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
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.
Journal 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>
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>
Mao L, Zabel C, Wacker MA, Nebrich G, Sagi D, Schrade P, Bachmann S, Kowald A, Klose J. 2006, Estimation of the mtDNA mutation rate in aging mice by proteome analysis and mathematical modeling. Experimental Gerontology, 41, 11-24.
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>
Schaber J, et al. (2005). Putative gene expression levels influence amino acid usage and evolutionary rates in endosymbiontic bacteria. Gene 352:109-117. <PubMed> <pdf>
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>
Kowald A, Jendrach M, Pohl S, Bereiter-Hahn J, Hammerstein P. 2005, On the relevance of mitochondrial fusions for the accumulation of mitochondrial deletion mutants: a modelling study. Aging Cell 4:273-283. <PubMed>
Jendrach M, Pohl S, Voth M, Kowald A, Hammerstein P, Bereiter-Hahn J. 2005, Morpho-dynamic changes of mitochondria during ageing of human endothelial cells. Mech. Ageing Dev. 126:813-821. <PubMed>
Lueking A, Huber O, Wirths C, Schulte K, Stieler KM, Blume-Peytavi U, Kowald A, Hensel-Wiegel K, Tauber R, Lehrach H, Meyer HE, Cahill DJ. 2005 Profiling of alopecia areata autoantigens based on protein microarray technology. Mol. Cell. Proteomics 4:1382-1390. <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>
Liebermeister, W. 2005. Response to temporal parameter fluctuations in biochemical networks, Journal of Theoretical Biology, 234, 423–438.
Zintzaras, E., Brown, N. and Kowald, A. 2006 Non-Parametric Classification of Protein Secondary Structures. Computers in Biology and Medicine, 36, 145-156.<PubMed>
Toedling, J., Schmeier, S., Heinig, M., Georgi, B. and Roepcke, S. 2005. MACAT - MicroArray Chromosome Analysis Tool. Bioinformatics, 21(9):2112-3.
Kowald, A and Demetrius, L. 2005. Directionality theory: A computational study of an entropic principle in evolutionary processes. Proceedings of the Royal Society, Series B, 272(1564):741-9.
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>
2003 and before
Liebermeister, W., Klipp, E., Schuster, S. & Heinrich, R., 2003, A theory of optimal differential gene expression. BioSystems, 76, 261-278. <PubMed>
Storm T., Rath S., Mohamed S.A., Bruse P., Kowald A., Oehmichen M., Meissner C. 2002. Mitotic brain cells are just as prone to mitochondrial deletions as neurons: a large-scale single-cell PCR investigation of the human caudate nucleus. Experimental Gerontology, 37, 1389-1400
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.
Zintzaras E., Bouka P. & Kowald A., 2002, Biometrical evaluation of bioequivalence using a bootstrap individual direct curve comparison method.Eur. J. Drug Metabolism & Pharmacokinetics, 27, 11-16
Kowald A., 2002, Lifespan does not measure ageing. Biogerontology, 3, 187-190.
Kowald A., 2001, The mitochondrial theory of aging. Biological Signals and Receptors, 10, 162-175
Liebermeister W., 2002, Linear modes of gene expression. determined by independent component analysis. Bioinformatics 18, 51-60
Liebermeister W., Rapoport T. A., Heinrich R., 2001, Ratcheting in post-translational protein translocation: a. mathematical model, J. Mol. Biol. 305, 643-56.