Publications

1. R Heinrich, E Hoffmann and H G Holzhütter.
   Calculation of kinetic parameters of a reversible enzymatic reaction in states of maximal activity.
   Biomed. Biochim. Acta 49(8/9):891–902, 1990.
   URL

2. R Heinrich and E Hoffmann.
   Kinetic parameters of enzymatic reactions in states of maximal activity; an evolutionary approach.
   J. Theor. Biol. 151 (2):249–283, July 1991.
   URL

3. R Heinrich, E Klipp, A Stephani and T Wilhelm.
   Evolutionary optimization of enzyme on the basis of kinetic and thermodynamic principles.
   In E Gnaiger, F N Gellerich and M Wyss (eds.). What is Controlling Life? 50 Years after Erwin Schroedinger's What is Life? (Modern Trends in Biothermokinetics 3). Insbruck University Press, 1994, pages 99-102.
   

4. T Wilhelm, E Hoffmann-Klipp and R Heinrich.
   An evolutionary approach to enzyme kinetics: optimization of ordered mechanisms.
   Bull. Math. Biol. 56 (1):65–106, January 1994.
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5. E Klipp and R Heinrich.
   Evolutionary optimization of enzyme kinetic parameters; effect of constraints.
   J. Theor. Biol. 171 (3):309–323, December 1994.
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6. E Klipp.
   Evolutionary optimization of enzyme kinetic parameters.
   J Biol. Syst. 3 (2):363–376, June 1995.
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7. E Klipp.
   Maximization of enzyme activity under consideration of various constraints.
   In D N Ghista (ed.). Biomedical and Life Physics. Vieweg, 1996, pages 71-84.
   

8. E Klipp and R Heinrich.
   Kinetic optimization of multienzyme systems.
   In H V Westerhoff, J L Snoep, F E Sluse, J E Wijker and B N Kholodenko (eds.). Biothermokinetics of the Living Cell. Biothermokinetic Press, 1996, pages 210-13.
   

9. R Heinrich and E Klipp.
   Control analysis of unbranched enzymatic chains in states of maximal activity.
   J. Theor. Biol. 182 (3):243–252, October 1996.
   URL

10. R Heinrich, F Montero, E Klipp, T G Waddell and E Meléndez-Hevia.
    Theoretical approaches to the evolutionary optimization of glycolysis. Thermodynamic and kinetic constraints.
    Eur. J. Biochem. 243 (1/2):191–201, January 1997.
    URL

11. R Heinrich, F Montero, E Klipp, T G Waddell and E Melendez-Hevia.
    Kinetic and thermodynamic constraints for the structural design of glycolysis.
    Nonlinear Anal. 30 (3):1793–1804, December 1997.
    URL

12. E Klipp.
    Relations between flux control coefficients and enzyme concentrations in states of minimized total amount of enzyme.
    In C Larsson, I L Pahlman and L Gustafsson (eds.). BioThermoKinetics. In the Post Genomic Era. University, Chalmers Reproservice, 1998, pages 27-9.
    

13. E Klipp and R Heinrich.
    Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control.
    BioSystems 54 (1/2):1–14, December 1999.
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14. B M Bakker, H E Assmus, F Bruggeman, J R Haanstra, E Klipp and H Westerhoff.
    Network-based selectivity of antiparasitic inhibitors.
    Molecular biology reports 29 (1/2):1–5, 2002.
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15. E Klipp, R Heinrich and H-G Holzhütter.
    Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities.
    Eur. J. Biochem. 269 (22):5406–5413, November 2002.
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16. J Hakenberg, S Schmeier, A Kowald, E Klipp and U Leser.
    Finding kinetic parameters using text mining.
    OMICS J. Integrat. Biol. 8 (2):131–152, 2004.
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17. E Klipp, W Liebermeister and C Wierling.
    Inferring dynamic properties of biochemical reaction networks from structural knowledge.
    Genome Inform. 15 (1):125–137, 2004.
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18. E Klipp, B Nordlander, B Kofahl and S Hohmann.
    Shutting the MAP off–and on again?.
    Curr. Genomics 5 (8):637-647, 2004.
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19. W Liebermeister, E Klipp, S Schuster and R Heinrich.
    A theory of optimal differential gene expression.
    BioSystems 76 (1/3):261–278, 2004.
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20. A Kowald and E Klipp.
    Alternative pathways might mediate toxicity of high concentrations of superoxide dismutase.
    Ann. N. Y. Acad. Sci. 1019:370–374, June 2004.
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21. B Kofahl and E Klipp.
    Modelling the dynamics of the yeast pheromone pathway.
    Yeast 21 (10):831–850, July 2004.
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22. E Klipp and S Hohmann.
    Simulation von Lebensprozessen.
    BIOForum 28 (10):60–61, 2005.
    

23. B Nordlander, E Klipp, B Kofahl and S Hohmann.
    Modelling signalling pathways –a yeast approach.
    In L Alberghina and H V Westerhoff (eds.). Systems Biology. Definitions and Perspectives (Topics Curr. Gen. 13). Springer, 2005, pages 277-302.
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24. E Klipp, B Nordlander, R Krüger, P Gennemark and S Hohmann.
    Integrative model of the response of yeast to osmotic shock.
    Nat. Biotechnol. 23 (8):975–982, August 2005.
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25. W Liebermeister, U Baur and E Klipp.
    Biochemical network models simplified by balanced truncation.
    FEBS J. 272 (16):4034–4043, August 2005.
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26. W Liebermeister and E Klipp.
    Biochemical networks with uncertain parameters.
    IEE Proc. Syst. Biol. 152 (3):97–107, September 2005.
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27. N Le Novère, A Finney, M Hucka, U S Bhalla, F Campagne, J Collado-Vides, E J Crampin, M Halstead, E Klipp, P Mendes, P Nielsen, H Sauro, B Shapiro, J L Snoep, H D Spence and B L Wanner.
    Minimum information requested in the annotation of biochemical models (MIRIAM).
    Nat. Biotechnol. 23 (12):1509–1515, December 2005.
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28. S Borger, W Liebermeister and E Klipp.
    Prediction of enzyme kinetic parameters based on statistical learning.
    Genome Inform. 17 (1):80–87, 2006.
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29. E Klipp and J Schaber.
    Modelling of signal transduction in yeast –Sensitivity and model analysis.
    In M Cánovas, J L Iborra and Arturo Manjón (eds.). Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine. Fundación CajaMurcia, 2006, pages 15-30.
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30. M Schulz, J Uhlendorf, E Klipp and W Liebermeister.
    SBMLmerge, a system for combining biochemical network models.
    Genome Inform. 17 (1):62–71, 2006.
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31. S Schuster, E Klipp and M Marhl.
    The predictive power of molecular network modelling –case studies of predictions with subsequent experimental verification.
    In F Eisenhaber (ed.). Discovering Biomolecular Mechanisms with Computational Biology. Landes Bioscience, Georgetown and Springer, 2006, pages 95-106.
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32. A Kowald, H Lehrach and E Klipp.
    Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.
    J. Theor. Biol. 238 (4):828–840, February 2006.
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33. J Schaber, B Kofahl, A Kowald and E Klipp.
    A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast.
    FEBS J. 273 (15):3520–3533, August 2006.
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34. E Klipp and W Liebermeister.
    Mathematical modeling of intracellular signaling pathways.
    BMC Neurosci. 7 (Suppl 1):S10, October 2006.
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35. Z Zi and E Klipp.
    SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
    Bioinformatics 22 (21):2704–2705, November 2006.
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36. W Liebermeister and E Klipp.
    Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.
    Theor. Biol. Med. Model. 3:41, December 2006.
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37. W Liebermeister and E Klipp.
    Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data.
    Theor. Biol. Med. Model. 3:42, December 2006.
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38. M Barberis and E Klipp.
    Insights into the network controlling the G1/S transition in budding yeast.
    Genome Inform. 18:85–99, 2007.
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39. M Barberis, E Klipp, M Vanoni and L Alberghina.
    Modeling of the G(1)/S transition in yeast cell cycle.
    FEBS J. 274 (Suppl. S1):248, 2007.
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40. S Borger, W Liebermeister, J Uhlendorf and E Klipp.
    Automatically generated model of a metabolic network.
    Genome Inform. 18:215–224, 2007.
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41. E Klipp.
    Modeling of yeast cell stress response.
    FEBS J. 274 (Suppl. s1):53, 2007.
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42. C Kühn, A Kühn, A J Poustka and E Klipp.
    Modeling development: spikes of the sea urchin.
    Genome Inform. 18:75–84, 2007.
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43. Z Zi and E Klipp.
    Steady state analysis of signal response in receptor trafficking networks.
    Genome Inform. 18:100–108, 2007.
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44. M Barberis, E Klipp, M Vanoni and L Alberghina.
    Cell size at S phase initiation: an emergent property of the G1/S network.
    PLoS Comput. Biol. 3 (4):e64, April 2007.
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45. E Klipp, W Liebermeister, A Helbig, A Kowald and J Schaber.
    Systems biology standards -the community speaks.
    Nat. Biotechnol. 25 (4):390–391, April 2007.
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46. Z Zi and E Klipp.
    Constraint-based modeling and kinetic analysis of the Smad dependent TGF-β signaling pathway.
    PLoS ONE 2 (9):e936, September 2007.
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47. Z Zi and E Klipp.
    Cellular signaling is potentially regulated by cell density in receptor trafficking networks.
    FEBS Lett. 581 (24):4589–4595, October 2007.
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48. E Klipp.
    Modelling dynamic processes in yeast.
    Yeast 24 (11):943–959, November 2007.
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49. M Ralser, M M Wamelink, A Kowald, B Gerisch, G Heeren, E A Struys, E Klipp, C Jakobs, M Breitenbach, H Lehrach and S Krobitsch.
    Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress.
    J. Biol. 6 (4):10, December 2007.
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50. M Barberis and E Klipp.
    Sic1 can regulate the fundamental events in the budding yeast cell cycle.
    FEBS J. 275 (Suppl. s1):441, 2008.
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51. J Bruck, W Liebermeister and E Klipp.
    Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis.
    Genome Inform. 20:1–14, 2008.
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52. M Cvijovic, H Soueidan, D J Sherman, E Klipp and M Nikolski.
    Exploratory simulation of cell ageing using hierarchical models.
    Genome Inform. 21:114–125, 2008.
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53. M Flöttmann, J Schaber, S Hoops, E Klipp and P Mendes.
    ModelMage: a tool for automatic model generation, selection and management.
    Genome Inform. 20:52–63, 2008.
    URL

54. E Klipp and J Schaber.
    Modeling the dynamics of stress activated protein kinases (SAPK) in cellular stress response.
    In F Posas and A R Nebreda (eds.). Stress-Activated Protein Kinases (Topics Curr. Gen. 20). Springer, 2008, pages 205–224.
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55. C Kühn, E Petelenz, B Nordlander, J Schaber, S Hohmann and E Klipp.
    Exploring the impact of osmoadaptation on glycolysis using time-varying response-coefficients.
    Genome Inform. 20:77–90, 2008.
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56. J Schaber and E Klipp.
    Short-term volume and turgor regulation in yeast.
    Essays Biochem. 45:147–160, 2008.
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57. S Gerber, H Aßmus, B Bakker and E Klipp.
    Drug-efficacy depends on the inhibitor type and the target position in a metabolic network –A systematic study.
    J. Theor. Biol. 252 (3):442–455, June 2008.
    URL

58. Z Zi, Y Zheng, A E Rundell and E Klipp.
    SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.
    BMC Bioinform. 9:342, August 2008.
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59. M J Herrgård, N Swainston, P Dobson, W B Dunn, K Y Arga, M Arvas, N Blüthgen, S Borger, R Costenoble, M Heinemann, M Hucka, N Le Novère, P Li, W Liebermeister, M L Mo, A P Oliveira, D Petranovic, S Pettifer, E Simeonidis, K Smallbone, I Spasić, D Weichart, R Brent, D S Broomhead, H V Westerhoff, B Kirdar, M Penttilä, E Klipp, B Ø Palsson, U Sauer, S G Oliver, P Mendes, J Nielsen and D B Kell.
    A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
    Nat. Biotechnol. 26 (10):1155–1160, October 2008.
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60. N Erjavec, M Cvijovic, E Klipp and T Nyström.
    Selective benefits of damage partitioning in unicellular systems and its effects on aging.
    Proc. Natl. Acad. Sci. USA 105 (48):18764–18769, December 2008.
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61. M Krantz, D Ahmadpour, L-G Ottosson, J Warringer, C Waltermann, B Nordlander, E Klipp, A Blomberg, St Hohmann and H Kitano.
    Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway.
    Mol. Syst. Biol. 5:281, 2009.
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62. J Schaber, W Liebermeister and E Klipp.
    Nested uncertainties in biochemical models.
    IET Syst. Biol. 3 (1):1–9, January 2009.
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63. T W Spiesser, E Klipp and M Barberis.
    A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae.
    Mol. Genet. Genomics 282 (1):25–35, July 2009.
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64. C Kühn, C Wierling, A Kühn, E Klipp, G Panopoulou, H Lehrach and A J Poustka.
    Monte Carlo analysis of an ODE model of the sea urchin endomesoderm network.
    BMC Syst. Biol. 3:83, August 2009.
    URL

65. R Alfieri, M Barberis, F Chiaradonna, D Gaglio, L Milanesi, M Vanoni, E Klipp and L Alberghina.
    Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation.
    BMC Bioinform. 10 (Suppl 12):S16, October 2009.
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66. M Schulz, B M Bakker and E Klipp.
    TIde: a software for the systematic scanning of drug targets in kinetic network models.
    BMC Bioinform. 10:344, October 2009.
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67. E Klipp.
    Timing matters.
    FEBS Lett. 583 (24):4013–4018, December 2009.
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68. S Gerber, G Hasenbrink, W Hendriksen, P Van Heusden, J Ludwig, E Klipp and H Lichtenberg-Fraté.
    Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK1|2 and PBMH1|2 promoter region.
    Genome Inform. 22:11–20, January 2010.
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69. C Kühn, K V S Prasad, E Klipp and P Gennemark.
    Formal representation of the high osmolarity glycerol pathway in yeast.
    Genome Inform. 22:69–83, 2010.
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70. J Schaber, M A Adrover, E Eriksson, S Pelet, E Petelenz-Kurdziel, D Klein, F Posas, M Goksör, M Peter, S Hohmann and E Klipp.
    Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation..
    Eur. Biophys. J. 39 (11):1547–1556, 2010.
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71. Schulz M. and E Klipp.
    Introduction to systems biology.
    In F Tretter, G Winterer, P J Gebicke-Haerter and E R Mendoza (eds.). Systems Biology in Psychiatric Research. From High-Throughput Data to Mathematical Modeling. Wiley-VCH, 2010, pages 81-96.
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72. S Stoma and E Klipp.
    Spatio-temporal simulation environment: a microscopy image based modelization framework.
    Microsc. Microanal. 16 (Suppl. S2):734–735, 2010.
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73. F Krause, J Uhlendorf, T Lubitz, M Schulz, E Klipp and W Liebermeister.
    Annotation and merging of SBML models with semanticSBML.
    Bioinformatics 26 (3):421–422, February 2010.
    URL

74. Z Zi, W Liebermeister and E Klipp.
    A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae.
    PLoS ONE 5 (3):e9522, March 2010.
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75. T W Spiesser, C Diener, M Barberis and E Klipp.
    What influences DNA replication rate in budding yeast?.
    PLoS ONE 5 (4):e10203, April 2010.
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76. M Barberis, T W Spiesser and E Klipp.
    Replication origins and timing of temporal replication in budding yeast: how to solve the conundrum?.
    Curr. Genomics 11 (3):199–211, May 2010.
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77. W Liebermeister, J Uhlendorf and E Klipp.
    Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.
    Bioinformatics 26 (12):1528–1534, June 2010.
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78. F Podo, L M C Buydens, H Degani, R Hilhorst, E Klipp, I S Gribbestad, S Van Huffel, H W M Van Laarhoven, J Luts, D Monleon, G J Postma, N Schneiderhan-Marra, F Santoro, H Wouters, H G Russnes, T Sørlie, E Tagliabue and A-L Børresen-Dale (for the FEMME Consortium).
    Triple-negative breast cancer: present challenges and new perspectives.
    Mol. Oncol. 4 (3):209–229, June 2010.
    URL

79. E Klipp, R C Wade and U Kummer.
    Biochemical network-based drug-target prediction.
    Curr. Opin. Biotechnol. 21 (4):511–516, August 2010.
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80. C Waltermann and E Klipp.
    Signal integration in budding yeast.
    Biochem. Soc. Trans. 38 (5):1257–1264, October 2010.
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81. T Lubitz, M Schulz, E Klipp and W Liebermeister.
    Parameter balancing in kinetic models of cell metabolism.
    J Phys. Chem. B 114 (49):16298–16303, December 2010.
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82. P Kahlem, A DiCara, M Durot, J M Hancock, E Klipp, V Schächter, E Segal, I Xenarios, Birney E and L Mendoza.
    Strengths and weaknesses of selected modeling methods used in systems biology.
    In N-S Yang (ed.). Systems and Computational Biology–Bioinformatics and Computational Modeling. InTech Open Access Publisher, 2011, pages 77-98.
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83. E Klipp.
    Computational yeast systems biology: a case study for the MAP kinase cascade.
    In J I Castrillo and S G Oliver (eds.). Yeast Systems Biology: Methods and Protocols (Meth. Mol. Biol. 759). Humana Press, 2011, pages 323–343.
    URL, DOI

84. N Mah, Y Wang, M-C Liao, A Prigione, J Jozefczuk, B Lichtner, K Wolfrum, M Haltmeier, M Flöttmann, M Schaefer, A Hahn, R Mrowka, E Klipp, M A Andrade-Navarro and J Adjaye.
    Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network.
    PLoS ONE 6 (8):e24351, 2011.
    URL

85. Tyc K M and E Klipp.
    Modeling dissemination of pathogenic fungi within a host: a cartoon for the interactions of two complex systems.
    J. Comp. Sci. Syst. Biol. S1:001, 2011.
    URL

86. J Schaber and E Klipp.
    Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks.
    Curr. Opin. Biotechnol. 22 (1):109–116, February 2011.
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87. J Schaber, M Flöttmann, J Li, C-F Tiger, S Hohmann and E Klipp.
    Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway.
    PLoS ONE 6 (3):e14791, March 2011.
    URL

88. S Stoma, M Fröhlich, S Gerber and E Klipp.
    STSE: spatio-temporal simulation environment dedicated to biology.
    BMC Bioinform. 12:126, April 2011.
    URL

89. D Waltemath, R Adams, D A Beard, F T Bergmann, U S Bhalla, R Britten, V Chelliah, M T Cooling, J Cooper, E J Crampin, A Garny, S Hoops, M Hucka, P Hunter, E Klipp, C Laibe, A K Miller, I Moraru, D Nickerson, P Nielsen, M Nikolski, S Sahle, H M Sauro, H Schmidt, J L Snoep, D Tolle, O Wolkenhauer and N Le Novère.
    Minimum information about a simulation experiment (MIASE).
    PLoS Comput. Biol. 7 (4):e1001122, April 2011.
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90. Z Zi, Z Feng, D A Chapnick, M Dahl, D Deng, E Klipp, A Moustakas and X Liu.
    Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamics.
    Mol. Syst. Biol. 7:492, May 2011.
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91. M Schulz, F Krause, N Le Novère, E Klipp and W Liebermeister.
    Retrieval, alignment, and clustering of computational models based on semantic annotations.
    Mol. Syst. Biol. 7:512, July 2011.
    URL

92. M À Adrover, Z Zi, A Duch, J Schaber, A González-Novo, J Jimenez, M Nadal-Ribelles, J Clotet, E Klipp and F Posas.
    Time-dependent quantitative multicomponent control of the G₁-S network by the stress-activated protein kinase Hog1 upon osmostress.
    Sci. Signal. 4 (192):ra63, September 2011.
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93. M Barberis, C Beck, A Amoussouvi, G Schreiber, C Diener, A Herrmann and E Klipp.
    A low number of SIC1 mRNA molecules ensures a low noise level in cell cycle progression of budding yeast.
    Mol. Biosyst. 7 (10):2804–2812, October 2011.
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94. C Waltermann and E Klipp.
    Information theory based approaches to cellular signaling.
    Biochim. Biophys. Acta 1810 (10):924–932, October 2011.
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95. M Barberis, C Linke, M À Adrover, A González-Novo, H Lehrach, S Krobitsch, F Posas and E Klipp.
    Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins.
    Biotechnol. Adv. 30 (1):108–130, 2012.
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96. M Floettmann, T Scharp and E Klipp.
    Computational modeling of biochemical processes and cell differentiation.
    In M K Stachowiak and E S Tzanakakis (eds.). Stem Cells. From Mechanisms to Technologies. World Scientific, 2012, pages 3-29.
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97. M Flöttmann, T Scharp and E Klipp.
    A stochastic model of epigenetic dynamics in somatic cell reprogramming.
    Front. Physiol. 3:216, 2012.
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98. M Hoffman-Sommer, A Supady and E Klipp.
    Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates.
    Front. Physiol. 3:287, 2012.
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99. C Kühn and E Klipp.
    Zooming in on yeast osmoadaptation.
    Adv. Exp. Med. Biol. 736:293–310, 2012.
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100. M D Leach, K M Tyc, A J P Brown and E Klipp.
     Modelling the regulation of thermal adaptation in Candida albicans, a major fungal pathogen of humans.
     PLoS ONE 7 (3):e32467, 2012.
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101. Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten Dijl, Michael Hecker, Uwe Völker, Philippe Bessières and Philippe Noirot.
     Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis.
     Science 335(6072):1103-1106, 2012.
     URL, DOI

102. F Rubelt, V Sievert, F Knaust, C Diener, T S Lim, K Skriner, E Klipp, R Reinhardt, H Lehrach and Z Konthur.
     Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires.
     PLoS ONE 7 (11):e49774, 2012.
     URL

103. J Schaber, R Baltanas, A Bush, E Klipp and A Colman-Lerner.
     Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast.
     Mol. Syst. Biol. 8:622, 2012.
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104. M Schulz, E Klipp and W Liebermeister.
     Propagating semantic information in biochemical network models.
     BMC Bioinform. 13:18, January 2012.
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105. T Handorf and E Klipp.
     Modeling mechanistic biological networks: an advanced Boolean approach.
     Bioinformatics 28 (4):557–563, February 2012.
     URL

106. G Schreiber, M Barberis, S Scolari, C Klaus, A Herrmann and E Klipp.
     Unraveling interactions of cell cycle-regulating proteins Sic1 and B-type cyclins in living yeast cells: a FLIM-FRET approach.
     FASEB J. 26 (2):546–554, February 2012.
     URL

107. J M Buescher, W Liebermeister, M Jules, M Uhr, J Muntel, E Botella, B Hessling, R J Kleijn, L Le Chat, F Lecointe, U Mäder, P Nicolas, S Piersma, F Rügheimer, D Becher, P Bessieres, E Bidnenko, E L Denham, E Dervyn, K M Devine, G Doherty, S Drulhe, L Felicori, M J Fogg, A Goelzer, A Hansen, C R Harwood, M Hecker, S Hubner, C Hultschig, H Jarmer, E Klipp, A Leduc, P Lewis, F Molina, P Noirot, S Peres, N Pigeonneau, S Pohl, S Rasmussen, B Rinn, M Schaffer, J Schnidder, B Schwikowski, J M Van Dijl, P Veiga, S Walsh, A J Wilkinson, J Stelling, S Aymerich and U Sauer.
     Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
     Science 335 (6072):1099–1103, March 2012.
     URL

108. P Nicolas, U Mäder, E Dervyn, T Rochat, A Leduc, N Pigeonneau, E Bidnenko, E Marchadier, M Hoebeke, S Aymerich, D Becher, P Bisicchia, E Botella, O Delumeau, G Doherty, E L Denham, M J Fogg, V Fromion, A Goelzer, A Hansen, E Härtig, C R Harwood, G Homuth, H Jarmer, M Jules, E Klipp, L Le Chat, F Lecointe, P Lewis, W Liebermeister, A March, R A T Mars, P Nannapaneni, D Noone, S Pohl, B Rinn, F Rügheimer, P K Sappa, F Samson, M Schaffer, B Schwikowski, L Steil, J Stülke, T Wiegert, K M Devine, A J Wilkinson, J M Van Dijl, M Hecker, U Völker, P Bessières and P Noirot.
     Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
     Science 335 (6072):1103–1106, March 2012.
     URL

109. C-F Tiger, F Krause, G Cedersund, R Palmér, E Klipp, S Hohmann, H Kitano and M Krantz.
     A framework for mapping, visualisation and automatic model creation of signal-transduction networks.
     Mol. Syst. Biol. 8:578, April 2012.
     URL

110. A Kowald, A Hamann, S Zintel, S Ullrich, E Klipp and H D Osiewacz.
     A systems biological analysis links ROS metabolism to mitochondrial protein quality control.
     Mech. Ageing Dev. 133 (5):331–337, May 2012.
     URL

111. M D Leach, E Klipp, L E Cowen and A J P Brown.
     Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs.
     Nat. Rev. Microbiol. 10 (10):693–704, October 2012.
     URL

112. T W Spiesser, C Müller, G Schreiber, M Krantz and E Klipp.
     Size homeostasis can be intrinsic to growing cell populations and explained without size sensing or signalling.
     FEBS J. 279 (22):4213–4230, November 2012.
     URL

113. C Linke, E Klipp, H Lehrach, M Barberis and S Krobitsch.
     Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions.
     Front. Physiol. 4:173, 2013.
     URL

114. E Petelenz-Kurdziel, C Kuehn, B Nordlander, D Klein, K-K Hong, T Jacobson, P Dahl, J Schaber, J Nielsen, S Hohmann and E Klipp.
     Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress.
     PLoS Comput. Biol. 9 (6):e1003084, 2013.
     URL

115. N J Stanford, T Lubitz, K Smallbone, E Klipp, P Mendes and W Liebermeister.
     Systematic construction of kinetic models from genome-scale metabolic networks.
     PLoS ONE 8 (11):e79195, 2013.
     URL

116. J A H Wodke, J Puchałka, M Lluch-Senar, J Marcos, E Yus, M Godinho, R Gutiérrez-Gallego, V A P Martins dos Santos, L Serrano, E Klipp and T Maier.
     Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.
     Mol. Syst. Biol. 9:653, 2013.
     URL

117. F Krause, M Schulz, B Ripkens, M Flöttmann, M Krantz, E Klipp and T Handorf.
     Biographer: web-based editing and rendering of SBGN compliant biochemical networks.
     Bioinformatics 29 (11):1467–1468, June 2013.
     URL

118. M Flöttmann, F Krause, E Klipp and M Krantz.
     Reaction-contingency based bipartite Boolean modelling.
     BMC Syst. Biol. 7:58, July 2013.
     URL

119. A Supady, E Klipp and M Barberis.
     A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae.
     J. Biotechnol. 168 (2):174–184, October 2013.
     URL

120. M Bock, T Scharp, C Talnikar and E Klipp.
     BooleSim: an interactive Boolean network simulator.
     Bioinformatics 30 (1):131–132, January 2014.
     URL

121. G M De Hijas-Liste, E Klipp, E Balsa-Canto and J R Banga.
     Global dynamic optimization approach to predict activation in metabolic pathways.
     BMC Syst. Biol. 8:1, January 2014.
     URL

122. D Hosiner, S Gerber, H Lichtenberg-Fraté, W Glaser, C Schüller and E Klipp.
     Impact of acute metal stress in Saccharomyces cerevisiae.
     PLoS ONE 9 (1):e83330, 2014.
     URL

123. A Kowald and E Klipp.
     Mathematical models of mitochondrial aging and dynamics.
     In H D Osiewacz (ed.). The Mitochonrion in Aging and Disease (Prog. Mol. Biol. Transl. Sci. 127). Elsevier, 2014, pages 63-92.
     URL

124. S Kummer, M Flöttmann, B Schwanhäusser, C Sieben, M Veit, M Selbach, E Klipp and A Herrmann.
     Alteration of protein levels during influenza virus H1N1 infection in host cells: a proteomic survey of host and virus reveals differential dynamics.
     PLoS ONE 9 (4):e94257, 2014.
     URL

125. K Tummler, T Lubitz, M Schelker and E Klipp.
     New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.
     FEBS J. 281 (2):549–571, January 2014.
     URL

126. K M Tyc, C Kühn, D Wilson and E Klipp.
     Assessing the advantage of morphological changes in Candida albicans: a game theoretical study.
     Front. Microbiol. 5:41, 2014.
     URL

127. S Vaga, M Bernardo-Faura, T Cokelaer, A Maiolica, C A Barnes, L C Gillet, B Hegemann, F Van Drogen, H Sharifian, E Klipp, M Peter, J Saez-Rodriguez and R Aebersold.
     Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
     Mol. Syst. Biol. 10 (12):767, 2014.
     URL

128. R García-Salcedo, T Lubitz, G Beltran, K Elbing, Y Tian, S Frey, O Wolkenhauer, M Krantz, E Klipp and S Hohmann.
     Glucose de-repression by yeast AMP-activated protein kinase SNF1 is controlled via at least two independent steps.
     FEBS J. 281 (7):1901–1917, April 2014.
     URL

129. J G Rodriguez Plaza, R Morales-Nava, C Diener, G Schreiber, Z D Gonzalez, M T Lara Ortiz, I Ortega Blake, O Pantoja, R Volkmer, E Klipp, A Herrmann and G Del Rio.
     Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin.
     J. Biol. Chem. 289 (21):14448–14457, May 2014.
     URL

130. C Diener, G Schreiber, W Giese, G Del Rio, A Schröder and E Klipp.
     Yeast mating and image-based quantification of spatial pattern formation.
     PLoS Comput. Biol. 10 (6):e1003690, June 2014.
     URL

131. M Hilsch, B Goldenbogen, C Sieben, C T Höfer, J P Rabe, E Klipp, A Herrmann and S Chiantia.
     Influenza A matrix protein M1 multimerizes upon binding to lipid membranes.
     Biophys. J. 107 (4):912–923, August 2014.
     URL

132. M Cvijovic, J Almquist, J Hagmar, S Hohmann, H-M Kaltenbach, E Klipp, M Krantz, P Mendes, S Nelander, J Nielsen, A Pagnani, N Przulj, A Raue, J Stelling, S Stoma, F Tobin, J A H Wodke, R Zecchina and M Jirstrand.
     Bridging the gaps in systems biology.
     Mol. Genet. Genomics 289 (5):727–734, October 2014.
     URL

133. M Floettmann, J Uhlendorf, T Scharp, E Klipp and T W Spiesser.
     SensA: web-based sensitivity analysis of SBML models.
     Bioinformatics 30 (19):2830–2831, October 2014.
     URL

134. F Guillaud, S Dröse, A Kowald, U Brandt and E Klipp.
     Superoxide production by cytochrome bc1 complex: a mathematical model.
     Biochim. Biophys. Acta 1837 (10):1643–1652, October 2014.
     URL

135. F Uschner and E Klipp.
     Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system.
     Syst. Synth. Biol. 8 (4):297–306, December 2014.
     URL

136. X Cheng, E Dimou, H Alborzinia, F Wenke, A Göhring, S Reuter, N Mah, H Fuchs, M A Andrade-Navarro, J Adjaye, S Gul, C Harms, J Utikal, E Klipp, R Mrowka and S Wölfl.
     Identification of 2-[4-[(4-methoxyphenyl)methoxy]-phenyl]acetonitrile and derivatives as potent Oct3/4 inducers.
     J. Med. Chem. 58 (12):4976–4983, 2015.
     URL

137. W Giese, M Eigel, S Westerheide, C Engwer and E Klipp.
     Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models.
     Phys. Biol. 12 (6):066014, 2015.
     URL

138. T Lubitz, N Welkenhuysen, S Shashkova, L Bendrioua, S Hohmann, E Klipp and M Krantz.
     Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review.
     npj Syst. Biol. Appl. 1:15007, 2015.
     URL

139. T Mori, M Flöttmann, M Krantz, T Akutsu and E Klipp.
     Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks.
     BMC Syst. Biol. 9:45, 2015.
     URL

140. A Raue, B Steiert, M Schelker, C Kreutz, T Maiwald, H Hass, J Vanlier, C Tönsing, L Adlung, R Engesser, W Mader, T Heinemann, J Hasenauer, M Schilling, T Höfer, E Klipp, F Theis, U Klingmüller, B Schöberl and J Timmer.
     Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
     Bioinformatics 31 (21):3558–3560, 2015.
     URL

141. B Spiesschaert, B Goldenbogen, S Taferner, M Schade, M Mahmoud, E Klipp, N Osterrieder and W Azab.
     Role of gB and pUS3 in equine herpesvirus 1 transfer between peripheral blood mononuclear cells and endothelial cells: a dynamic in vitro model.
     J. Virol. 89 (23):11899–11908, 2015.
     URL

142. T W Spiesser, C Kühn, M Krantz and E Klipp.
     Bud-localization of CLB2 mRNA can constitute a growth rate dependent daughter sizer.
     PLoS Comput. Biol. 11 (4):e1004223, 2015.
     URL

143. K Tummler, C Kühn and E Klipp.
     Dynamic metabolic models in context: biomass backtracking.
     Integr. Biol. 7 (8):940–951, 2015.
     URL

144. L C Barros de Andrade e Sousa, C Kühn, K M Tyc and E Klipp.
     Dosage and dose schedule screening of drug combinations in agent-based models reveals hidden synergies.
     Front. Physiol. 6:398, 2016.
     URL

145. S Gerber, M Fröhlich, H Lichtenberg-Fraté, S Shabala, L Shabala and E Klipp.
     A thermodynamic model of monovalent cation homeostasis in the yeast Saccharomyces cerevisiae.
     PLoS Comput. Biol. 12 (1):e1004703, 2016.
     URL

146. B Goldenbogen, W Giese, M Hemmen, J Uhlendorf, A Herrmann and E Klipp.
     Dynamics of cell wall elasticity pattern shapes the cell during yeast mating morphogenesis.
     Open Biol. 6 (9):160136, 2016.
     URL

147. E Klipp, L Liebermeister, C Wierling and A Kowald.
     Systems Biology. A Textbook. (second revised edition).
     Wiley-Blackwell, 2016.
     978-3-527-33636-4">URL

148. L Losensky, B Goldenbogen, G Holland, M Laue, A Petran, J Liebscher, H A Scheidt, A Vogel, D Huster, E Klipp and A Arbuzova.
     Micro -and nano-tubules built from loosely and tightly rolled up thin sheets.
     Phys. Chem. Chem. Phys. 18 (2)(2):1292–1301, 2016.
     URL

149. T Lubitz, J Hahn, F T Bergmann, E Noor, E Klipp and W Liebermeister.
     SBtab: a flexible table format for data exchange in systems biology.
     Bioinformatics 32 (16):2559–2561, 2016.
     URL

150. J Pauling and E Klipp.
     Computational lipidomics and lipid bioinformatics: filling In the blanks.
     J. Integr. Bioinform. 13 (1):299, 2016.
     URL

151. M Schelker, C M Mair, F Jolmes, R-W Welke, E Klipp, A Herrmann, M Flöttmann and C Sieben.
     Viral RNA degradation and diffusion act as a bottleneck for the influenza A virus infection efficiency.
     PLoS Comput. Biol. 12 (10):e1005075, 2016.
     URL

152. V Schützhold, J Hahn, K Tummler and E Klipp.
     Computational modeling of lipid metabolism in yeast.
     Front. Mol. Biosci. 3:57, 2016.
     URL

153. T Spiesser, C Kühn, M Krantz and E Klipp.
     The MYpop toolbox: putting yeast stress responses in cellular context on single cell and population scales.
     Biotechnol. J. 11 (9):1158–1168, 2016.
     URL

154. S R Talemi, C-F Tiger, M Andersson, R Babazadeh, N Welkenhuysen, E Klipp, S Hohmann and J Schaber.
     Systems level analysis of the yeast osmo-stat.
     Sci. Rep. 6:30950, 2016.
     URL

155. K M Tyc, S E Herwald, J A Hogan, J V Pierce, E Klipp and C A Kumamoto.
     The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression.
     BMC Syst. Biol. 10:20, 2016.
     URL

156. A Auconi, A Giansanti and E Klipp.
     Causal influence in linear Langevin networks without feedback.
     Physical Rev. E 95 (4-1):042315, 2017.
     URL

157. G Del Rio, E Klipp and A Herrmann.
     Using confocal microscopy and computational modeling to investigate the cell-penetrating properties of antimicrobial peptides.
     Methods Mol. Biol. 1548:191–199, 2017.
     URL

158. C Linke, A Chasapi, A González-Novo, I Al Sawad, S Tognetti, E Klipp, M Loog, S Krobitsch, F Posas, I Xenarios and M Barberis.
     A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle.
     npj Syst. Biol. Appl. 3:7, 2017.
     URL

159. U Münzner, T Lubitz, E Klipp and M Krantz.
     Toward genome-scale models of signal transduction networks.
     In J Nielsen and S Hohmann (eds.). Systems Biology. Wiley-VCH, 2017, pages 215–242.
     URL

160. M Schelker, S Feau, J Du, N Ranu, E Klipp, G MacBeath, B Schoeberl and A Raue.
     Estimation of immune cell content in tumour tissue using single-cell RNA-seq data.
     Nat. Commun. 8:2032, 2017.
     URL

161. K Stojanovski, T Ferrar, H Benisty, F Uschner, J Delgado, J Jimenez, C Solé, E Nadal, E Klipp, F Posas, L Serrano and C Kiel.
     Interaction dynamics determine signaling and output pathway responses.
     Cell Rep. 19 (1):136–149, 2017.
     URL

162. M Heiske, T Letellier and E Klipp.
     Comprehensive mathematical model of oxidative phosphorylation valid for physiological and pathological conditions..
     FEBS J. 284 (17):2802–2828, September 2017.
     URL

163. Aouefa Amoussouvi, Lotte Teufel, Matthias Reis, Martin Seeger, Julia Katharina Schlichting, Gabriele Schreiber, Andreas Herrmann and Edda Klipp.
     Transcriptional timing and noise of yeast cell cycle regulators–a single cell and single molecule approach.
     npj Systems Biology and Applications 4(1):17, 2018.
     URL

164. Vladimir J Arellano, Paula Martinell García, Jonathan G Rodríguez Plaza, Maria T Lara Ortiz, Gabriele Schreiber, Rudolf Volkmer, Edda Klipp and Gabriel Del Rio.
     An Antimicrobial Peptide Induces FIG1-Dependent Cell Death During Cell Cycle Arrest in Yeast.
     Front Microbiol 9:1240, 2018.
     URL, DOI

165. M Reis, J A Kromer and E Klipp.
     General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks.
     J. Math. Biol. 20 January 2018:Epub ahead of print, 2018.
     URL

166. K Tummler, M Zimmermann, O T Schubert, R Aebersold, C Kühn, U Sauer and E Klipp.
     Two parallel pathways implement robust propionate catabolism and detoxification in mycobacteria.
     bioRxiv, 2018.
     URL

167. K Tummler and E Klipp.
     The discrepancy between data for and expectations on metabolic models: How to match experiments and computational efforts to arrive at quantitative predictions?.
     Curr. Opin. Syst. Biol. 8:1–6, 2018.
     URL

168. J Theobald, X Cheng, A Ghanem, H Gaitantzi, G Song, E Klipp, J Wodke, H Becker, R Mrowka, K Breitkopf-Heinlein, S Dooley and S Wölfl.
     Monitoring cytochrome P450 activity in living hepatocytes by chromogenic substrates in response to drug treatment or during cell maturation.
     Arch. Toxicol. 92(3):1133–1149, March 2018.
     URL

169. Arturo Blazquez-Navarro, Thomas Schachtner, Ulrik Stervbo, Anett Sefrin, Maik Stein, Timm H Westhoff, Petra Reinke, Edda Klipp, Nina Babel, Avidan U Neumann and Michal Or-Guil.
     Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.
     PLOS Computational Biology 14(5):1-20, May 2018.
     URL, DOI

170. Raphaela Fritsche-Guenther, Christin Zasada, Guido Mastrobuoni, Nadine Royla, Roman Rainer, Florian Roßner, Matthias Pietzke, Edda Klipp, Christine Sers and Stefan Kempa.
     Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations.
     Scientific Reports 8(1):9204, June 2018.
     URL

171. Tom Altenburg, Björn Goldenbogen, Jannis Uhlendorf and Edda Klipp.
     Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae.
     npj Systems Biology and Applications 5(1):34, 2019.
     URL

172. Andrea Auconi, Andrea Giansanti and Edda Klipp.
     Information Thermodynamics for Time Series of Signal-Response Models.
     Entropy 21(2), 2019.
     URL, DOI

173. Ana Bulović, Stephan Fischer, Marc Dinh, Felipe Golib, Wolfram Liebermeister, Christian Poirier, Laurent Tournier, Edda Klipp, Vincent Fromion and Anne Goelzer.
     Automated generation of bacterial resource allocation models.
     Metabolic Engineering 55:12 -22, 2019.
     URL, DOI

174. Lotte Teufel, Katja Tummler, Max Flöttmann, Andreas Herrmann, Naama Barkai and Edda Klipp.
     A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle.
     Scientific Reports 9(1):3343, 2019.
     URL

175. Ulrike Münzner, Edda Klipp and Marcus Krantz.
     A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae.
     Nat. Commun. 10:2041-1723, March 2019.
     URL, DOI

176. Friedemann Uschner and Edda Klipp.
     Signaling pathways in context.
     Curr. Opin. Syst. Biol. 58:155-160, April 2019.
     URL, DOI

177. Maria Krantz and Edda Klipp.
     Moonlighting proteins -an approach to systematize the concept..
     In silico biology, November 2019.
     

178. Stephan O Adler and Edda Klipp.
     Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality..
     Entropy (Basel, Switzerland) 22, January 2020.
     

179. B Goldenbogen, SO Adler, O Bodeit, JAH Wodke, A Korman, L Bonn, X Escalera-Fanjul, JEL Haffner, M Karnetzki, M Krantz, I Maintz, L Mallis, RU Moran Torres, H Prawitz, PS Segelitz, M Seeger, R Linding and E Klipp.
     Geospatial precision simulations of community confined human interactions during SARS-CoV-2 transmission reveals bimodal intervention outcomes.
     medRxiv, 2020.
     URL, DOI

180. Maria Krantz and Edda Klipp.
     Moonlighting proteins -an approach to systematize the concept..
     In silico biology 14:71-83, 2020.
     

181. Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman Malik S Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev and Cheng Zhang.
     Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
     Nature biotechnology 38(4):504–504, 2020.
     URL

182. Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev and Cheng Zhang.
     MEMOTE for standardized genome-scale metabolic model testing..
     March 2020.
     

183. Kristin Habermann, Bhavika Tiwari, Maria Krantz, Stephan O Adler, Edda Klipp, Asif M Arif and Wolfgang Frank.
     Identification of small non-coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana..
     The Plant journal : for cell and molecular biology 104:138-155, September 2020.
     

184. Maria Krantz, Julia Legen, Yang Gao, Reimo Zoschke, Christian Schmitz-Linneweber and Edda Klipp.
     Modeling indicates degradation of mRNA and protein as a potential regulation mechanisms during cold acclimation.
     Journal of Plant Research 134(4):873–883, 2021.
     URL

185. Maria Krantz, David Zimmer, Stephan O Adler, Anastasia Kitashova, Edda Klipp, Timo Mühlhaus and Thomas Nägele.
     Data Management and Modeling in Plant Biology.
     Frontiers in Plant Science 12, 2021.
     URL, DOI

186. Veera Raghavan Thangapandi, Oskar Knittelfelder, Mario Brosch, Eleonora Patsenker, Olga Vvedenskaya, Stephan Buch, Sebastian Hinz, Alexander Hendricks, Marina Nati, Alexander Herrmann, Devavrat Ravindra Rekhade, Thomas Berg, Madlen Matz-Soja, Klaus Huse, Edda Klipp, Josch K Pauling, Judith AH Wodke, Jacobo Miranda Ackerman, Malte Bonin, Elmar Aigner, Christian Datz, Witigo Schönfels, Sophie Nehring, Sebastian Zeissig, Christoph Röcken, Andreas Dahl, Triantafyllos Chavakis, Felix Stickel, Andrej Shevchenko, Clemens Schafmayer, Jochen Hampe and Pallavi Subramanian.
     Loss of hepatic Mboat7 leads to liver fibrosis.
     Gut 70(5):940–950, 2021.
     URL, DOI

187. Olga Vvedenskaya, Tim Daniel Rose, Oskar Knittelfelder, Alessandra Palladini, Judith Andrea Heidrun Wodke, Kai Schuhmann, Jacobo Miranda Ackerman, Yuting Wang, Canan Has, Mario Brosch, Veera Raghavan Thangapandi, Stephan Buch, Thomas Züllig, Jürgen Hartler, Harald C Köfeler, Christoph Röcken, Ünal Coskun, Edda Klipp, Witigo Schoenfels, Justus Gross, Clemens Schafmayer, Jochen Hampe, Josch Konstantin Pauling and Andrej Shevchenko.
     Nonalcoholic fatty liver disease stratification by liver lipidomics.
     Journal of Lipid Research 62:100104, 2021.
     URL, DOI

188. Tatjana Kleine, Thomas Nägele, Ekkehard H Neuhaus, Christian Schmitz-Linneweber, Alisdair R Fernie, Peter Geigenberger, Bernhard Grimm, Kerstin Kaufmann, Edda Klipp, Jörg Meurer, Torsten Möhlmann, Timo Mühlhaus, Belen Naranjo, Jörg Nickelsen, Andreas Richter, Hannes Ruwe, Michael Schroda, Serena Schwenkert, Oliver Trentmann, Felix Willmund, Reimo Zoschke and Dario Leister.
     Acclimation in plants -the Green Hub consortium..
     The Plant journal : for cell and molecular biology 106:23-40, April 2021.
     

189. Jorin Diemer, Jens Hahn, Björn Goldenbogen, Karin Müller and Edda Klipp.
     Sperm migration in the genital tract—In silico experiments identify key factors for reproductive success.
     PLOS Computational Biology 17(7):1-17, July 2021.
     URL, DOI

190. Martin Seeger, James Longden, Edda Klipp and Rune Linding.
     Deep Hidden Physics Modeling of Cell Signaling Networks..
     Current genomics 22:239-243, December 2021.
     

191. Björn Goldenbogen, Stephan O Adler, Oliver Bodeit, Judith A H Wodke, Ximena Escalera-Fanjul, Aviv Korman, Maria Krantz, Lasse Bonn, Rafael Morán-Torres, Johanna E L Haffner, Maxim Karnetzki, Ivo Maintz, Lisa Mallis, Hannah Prawitz, Patrick S Segelitz, Martin Seeger, Rune Linding and Edda Klipp.
     Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination.
     Advanced Science n/a(n/a):2200088, 2022.
     URL, DOI

192. Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp and Tatsuya Akutsu.
     Identification of periodic attractors in Boolean networks using a priori information.
     PLOS Computational Biology 18(1):1-27, January 2022.
     URL, DOI

193. Stephan O Adler, Thomas W Spiesser, Friedemann Uschner, Ulrike Münzner, Jens Hahn, Marcus Krantz and Edda Klipp.
     A yeast cell cycle model integrating stress, signaling, and physiology..
     FEMS yeast research 22, June 2022.
     URL, DOI

194. Willow Carretero Chavez, Marcus Krantz, Edda Klipp and Irina Kufareva.
     kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models.
     BMC Bioinformatics 24(1):246, 2023.
     URL, DOI

195. Anastasia Kitashova, Stephan O Adler, Andreas S Richter, Svenja Eberlein, Dejan Dziubek, Edda Klipp and Thomas Nägele.
     Limitation of sucrose biosynthesis shapes carbon partitioning during plant cold acclimation.
     Plant, Cell & Environment 46(2):464-478, 2023.
     URL, DOI

196. Martin Seeger, Max Flöttmann and Edda Klipp.
     A dynamical stochastic model of yeast translation across the cell cycle.
     Heliyon 9(2):e13101, 2023.
     URL, DOI