OA Publications of the Max Planck Institute

Max Planck Institute for Dynamics of Complex Technical Systems

Journal Article (1119)

2013

Journal Article

Behne, A.; Muth, T.; Borowiak, M.; Reichl, U.; Rapp, E.: glyXalign: High-throughput migration time alignment preprocessing of electrophoretic data retrieved via multiplexed capillary gel electrophoresis with laser-induced fluorescence detection-based glycoprofiling. Electrophoresis 34 (16), pp. 2311 - 2315 (2013)

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Benner, P.; Ezzatti, P.; Mena, H.; Quintana-Ortí, E. S.; Remón, A.: Solving Matrix Equations on Multi-Core and Many-Core Architectures. Algorithms 6 (4), pp. 857 - 870 (2013)

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Benner, P.; Saak, J.; Stoll, M.; Weichelt, H. K.: Efficient Solution of Large-Scale Saddle Point Systems Arising in Riccati-Based Boundary Feedback Stabilization of Incompressible Stokes Flow. SIAM Journal on Scientific Computing 35 , pp. S150 - S170 (2013)

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Borchers, S.; Freund, S.; Rath, A.; Streif, S.; Reichl, U.; Findeisen, R.: Identification of Growth Phases and Influencing Factors in Cultivations with AGE1.HN Cells Using Set-Based Methods. PLoS One 8 (8), e68124 (2013)

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Carius, L.; Carius, A. B.; McIntosh, M.; Grammel, H.: Quorum sensing influences growth and photosynthetic membrane production in high-cell-density cultivations of Rhodospirillum rubrum. BMC Microbiology 13, 189 (2013)

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Chaoiya, C.; Berenguier, D.; Keating, S. M.; Naldi, A.; van Iersel, M. P.; Rodriguez, N.; Dräger, A.; Büchel, F.; Cokelaer, T.; Kowal, B. et al.; Wicks, B.; Gonçalves, E.; Dorier, J.; Page, M.; Monteiro, P. T.; Kamp von, A.; Xenarius , I.; de Jong, H.; Hucka, M.; Klamt, S.; Thieffrey, D.; Le Novère, N.; Saez-Rodriguez, J.; Helikar, T.: SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formlisms and tools. BMC Systems Biology 7, 135 (2013)

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Frensing, T.; Heldt, S.; Pflugmacher, A.; Behrendt, I.; Jordan, I.; Flockerzi, D.; Genzel, Y.; Reichl, U.: Continuous Influenza Virus Production in Cell Culture Shows a Periodic Accumulation of Defective Interfering Particles. PLoS One 8 (9), e72288 (2013)

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Gonçalves, E.; Bucher, J.; Ryll, A.; Niklas, J.; Mauch, K.; Klamt, S.; Rocha, M.; Saez-Rodriguez, J.: Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems 9 (7), pp. 1576 - 1583 (2013)

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Gruchattka, E.; Hädicke, O.; Klamt, S.; Schuetz, V.; Kayser , O.: In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microbial Cell Factories 12, 84 (2013)

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Heldt, S.; Frensing, T.; Pflugmacher, A.; Gröpler, R.; Peschel, B.; Reichl, U.: Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals. PLoS Computational Biology 9 (11), e1003372 (2013)

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Jordan, I.; Lohr, V.; Genzel, Y.; Reichl, U.; Sandig, V.: Elements in the Development of a Production Process for Modified Vaccinia Virus Ankara. Microorganisms 1 (1), pp. 100 - 121 (2013)

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Jungreuthmeyer, C.; Nair, G.; Klamt, S.; Zanghellini, J.: Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14 (1), 318 (2013)

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Kolarich, D.; Rapp, E.; Struwe, W. B.; Haslam, S. M.; Zaia, J.; McBride, R.; Agravat, S.; Campell, M. P.; Kato, M.; Ranzinger, R. et al.; Kettner, C.; York, W. S.: The Minimum Information Required for a Glycomics Experiment (MIRAGE) Project: Improving the Standards for Reporting Mass-spectrometry-based Glycoanalytic Data. Molecular and Cellular Proteomics 12 (4), pp. 991 - 995 (2013)

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Kottler, R.; Mank, M.; Hennig, R.; Müller-Werner, B.; Stahl, B.; Reichl, U.; Rapp, E.: Development of a high-throughput glycoanalysis method for the characterization of oligosaccharides in human milk utilizing multiplexed capillary gel electrophoresis with laser-induced fluorescence detection. Electrophoresis 34 (16), pp. 2323 - 2336 (2013)

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Melas, I. N.; Samaga, R.; Alexopoulos, L. G.; Klamt, S.: Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. PLoS Computational Biology 9 (9), e1003204 (2013)

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Muth, T.; Benndorf, D.; Reichl, U.; Rapp, E.; Martens, L.: Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Molecular BioSystems 9 (4), pp. 578 - 585 (2013)

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Pearson, J. W.; Stoll, M.: Fast Iterative Solution of Reaction-Diffusion Control Problems Arising from Chemical Processes. SIAM Journal on Scientific Computing 35 (5), pp. B987 - B1009 (2013)

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Pinna, A.; Heise, S.; Flassig, R.; de la Fuente, A.; Klamt, S.: Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. BMC Systems Biology 7, 73 (2013)

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Rodriguez-Fernandez, M.; Rehberg, M.; Kremling, A.; Banga, J. R.: Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Systems Biology 7, 76 (2013)

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Samaga, R.; Klamt, S.: Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Communication and Signaling 11 (1), 43 (2013)

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Sharma, P.; Stagge, S.; Bekker, M.; Bettenbrock, K.; Hellingwerf, K. J.: Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone. PLoS One 8 (10), e7541 (2013)

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2012

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Benner, P.; Breiten, T.: Interpolation-Based H₂-Model Reduction of Bilinear Control Systems. SIAM Journal on Matrix Analysis and Applications 33 (3), pp. 859 - 885 (2012)

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Benner, P.; Mach, T.: Computing All or Some Eigenvalues of Symmetric ℋ_ℓ-Matrices. SIAM Journal on Scientific Computing 34 (1), pp. A485 - A496 (2012)

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Conradi, C.; Flockerzi, D.: Switching in mass action networks based on linear inequalities. SIAM Journal on Applied Dynamical Systems 11 (1), pp. 110 - 134 (2012)

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Flassig, R.; Sundmacher, K.: Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks. Bioinformatics 28 (23), pp. 3089 - 3096 (2012)

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Kolczyk, K.; Samaga, R.; Conzelmann, H.; Mirschel, S.; Conradi, C.: The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics 13, 251 (2012)

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Kremling, A.; Goehler, A.; Jahreis, K.; Nees, M.; Auerbach, B.; Schmidt-Heck, W.; Kökpinar, Ö.; Geffers, R.; Rinas, U.; Bettenbrock, K.: Analysis and Design of Stimulus Response Curves of E. coli. Metabolites 2 (4), pp. 844 - 871 (2012)

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Lohr, V.; Genzel, Y.; Jordan, I.; Katinger, D.; Mahr, S.; Sandig, V.; Reichl, U.: Live attenuated influenza viruses produced in a suspension process with avian AGE1.CR.pIX cells. BMC Biotechnology 12, 79 (2012)

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Mangold, M.; Krasnyk, M.: Modellreduktion von Populationssystemen mit Hilfe von Proper Orthogonal Decomposition. At-Automatisierungstechnik 60 (9), pp. 561 - 573 (2012)

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Palis, S.; Kienle, A.: Diskrepanzbasierte Regelung der kontinuierlichen Kristallisation. at - Automatisierungstechnik 60 (3), pp. 145 - 154 (2012)

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Pandelia, M.-E.; Infossi, P.; Stein, M.; Guidici-Orticoni, M.-T.; Lubitz, W.: Spectroscopic characterization of the key catalytic intermediate Ni-C in the O₂-tolerant [NiFe] hydrogenase I from Aquifex aeolicus: evidence of a weakly bound hydride. Chemical Communications 48 (6), pp. 823 - 825 (2012)

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Pearson, J. W.; Stoll, M.; Wathen, A. J.: Regularization-Robust Preconditioners for Time-Dependent PDE-Constrained Optimization Problems. SIAM Journal on Matrix Analysis and Applications 33 (4), pp. 1126 - 1152 (2012)

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Popov, M.; Nacheva, G.; Reichl, U.; Ivanov, I.: Effect of the 3’-terminal truncation of the human interferon-gamma gene on plasmid segregation in escherichia coli. Biotechnology and Biotechnological Equipment 26 (2), pp. 2930 - 2936 (2012)

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Sommer, S.; Kienle, A.: Auto-Tuning of Multivariable PID Controllers Using Iterative Feedback Tuning. at - Automatisierungstechnik 60 (1), pp. 20 - 27 (2012)

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Stein, M.; Pilli, M.; Bernauer, S.; Habermann, B. H.; Zerial, M.; Wade, R. C.: The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity. PLoS ONE 7 (4), e34870 (2012)

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Vidaković-Koch, T.; González Martinez, I.; Kuwertz, R.; Kunz, U.; Turek, T.; Sundmacher, K.: Electrochemical Membrane Reactors for Sustainable Chlorine Recycling. Membranes 2 (3), pp. 510 - 528 (2012)

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Yu, E.H.; Wang, Y.; Krewer, U.; Li, L.; Scott, K.: Direct oxidation alkaline fuel cells: from materials to systems. Energy & Environmental Science 5 (2), pp. 5668 - 5680 (2012)

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2011

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Baur, U.; Beattie, C.; Benner, P.; Gugercin, S.: Interpolatory Projection Methods for Parameterized Model Reduction. SIAM Journal on Scientific Computing 33 (5), pp. 2489 - 2518 (2011)

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Benner, P.; Damm, T.: Lyapunov Equations, Energy Functionals, and Model Order Reduction of Bilinear and Stochastic Systems. SIAM Journal on Control and Optimization 49 (2), pp. 686 - 711 (2011)

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Chen, L.; Zhou, T.; Chen, L.; Ye, Y.; Qi, Z.; Freund, H.; Sundmacher, K.: Selective Oxidation of Cyclohexanol to Cyclohexanone in the Ionic Liquid 1-Octyl-3-Methylimidazolium Chloride. Chemical Communications 47 (33), pp. 9354 - 9356 (2011)

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Hädicke, O.; Grammel, H.; Klamt, S.: Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. BMC Systems Biology 5, 150 (2011)

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Hamel, C.; Wolff, T.; Seidel-Morgenstern, A.: Compatibility of Transport and Reaction in Membrane Reactors Used for the Oxidative Dehydrogenation of Short-Chain Hydrocarbons. International Journal of Chemical Reactor Engineering 9, A12 (2011)

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Kolvenbach, B. A.; Lenz, M.; Benndorf, D.; Rapp, E.; Fousek, J.; Vlcek, C.; Schäffer, A.; Gabriel, F. L.; Kohler, H.-P. E.; Corvini, P. F.: Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3. AMB Express 1, 8 (2011)

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Lu, H.; Rihko-Struckmann, L.; Sundmacher, K.: Spontaneous oscillations of cell voltage, power density, and anode exit CO concentration in a PEM fuel cell. Physical Chemistry Chemical Physics 13 (40), pp. 18179 - 18185 (2011)

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Petiot, E.; Jacob, D.; Lanthier, S.; Lohr, V.; Ansorge, S.; Kamen, A. A.: Metabolic and Kinetic analyses of influenza production in perfusion HEK293 cell culture. BMC Biotechnology 11, 84 (2011)

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Popov, M.; Petrov, S. A.; Nacheva, G.; Ivanov, I.; Reichl, U.: Effects of a recombinant gene expression on ColE1-like plasmid segregation in Escherichia coli. BMC Biotechnology 11, 18 (2011)

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Roedig, J.; Rapp, E.; Höper, D.; Genzel, Y.; Reichl, U.: Impact of Host Cell Line Adaptation on Quasispecies Composition and Glycosylation of Influenza A Virus Hemagglutinin. PLoS One 6 (12), e27989 (2011)

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Ryll, A.; Samaga, R.; Schaper, F.; Alexopoulos, L.G.; Klamt, S.: Large-scale models of IL-1 and IL-6 signaling and their hepatocellular specification. Molecular BioSystems 7 (12), pp. 3253 - 3270 (2011)

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Shalaby, R.; Schauer, T.; Liedecke, W.; Raisch, J.: Amplifier design for EMG recording from stimulation electrodes during functional electrical stimulation leg cycling ergometry. Biomedizinische Technik 56 (1), pp. 23 - 33 (2011)

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Zenith, F.; Krewer, U.: Simple and reliable model for estimation of methanol cross-over in direct methanol fuel cells and its application on methanol-concentration control. Energy & Environmental Science 4 (2), pp. 519 - 527 (2011)

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