Hier findet sich eine komplette Publikationsliste der Fachgruppe ARB. Separate Publikationslisten für den Gruppenleiter Steffen Klamt bzw. die Teamleiterin Katja Bettenbrock finden sich hier: Steffen Klamt / Katja Bettenbrock.


  • Frohwitter J, Behrendt G, Klamt S, Bettenbrock K (2024) A new Zymomonas mobilis platform strain for the efficient production of chemicals. Microbial Cell Facories 23:143. Open Access 
  • Espinel-Ríos S, Behrendt G, Bauer J, Morabito B , Pohlodek J, Schütze A,  Findeisen R, Bettenbrock K, Klamt S (2024) Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. Process Biochemistry 143:174-185. Open Access
  • Bauer J, Klamt S (2024) OptMSP: A toolbox for designing optimal multi-stage (bio)processes. Journal of Biotechnology 383:94-102. Open Access
  • Behrendt G, Vlachonikolou M, Tietgens H, Bettenbrock K (2024) Construction and comparison of different vehicles for heterologous gene expression in Zymomonas mobilis. Microbial Biotechnology 17:e14381.Open Access
  • Huber N, Alcalá-Orozco, EA, Rexer T, Reichl U, Klamt S (2024) Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metabolic Engineering 81:10-25. Open Access
  • Espinel Ríos S, Morabito B, Pohlodek J, Bettenbrock K, Klamt S, Findeisen R (2024) Toward a modeling, optimization, and predictive control framework for fed‐batch metabolic cybergenetics. Biotechnology and Bioengineering 121:366-379. Open Access


  • von Kamp A, Klamt S (2023) Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. Bioinformatics 39:btad600 Open Access
  • Hülsmann J, Fraune T, Dodawatta B, Reuter F, Beutner M, Beck V, Hackert-Oschätzen M, Ohl K D, Bettenbrock K, Jaiga G, Wippermann J, Wacker, M (2023) Integrated biophysical matching of bacterial nanocellulose coronary artery bypass grafts towards bioinspired artery typical functions. Sci Rep 13:18274 Open Access
  • Alcalá-Orozco E A, Grote V, Fiebig T, Klamt S, Reichl U, Rexer T (2023) A Cell-Free Multi-enzyme Cascade Reaction for the Synthesis of CDP-Glycerol. ChemBioChem 24: e202300463. Open Access
  • Boecker S, Schulze P, Klamt S (2023) Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. Biotechnology for Biofuels and Bioproducts 16:148. Open Access
  • Bekiaris PS, Klamt S (2023) Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions. Nature Communications 14:4660. Open Access
  • Espinel-Ríos S, Bettenbrock K, Klamt S, Avalos J L, Findeisen R (2023) Machine learning-supported cybergenetic modeling, optimization and control for synthetic microbial communities. Computer Aided Chemical Engineering 52:2601-2605. Open Access
  • Wichmann J, Behrendt G, Boecker S, Klamt S (2023) Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering. Metabolic Engineering 77:199-207. Open Access


  • Espinel-Ríos S, Morabito B, Bettenbrock K, Klamt S, Findeisen R (2022) Soft sensor for monitoring dynamic changes in cell composition. IFAC-PapersOnLine 55:98-103. Open Access
  • Espinel-Ríos S, Morabito B, Pohlodek J, Bettenbrock K, Klamt S, Findeisen R (2022) Optimal control and dynamic modulation of the ATPase gene expression for enforced ATP wasting in batch fermentations. IFAC-PapersOnLine 55:174-180. Open Access
  • Espinel-Ríos S, Huber N, Alcalá Orozco E A, Morabito B, Rexer T, Reichl U, Klamt S, Findeisen R (2022) Cell-free biosynthesis meets dynamic optimization and control: a fed-batch framework. IFAC-PapersOnLine 55:92-97. Open Access
  • Li Z, Nees M, Bettenbrock K, Rinas U (2022) Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. Microbial Cell Factories 21:67. Open Access
  • Schneider P, Bekiaris PS, von Kamp AKlamt S (2022) StrainDesign: a comprehensive Python package for computational design of metabolic networks. Bioinformatics 38:4981-4983. Open Access
  • Behrendt G, Frohwitter J, Vlachonikolou M, Klamt S, Bettenbrock K (2022) Zymo-Parts: A Golden Gate Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. ACS Synthtic Biology 11:3855-3864. Open Access
  • Wichmann J, Eggert A, Elbourne LDH, Paulsen, IT, Lauersen KJ, Kruse O (2022) Farnesyl pyrophosphate compartmentalization in the green microalga Chlamydomonas reinhardtii during heterologous (E)-α-bisabolene production. Microbial Cell Factories 21:190. Open Access
  • Boecker S, Espinel-Ríos S, Bettenbrock K, Klamt S (2022) Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering 73:50-57. Open Access
  • Klamt S, von Kamp A (2022) Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks. Metabolites 12: 585. Open Access
  • Espinel-Ríos S, Bettenbrock K, Klamt S, Findeisen R (2022) Maximizing batch fermentation efficiency by constrained model-based optimization and predictive control of adenosinetriphosphate turnover. AIChE Journal 68:e17555. Open Access
  • Thiele S, von Kamp A, Bekiaris PS, Schneider P, Klamt S (2022) CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks. Bioinformatics 38:1467-1469. Open Access
  • Mahour R, Lee JW, Grimpe P, Boecker S, Grote V, Klamt S, Seidel-Morgenstern A, Rexer TFT, Reichl U (2022) Cell-Free Multi-Enzyme Synthesis and Purification of Uridine Diphosphate Galactose. ChemBioChem 23:e202100361. Link
  • Petras D, ..., Boecker S, ..., Wang M (2022) GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods 19:134-136. Link


  • Boecker S, Slaviero G, Schramm T, Szymanski W, Steuer R, Link H, Klamt S (2021) Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology 17:e10504. Open Access
  • Schneider P, Radhakrishnan M, Klamt S (2021) Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs. Biotechnology Journal 16:e2100236. Link
  • Harriehausen I, Bollmann J, Carneiro T, Bettenbrock K, Seidel-Morgenstern A (2021) Characterization of an Immobilized Amino Acid Racemase for Potential Application in Enantioselective Chromatographic Resolution Processes. Catalysts 11:726. Link
  • Bekiaris PS, Klamt S (2021) Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Computational Biology 17:e1009093. Link
  • Boecker S, Harder B-J, Kutscha R, Pflügl S, Klamt S (2021) Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli. Microbial Cell Factories 20:63. Link
  • Novak K, Neuendorf CS, Kofler I, Kieberger N, Klamt S, Pflügl S (2021) Blending industrial blast furnace gas with H2 enables Acetobacterium woodii to efficiently co-utilize CO, CO2 and H2. Bioresource Technology 323:124573. Link


  • Zahoor A, Messerschmidt K, Boecker S, Klamt S (2020) ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. Biotechnology for Biofuels 13:185. Link
  • Klamt S, Mahadevan R, von Kamp A (2020) Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinformatics 21:510. Link
  • Carneiro T, Wrzosek K, Bettenbrock K, Lorenz H, Seidel-Morgenstern A (2020) Immobilization of an amino acid racemase for application in crystallization‐based chiral resolutions of asparagine monohydrate. Engineering in Life Sciences 20:551-560. Open Access
  • Kalnenieks U, Pappas KM, Bettenbrock K (2020). Zymomonas mobilis metabolism: Novel tools and targets for its rational engineering. Adv Microbial Phys 77:37-88. Link
  • Rexer T, Wenzel L, Hoffmann M, Tischlik S, Bergmann C, Grote V, Boecker S, Bettenbrock K, Schildbach A, Kottler R, Mahour R, Rapp E, Pietzsch M, Reichl U (2020) Synthesis of lipid-linked oligosaccharides by a compartmentalized multi-enzyme cascade for the in vitro N-glycosylation of peptides. Journal of Biotechnology 322(10):54-65. Link
  • Schneider P, von Kamp A, Klamt S (2020) An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. PLOS Computational Biology 16(7):e1008110. Open access
  • von Kamp A, Klamt S (2020) MEMO: A method for computing metabolic modules for cell-free production systems. ACS Synth Biol 9(3):556-566. Open Access
  • Lieven C, ..., Klamt S, ..., Zhang C (2020) MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology 38(3):272-276. Link
  • Schütze A, Benndorf D, Püttker S, Kohrs F, Bettenbrock K (2020) The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12. Frontiers in Microbiology 11:233. Open Access
  • Bekiaris PS, Klamt S (2020) Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 21:19. Open Access


  • Kalnenieks U, Balodite E, Strähler S, Strazdina I, ... , Bettenbrock K (2019) Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism. Frontiers in Microbiology 10: 2533. Open Access
  • Witt A, Pozzi R, Diesch S, Hädicke O, Grammel H (2019) New light on ancient enzymes – in vitro CO2 Fixation by Pyruvate Synthase of Desulfovibrio africanus and Sulfolobus acidocaldarius. The FEBS Journal 286(22):4494-4508. Link
  • Zahoor A , Küttner FTK, Blank LM, Ebert BE (2019) Evaluation of pyruvate decarboxylase‐negative Saccharomyces cerevisiae strains for the production of succinic acid. Engineering in Life Sciences 19(10):711-7120. Open Access
  • Boecker S, Zahoor A, Schramm T, Link H, Klamt S (2019) Broadening the scope of enforced ATP wasting as a tool for metabolic engineering in Escherichia coli. Biotechnology Journal 14(9):1800438. Open Access
  • Schneider P, Klamt S (2019) Characterizing and ranking computed metabolic engineering strategies. Bioinformatics 35(17): 3063–3072. Open Access
  • Thiele S, Heise S, Hessenkemper W, Bongartz H, Fensky M, Schaper F, Klamt S (2019) Designing optimal experiments to discriminate interaction graph models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 16:925-935. Open Access
  • Weinrich S, Koch S, Bonk F, Popp D, Benndorf D, Klamt S, Centler F (2019) Augmenting biogas process modeling by resolving intracellular metabolic activity. Frontiers in Microbiology 10:1095. Open Access
  • Klamt S, von Kamp A, Harder B-J (2019) Computergestütztes Design mikrobieller Zellfabriken. BIOspektrum 25:156-158. Open Access
  • Koch S, Kohrs F, Lahmann P, Bissinger T, Wendschuh S, Benndorf D, Reichl U, Klamt S (2019) RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PLoS Computational Biology 15(2):e1006759. Open Access


  • Venayak N, von Kamp A, Klamt S, Mahadevan R (2018) MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications 9:5332. Open Access
  • Hädicke O, von Kamp A, Aydogan T, Klamt S (2018) OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PLoS Computational Biology 14:e1006492. Open Access
  • Kyselova L, Kreitmayer D, Kremling A & Bettenbrock K (2018) Type and capacity of glucose transport influences succinate yield in two-stage cultivations. Microbial Cell Factories 17:132. Springer
  • Mahour R, Klapproth J, Rexer T, Schildbach A, Klamt S, Pietzsch M, Rapp E, Reichl U (2018) Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 283:120 - 129. Artikel
  • Bosch J, Klamt S, Stoll M (2018) Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics 78:1350 - 1377. Artikel
  • Nitzschke A, Bettenbrock K (2018) All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K 12. PLoS One 13:20194699. Open Access
  • Klamt S, Müller S, Regensburger J, Zanghellini J (2018) A mathematical framework for yield (vs. rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 47:153-169. Open Access
  • Klamt S, Mahadevan R, Hädicke O (2018) When do two-stage processes outperform one-stage processes? Biotechnology Journal 13:1700539. Open Access
  • Harder B-J, Bettenbrock K, Klamt S (2018) Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 115 :156-164. Open Access


  • von Kamp A, Thiele S, Hädicke O, Klamt S (2017) Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 261 :221-228. Open Access
  • von Kamp A, Klamt S (2017) Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 8:15956. Open Access
  • Zander D, Samaga D, Straube R, Bettenbrock K (2017) Bistability and nonmonotonic induction of the lac operon in the natural lactose uptake system. Biophysical Journal 112:1984-1996. PubMed
  • Klamt S, Regensburger G, Gerstl MP, 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 constraints. PLoS Comput Biol 13:e1005409. Open Access
  • Prigent S, Frioux C, Dittami SM, Thiele S,... (2017) Meneco, a topolpoy-based gap-filling tool applicable to degraded genome-wide metabolic networks. PLoS Comput Biol 13:e1005276. Open Access
  • Hädicke O, Klamt S (2017) EColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent model. Scientific Reports 7:39647. Open Access


  • Wu H, von Kamp A, Leoncikas V, ...., Klamt S, ... Kierzek AM (2016) MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 2:16032. Open Access
  • Ud-Dean SM, 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 17:252. PubMed
  • Harder B-J, Bettenbrock K, Klamt S (2016) Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 38:29-37. PubMed
  • Wrzosek K, Rivera MA, Bettenbrock K, Seidel-Morgenstern A (2016) Racemization of undesired enantiometers: Immobization of mandelate racements and application in a fixed bed reactor. Biotechnol. J 11:453-463. Open Access
  • Kolczyk K, Conradi C (2016) Challenges in horizontal model integration. BMC Systems Biology 10:28. OpenAccess
  • Gerstl MP, Klamt S, Jungreuthmayer C, Zanghellini J (2016) Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 32:730-737. OpenAccess
  • Koch S, Benndorf D, Fronk K, Reichl U, Klamt S (2016) Predicting compositions of communities from stoichiometric models with applications for the biogas process. Biotechnology for Biofuels  9:17. OpenAccess


  • Bordron P,  Latorre M, Cortés MP, González M, Thiele S, Siegel A, Maas A, Eveillard D (2015) Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. MicrobiologyOpen accepted. OpenAccess
  • Hädicke O, Klamt S (2015) Manipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions 43:1140-1145. PubMed
  • Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziolowski C, Klamt S (2015) Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 16:345. Open Access
  • Hädicke O, Bettenbrock K, Klamt S (2015) Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnology & Bioengineering 112:2195-2199. PubMed
  • Mahadevan R, von Kamp A, Klamt S (2015) Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 31:2844-2851. PubMed
  • Erdrich P, Steuer R, Klamt S (2015) An algorithm for the reduction of genome-scale metabolic network models to meaningful core models.  BMC Systems Biology 9:48. Open Access
  • Klamt S, Mahadevan R (2015) On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 30:166-178. PubMed
  • Michailidou M, Melas IN, Messinis DE, Klamt S, Alexopoulos LG, Kolisis FN, Loutrari H (2015) Network-based analysis of nutraceuticals in human hepatocellular carcinomas reveals mechanisms of chemopreventive action. CPT: Pharmacometrics & Systems Pharmacology 4: 350-361. Open Access
  • D`Alessandro LA, Samaga R, Maiwald T, Rho SH, 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 Combining Qualitative and Quantitative Modeling. PLOS Computational Biology 11(4): e1004192. Open Access
  • Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho K-H, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN (2015) Silence on the relevant literature and errors in implementation. Nature Biotechnology 33:336–339. PubMed
  • Müller 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 hepatocytes. Molecular Systems Biology 11:795. Open Access
  • Conradi C, Shiu A (2015) A Global Convergence Result for Processive Multisite Phosphorylation Systems. Bulletin of Mathematical Biology 77:126-155. Springer
  • Wiechert W, Klamt S (2015) Computational Systems Biology - neues Fach in den Lebenswissenschaften. BIOspektrum21:46-48. Springer
  • Müller S, Feliu E, Regensburger G, Conradi C, Shiu A, Dickenstein A (2015) Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry. Foundations of Computational Mathematics 15(70). Springer


  • Flockerzi D, Holstein K, Conradi C (2014) N-site phosphorylation systems with 2N-1 steady states. Bulletin of Mathematical Biology 76:1892-1916. Springer
  • Klamt S, Hädicke O, von Kamp A (2014) Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. Large-Scale Networks in Engineering and Life Sciences. Edited by Benner P, Findeisen R, Flockerzi D, Reichl U and Sundmacher K, Springer, pp.263-316. Springer
  • Varnicic M, Bettenbrock K, Hermsdorf D, Vidakivic-Koch T, Sundmacher K (2014) Combined electrochemical and microscopic study of porous enzymatic electrodes with direct electron transfer mechanism. RSC Advances 4:36471-36479. Open Access
  • Henkel SG, Beek AT, Steinsiek S, Stagge S, Bettenbrock K, Teixeira de Mattos J, Sauter T, Sawodny O, Ederer M (2014) Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions. PLoS ONE 9(9):e107640. Open Access
  • Erdrich P, Steuer R, Knoop H, Klamt S (2014) Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 13:128. Open Access
  • Prigent S, Collet G, Dittami S, Delage L, Ethis de Corny F, Dameron O, Eveillard D, Thiele S, Cambefort J, Boyen C, Siegel A, Tonon T (2014) The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. The Plant Journal 80:367–381. Open Access
  • 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 models. BioSystems 124:26–38. PubMed
  • Lohr V, Haedicke O, Genzel Y, Jordan I , Buentemeyer H, Klamt S, Reichl U (2014) The avian cell line AGE1.CR.pIX characterized my metabolic flux analysis. BMC Biotechnology 14:72. Open Access
  • Kramer B , Conradi C (2014) Identifying network structures that can cause multistationarity. In Proceedings of 21st International Symposium on Mathematical Theory of Networks and Systems pp. 1548-1555.
  • Bettenbrock K , Bai H, Ederer M, Green J, Hellingwerf KJ, Holcombe M, Kunz S, Rolfe MD, Sanguinetti G, Sawodny O, Sharma P, Steinsiek S, Poole R (2014) Towards a Systems Level Understanding of the Oxygen Response of Escherichia coli. Advances in Microbial Physiology 64 :65-114. Open Access
  • Straube R (2014) Reciprocal regulation as a source of ultrasensitivity in two-component systems with a bifunctional sensor kinase. PLoS Computational Biology 10(5):e1003614. Open Access
  • Heise S, Flassig RJ, Klamt S (2014) Benchmarking a Simple Yet Effective Approach for Inferring Gene Regulatory Networks from Sytems Genetics Data In: Gene Network Inference: Verification of Methods for Systems Genetics Data. Edited by de la Fuenta A, Springer, pp.33-47. Springer
  • Ederer M, Steinsiek S, Stagge S, Rolfe M, Beek AT, Knies D, Teixeira de Mattos J, Sauter T, Green J, Poole R, Bettenbrock K, Sawodny O (2014) A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Frontiers in Microbiology 5:124. Open Access
  • Conradi C, Mincheva M (2014) Catalytic contants enable the emergence of bistability in dual phosphorylation. J.R.Soc. Interface 11(95):20140158. Open Access
  • Steinsiek S, Stagge S, Bettenbrock K (2014) Analysis of Escherichia coli Mutants with a Linear Respiratory Chain. PLoS ONE 9(1):e87307. Open Access
  • von Kamp A, Klamt S (2014) Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Computational Biology 10(1):e1003378. Open Access


  • Chaouiya C, Berenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer F, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT,  von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry 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 formalisms and tools. BMC Systems Biology 7:135. OpenAccess
  • Holstein K, Flockerzi D, Conradi C (2013) Multistationary in Sequential Distributed Multisite Phosphorylation Networks. Bulletin of Mathematical Biology 75(11):2028-2058. PubMed
  • Jungreuthmayer C, Nair G, Klamt S, Zanghellini J (2013) Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14:318. Open Access
  • Carius L, Carius AB, McIntosh M, Grammel H (2013) Quorum sensing influences growth and photosynthetic membrane production in high-cell-density cultivations of Rhodospirillum rubrum. BMC Microbiology 13:189. Open Access
  • Gruchattka E, Hädicke O, Klamt S, Schuetz V, Kayser O (2013) In silicio profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 12:84 Open Access
  • Jahn S, Haverkorn van Rijsevijk BR, Sauer U, Bettenbrock K (2013) A role for EIIANtr in controlling fluxes in the central metabolism of E. coli K12. Biochimica et Biophysica Acta - Molecular Cell Research 12:2879-2889. Pubmed
  • Sharma P, Stagge S, Bekker M, Bettenbrock K, Hellingwerf KJ (2013) Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone. PLOS One 8:e7541. Open Access
  • Straube R (2013) Senitivity and Robustness in Convalent Modification Cycles with a Bifunctional Converter Enzyme. Biophysical Journal 105:1925-1933. Pubmed
  • Pinna A, Heise S, Flassig RJ, de la Fuente A, Klamt S (2013) Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 7:73. Open Access
  • Straube R, Conradi C (2013) Reciprocal enzyme regulation as a source of bistability in covalent modification cycles. Journal of Theoretical Biology 330:56-74. PubMed
  • Samaga R, Klamt S (2013) Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 11:43. Open Access
  • Hädicke O, Lohr V, Genzel Y, Reichl U, Klamt S (2013) Evaluating differences of metabolic performances: Statistical methods and their application to animal cell cultivations. Biotechnology and Bioengineering 10: 2633-2643. PubMed
  • Goncalves 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 models. Molecular BioSystems 9:1576-1583. PubMed
  • Waddell SJ, von Kamp A, Klamt S, Neyrolles O (2013) Host-pathogen interactions. In: Systems Biology of Tuberculosis. Edited by McFadden J, Beste DJV, Kierzek AM. New York, Springer, pp.73-96. Online version.
  • Melas IN, Samaga R, Alexopoulos LG, Klamt S (2013) Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology9:e1003204. Open Access
  • 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


  • 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
  • Marbach A, BettenbrockK (2012) lac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. J. Biotechnol.157: 82-88. PubMed
  • Steinsiek S,  BettenbrockK  (2012) Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems. J. Bacteriol.194:5897-5908. PubMed
  • Kremling A, Goehler A, Jahreis K, Nees M, Auerbach B, Schmidt-Heck W, Kökpinar Ö, Geffers R, Rinas U, Bettenbrock K (2012) Analysis and design of stimulus response curves in central metabolism of  E. coli. Metabolites2: 844-871. Open Access


  • 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 E83:021919. PubMed
  • Steinsiek S, Frixel A, Stagge S, SUMO, Bettenbrock K (2011) Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels. J. Biotechnol.154:35-45. 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
  • 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. preprintDOI:10.1137/100782620
  • Vester D, Lagoda A, Seitz C, Heldt S, Bettenbrock K, Genzel Y und Reichl U (2010) Real-time RT-qPCR assay for the analysis of human influenza A virus transcription and replication dynamics. J Virol Methods168:63-71. PubMed


  • 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. abstractDOI: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
  • Kremling A, Fischer S, Bettenbrock K (2009) Catabolite repression in Escherichia col i- a comparison of modelling approaches.  FEBS J.276: 594-602. PubMed


  • 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.
  • 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. abstractPubMed
  • Flockerzi D and Conradi C (2008) Subnetwork analysis for multistationarity in mass action kinetics. Journal of Physics - Conference Series 138:012006. abstractDOI:10.1088/1742-6596/138/1/012006
  • Kremling A, Bettenbrock K, Gilles ED (2008) A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. Bioinformatics 2008 abstract DOI:10.1093/bioinformatics/btn010A. PubMed


  • 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). preprintPubMed
  • 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. preprintDOI: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
  • Bettenbrock K, Sauter T, Jahreis K, Lengeler JW and Gilles ED (2007) Analysis of the correlation between growth rates, EIIACrr phosphorylation, and intracellular cAMP levels in Escherichia coli K-12. J. Bacteriol.189: 6891-6900. PubMed
  • Kremling A, BettenbrockK, Gilles ED (2007) Analysis of global control of Escherichia coli carbohydrate uptake. BMC Systems Biology, 1:42 (13. Sept. 2007). 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
  • 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
  • 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.
  • Bettenbrock K, Fischer S,Kremling A, Jahreis K, Sauter T, Gilles ED (2006) A quantitative approach to catabolite repression in Escherichia coli. J. Biol. Chem. Vol. 2815:2578-2584. PubMed


  • 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. abstractPubMed
  • 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. abstractPubMed
  • 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. abstractPubMed
  • Kremling A, Stelling J, Bettenbrock K, Fischer S, Gilles ED (2005) Metabolic Networks: Biology meets engineering sciences. In : Systems Biology Definitions and Perspectives, pp 215-234. Springer


  • 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 20:226-234. 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
  • Kremling A, Fischer S, Sauter T, BettenbrockK, Gilles ED (2004) Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. Biosystems Vol. 73, pp 57-71. PubMed
  • Saez-Rodriguez J, Kremling A, Conzelmann H, Bettenbrock K, Gilles ED (2004) Modular analysis of signal transduction networks. IEEE Control Systems Magazine24: 35-52. 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
  • 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. abstractDOI:10.1524/zpch.217.11.1427.20485


  • 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 Reports29(1-2):233-236. PubMed
  • Klamt S and Schuster S (2002) Calculating as many fluxes as possible in underdetermined metabolic networks. Molecular Biology Reports29(1-2):243-248. PubMed
  • Schuster S and Klamt S (2002) Applying metabolic pathway analysis to make good use of methanol. Trends in Biotechnology20(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 & Bioengineering77(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 Engineering24(6):363-372. publisher page
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