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Niebel, B., Leupold, S., & Heinemann, M. (2019). An upper limit on Gibbs energy dissipation governs cellular metabolism. Nature Metabolism, 1, 125-131.


Kimkes, T. E. P., & Heinemann, M. (2018). Reassessing the role of the Escherichia coli CpxAR system in sensing surface contact. PLoS ONE, 13(11), [e0207181].
Takhaveev, V., & Heinemann, M. (2018). Metabolic heterogeneity in clonal microbial populations. Current Opinion in Microbiology, 45, 30-38.
Bley Folly, B., Ortega, A. D., Hubmann, G., Bonsing-Vedelaar, S., Wijma, H. J., van der Meulen, P., ... Heinemann, M. (2018). Assessment of the interaction between the flux-signaling metabolite fructose-1,6-bisphosphate and the bacterial transcription factors CggR and Cra. Molecular Microbiology, 109(3), 278-290.
von Borzyskowski, L. S., Carrillo, M., Leupold, S., Glatter, T., Kiefer, P., Weishaupt, R., ... Erb, T. J. (2018). An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metabolic Engineering, 47, 423-433.
Litsios, A., Ortega, Á. D., Wit, E. C., & Heinemann, M. (2018). Metabolic-flux dependent regulation of microbial physiology. Current Opinion in Microbiology, 42, 71-78.
Zhang, Z., Milias-Argeitis, A., & Heinemann, M. (2018). Dynamic single-cell NAD(P)H measurement reveals oscillatory metabolism throughout the E. coli cell division cycle. Scientific Reports, 8(1), [2162].
Garcia, H. G., Benzinger, D., Rullan, M., Milias-Argeitis, A., Khammash, M., Deutschbauer, A. M., ... Gladfelter, A. S. (2018). Principles of Systems Biology, No. 30. Cell systems, 7(1), 1-2.
Rullan, M., Benzinger, D., Schmidt, G. W., Milias-Argeitis, A., & Khammash, M. (2018). An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation. Molecular Cell, 70(4), 745-756.e6.
Milias Argeitis, A., & Kurdyaeva, T. (2018). Analytical calculation of Sobol sensitivity indices for Gaussian Processes with a squared exponential covariance function.


Filer, D., Thompson, M. A., Takhaveev, V., Dobson, A. J., Kotronaki, I., Green, J. W. M., ... Alic, N. (2017). RNA polymerase III limits longevity downstream of TORC1. Nature, 552(7684), 263-267.
Papagiannakis, A., Niebel, B., Wit, E., & Heinemann, M. (2017). A CDK-independent metabolic oscillator orchestrates the budding yeast cell cycle. Febs Journal, 284(S1), 54. [S.5.4-002].
Heinemann, M., & Pilpel, Y. (2017). Editorial overview: Systems biology for biotechnology. Current Opinion in Biotechnology, 46, iv-v.
Papagiannakis, A., de Jonge, J. J., Zhang, Z., & Heinemann, M. (2017). Quantitative characterization of the auxin-inducible degron: a guide for dynamic protein depletion in single yeast cells. Scientific Reports, 7, [4704].
Papagiannakis, A., Niebel, B., Wit, E. C., & Heinemann, M. (2017). Autonomous Metabolic Oscillations Robustly Gate the Early and Late Cell Cycle. Molecular Cell, 65(2), 285-295.
Radzikowski, J. L., Schramke, H., & Heinemann, M. (2017). Bacterial persistence from a system-level perspective. Current Opinion in Biotechnology, 46, 98-105.
Kuzmanovska, I., Milias Argeitis, A., Mikelson, J., Zechner, C., & Khammash, M. (2017). Parameter inference for stochastic single-cell dynamics from lineage tree data. BMC Systems Biology, 11(52), [52].


Radzikowski, J. L., Vedelaar, S., Siegel, D., Ortega, Á. D., Schmidt, A., & Heinemann, M. (2016). Bacterial persistence is an active σS stress response to metabolic flux limitation. Molecular Systems Biology, 12(9), 1-18. [882].
van Rijsewijk, B. R. B. H., Kochanowski, K., Heinemann, M., & Sauer, U. (2016). Distinct transcriptional regulation of the two Escherichia coli transhydrogenases PntAB and UdhA. Microbiology-Reading, 162(9), 1672-1679.
Heinemann, M. (2016). Flux Controls Flux – a Key Challenge for Metabolic Engineering. Chemie-Ingenieur-Technik, 88(9).
Schmidt, A., Kochanowski, K., Vedelaar, S., Ahrné, E., Volkmer, B., Callipo, L., ... Heinemann, M. (2016). The quantitative and condition-dependent Escherichia coli proteome. Nature Biotechnology, 34(1), 104-110.
Milias-Argeitis, A., Oliveira, A. P., Gerosa, L., Falter, L., Sauer, U., & Lygeros, J. (2016). Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection. PLoS Computational Biology, 12(3), 1-27. [e1004784].
Milias-Argeitis, A., & Khammash, M. (2016). Adaptive Model Predictive Control of an optogenetic system. In 2015 54th IEEE Conference on Decision and Control, CDC 2015 (Vol. 2016-February, pp. 1265-1270). [7402385] Institute of Electrical and Electronics Engineers Inc..
Milias-Argeitis, A., Rullan, M., Aoki, S. K., Buchmann, P., & Khammash, M. (2016). Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. Nature Communications, 7, [12546].


Janssens, G. E., Meinema, A. C., Gonzalez, J., Wolters, J. C., Schmidt, A., Guryev, V., ... Heinemann, M. (2015). Protein biogenesis machinery is a driver of replicative aging in yeast. eLife, 4, [e08527].
Milias-Argeitis, A., & Khammash, M. (2015). Optimization-based Lyapunov function construction for continuous-time Markov chains with affine transition rates. In Proceedings of the IEEE Conference on Decision and Control (pp. 4617-4622). (Proceedings of the IEEE Conference on Decision and Control; Vol. 2015-February). Institute of Electrical and Electronics Engineers Inc..
Ruess, J., Parise, F., Milias-Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. Proceedings of the National Academy of Sciences, 112(26), 8148-8153.
Milias-Argeitis, A., Engblom, S., Bauer, P., & Khammash, M. (2015). Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks. Journal of the Royal Society Interface, 12, 1-32.


Daszczuk, A., Dessalegne, Y., Drenth, I., Hendriks, E., Jo, E., van Lente, T., ... Veening, J-W. (2014). Bacillus subtilis Biosensor Engineered To Assess Meat Spoilage. ACS Synthetic Biology, 3(12), 999-1002.
Huberts, D. H. E. W., Gonzalez Hernandez, J., Lee, S. S., Litsios, A., Hubmann, G., Wit, E. C., & Heinemann, M. (2014). Calorie restriction does not elicit a robust extension of replicative lifespan in Saccharomyces cerevisiae. Proceedings of the National Academy of Science of the United States of America, 111(32), 11727-11731.
Kotte, O., Volkmer, B., Radzikowski, J. L., & Heinemann, M. (2014). Phenotypic bistability in Escherichia coli's central carbon metabolism. Molecular Systems Biology, 10(7), [736].
Milias-Argeitis, A., Lygeros, J., & Khammash, M. (2014). Fast variance reduction for steady-state simulation and sensitivity analysis of stochastic chemical systems using shadow function estimators. Journal of Chemical Physics, 141(2), [024104].


Huberts, D. H. E. W., Janssens, G. E., Lee, S. S., Vizcarra, I. A., & Heinemann, M. (2013). Continuous High-resolution Microscopic Observation of Replicative Aging in Budding Yeast. Journal of visualized experiments : JoVE, (78), [50143].
Huberts, D. H. E. W., Sik Lee, S., Gonzáles, J., Janssens, G. E., Vizcarra, I. A., & Heinemann, M. (2013). Construction and use of a microfluidic dissection platform for long-term imaging of cellular processes in budding yeast. Nature protocols, 8(6), 1019-1027.
Ibáñez, A. J., Fagerer, S. R., Schmidt, A. M., Urban, P. L., Jefimovs, K., Geiger, P., ... Zenobi, R. (2013). Mass spectrometry-based metabolomics of single yeast cells. Proceedings of the National Academy of Sciences of the United States of America, 110(22), 8790-8794.
Gerosa, L., Kochanowski, K., Heinemann, M., & Sauer, U. (2013). Dissecting specific and global transcriptional regulation of bacterial gene expression. Molecular Systems Biology, 9, [658].
Zampar, G. G., Kümmel, A., Ewald, J., Jol, S., Niebel, B., Picotti, P., ... Heinemann, M. (2013). Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Molecular Systems Biology, 9, 651-1-651-13. [651].
Kochanowski, K., Volkmer, B., Gerosa, L., Haverkorn van Rijsewijk, B. R., Schmidt, A., & Heinemann, M. (2013). Functioning of a metabolic flux sensor in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 110(3), 1130-1135.
Ruess, J., Milias-Argeitis, A., & Lygeros, J. (2013). Designing experiments to understand the variability in biochemical reaction networks. Journal of the Royal Society Interface, 10(88), 20130588.
Milias-Argeitis, A., & Lygeros, J. (2013). Steady-state simulation of metastable stochastic chemical systems. Journal of Chemical Physics, 138(18), [184109].
Esfahani, P. M., Milias-Argeitis, A., & Chatterjee, D. (2013). Analysis of controlled biological switches via stochastic motion planning. In 2013 European Control Conference, ECC 2013 (pp. 93-98). [6669626]


Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters. PLoS Computational Biology, 8(7), [e1002575].
Schuetz, R., Zamboni, N., Zampieri, M., Heinemann, M., & Sauer, U. (2012). Multidimensional optimality of microbial metabolism. Science, 336(6081), 601-604.
Lee, S. S., Avalos Vizcarra, I., 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.
Jol, S. J., Kümmel, A., Terzer, M., Stelling, J., & Heinemann, M. (2012). System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PLoS Computational Biology, 8(3), [e1002415].
Huberts, D. H. E. W., Niebel, B., & Heinemann, M. (2012). A flux-sensing mechanism could regulate the switch between respiration and fermentation. Fems Yeast Research, 12(2), 118-128.


Urban, P. L., Schmidt, A. M., Fagerer, S. R., Amantonico, A., Ibañez, A., Jefimovs, K., ... Zenobi, R. (2011). Carbon-13 labelling strategy for studying the ATP metabolism in individual yeast cells by micro-arrays for mass spectrometry. Molecular BioSystems, 7(10), 2837-2840.
Volkmer, B., & Heinemann, M. (2011). Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling. PLoS ONE, 6(7), [23126].
Sturm, A., Heinemann, M., Arnoldini, M., Benecke, A., Ackermann, M., Benz, M., ... Hardt, W-D. (2011). The cost of virulence: retarded growth of Salmonella Typhimurium cells expressing type III secretion system 1. PLoS Pathogens, 7(7), [1002143].
Bujara, M., Schümperli, M., Pellaux, R., Heinemann, M., & Panke, S. (2011). Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis. Nature Chemical Biology, 7(5), 271-277.
Costenoble, R., Picotti, P., Reiter, L., Stallmach, R., Heinemann, M., Sauer, U., & Aebersold, R. (2011). Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology, 7(1), 464-1-464-13. [464].
Heinemann, M., & Zenobi, R. (2011). Single cell metabolomics. Current Opinion in Biotechnology, 22(1), 26-31.
Heinemann, M., & Sauer, U. (2011). From good old biochemical analyses to high-throughput omics measurements and back. Current Opinion in Biotechnology, 22(1), 1-2.
Milias-Argeitis, A., Summers, S., Stewart-Ornstein, J., Zuleta, I., Pincus, D., El-Samad, H., ... Lygeros, J. (2011). In silico feedback for in vivo regulation of a gene expression circuit. Nature Biotechnology, 29, 1114-1116.
Ruess, J., Milias-Argeitis, A., Summers, S., & Lygeros, J. (2011). Moment estimation for chemically reacting systems by extended Kalman filtering. Journal of Chemical Physics, 135(16), [165102].


Jol, S. J., Kümmel, A., Hatzimanikatis, V., Beard, D. A., & Heinemann, M. (2010). Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. Biophysical Journal, 99(10), 3139-3144.
Kleijn, R., Fendt, S-M., Schuetz, R., Heinemann, M., Zamboni, N., & Sauer, U. (2010). Transcriptional control of metabolic fluxes and computational identification of the governing principles. Febs Journal, 277, 27-27.
Heinemann, M., & Sauer, U. (2010). Systems biology of microbial metabolism. Current Opinion in Microbiology, 13(3), 337-343.
Kummel, A., Ewald, J. C., Fendt, S-M., Jol, S. J., Picotti, P., Aebersold, R., ... Heinemann, M. (2010). Differential glucose repression in common yeast strains in response to HXK2 deletion. Fems Yeast Research, 10(3), 322-332.
Kotte, O., Zaugg, J. B., & Heinemann, M. (2010). Bacterial adaptation through distributed sensing of metabolic fluxes. Molecular Systems Biology, 82(9), 1492-1493. [355].
Bujara, M., Schümperli, M., Billerbeck, S., Heinemann, M., & Panke, S. (2010). Exploiting Cell-Free Systems: Implementation and Debugging of a System of Biotransformations. Biotechnology and Bioengineering, 106(3), 376-389.
Ramponi, F., Chatterjee, D., Milias-Argeitis, A., Hokayem, P., & Lygeros, J. (2010). Attaining mean square boundedness of a marginally stable stochastic linear system with a bounded control input. IEEE Transactions on Automatic Control, 55(10), 2414-2418.
Milias-Argeitis, A., Porreca, R., Summers, S., & Lygeros, J. (2010). Bayesian model selection for the yeast GATA-factor network: A comparison of computational approaches. In 2010 49th IEEE Conference on Decision and Control, CDC 2010 (pp. 3379-3384). [5717307]


Graaf, A. A. D., Freidig, A. P., Roos, B. D., Jamshidi, N., Heinemann, M., Rullmann, J. A. C., ... Ommen, B. V. (2009). Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology. PLoS Computational Biology, 5(11), [e1000554].
Cook, G. M., Berney, M., Gebhard, S., Heinemann, M., Cox, R. A., Danilchanka, O., & Niederweis, M. (2009). Physiology of mycobacteria. Advances in microbial physiology, 55, 81-182.
Kotte, O., & Heinemann, M. (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4), 519-525.
Cinquemani, E., Milias-Argeitis, A., Summers, S., & Lygeros, J. (2009). Local identification of piecewise deterministic models of genetic networks. In Hybrid Systems: Computation and Control - 12th International Conference, HSCC 2009, Proceedings (Vol. 5469, pp. 105-119). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5469).


Zamboni, N., Kümmel, A., & Heinemann, M. (2008). anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. Bmc Bioinformatics, 9(199), [199].
Amantonico, A., Oh, J. Y., Sobek, J., Heinemann, M., & Zenobi, R. (2008). Mass Spectrometric Method for Analyzing Metabolites in Yeast with Single Cell Sensitivity. Angewandte Chemie International Edition, 47(29), 5382-5385.
Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., ... Kell, D. B. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26(10), 1155-1160.
Cinquemani, E., Milias-Argeitis, A., Summers, S., & Lygeros, J. (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics (Oxford, England), 24(23), 2748-2754.


Hübscher, J., Jansen, A., Kotte, O., Schäfer, J., Majcherczyk, P. A., Harris, L. G., ... Berger-Bächi, B. (2007). Living with an imperfect cell wall: compensation of femAB inactivation in Staphylococcus aureus. BMC Genomics, 8, [307].
Sauer, U., Heinemann, M., & Zamboni, N. (2007). Genetics - Getting closer to the whole picture. Science, 316(5824), 550-551.
Makart, S., Heinemann, M., & Panke, S. (2007). Characterization of the AlkS/P-alkB-expression system as an efficient tool for the production of recombinant proteins in Escherichia coli fed-batch fermentations. Biotechnology and Bioengineering, 96(2), 326-336.


Kümmel, A., Panke, S., & Heinemann, M. (2006). Systematic assignment of thermodynamic constraints in metabolic network models. Bmc Bioinformatics, 7(512).,
Heinemann, M., & Panke, S. (2006). Synthetic biology--putting engineering into biology. Bioinformatics, 22(22), 2790-2799.
Seggewib, J., Becker, K., Kotte, O., Eisenacher, M., Khoschkhoi Yazdi, M. R., Fischer, A., ... von Eiff, C. (2006). Detailed survey of genome-wide expression differences between a Staphylococcus aureus mutant displaying the small colony variant phenotype and its parental strain. International journal of medical microbiology, 296, 132-133.
Bechtold, M., Heinemann, M., & Panke, S. (2006). Suitability of teicoplanin-aglycone bonded stationary phase for simulated moving bed enantio separation of racemic amino acids employing composition-constrained eluents. Journal of Chromatography A, 1113(1-2), 167-176.
Bechtold, M., Makart, S., Heinemann, M., & Panke, S. (2006). Integrated operation of continuous chromatography and biotransformations for the generic high yield production of fine chemicals. Journal of Biotechnology, 124(1), 146-162.
Davidescu, F. P., Madsen, H., Schümperli, M., Heinemann, M., Panke, S., & Jørgensen, S. B. (2006). Stochastic grey box modeling of the enzymatic biochemical reaction network of E. coli mutants. In Proceedings of the 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering (21 ed., pp. 161-166). Elsevier.
Kümmel, A., Panke, S., & Heinemann, M. (2006). Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Molecular Systems Biology, 2, 2006.0034.
Seggewiß, J., Becker, K., Kotte, O., Eisenacher, M., Khoschkhoi Yazdi, M. R., Fischer, A., ... Eiff, C. V. (2006). Reporter Metabolite Analysis of Transcriptional Profiles of a Staphylococcus aureus Strain with Normal Phenotype and Its Isogenic hemB Mutant Displaying the Small-Colony-Variant Phenotype. Journal of Bacteriology, 188(22), 7765-7777.


Schumperli, M., Heinemann, M., Gomolka, S., Kummel, A., & Panke, S. (2005). A new approach for the production of DHAP: The system of biotransformations. Journal of Biotechnology, 118, S90-S90.
Kummel, A., Schumperli, M., & Heinemann, M. (2005). Design of a system of biotransformations by means of stoichiometric network analysis. Journal of Biotechnology, 118, S105-S105.
Kluge, J., Kummel, A., Panke, S., & Heinemann, M. (2005). Model-based identification of regulation patterns controlling metabolic redundancy in central carbon metabolism. Journal of Biotechnology, 118, S3-S3.
Heinemann, M., Meinberg, H., Büchs, J., Koß, H-J., & Ansorge-Schumacher, M. B. (2005). Method for Quantitative Determination of Spatial Polymer Distribution in Alginate Beads Using Raman Spectroscopy. Applied Spectroscopy, 59(3), 280-285.
Buthe, A., Recker, T., Heinemann, M., Hartmeier, W., Büchs, J., & Ansorge-Schumacher, M. B. (2005). pH-optima in lipase-catalysed esterification. Biocatalysis and Biotransformation, 23(5), 307-314.
Trivedi, A., Heinemann, M., Spiess, A. C., Daussmann, T., & Büchs, J. (2005). Optimization of Adsorptive Immobilization of Alcohol Dehydrogenases. Journal of Bioscience and Bioengineering, 99(4), 340-347.
Heinemann, M., Kümmel, A., Ruinatscha, R., & Panke, S. (2005). In Silico Genome-Scale Reconstruction and Validation of the Staphylococcus aureus Metabolic Network. Biotechnology and Bioengineering, 92(7), 850-864.


Panke, S., Kümmel, A., Schümperli, M., & Heinemann, M. (2004). Industrial multi-step biotransformations. Chimica Oggi-Chemistry Today, 22(9), 44-47.
Ferloni, C., Heinemann, M., Hummel, W., Daussmann, T., & Büchs, J. (2004). Optimization of enzymatic gas-phase reactions by increasing the long-term stability of the catalyst. Biotechnology Progress, 20(3), 975-978.
Heinemann, M., Limper, U., & Büchs, J. (2004). New insights in the spatially resolved dynamic pH measurement in macroscopic large absorbent particles by confocal laser scanning microscopy. Journal of Chromatography A, 1024(1), 45-53.


Heinemann, M., Kümmel, A., Giesen, R., Ansorge-Schumacher, M. B., & Büchs, J. (2003). Experimental and Theoretical Analysis of Phase Equilibria in a Two-phase System Used for Biocatalytic Esterifications. Biocatalysis and Biotransformation, 21(3), 115-121.


Heinemann, M., Wagner, T., Doumèche, B., Ansorge-Schumacher, M., & Büchs, J. (2002). A new approach for the spatially resolved qualitative analysis of the protein distribution in hydrogel beads based on confocal laser scanning microscopy. Biotechnology Letters, 24(10), 845-850.
Doumèche, B., Heinemann, M., Büchs, J., Hartmeier, W., & Ansorge-Schumacher, M. B. (2002). Enzymatic catalysis in gel-stabilized two-phase systems: improvement of the solvent phase. Journal of Molecular Catalysis B: Enzymatic, 18(1), 19-27.
Last modified:10 November 2016 11.00 a.m.