism of the hemin-hydrogen-peroxide-sulfite oscillator. Zeitschrift für Physikalische Chemie 217(11):1427-1442. abstract DOI:10.1524/zpch.217.11.1427.20485

2002

• 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