Journal Article (736)

2014
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Lohr, V.; Hädicke, O.; Genzel, Y.; Jordan, I.; Buentemeyer, H.; Klamt, S.; Reichl, U.: The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnology 14, p. 72 (2014)
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Lorenz, H.; Seidel-Morgenstern, A.: Processes To Separate Enantiomers. Angewandte Chemie International Edition 53 (5), pp. 1218 - 1250 (2014)
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Mangold, M.; Khlopov, D.; Danker, G.; Palis, S.; Svjantyj, V.; Kienle, A.: Development and Nonlinear Analysis of Dynamic Plant Models in ProMoT /Diana. Chemie Ingenieur Technik 86 (7), pp. 1107 - 1116 (2014)
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Orthaber, A.; Karnahl, M.; Tschierlei, S.; Streich, D.; Stein, M.; Ott, S.: Coordination and conformational isomers in mononuclear iron complexes with pertinence to the [FeFe] hydrogenase active site. Dalton Transactions 43, pp. 4537 - 4549 (2014)
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Qamar, S.; Abbasi, J. N.; Javeed, S.; Seidel-Morgenstern, A.: Analytical solutions and moment analysis of general rate model for linear liquid chromatography. Chemical Engineering Science 107, pp. 192 - 205 (2014)
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Qamar, S.; Bibi, S.; Khan, F. U.; Shah, M.; Javeed, S.; Seidel-Morgenstern, A.: Irreversible and Reversible Reactions in a Liquid Chromatographic Column: Analytical Solutions and Moment Analysis. Industrial and Engineering Chemistry Research 53 (6), pp. 2461 - 2472 (2014)
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Qamar, S.; Khan, . U.; Mehmood, Y.; Seidel-Morgenstern, A.: Analytical solution of a two-dimensional model of liquid chromatography including moment analysis. Chemical Engineering Science 116, pp. 576 - 589 (2014)
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Rehberg, M.; Rath, A.; Ritter, J.; Genzel, Y.; Reichl, U.: Changes in intracellular metabolite pools during growth of adherent MDCK cells in two different media. Applied Microbiology and Biotechnology 98 (1), pp. 385 - 397 (2014)
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Rehberg, M.; Ritter, J.; Reichl, U.: Glycolysis Is Governed by Growth Regime and Simple Enzyme Regulation in Adherent MDCK Cells. PLoS Computational Biology 10 (10), p. e1003885 (2014)
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Rüger, M.; Ackermann, M.; Reichl, U.: Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry. BMC Microbiology 14, p. 56 - 56 (2014)
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Schaber, J.; Lapytsko, A.; Flockerzi, D.: Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. Interface: Journal of the Royal Society 11 (91), p. 20130971 (2014)
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Seel, T.; Raisch, J.; Schauer, T.: IMU-based joint angle measurement for gait analysis. Sensors 14 (4), pp. 6891 - 6909 (2014)
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Steinsiek, S.; Stagge, S.; Bettenbrock, K.: Analysis of Escherichia coli Mutants with a Linear Respiratory Chain. PLoS One 9 (1), p. e87307 (2014)
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Straube, R.: Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase. PLoS Computational Biology 10 (5), p. e1003614 (2014)
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Varničić, M.; Bettenbrock, K.; Hermsdorf, D.; Vidaković-Koch, T.; Sundmacher, K.: Combined electrochemical and microscopic study of porous enzymatic electrodes with direct electron transfer mechanism. RSC Advances 4 (69), pp. 36471 - 36479 (2014)
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York, W.S.; Agravat, S.; Aoki-Kinoshita, K.F.; Mcbride, R.; Campell, F.; Castello, C.E.; Dell, A.; Feizi, T.; Haslam, S.M.; Karlsson, N. et al.; Khoo, K.-H.; Kolarich, D.; Liu, Y.; Novotny, M.; Packer, N.H.; Paulson, J.C.; Rapp, E.; Ranzinger, R.; Rudd, P.M.; Smith, D.F.; Struwe, W.B.; Tiemeyer, M.; Wells, L.; Zaia, J.; Kettner, C.: MIRAGE: The minimum information required for a glycomics experiment. Glycobiology 24 (5), pp. 402 - 406 (2014)
2013
Journal Article
Bakovic, M.P.; Selman, M.H.J.; Hoffmann, M.; Rudan, I.; Campbell, H.; Deelder, A.M.; Lauc, G.; Wuhrer, M.: High-Throughput IgG Fc N-Glycosylation Profiling by Mass Spectrometry of Glycopeptides. Journal of Proteome Research 12 (2), pp. 821 - 831 (2013)
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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 (5 - Special Section: 2012 Copper Mountain Conference), 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), p. 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, p. 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, p. 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), p. 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), p. 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), p. 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)
Journal Article
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), p. 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, p. 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), p. 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), p. e7541 (2013)
2012
Journal Article
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-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, p. 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, p. 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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