Dr. Edda Klipp - Publications
Textbook

Klipp, E., Herwig, R., Kowald, A., Wierling, C. and Lehrach, H. 2005. Systems Biology in Practice: Concepts, Implementation and Application. Wiley-VCH, Weinheim.
ISBN 3-527-31078-9

systems biology in practice

Book chapters

Schaber, J. & Klipp, E. 2008. Short-term volume and turgor regulation in yeast. In: Systems Biology (Editor: Wolkenhauer, O.), Series: Essays in Biochemistry. In press.

Klipp, E. & Schaber, J. 2008. Modeling the dynamics of stress activated protein kinases (SAPK) in cellular stress response. In: SAPK – Stress Activated Protein Kinase (Ed: Posas, F.). Series: Topics in Current Genetics. ISBN 978-3-540-75568-5. Springer-Verlag Berlin Heidelberg.

Klipp E & Schaber J. 2006. Modelling of Signal Transduction in Yeast – Sensitivity and Model Analysis. In "Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine" (M. Cánovas, J.L. Iborra and A. Manjón, Editors). Murcia.

Nordlander B, Klipp, E., Kofahl B, and Hohmann S. 2005. Modelling signalling pathways - a yeast approach In: "Systems Biology. Definitions and Perspectives", Alberghina L, Westerhoff HV (editors) In Series "Topics in Current Genetics" (Hohmann S, series editor), Springer-Verlag Heidelberg, 277-302.
ISBN: 3-540-22968-X.

Schuster, S., Klipp, E., and Marhl, M. The predictive power of molecular network modelling - case studies of predictions with subsequent experimental verification. In: "Discovering Biomolecular Mechanisms with Computational Biology" (Frank Eisenhaber, ed.) Landes Bioscience, Georgetown, 115-127.

Lachmann M., Blackstone NW., Haig D., Kowald A., Michod RE., Szathmary E., Werren JH., Wolpert L. 2003. Cooperation and conflict in the evolution of genomes, self, and multicellular organisms. In: Genetic and Cultural Evolution of Cooperation (Hammerstein P. ed), p. 327-356, Cambridge, MA: The MIT Press.

Articles

2008

Zi, Z., Zheng, Y., Rundell, A.E. & Klipp, E. 2008. SBML-SAT: A systems biology markup language (SBML) based sensitivity analysis tool. BMC Bioinformatics, 9:342.    <FullText>

Kühn, C., Petelenz, E., Nordlander, B., Schaber, J., Hohmann, S. & Klipp, E. 2008 Exploring the impact of osmoadaptation on glycolysis using time-varying response coefficients. Genome Informatics, in press.

Bruck, J., Liebermeister, W. & Klipp, E. 2008. Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis. Genome Informatics, in press.

Gerber, S., Aßmus, H., Bakker, B.M., & Klipp, E. 2008. 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. <PubMed> <FullText>  doi:10.1016/j.jtbi.2007.09.027 .

2007

Ralser, M., Wamelink, M.M., Kowald, A., Gerisch,B., Heeren, G., Struys, E., Klipp, E., Jakobs, C., Breitenbach, M., Lehrach, H., Krobitsch, S. 2007. Dynamic re-routing of the carbohydrate flux is key in counteracting oxidative stress. J. Biol. Dec 21, 6(4), 10. <PubMed>  <pdf>

   !!! BioMedCentral Research Award Biology, 2007

Zi, Z. & Klipp, E. 2007.Constraint-Based Modeling and Kinetic Analysis of the Smad Dependent TGF-β Signaling Pathway. PLoS ONE. 2, e936 <PubMed>  <pdf>

Klipp, E. 2007. Modeling dynamic processes in yeast. Review. Yeast. DOI: 10.1002/yea.1544. <PubMed> <pdf>

Zi, Z. & Klipp, E. 2007.Cellular signaling is potentially regulated by cell density in receptor trafficking networks. FEBS Letters. 581, 4589–4595. <PubMed>

Barberis, M. & Klipp, E. 2007. Insights into the network controlling the G1/S transition in budding yeast. Genome Informatics. 18(1), 85-99.<PubMed> <pdf>

Kühn, C., Poustka, A. & Klipp, E. 2007. Modeling development: Spikes of the Sea Urchin. Genome Informatics. 18(1), 75-84.<PubMed>  <pdf>

Zi, Z. & Klipp, E. 2007. Steady state analysis of signal response in receptor trafficking networks. Genome Informatics. 18(1), 100-108.<PubMed> <pdf>

Borger, S., Liebermeister, W., Uhlendorf, J. & Klipp, E. 2007. Automatically generated model of a metabolic network. Genome Informatics. 18(1), 215-224. <PubMed> <pdf>

Klipp E, Liebermeister W, Helbig A, Kowald A & Schaber J. 2007. Systems Biology standards – the community speaks. Nature Biotechnology, 25(4), 390-391. <PubMed> <pdf>

Barberis M, Klipp E, Vanoni M & Alberghina A. 2007. Cell Size at S Phase Initiation: an Emergent Property of the G1/S Network. PLoS Comp. Biol., 3(4), e64.<PubMed> <pdf>

2006

Liebermeister W, Klipp E. 2006 Bringing metabolic networks to life: convenien-ce rate law and thermodynamic constraints. TBioMed, 3:41, doi:10.1186/1742-4682-3-41.<PubMed> <pdf>

Liebermeister W & Klipp E. 2006 Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. TBioMed, 3:42, doi:10.1186/1742-4682-3-42.<PubMed> <pdf>

Schulz M, Uhlendorf J, Klipp E & Liebermeister W. 2006. SBMLmerge, a system for combining biochemical network models. Genome Informatics, 17(1), 62-71.<PubMed> <pdf>

Borger S, Liebermeister W & Klipp E. 2006. Prediction of enzyme kinetic parameters based on statistical learning. Genome Informatics, 17(1), 80-87.<PubMed> <pdf>

Zi Z & Klipp E. 2006. SBML-PET: A Systems Biology Markup Language based Parameter Estimation Tool. Bioinformatics, 22(21), 2704-2705. 2006 Aug 22; [Epub ahead of print] .<PubMed> <pdf>

Klipp E & Liebermeister W. 2006. Mathematical modeling of intracellular signaling pathways. BMC Neuroscience. 7 Suppl 1:S10.<PubMed>  <pdf>

Schaber J, Kofahl B, Kowald A & Klipp E. 2006. A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker’s yeast. FEBS Journal. 273, 3520-3533.<PubMed>  <pdf>


2005

Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. 2005 Minimum Information Requested In the Annotation of biochemical Models (MIRIAM) Nature Biotechnology, 23(12), 1509-1515. <PubMed><pdf>

Klipp, E. & Hohmann, S. 2005. Simulation von Lebensprozessen. BIOForum, 10, 60-61.

Liebermeister, W. & Klipp, E. 2005. Biochemical networks with uncertain parameters. IEE Systems Biology, 152 (3), 97-107. <PubMed>

Kowald A, Lehrach H & Klipp E. 2005, Alternative Pathways as Mechanism for the Negative Effects Associated with Overexpression of Superoxide
Dismutase, Journal Theoretical Biology, 238(4):828-40. <PubMed> 

Klipp, E, Nordlander, B, Krüger, R, Gennemark, P & Hohmann, S. 2005. The dynamic response of yeast cells to osmotic shock – a systems biology approach. Nature Biotechnology, 23, 975-982. <PubMed>

Liebermeister, W, Baur, U, and Klipp, E. 2005. Complexity reduction of biochemical network models by balanced truncation. FEBS Journal, 272(16):4034-43. <PubMed>

Klipp, E. 2005. Dynamic modeling of yeast cell stress response. Proceedings of the he First Annual RECOMB Satellite Workshop on Systems Biology and The Second Annual RECOMB Satellite Workshop on Regulatory Genomics. December 2-4, 2005. University of California, San Diego, U.S.A.

Borger, S., Liebermeister, W. & Klipp, E. 2005. Distribution of a bifurcation parameter in a genetic network with uncertain parameters. Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks, (Kummer, U. et al., eds) Logos, Berlin, pp. 95-101.

2004

Klipp, E., Nordlander, B., Kofahl, B., and Hohmann, S. 2004. Shutting the MAP off – and on again? Current Genomics, 5, 637-647.

Kowald A., and Klipp E. 2004. Alternative pathways might mediate toxicity of high concentrations of superoxide dismutase. Annals of the New York Academy of Sciences,1019, 370-374

Klipp E., Liebermeister W., and Wierling C. 2004. Inferring Dynamic Properties of Biochemical Reaction Networks from Structural Knowledge. Genome Informatics 15(1): 125-137. <PubMed>

Hakenberg, J., Schmeier, S., Kowald, A., Klipp, E. and Leser, U. 2004. Finding kinetic parameters using text mining. OMICS – journal of integrative biology. 8(2), 131-152. <PubMed>

Kofahl B. & Klipp E. 2004. Modeling the Dynamics of the Yeast Pheromone Pathway. YEAST, 21, 831-850. <PubMed>

Liebermeister, W., Klipp, E., Schuster, S. & Heinrich, R., 2004, A theory of optimal differential gene expression. BioSystems, 76, 261-278. <PubMed>

before 2003

Schmeier, S., Hakenberg, J., Kowald, A., Klipp, E. & Leser, U. Text Mining for Systems Biology Using Statistical Learning Methods. Proceedings der Workshop-Woche “Lehren – Lernen – Wissen – Adaptivität (LLWA 2003)“, Oktober 2003, Karlsruhe.

Klipp E, Mathematical modeling of signal transduction in yeast. YEAST 20: S286-S286 Suppl. 1 JUL 2003

Klipp, E., Heinrich, R. and Holzhütter, H.-G., 2002, Prediction of temporal gene expression. Metabolic optimisation by re-distribution of enzyme activities. Eur. J. Biochem., 269, 1-8.

Bakker BM, Assmus HE, Bruggeman F, Haanstra JR, Klipp E & Westerhoff H 2002. Network-based selectivity of antiparasitic inhibitors. Mol. Biol. Rep. 29 (1-2): 1-5.

Liebermeister, W., Schuster, S., Heinrich, R. & Klipp, E. 2002. Relating gene expression to function by an optimality postulate. Proceedings of the European Conference on Cell Biology (ECCB) 2002.

Klipp, E. 2001. Reprogramming the metabolic system. In Trends in Nonlinear Analysis. Theory, Modelling and Computation. Heidelberg, 126-128.

Klipp, E., Holzhütter, H.-G. & Heinrich, R. 2000. Reprogramming the metabolic system by altering gene expression. In Animating the cellular map, Proceedings of the 9th Int. Meeting on BioThermoKinetics, Stellenbosch (Hofmeyr, J.-H.S., Rohwer, J.M. & Snoep, J.L., eds), 165-170.

Klipp E. & Heinrich R. 1999. Competition for enzymes in metabolic pathways. BioSystems, 54, 1-14.

Klipp, E. (1998) Relations between flux control coefficients and enzyme concentrations in states of minimized total amount of enzyme. In: Larsson, C., Påhlman, I.-L., and Gustafsson, L. (eds.) BioThermoKinetics. In the Post Genomic Era. Göteborg: Göteborg University, 27-29.

Heinrich, R., Montero, F., Klipp, E., Waddell, T.G., and Meléndez-Hevia, E. (1997) Kinetic and thermodynamic constraints for the structural design of glycolysis. Nonlinear Anal. Theor. Meth. & Appl. 30, 1793-1804.

Heinrich R, Montero F, Klipp E, Waddell TG & Meléndez-Hevia E. 1997. Theoretical approaches to the evolutionary optimization of glycolysis. Thermodynamic and kinetic constraints. Eur.J.Biochem. 243, 191-201.

Heinrich R & Klipp E. 1996. Control analysis of unbranched enzymatic chains in states of maximal activity. J.theor.Biol. 182,243-252.

Klipp, E. (1996) Maximization of enzymic activity under consideration of various constraints. In: Ghista, D.N. (Ed.) Biomedical and Life Physics. Proceedings of the Second Gauss Symposium, August 2-8, 1993, Munich. Braunschweig: Vieweg, 71-84.

Klipp, E. and Heinrich, R. (1996) Kinetic optimization of multi-enzyme systems. In: Westerhoff, H.V., Snoep, J.L., Sluse, F.E., Wijker, J.E., and Kholodenko, B.N. (eds.) Biothermokinetics of the Living Cell. Amsterdam: Biothermokinetic Press, 210-213.

Klipp, E. (1995) Evolutionary optimization of enzyme kinetic parameters. J. Biol. Syst. 3, 363-376.

Klipp E & Heinrich R. 1994, Evolutionary optimization of enzyme kinetic parameters; effect of constraints. J.theor.Biol. 171, 309-323.

Wilhelm T, Hoffmann-Klipp E & Heinrich R. 1994, An evolutionary approach to enzyme kinetics; optimization of ordered mechanisms. Bull.Math.Biol. 56, 65-106.

Heinrich, R., Klipp, E., Stephani, A., and Wilhelm, T. (1994) Evolutionary optimization of enzymes on the basis of kinetic and thermodynamic principles. In: Gnaiger, E., Gellerich, F.N., and Wyss, M. (eds.) What is Controlling Life?. Innsbruck: Innsbruck University Press, 99-102.

Heinrich, R., Hoffmann, E., and Holzhütter, H.-G. (1994) Kinetic parameters of enzymes in states of maximal activity. In: Westerhoff, H.V. (Ed.) Biothermokinetics. Andover: Intercept Ltd., 81-91.

Heinrich, R. and Hoffmann, E. (1993) Genetics and evolutionary dynamics. An evolutionary approach to enzyme catalysis. In: Demongeot, J. and Capasso, V. (eds.) Mathematics Applied to Biology and Medicine. Proceedings of the 1. European Conference, Grenoble, January 1991. Winnipeg: Wuerz Publishing Ltd., 315-319.

Heinrich R & Hoffmann E. 1991. Kinetic parameters of enzymatic reactions in states of maximal activity; an evolutionary approach. J.theor.Biol. 151,249-283.

Heinrich R, Hoffmann E & Holzhütter HG. 1990. Calculation of kinetic parameters of a reversible enzymatic reaction in states of maximal activity. Biomed. Biochim.Acta 49, 891-902.