OA Publications of the Max Planck Institute

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

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)

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)

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)

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)

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)

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)

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)

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

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)

Benner, P.: Balancing-Related Model Reduction for Parabolic Control Systems. 1st IFAC Workshop on Control of Systems Governed by Partial Differential Equations - CPDE 2013, Paris, France, September 25, 2013 - September 27, 2013. IFAC Proceedings Volumes 46 (26), pp. 257 - 262 (2013)

Benner, P.; Stoll, M.: Optimal Control for Allen-Cahn Equations Enhanced by Model Predictive Control. 1st IFAC Workshop on Control of Systems Governed by Partial Differential Equations - CPDE 2013, Paris, France, September 25, 2013 - September 27, 2013. IFAC Proceedings Volumes 46 (26), pp. 139 - 143 (2013)

Palis, S.; Bück, A.; Kienle, A.: Adaptive Discrepancy Based Control of Continuous Fluidized Bed Spray Granulation with Internal Classification. 9th IFAC Symposium on Nonlinear Control Systems, 2013, Toulouse, September 04, 2013 - September 06, 2013. IFAC Proceedings Volumes 46 (23), pp. 400 - 405 (2013)

Palis, S.; Kienle, A.; Bück, A.: Discrepancy based control of systems of population balances. 1st IFAC Workshop on Control of Systems Governed by Partial Differential Equations - CPDE 2013, Paris, France, September 25, 2013 - September 27, 2013. IFAC Proceedings Volumes 46 (26), pp. 172 - 176 (2013)

Rehberg, M.; Wetzel, M.; Ritter, J.; Reichl, U.: The Regulation of Glutaminolysis and Citric Acid Cycle Activity During Mammalian Cell Cultivation. 12th IFAC Symposium on Computer Applications in Biotechnology - CAB 2013, Mumbai, India, December 16, 2013 - December 18, 2013. IFAC Proceedings Volumes 46 (31), pp. 48 - 53 (2013)

Zhang, J.-H.; Raisch, J.: Hybrid-Data-Driven Fuzzy Recognition of Operator Cognitive State in Human-Machine Cooperative Control System. 13th IFAC Symposium on Large Scale Complex Systems: Theory and Applications, 2013, Shanghai Jiao Tong University, Shanghai, China, July 07, 2013 - July 10, 2013. IFAC Proceedings Volumes 46 (13), pp. 327 - 334 (2013)