Publications ARB group

Journal Article (98)

1. 2018
   MPG.PuRe
   Bosch, J.; Klamt, S.; Stoll, M.: Generalizing diffuse interface methods on graphs: non-smooth potentials and hypergraphs. SIAM Journal on Applied Mathematics (accepted)
2. MPG.PuRe DOI PDF
   Harder, B.-J.; Bettenbrock, K.; Klamt, S.: Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli. Biotechnology and Bioengineering 115 (1), pp. 156 - 164 (2018)
3. MPG.PuRe DOI PDF
   Klamt, S.; Mahadevan, R.; Hädicke, O.: When do two-stage processes outperform one-stage processes? Biotechnology Journal 13 (2), 1700539 (2018)
4. MPG.PuRe DOI PDF
   Klamt, S.; Müller, S.; Regensburger, G.; Zanghellini, J.: A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. Metabolic Engineering 47, pp. 153 - 169 (2018)
5. MPG.PuRe DOI
   Liu, X.; Reitsma, J. M.; Mamrosh, J. L.; Zhang, Y.; Straube, R.; Deshaies, R. J.: Cand1-Mediated Adaptive Exchange Mechanism Enables Variation in F-Box Protein Expression. Molecular Cell 69 (5), pp. 773 - 786 (2018)
6. MPG.PuRe DOI
   Thiele, S.; Heise, S.; Hessenkemper, W.; Bongartz, H.; Fensky, M.; Schaper, F.; Klamt, S.: Designing optimal experiments to discriminate interaction graph models. IEEE ACM Transactions on Computational Biology and Bioinformatics (accepted)
7. 2017
   MPG.PuRe DOI PDF
   Hädicke, O.; Klamt, S.: EColiCore2: a reference model of the central metabolism of Escherichia coli and the relationships to its genome-scale parent model. Scientific Reports 7, 39647 (2017)
8. MPG.PuRe DOI PDF
   Kamp von, A.; Thiele, S.; Hädicke, O.; Klamt, S.: Use of CellNetAnalyzer in biotechnology and metabolic engineering. Journal of Biotechnology 261, pp. 221 - 228 (2017)
9. MPG.PuRe DOI PDF
   Kamp von, A.; Klamt, S.: Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. Nature Communications 8, 15926 (2017)
10. MPG.PuRe DOI PDF
    Klamt, S.; Regensburger, G.; Gerstl, P.M.; Jungreuthmayer, C.; Schuster, S.; Mahadevan, R.; Zanghellini, J.; Müller, S.: From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology 13 (4), e1005409 (2017)
11. MPG.PuRe DOI PDF
    Prigent, S.; Frioux, C.; Dittami, S. M.; Thiele, S.; Larhlimi, A.; Collet, G.; Gutknecht, F.; Got, J.; Eveillard, D.; Bourdon, J. et al.; Plewniak, F.; Tonon, T.; Siegel, A.: Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Computational Biology 13, e1005276 (2017)
12. MPG.PuRe DOI
    Straube, R.: Analysis of network motifs in cellular regulation: Structural similarities, input–output relations and signal integration. Biosystems 162, pp. 2015 - 232 (2017)
13. MPG.PuRe DOI PDF
    Straube, R.; Shah, M.; Flockerzi, D.; Wolf, D.A.: Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire. PLoS Computational Biology 13 (11), e1005869 (2017)
14. MPG.PuRe DOI
    Zander, D.; Samaga, D.; Straube, R.; Bettenbrock, K.: Bistability and Nonmonotonic Induction of the lac Operon in the Natural Lactose Uptake System. Biophysical Journal 112 (9), pp. 1984 - 1996 (2017)
15. 2016
    MPG.PuRe DOI PDF
    Bordron, P.; Latorre, M.; Cortés, M.-P.; González, M.; Thiele, S.; Siegel, A.; Maass, A.; Eveillard, D.: Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. MicrobiologyOpen 5 (1), pp. 106 - 117 (2016)
16. MPG.PuRe DOI PDF
    Gerstl, M. P.; Klamt, S.; Jungreuthmayer, C.; Zanghellini, J.: Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 32 (5), pp. 730 - 737 (2016)
17. MPG.PuRe DOI
    Harder, B.-J.; Bettenbrock, K.; Klamt, S.: Model-Based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metabolic Engineering 38, pp. 29 - 37 (2016)
18. MPG.PuRe DOI PDF
    Koch, S.; Benndorf, D.; Fronk, K.; Reichl, U.; Klamt, S.: Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnology for Biofuels 9, 17 (2016)
19. MPG.PuRe DOI PDF
    Kolczyk, K.; Conradi, C.: Challenges in horizontal model integration. BMC Systems Biology (10), 28 (2016)
20. MPG.PuRe DOI
    Müller, S.; Feliu, E.; Regensburger, G.; Conradi, C.; Shiu, A.; Dickenstein, A.: Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry. Foundations of Computational Mathematics 16 (1), pp. 69 - 97 (2016)
21. MPG.PuRe DOI PDF
    Ud-Dean, S.; Heise, S.; Klamt, S.; Gunawan, R.: TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics 17 (17), 252 (2016)
22. MPG.PuRe DOI PDF
    Wrzosek, K.; García Rivera, M. A.; Bettenbrock, K.; Seidel-Morgenstern, A.: Racemization of undesired enantiomers: Immobilization of mandelate racemase and application in a fixed bed reactor. Biotechnology Journal 11 (4), pp. 453 - 463 (2016)
23. MPG.PuRe DOI PDF
    Wu, H.; Kamp von, A.; Leoncikas, V.; Mori, W.; Sahin, M.; Gevorgyan, A.; Linley, C.; Grabowski, M.; Mannan, A. A.; Stoy, N. et al.; Steward, G. R.; Ward, L. T.; Lewis, D.J.M.; Sroca, J.; Matsuno, H.; Klamt, S.; Westerhoff, H.V.; McFadden, J.; Plant, N.J.; Kierzek, A.M.: MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 2, 16032 (2016)
24. 2015
    MPG.PuRe DOI
    Bastiaens, P. I.H.; Birtwistle, M.; Blüthgen, N.; Bruggeman, F.; Cho, K.-H.; de la Fuente, A.; Hoek, J.; Kiyatkin, A.; Klamt, S.; Kolch, W. et al.; Legewie, S.; Mendes, P.; Naka, T.; Santra, T.; Sontag, E.; Westerhoff, H.; Kholodenko, B.: Silence on the relevant literature and errors in implementation. Nature Biotechnology 33 (4), pp. 336 - 339 (2015)
25. MPG.PuRe DOI
    Conradi, C.; Shiu, A.: A Global Convergence Result for Processive Multisite Phosphorylation Systems. Bulletin of mathematical biology 77 (1), pp. 126 - 155 (2015)
26. MPG.PuRe DOI PDF
    D`Allessandro, L. A.; Samaga, R.; Maiwald, T.; Rho, S.-H.; Bonefas, S.; Raue, A.; Iwamoto, N.; Kienast, A.; Waldow, K.; Meyer, R. et al.; Schilling, M.; Timmer, J.; Klamt, S.; Klingmüller, U.: Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Computational Biology 11 (4), e1004192 (2015)
27. MPG.PuRe DOI PDF
    Erdrich, P.; Steuer, R.; Klamt, S.: An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Systems Biology 9, 48 (2015)
28. MPG.PuRe DOI PDF
    Hädicke, O.; Bettenbrock, K.; Klamt, S.: Enforced ATP futile cycling increases specific productivity and yield of anaerobic lactate production in Escherichia coli. Biotechnology and Bioengineering 112 (10), pp. 2195 - 2199 (2015)
29. MPG.PuRe DOI PDF
    Hädicke, O.; Klamt, S.: Manipulation of the ATP pool as a tool for metabolic engineering. Biochemical Society Transactions (London) 43 (6), pp. 1140 - 1145 (2015)
30. MPG.PuRe DOI
    Klamt, S.; Mahadevan, R.: On the feasibility of growth-coupled product synthesis in microbial strains. Metabolic Engineering 30, pp. 166 - 178 (2015)
31. MPG.PuRe DOI
    Mahadevan, R.; Kamp von, A.; Klamt, S.: Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics 31 (17), pp. 2844 - 2851 (2015)
32. MPG.PuRe DOI PDF
    Michailidou, M.; Melas, I.; Messinis, D.; Klamt, S.; Alexopoulos, L.; Kolisis, F.; Loutrari, H.: Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action. CPT: Pharmacometrics & Systems Pharmacology 4 (6), pp. 350 - 361 (2015)
33. MPG.PuRe DOI PDF
    Mueller, S.; Huard, J.; Waldow, K.; Huang, X.; D'Alessandro, L.; Bohl, S.; Börner, K.; Grimm, D.; Klamt, S.; Klingmüller, U. et al.; Schilling, M.: T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes. Molecular Systems Biology 11, 795 (2015)
34. MPG.PuRe DOI
    Straube, R.: Analysis of Substrate Competition in Regulatory Network Motifs: Stimulus-Response Curves, Thresholds and Ultrasensitivity. Journal of Theoretical Biology 380, pp. 74 - 82 (2015)
35. MPG.PuRe DOI PDF
    Thiele, S.; Cerone, L.; Saez-Rodriguez, J.; Siegel, A.; Guciolowski, C.; Klamt, S.: Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinformatics 16 (1), 345 (2015)
36. MPG.PuRe DOI
    Wiechert, W.; Klamt, S.: Computational Systems Biology — neues Fach in den Lebenswissenschaften. Biospektrum 21 (1), pp. 46 - 48 (2015)
37. 2014
    MPG.PuRe DOI
    Carius, L.; Rumschinski, P.; Faulwasser, T.; Flockerzi, D.; Grammel, H.; Findeisen, R.: Model-based derivation, analysis and control of unstable microaerobic steady-states-Considering Rhodospirillum rubrum as an example. Biotechnology and Bioengineering 111 (4), pp. 734 - 747 (2014)
38. MPG.PuRe DOI
    Conradi, C.; Mincheva, M.: Catalytic constants enable the emergence of bistability in dual phosphorylation. Interface: Journal of the Royal Society 6 (11), 95, pp. 1742 - 5662 (2014)
39. MPG.PuRe DOI PDF
    Ederer, M.; Steinsiek, S.; Stagge, S.; Rolfe, M. D.; TerBeek, A.; Knies, D.; Teixeira de Mattos, M. J.; Sauter , T.; Green , J.; Poole, R. K. et al.; Bettenbrock, K.; Sawodny, O.: A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Frontiers in Microbiology 5, 124, p. 124 (2014)
40. MPG.PuRe DOI PDF
    Erdrich, P.; Knoop, H.; Steuer, R.; Klamt, S.: Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microbial Cell Factories 13, p. 128 - 128 (2014)
41. MPG.PuRe DOI
    Flockerzi, D.; Holstein, K.; Conradi, C.: N-site Phosphorylation Systems with 2N-1 Steady States. Bulletin of Mathematical Biology 76 (8), pp. 1892 - 1916 (2014)
42. MPG.PuRe DOI PDF
    Henkel, S.; Beek, A. T.; Steinsiek, S.; Stagge, S.; Bettenbrock, K.; M. Joost Teixeira de Mattos, M.; Sawodny, O.; Ederer, M.; Sauter, T.: Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions. PLoS One 9 (9), p. e107640 (2014)
43. MPG.PuRe DOI PDF
    Kamp von, A.; Klamt, S.: Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. PLoS Computational Biology 10 (1), e1003378 (2014)
44. MPG.PuRe DOI PDF
    Lohr, V.; Hädicke, O.; Genzel, Y.; Jordan, I.; Buentemeyer, H.; Klamt, S.; Reichl, U.: The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnology 14, p. 72 (2014)
45. MPG.PuRe DOI
    Prigent, S.; Collet, G.; Dittami, S. M.; Delage, L.; Ethis de Corny, F.; Dameron, O.; Eveillard, D.; Thiele, S.; Cambefort, J.; Siegel, A. et al.; Tonon, T.: The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. The Plant Journal 80 (2), pp. 367 - 381 (2014)
46. MPG.PuRe DOI
    Ryll, A.; Bucher, J.; Bonin, A.; Bongard, S.; Gonçalves , E.; Saez- Roidriguez, J.; Niklas, J.; Klamt, S.: A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosystems 124, pp. 26 - 38 (2014)
47. MPG.PuRe DOI PDF
    Steinsiek, S.; Stagge, S.; Bettenbrock, K.: Analysis of Escherichia coli Mutants with a Linear Respiratory Chain. PLoS One 9 (1), p. e87307 (2014)
48. MPG.PuRe DOI PDF
    Straube, R.: Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase. PLoS Computational Biology 10 (5), p. e1003614 (2014)
49. MPG.PuRe DOI PDF
    Varničić, M.; Bettenbrock, K.; Hermsdorf, D.; Vidaković-Koch, T.; Sundmacher, K.: Combined electrochemical and microscopic study of porous enzymatic electrodes with direct electron transfer mechanism. RSC Advances 4 (69), pp. 36471 - 36479 (2014)
50. 2013
    MPG.PuRe DOI
    Carius, L.; Hädicke, O.; Grammel, H.: Stepwise reduction of the culture redox potential allows the analysis of microaerobic metabolism and photosynthetic membrane synthesis in Rhodospirillum rubrum. Biotechnology and Bioengineering 110 (2), pp. 573 - 585 (2013)