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Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Shimobayashi, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

Sarraf-Zadeh, Ladan; Christen, Stefan; Sauer, Uwe; Cognigni, Paola; Miguel-Aliaga, Irene; Stocker, Hugo; Köhler, Katja; Hafen, Ernst (2013). Local requirement of the Drosophila insulin binding protein imp-L2 in coordinating developmental progression with nutritional conditions. Developmental Biology, 381(1):97-106.

Busetto, Alberto Giovanni; Hauser, Alain; Krummenacher, Gabriel; Sunnåker, Mikael; Dimopoulos, Sotiris; Ong, Cheng Soon; Stelling, Jörg; Buhmann, Joachim M (2013). Near-optimal experimental design for model selection in systems biology. Bioinformatics:online.

Zampar, Guillermo G; Kümmel, Anne; Ewald, Jennifer; Jol, Stefan; Niebel, Bastian; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2013). Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Molecular Systems Biology, 9:651.


Mülleder, Michael; Capuano, Floriana; Pir, Pınar; Christen, Stefan; Sauer, Uwe; Oliver, Stephen G; Ralser, Markus (2012). A prototrophic deletion mutant collection for yeast metabolomics and systems biology. Nature Biotechnology, 30(12):1176-1178.

Gonnet, Pedro; Dimopoulos, Sotiris; Widmer, Lukas; Stelling, Jörg (2012). A specialized ODE integrator for the efficient computation of parameter sensitivities. BMC Systems Biology, 6:46.

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Pelet, Serge; Dechant, Reinhard; Lee, Sung Sik; van Drogen, Frank; Peter, Matthias (2012). An integrated image analysis platform to quantify signal transduction in single cells. Integrative Biology, 4:1274-82.

Lee, Sung Sik; Horvath, Peter; Pelet, Serge; Hegemann, Björn; Lee, Luke P; Peter, Matthias (2012). Quantitative and dynamic assay of single cell chemotaxis. Integrative Biology, 4(4):381.

Oliveira, Ana Paula; Ludwig, Christina; Picotti, Paola; Kogadeeva, Maria; Aebersold, Ruedi; Sauer, Uwe (2012). Regulation of yeast central metabolism by enzyme phosphorylation. Molecular Systems Biology, 8:online.

Jol, Stefan J; Kümmel, Anne; Terzer, Marco; Stelling, Jörg; Heinemann, Matthias (2012). System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. PLoS Computational Biology, 8(3):e1002415.

Lee, S S; Vizcarra, I A; Huberts, D H E W; Lee, L P; Heinemann, M (2012). Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform. Proceedings of the National Academy of Sciences of the United States of America, 109(13):4916-4920.


Loewith, Robbie; Hall, Michael N (2011). Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control. Genetics, 189:1177 -1201.

Zamora-Sillero, E; Hafner, M; Ibig, A; Stelling, J; Wagner, A (2011). Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Systems Biology, 5:142.

Raman, K; Wagner, A (2011). Evolvability and robustness in a complex signalling circuit. Molecular BioSystems, 7(4):1081-1092.

Zinzalla, Vittoria; Stracka, Daniele; Oppliger, Wolfgang; Hall, Michael N (2011). Activation of mTORC2 by Association with the Ribosome. Cell, 144:757-768.

Huberts, Daphne H E W; Niebel, Bastian; Heinemann, Matthias (2011). A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Research, 12(2):118-128.

Costenoble, Roeland; Picotti, Paola; Reiter, Lukas; Stallmach, Robert; Heinemann, Matthias; Sauer, Uwe; Aebersold, Ruedi (2011). Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology, 7:464.

Pelet, Serge; Peter, Matthias (2011). Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells. In: Koeppl, Heinz; Densmore, Douglas; Setti, Gianluca; di Bernardo, Mario. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology. New York, USA: Springer, 369-394.

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.


Milias-Argeitis, Andreas; Porreca, Riccardo; Summers, Sean; Lygeros, John (2010). Bayesian model selection for the yeast GATA-factor network: a comparison of computational approaches. In: 49th IEEE Conference on Decision and Control, Atlanta, GA, 15 December 2010 - 17 December 2010, 3379-84.

Porreca, Riccardo; Cinquemani, Eugenio; Lygeros, John; Ferrari-Trecate, Giancarlo (2010). Structural identification of unate-like genetic network models from time-lapse protein concentration measurements. In: 49th IEEE Conference on Decision and Control, Atlanta, GA, 15 December 2010 - 17 December 2010, 2529-34.

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. The EMBO Journal, 29(15):2515-2526.

Kümmel, Anne; Ewald, Jennifer Christina; Fendt, Sarah-Maria; Jol, Stefan Jasper; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2010). Differential glucose repression in common yeast strains in response to HXK2 deletion. FEMS Yeast Research, 10(3):322-332.

Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias (2010). Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks. Biophysical Journal, 99(10):3139-3144.

Fendt, Sarah-Maria; Buescher, Joerg Martin; Rudroff, Florian; Picotti, Paola; Zamboni, Nicola; Sauer, Uwe (2010). Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Molecular Systems Biology, 6:356.

Fendt, Sarah-Maria; Sauer, Uwe (2010). Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates. BMC Systems Biology, 4(1):12.

Fendt, Sarah-Maria; Oliveira, Ana Paula; Christen, Stefan; Picotti, Paola; Dechant, Reinhard Christoph; Sauer, Uwe (2010). Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Molecular Systems Biology, 6:432.


Cinquemani, Eugenio; Porreca, Riccardo; Lygeros, John; Ferrari-Trecate, Giancarlo (2009). Canalizing structure of genetic network dynamics: modelling and identification via mixed-integer programming. In: Combined 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference, Shanghai, 15 December 2009 - 18 December 2009, 5618-23.

Bragg, J G; Wagner, A (2009). Protein material costs: single atoms can make an evolutionary difference. Trends in Genetics, 25(1):5-8.

Hafner, M; Koeppl, H; Hasler, M; Wagner, A (2009). 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biology, 5(10):e1000534.

Kotte, Oliver; Heinemann, Matthias (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4):519-525.


Ferrada, E; Wagner, A (2008). Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proceedings of the Royal Society B: Biological Sciences, 275(1643):1595-1602.

Wright, J; Wagner, A (2008). The Systems Biology Research Tool: evolvable open-source software. BMC Systems Biology, 2:55.

Wagner, A (2008). Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B: Biological Sciences, 275(1630):91-100.

Wagner, A (2008). Neutralism and selectionism: a network-based reconciliation. Nature Reviews. Genetics, 9(12):965-974.

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

This list was generated on Tue Jul 23 23:21:00 2024 CEST.