Stephan O Adler, Anastasia Kitashova, Ana Bulović, Thomas Nägele and Edda Klipp.
Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism..
NPJ systems biology and applications 11:28, 2025.
URL, DOI

Gabriele Schreiber, Facundo Rueda, Florian Renner, Asya Fatima Polat, Philipp Lorenz and Edda Klipp.
Expression Dynamics and Genetic Compensation of Cell Cycle Paralogues in Saccharomyces cerevisiae..
Cells 14, 2025.
URL, DOI

Pattarawan Intasian, Chalermroj Sutthaphirom, Oliver Bodeit, Duangthip Trisrivirat, Ninlapan Kimprasoot, Juthamas Jaroensuk, Barbara Bakker, Edda Klipp and Pimchai Chaiyen.
Enhancement of essential cofactors for in vivo biocatalysis..
Faraday discussions, 2024.
URL, DOI

Katja Tummler and Edda Klipp.
Data integration strategies for whole-cell modeling..
FEMS yeast research 24, 2024.
URL, DOI

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

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

Antoni Kowalski, Cristine Betzer, Sigrid Thirup Larsen, Emil Gregersen, Estella A Newcombe, Montaña Caballero Bermejo, Viktor Wisniewski Bendtsen, Jorin Diemer, Christina V Ernstsen, Shweta Jain, Alicia Espiña Bou, Annette Eva Langkilde, Lene N Nejsum, Edda Klipp, Robert Edwards, Birthe B Kragelund, Poul Henning Jensen and Poul Nissen.
Monomeric α-synuclein activates the plasma membrane calcium pump..
The EMBO journal 42:e111122, 2023.
URL, DOI

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

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, 2022.
URL, DOI

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

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, 2022.
URL, DOI

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, 2021.
URL, DOI

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, 2021.
URL, DOI

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

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

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

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

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.
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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.
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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, 1991.
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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.

E Klipp and R Heinrich.
Evolutionary optimization of enzyme kinetic parameters; effect of constraints.
J. Theor. Biol. 171 (3):309–323, 1994.
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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, 1994.
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E Klipp.
Evolutionary optimization of enzyme kinetic parameters.
J Biol. Syst. 3 (2):363–376, 1995.
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R Heinrich and E Klipp.
Control analysis of unbranched enzymatic chains in states of maximal activity.
J. Theor. Biol. 182 (3):243–252, 1996.
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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.

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.

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, 1997.
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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, 1997.
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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.

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, 1999.
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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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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, 2002.
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M Lachmann, N W Blackstone, D Haig, A Kowald, R E Michod, E Szathmary, J H Werren and L Wolpert.
Cooperation and conflict in the evolution of genomes, cells, and multicellular organisms.
In P Hammerstein (ed.). Genetic and Cultural Evolution of Cooperation. MIT Press, 2003, pages 327-56.
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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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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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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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B Kofahl and E Klipp.
Modelling the dynamics of the yeast pheromone pathway.
Yeast 21 (10):831–850, 2004.
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A Kowald and E Klipp.
Alternative pathways might mediate toxicity of high concentrations of superoxide dismutase.
Ann. N. Y. Acad. Sci. 1019:370–374, 2004.
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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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E Klipp and S Hohmann.
Simulation von Lebensprozessen.
BIOForum 28 (10):60–61, 2005.

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, 2005.
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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, 2005.
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W Liebermeister and E Klipp.
Biochemical networks with uncertain parameters.
IEE Proc. Syst. Biol. 152 (3):97–107, 2005.
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W Liebermeister, U Baur and E Klipp.
Biochemical network models simplified by balanced truncation.
FEBS J. 272 (16):4034–4043, 2005.
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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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S Borger, W Liebermeister and E Klipp.
Prediction of enzyme kinetic parameters based on statistical learning.
Genome Inform. 17 (1):80–87, 2006.
URL

O Ebenhöh and W Liebermeister.
Structural analysis of expressed metabolic subnetworks.
Genome Inform. 17 (1):163–172, 2006.
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E Klipp and W Liebermeister.
Mathematical modeling of intracellular signaling pathways.
BMC Neurosci. 7 (Suppl 1):S10, 2006.
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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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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, 2006.
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W Liebermeister and E Klipp.
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.
Theor. Biol. Med. Model. 3:41, 2006.
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W Liebermeister and E Klipp.
Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data.
Theor. Biol. Med. Model. 3:42, 2006.
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C Salazar, J Schütze and O Ebenhöh.
Bioinformatics meets systems biology.
Genome Biol. 7 (1):303, 2006.
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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, 2006.
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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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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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Z Zi and E Klipp.
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
Bioinformatics 22 (21):2704–2705, 2006.
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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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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, 2007.
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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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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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E Klipp.
Modelling dynamic processes in yeast.
Yeast 24 (11):943–959, 2007.
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E Klipp.
Modeling of yeast cell stress response.
FEBS J. 274 (Suppl. s1):53, 2007.
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E Klipp, W Liebermeister, A Helbig, A Kowald and J Schaber.
Systems biology standards -the community speaks.
Nat. Biotechnol. 25 (4):390–391, 2007.
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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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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, 2007.
URL

Z Zi and E Klipp.
Cellular signaling is potentially regulated by cell density in receptor trafficking networks.
FEBS Lett. 581 (24):4589–4595, 2007.
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Z Zi and E Klipp.
Constraint-based modeling and kinetic analysis of the Smad dependent TGF-β signaling pathway.
PLoS ONE 2 (9):e936, 2007.
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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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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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G Basler, Z Nikoloski, O Ebenhöh and T Handorf.
Biosynthetic potentials from species-specific metabolic networks.
Genome Inform. 20:135–148, 2008.
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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.
URL

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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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, 2008.
URL

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

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, 2008.
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T Handorf, N Christian, O Ebenhöh and D Kahn.
An environmental perspective on metabolism.
J. Theor. Biol. 252 (3):530–537, 2008.
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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, 2008.
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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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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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J Schaber and E Klipp.
Short-term volume and turgor regulation in yeast.
Essays Biochem. 45:147–160, 2008.
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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, 2008.
URL

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, 2009.
URL

N Christian, P May, S Kempa, T Handorf and O Ebenhöh.
An integrative approach towards completing genome-scale metabolic networks.
Mol. BioSyst. 5 (12):1889–1903, 2009.
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O Ebenhöh and T Handorf.
Functional classification of genome-scale metabolic networks.
EURASIP J. Bioinform. Syst. Biol. 2009:570456, 2009.
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E Klipp.
Timing matters.
FEBS Lett. 583 (24):4013–4018, 2009.
URL

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.
URL

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, 2009.
URL

J Schaber, W Liebermeister and E Klipp.
Nested uncertainties in biochemical models.
IET Syst. Biol. 3 (1):1–9, 2009.
URL

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, 2009.
URL

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, 2009.
URL

E Yus, T Maier, K Michalodimitrakis, V Noort, T Yamada, W-H Chen, J A H Wodke, M Güell, S Martínez, R Bourgeois, S Kühner, E Raineri, I Letunic, O V Kalinina, M Rode, R Herrmann, R Gutiérrez-Gallego, R B Russell, A-C Gavin, P Bork and L Serrano.
Impact of genome reduction on bacterial metabolism and its regulation.
Science 326 (5957):1263–1268, 2009.
URL

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, 2010.
URL

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, 2010.
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E Klipp, R C Wade and U Kummer.
Biochemical network-based drug-target prediction.
Curr. Opin. Biotechnol. 21 (4):511–516, 2010.
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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, 2010.
URL

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.
URL

W Liebermeister, J Uhlendorf and E Klipp.
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.
Bioinformatics 26 (12):1528–1534, 2010.
URL

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, 2010.
URL

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, 2010.
URL

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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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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J Schütze and J Wolf.
Spatio-temporal dynamics of glycolysis in cell layers. A mathematical model..
Biosystems 99:104–108, 2010.
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T W Spiesser, C Diener, M Barberis and E Klipp.
What influences DNA replication rate in budding yeast?.
PLoS ONE 5 (4):e10203, 2010.
URL

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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C Waltermann and E Klipp.
Signal integration in budding yeast.
Biochem. Soc. Trans. 38 (5):1257–1264, 2010.
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K Yizhak, T Benyamini, W Liebermeister, E Ruppin and T Shlomi.
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.
Bioinformatics 26 (12):i255–i260, 2010.
URL

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, 2010.
URL

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, 2011.
URL

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, 2011.
URL

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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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.
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A Kowald.
The glyoxalase system as an example of a cellular maintenance pathway with relevance to aging.
Aging 3 (1):17–18, 2011.
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A Kowald and T B L Kirkwood.
Evolution of the mitochondrial fusion-fission cycle and its role in aging.
Proc. Natl. Acad. Sci. USA 108 (25):10237–10242, 2011.
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A Kowald and S Schmeier.
Text mining for systems modeling.
Methods Mol. Biol. 696:305–318, 2011.
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A Kowald and C Wierling.
Standards, tools, and databases for the analysis of yeast 'omics data.
Methods Mol. Biol. 759:345–365, 2011.
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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

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, 2011.
URL

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, 2011.
URL

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, 2011.
URL

J Schütze, T Mair, M J B Hauser, M Falcke and J Wolf.
Metabolic synchronization by traveling waves in yeast cell layers.
Biophys. J. 100 (4):809–813, 2011.
URL

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

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

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, 2011.
URL

C Waltermann and E Klipp.
Information theory based approaches to cellular signaling.
Biochim. Biophys. Acta 1810 (10):924–932, 2011.
URL

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, 2011.
URL

M Barberis.
Molecular systems biology of Sic1 in yeast cell cycle regulation through multiscale modeling.
Adv. Exp. Med. Biol. 736:135–167, 2012.
URL

M Barberis.
Sic1 as a timer of Clb cyclin waves in the yeast cell cycle–design cycle –design principle of not just an inhibitor.
FEBS J. 279 (18):3386–3410, 2012.
URL

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.
URL

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, 2012.
URL

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.
URL

M Flöttmann, T Scharp and E Klipp.
A stochastic model of epigenetic dynamics in somatic cell reprogramming.
Front. Physiol. 3:216, 2012.
URL

G Fuellen, J Dengjel, A Hoeflich, J Hoeijemakers, H A Kestler, A Kowald, S Priebe, D Rebholz-Schuhmann, B Schmeck, U Schmitz, A Stolzing, J Sühnel, D Wuttke and J Vera.
Systems biology and bioinformatics in aging research: a workshop report.
Rejuvenation Res. 15 (6):631–641, 2012.
URL

C Geijer, I Pirkov, W Vongsangnak, A Ericsson, J Nielsen, M Krantz and S Hohmann.
Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response.
BMC Genom. 13:554, 2012.
URL

T Handorf and E Klipp.
Modeling mechanistic biological networks: an advanced Boolean approach.
Bioinformatics 28 (4):557–563, 2012.
URL

M Hoffman-Sommer, A Supady and E Klipp.
Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates.
Front. Physiol. 3:287, 2012.
URL

T B L Kirkwood and A Kowald.
The free-radical theory of ageing–older, wiser and still alive: modelling positional effects of the primary targets of ROS reveals new support.
Bioessays 34 (8):692–700, 2012.
URL

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, 2012.
URL

C Kühn and E Klipp.
Zooming in on yeast osmoadaptation.
Adv. Exp. Med. Biol. 736:293–310, 2012.
URL

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, 2012.
URL

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.
URL

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

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, 2012.
URL

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

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.
URL

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, 2012.
URL

M Schulz, E Klipp and W Liebermeister.
Propagating semantic information in biochemical network models.
BMC Bioinform. 13:18, 2012.
URL

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, 2012.
URL

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, 2012.
URL

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

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, 2013.
URL

C Kühn and P Gennemark.
Modeling yeast osmoadaptation at different levels of resolution.
J. Bioinform. Comput. Biol. 11 (2):1330001, 2013.
URL

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

T Maier, J Marcos, J A H Wodke, B Paetzold, M Liebeke, R Gutiérrez-Gallego and L Serrano.
Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae.
Mol. Biosyst. 9:1743–1755, 2013.
URL

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

M Rother, U Münzner, S Thieme and M Krantz.
Information content and scalability in signal transduction network reconstruction formats.
Mol. Biosyst. 9 (8):1993–2004, 2013.
URL

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

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, 2013.
URL

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

J Ariño, E Aydar, S Drulhe, D Ganser, J Jorrín, M Kahm, F Krause, S Petrezsélyová, L Yenush, O Zimmermannová, G P H Van Heusden, M Kschischo, J Ludwig, C Palmer, J Ramos and H Sychrová.
Systems biology of monovalent cation homeostasis in yeast: the translucent contribution.
Adv. Microb. Physiol. 64:1–63, 2014.
URL

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

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, 2014.
URL

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, 2014.
URL

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, 2014.
URL

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, 2014.
URL

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, 2014.
URL

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, 2014.
URL

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, 2014.
URL

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

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

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

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, 2014.
URL

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, 2014.
URL

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

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, 2014.
URL

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

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

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

P Groth, G Reuter and S Thieme.
Analysis of genomic data in a cloud computing environment.
In B Wang, R Li and W Perrizo (eds.). Big Data Analytics in Bioinformatics and Healthcare. IGI Global, 2015, pages 186-214.
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M Lluch-Senar, J Delgado, W-H Chen, V Lloréns-Rico, F J O'Reilly, J A H Wodke, E B Unal, E Yus, S Martínez, R J Nichols, T Ferrar, A Vivancos, A Schmeisky, J Stülke, V Van Noort, A-C Gavin, P Bork and L Serrano.
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
Mol. Syst. Biol. 11 (1):780, 2015.
URL

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

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

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

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

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

S F Thieme, J L Vahldiek, K Tummler, F Poch, O H Gemeinhardt, B Hiebl, K S Lehmann, B Hamm and S M Niehues.
Value or waste: perfusion imaging following radiofrequency ablation –early experience.
Clin. Hemorheol. Microcirc. 61 (2):323–331, 2015.
URL

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

J A H Wodke, A Alibés, L Cozzuto, A Hermoso, E Yus, M Lluch-Senar, L Serrano and G Roma.
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae.
Nucleic Acids Res. 43 (Database issue):D618–D623, 2015.
URL

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

W-H Chen, V Van Noort, M Lluch-Senar, M L Hennrich, J A H Wodke, E Yus, A Alibés, G Roma, D R Mende, C Pesavento, A Typas, A-C Gavin, L Serrano and P Bork.
Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances.
Nucleic Acids Res. 44 (3):1192–1202, 2016.
URL

M Cvijovic, T Höfer, J Aćimović, L Alberghina, E Almaas, D Besozzi, A Blomberg, T Bretschneider, M Cascante, O Collin, P De Atauri, C Depner, R Dickinson, M Dobrzynski, C Fleck, J Garcia-Ojalvo, D Gonze, J Hahn, H M Hess, S Hollmann, M Krantz, U Kummer, T Lundh, G Martial, V M Dos Santos, A Mauer-Oberthür, B Regierer, B Skene, E Stalidzans, J Stelling, B Teusink, C T Workman and S Hohmann.
Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.
npj Syst. Biol. Appl. 2:16011, 2016.
URL

D Davidi, E Noor, W Liebermeister, A Bar-Even, A Flamholz, K Tummler, U Barenholz, M Goldenfeld, T Shlomi and R Milo.
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.
Proc. Natl. Acad. Sci. U.S.A. 113 (12):3401–3406, 2016.
URL

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

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

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

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

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

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

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

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

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

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

D Waltemath, J R Karr, F T Bergmann, V Chelliah, M Hucka, M Krantz, W Liebermeister, P Mendes, C J Myers, P Pir, B Alaybeyoglu, N K Araganathan, K Baghalian, A T Bittig, P E Pinto Burke, M Cantarelli, Y H Chew, R S Costa, J Cursons, T Czauderna, A P Goldberg, H F Gómez, J Hahn, T Hameri, D F Hernandez Gardiol, D Kazakiewicz, I Kiselev, V Knight-Schrijver, C Knüpfer, M König, D Lee, A Lloret-Villas, N Mandrik, J K Medley, B Moreau, H Naderi-Meshkin, S K Palaniappan, D Priego-Espinosa, M Scharm, M Sharma, K Smallbone, N J Stanford, J-H Song, T Theile, M Tokic, N Tomar, V Touré, J Uhlendorf, T M Varusai, L H Watanabe, F Wendland, M Wolfien, J T Yurkovich, Y Zhu, A Zardilis, A Zhukova and F Schreiber.
Toward community standards and software for whole-cell modeling.
IEEE Trans. Biomed. Eng. 63 (10):2007–2014, 2016.
URL

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

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

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, 2017.
URL

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

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

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

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

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.
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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.
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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, 2018.
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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, 2018.
URL

Giese W, Milicic G, Schröder A and Klipp E..
Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction..
PLoS Comput. Biol. 14(4)(4):1-27, 2018.
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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.
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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, 2018.
URL

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

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

Andrea Auconi, Andrea Giansanti and Edda Klipp.
Information Thermodynamics for Time Series of Signal-Response Models.
Entropy 21(2), 2019.
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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.
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Maria Krantz and Edda Klipp.
Moonlighting proteins -an approach to systematize the concept..
In silico biology, 2019.
URL, DOI

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, 2019.
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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

Friedemann Uschner and Edda Klipp.
Signaling pathways in context.
Curr. Opin. Syst. Biol. 58:155-160, 2019.
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Stephan O Adler and Edda Klipp.
Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality..
Entropy (Basel, Switzerland) 22, 2020.
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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, 2020.
URL, DOI

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

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

Jesper Romers, Sebastian Thieme, Ulrike Münzner and Marcus Krantz.
A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models..
NPJ systems biology and applications 6:2, 2020.
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