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Research GBB Molecular Systems Biology



Smith, E. N., van Aalst, M., Tosens, T., Niinemets, Ü., Stich, B., Morosinotto, T., Alboresi, A., Erb, T., Gómez-Coronado, P. A., Tolleter, D., Finazzi, G., Curien, G., Heinemann, M., Ebenhöh, O., Hibberd, J. M., Schlüter, U., Sun, T., & Weber, A. P. M. (2023). Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives. Molecular Plant. Advance online publication.
Takhaveev, V., Özsezen, S., Smith, E. N., Zylstra, A., Chaillet, M. L., Chen, H., Papagiannakis, A., Milias-Argeitis, A., & Heinemann, M. (2023). Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle. Nature Metabolism, 5(2), 294-313.
Prins, F. L., Tomanin, D., Kamenz, J., & Azzopardi, G. (2023). Biometric Recognition of African Clawed Frogs. In N. Tsapatsoulis (Ed.), Computer Analysis of Images and Patterns: 20th International Conference, CAIP 2023 Limassol, Cyprus, September 25–28, 2023 Proceedings, Part II (pp. 151-161). (Lecture Notes in Computer Science; Vol. 14185). Springer.


Zylstra, A., & Heinemann, M. (2022). Metabolic dynamics during the cell cycle. Current Opinion in Systems Biology, 30, Article 100415.
Van den Bergh, B., Schramke, H., Michiels, J. E., Kimkes, T. E. P., Radzikowski, J. L., Schimpf, J., Vedelaar, S. R., Burschel, S., Dewachter, L., Lončar, N., Schmidt, A., Meijer, T., Fauvart, M., Friedrich, T., Michiels, J., & Heinemann, M. (2022). Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis. Nature Communications, 13(1), Article 546.
Losa, J., Leupold, S., Alonso-Martinez, D., Vainikka, P., Thallmair, S., Tych, K. M., Marrink, S. J., & Heinemann, M. (2022). Perspective: A stirring role for metabolism in cells. Molecular Systems Biology, 18(4), Article e10822.
Litsios, A., Goswami, P., Terpstra, H. M., Coffin, C., Vuillemenot, L-A., Rovetta, M., Ghazal, G., Guerra, P., Buczak, K., Schmidt, A., Tollis, S., Tyers, M., Royer, C. A., Milias-Argeitis, A., & Heinemann, M. (2022). The timing of Start is determined primarily by increased synthesis of the Cln3 activator rather than dilution of the Whi5 inhibitor. Molecular Biology of the Cell, 33(5), Article rp2.
Novarina, D., Koutsoumpa, A., & Milias-Argeitis, A. (2022). A user-friendly and streamlined protocol for CRISPR/Cas9 genome editing in budding yeast. STAR protocols, 3(2), Article 101358.
Kurdyaeva, T., & Milias-Argeitis, A. (2022). Propagation of initial condition uncertainty for linear dynamical systems: Beyond the Gaussian assumption. In 2022 European Control Conference, ECC 2022 (pp. 1391-1396). Institute of Electrical and Electronics Engineers Inc..
Guerra, P., Vuillemenot, L-A. P. E., van Oppen, Y. B., Been, M., & Milias-Argeitis, A. (2022). TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle. Journal of Cell Science, 135(18), Article 260378. Advance online publication.


Sellner, B., Prakapaitė, R., van Berkum, M., Heinemann, M., Harms, A., & Jenal, U. (2021). A New Sugar for an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection. mBio, 12(6), Article e03246-21.
Vedelaar, S. R., Radzikowski, J. L., & Heinemann, M. (2021). A Robust Method for Generating, Quantifying, and Testing Large Numbers of Escherichia coli Persisters. Methods in molecular biology (Clifton, N.J.), 2357, 41-62.
Ortega, A. D., Takhaveev, V., Vedelaar, S. R., Long, Y., Mestre-Farràs, N., Incarnato, D., Ersoy, F., Olsen, L. F., Mayer, G., & Heinemann, M. (2021). A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux. Cell Chemical Biology, 28(11), 1554-1568.e8. Article j.chembiol.2021.04.006. Advance online publication.
Alseekh, S., Aharoni, A., Brotman, Y., Contrepois, K., D'Auria, J., Ewald, J., C Ewald, J., Fraser, P. D., Giavalisco, P., Hall, R. D., Heinemann, M., Link, H., Luo, J., Neumann, S., Nielsen, J., Perez de Souza, L., Saito, K., Sauer, U., Schroeder, F. C., ... Fernie, A. R. (2021). Mass spectrometry-based metabolomics: A guide for annotation, quantification and best reporting practices. Nature Methods, 18(7), 747-756. Advance online publication.
Yang, X., Heinemann, M., Howard, J., Huber, G., Iyer-Biswas, S., Le Treut, G., Lynch, M., Montooth, K. L., Needleman, D. J., Pigolotti, S., Rodenfels, J., Ronceray, P., Shankar, S., Tavassoly, I., Thutupalli, S., Titov, D. V., Wang, J., & Foster, P. J. (2021). Physical bioenergetics: Energy fluxes, budgets, and constraints in cells. Proceedings of the National Academy of Sciences of the United States of America, 118(26), Article e2026786118.
Kruitbosch, H., Mzayek, Y., Omlor, S., Guerra, P., & Milias-Argeitis, A. (2022). A convolutional neural network for segmentation of yeast cells without manual training annotations. Bioinformatics (Oxford, England), 38(5), 1427-1433. Article btab835. Advance online publication.
Guerra, P., Vuillemenot, L-A., Rae, B., Ladyhina, V., & Milias-Argeitis, A. (2022). Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synthetic Biology, 11(3), 1129-1141. Article acssynbio.1c00387. Advance online publication.
Kurdyaeva, T., & Milias Argeitis, A. (2021). Moment-based uncertainty propagation for deterministic biochemical network models with rational reaction rates. In Proceedings of the European Control Conference 2021 EUCA.
Kurdyaeva, T., & Milias-Argeitis, A. (2021). Uncertainty propagation for deterministic models of biochemical networks using moment equations and the extended Kalman filter. Journal of the Royal Society Interface, 18(181), Article 20210331.
Novarina, D., Guerra, P., & Milias-Argeitis, A. (2021). Vacuolar Localization via the N-terminal Domain of Sch9 is Required for TORC1-dependent Phosphorylation and Downstream Signal Transduction. Journal of Molecular Biology, 433(24), Article 167326. Advance online publication.
Kamenz, J., Qiao, R., Yang, Q., & Ferrell, J. E. (2021). Real-Time Monitoring of APC /C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts. In Methods in Molecular Biology (pp. 29-38). (Methods in Molecular Biology; Vol. 2329). Humana Press.


Heinemann, M., Basan, M., & Sauer, U. (2020). Implications of initial physiological conditions for bacterial adaptation to changing environments. Molecular Systems Biology, 16(9), Article e9965.
Milias Argeitis, A., & Kurdyaeva, T. (2020). Derivation of moment equations for a nonlinear gene expression model with initial condition and parameter uncertainty.
Kamenz, J., Gelens, L., & Ferrell, J. E. (2021). Bistable, Biphasic Regulation of PP2A-B55 Accounts for the Dynamics of Mitotic Substrate Phosphorylation. Current Biology, 31(4), 794-808. Advance online publication.
Lockhead, S., Moskaleva, A., Kamenz, J., Chen, Y., Kang, M., Reddy, A. R., Santos, S. D. M., & Ferrell, J. E. (2020). The Apparent Requirement for Protein Synthesis during G2 Phase Is due to Checkpoint Activation. Cell reports, 32(2), Article 107901.


Kimkes, T. E. P., & Heinemann, M. (2020). How bacteria recognise and respond to surface contact. FEMS Microbiology Reviews, 44(1), 106-122. Advance online publication.
Niebel, B., Leupold, S., & Heinemann, M. (2019). An upper limit on Gibbs energy dissipation governs cellular metabolism. Nature Metabolism, 1, 125-131.
Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A., Collins, J. J., Dehio, C., Fortune, S., Ghigo, J-M., Hardt, W-D., Harms, A., Heinemann, M., Hung, D. T., Jenal, U., Levin, B. R., ... Zinkernagel, A. (2019). Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology, 17(7), 441-448. Advance online publication.
Litsios, A., Huberts, D. H. E. W., Terpstra, H. M., Guerra, P., Schmidt, A., Buczak, K., Papagiannakis, A., Rovetta, M., Hekelaar, J., Hubmann, G., Exterkate, M., Milias-Argeitis, A., & Heinemann, M. (2019). Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast. Nature Cell Biology, 21(11), 1382-1392.
Ozsezen, S., Papagiannakis, A., Chen, H., Niebel, B., Milias-Argeitis, A., & Heinemann, M. (2019). Inference of the High-Level Interaction Topology between the Metabolic and Cell-Cycle Oscillators from Single-Cell Dynamics. Cell systems, 9(4), 354-365. Advance online publication.
Zhang, Z., Kimkes, T. E. P., & Heinemann, M. (2019). Manipulating rod-shaped bacteria with optical tweezers. Scientific Reports, 9(1), Article 19086.
Monteiro, F., Hubmann, G., Takhaveev, V., Vedelaar, S. R., Norder, J., Hekelaar, J., Saldida, J., Litsios, A., Wijma, H. J., Schmidt, A., & Heinemann, M. (2019). Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor. Molecular Systems Biology, 15(12), Article e9071.
Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A., Collins, J. J., Dehio, C., Fortune, S., Ghigo, J-M., Hardt, W-D., Harms, A., Heinemann, M., Hung, D. T., Jenal, U., Levin, B. R., ... Zinkernagel, A. (2019). Publisher Correction: Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology, 17(7), 460-460. Advance online publication.
Leupold, S., Hubmann, G., Litsios, A., Meinema, A. C., Takhaveev, V., Papagiannakis, A., Niebel, B., Janssens, G., Siegel, D., & Heinemann, M. (2019). Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan. eLife, 8, Article e41046.
Yang, Y-S., Kato, M., Wu, X., Litsios, A., Sutter, B. M., Wang, Y., Hsu, C-H., Wood, N. E., Lemoff, A., Mirzaei, H., Heinemann, M., & Tu, B. P. (2019). Yeast Ataxin-2 Forms an Intracellular Condensate Required for the Inhibition of TORC1 Signaling during Respiratory Growth. Cell, 177(3), 697-710. Advance online publication.
Kurdyaeva, T., & Milias-Argeitis, A. (2019). Efficient global sensitivity analysis of biochemical networks using Gaussian process regression. In 2018 IEEE Conference on Decision and Control, CDC 2018 (pp. 2673-2678). Article 8618902 (Proceedings of the IEEE Conference on Decision and Control). Institute of Electrical and Electronics Engineers Inc..


von Borzyskowski, L. S., Carrillo, M., Leupold, S., Glatter, T., Kiefer, P., Weishaupt, R., Heinemann, M., & Erb, T. J. (2018). An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metabolic Engineering, 47, 423-433. Advance online publication.
Bley Folly, B., Ortega, A. D., Hubmann, G., Bonsing-Vedelaar, S., Wijma, H. J., van der Meulen, P., Milias-Argeitis, A., & 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. Advance online publication.
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), Article 2162.
Takhaveev, V., & Heinemann, M. (2018). Metabolic heterogeneity in clonal microbial populations. Current Opinion in Microbiology, 45, 30-38. Advance online publication.
Kimkes, T. E. P., & Heinemann, M. (2018). Reassessing the role of the Escherichia coli CpxAR system in sensing surface contact. PLoS ONE, 13(11), Article e0207181.
Milias Argeitis, A., & Kurdyaeva, T. (2018). Analytical calculation of Sobol sensitivity indices for Gaussian Processes with a squared exponential covariance function.
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.
Garcia, H. G., Benzinger, D., Rullan, M., Milias-Argeitis, A., Khammash, M., Deutschbauer, A. M., Langdon, E. M., & Gladfelter, A. S. (2018). Principles of Systems Biology, No. 30. Cell systems, 7(1), 1-2.
Thadani, R., Kamenz, J., Heeger, S., Munoz, S., & Uhlmann, F. (2018). Cell-Cycle Regulation of Dynamic ChromosomeAssociation of the Condensin Complex. Cell reports, 23(8), 2308-2317.


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. Advance online publication.
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. Article S.5.4-002.
Radzikowski, J. L., Schramke, H., & Heinemann, M. (2017). Bacterial persistence from a system-level perspective. Current Opinion in Biotechnology, 46, 98-105.
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, Article 4704.
Filer, D., Thompson, M. A., Takhaveev, V., Dobson, A. J., Kotronaki, I., Green, J. W. M., Heinemann, M., Tullet, J. M. A., & Alic, N. (2017). RNA polymerase III limits longevity downstream of TORC1. Nature, 552(7684), 263-267. Advance online publication.
Gupta, A., Milias-Argeitis, A., & Khammash, M. (2017). Dynamic disorder in simple enzymatic reactions induces stochastic amplification of substrate. Journal of the Royal Society Interface, 14(132), Article 20170311.
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), Article 52.
Kamenz, J., & Ferrell, J. E. (2017). The Temporal Ordering of Cell-Cycle Phosphorylation. Molecular Cell, 65(3), 371-373.
Kamenz, J., & Hauf, S. (2017). Time To Split Up: Dynamics of Chromosome Separation. Trends in Cell Biology, 27(1), 42-54.


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., 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. Article 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), 1392.
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). Article 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, Article 12546.
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. Article e1004784.


Schmidt, A., Kochanowski, K., Vedelaar, S., Ahrné, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R., & Heinemann, M. (2016). The quantitative and condition-dependent Escherichia coli proteome. Nature Biotechnology, 34(1), 104-110. Advance online publication.
Janssens, G. E., Meinema, A. C., Gonzalez, J., Wolters, J. C., Schmidt, A., Guryev, V., Bischoff, R., Wit, E. C., Veenhoff, L. M., & Heinemann, M. (2015). Protein biogenesis machinery is a driver of replicative aging in yeast. eLife, 4, Article e08527.
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., & 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). IEEE.
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.
Kamenz, J., Mihaljev, T., Kubis, A., Legewie, S., & Hauf, S. (2015). Robust Ordering of Anaphase Events by AdaptiveThresholds and Competing Degradation Pathways. Molecular Cell, 60, 446-459.


Daszczuk, A., Dessalegne, Y., Drenth, I., Hendriks, E., Jo, E., van Lente, T., Oldebesten, A., Parrish, J., Poljakova, W., Purwanto, A. A., van Raaphorst, R., Boonstra, M., van Heel, A., Herber, M., van der Meulen, S., Siebring, J., Sorg, R. A., Heinemann, M., Kuipers, O. P., & 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), Article 736.
Lee, S. S., Dechant, R., Vizcarra, I. A., Huberts, D. H. E. W., Lee, L. P., Heinemann, M., & Peter, M. (2014). Single cell analysis of yeast aging using microfluidic dissection. In 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014 (pp. 666-668). Chemical and Biological Microsystems Society .
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), Article 024104.
Fromm, S. A., Kamenz, J., Nöldeke, E. R., Neu, A., Zocher, G., & Sprangers, R. (2014). In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery. Angewandte Chemie - International Edition, 53(28), 7354-7359.
Kamenz, J., & Hauf, S. (2014). Slow checkpoint activation kinetics as a safety device in anaphase. Current Biology, 24(6), 646-651.


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.
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), Article 50143.
Gerosa, L., Kochanowski, K., Heinemann, M., & Sauer, U. (2013). Dissecting specific and global transcriptional regulation of bacterial gene expression. Molecular Systems Biology, 9, Article 658.
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.
Ibáñez, A. J., Fagerer, S. R., Schmidt, A. M., Urban, P. L., Jefimovs, K., Geiger, P., Dechant, R., Heinemann, M., & 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.
Zampar, G. G., Kümmel, A., Ewald, J., Jol, S., Niebel, B., Picotti, P., Aebersold, R., Sauer, U., Zamboni, N., & 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. Article 651.
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). Article 6669626
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), Article 20130588.
Milias-Argeitis, A., & Lygeros, J. (2013). Steady-state simulation of metastable stochastic chemical systems. Journal of Chemical Physics, 138(18), Article 184109.
Heinrich, S., Geissen, E-M., Kamenz, J., Trautmann, S., Widmer, C., Drewe, P., Knop, M., Radde, N., Hasenauer, J., & Hauf, S. (2013). Determinants of robustness in spindle assembly checkpoint signalling. Nature Cell Biology, 15, 1328-1339.


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.
Schuetz, R., Zamboni, N., Zampieri, M., Heinemann, M., & Sauer, U. (2012). Multidimensional optimality of microbial metabolism. Science, 336(6081), 601-604.
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), Article e1002575.
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), Article e1002415.
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.
Fromm, S. A., Truffault, V., Kamenz, J., Braun, J. E., Hoffmann, N. A., Izaurralde, E., & Sprangers, R. (2012). The structural basis of Edc3‐ and Scd6‐mediated activation of the Dcp1:Dcp2 mRNA decapping complex. The EMBO Journal, 31, 279-290.


Urban, P. L., Schmidt, A. M., Fagerer, S. R., Amantonico, A., Ibañez, A., Jefimovs, K., Heinemann, M., & 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.
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. Article 464.
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), Article 23126.
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.
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.
Heinemann, M., & Zenobi, R. (2011). Single cell metabolomics. Current Opinion in Biotechnology, 22(1), 26-31.
Sturm, A., Heinemann, M., Arnoldini, M., Benecke, A., Ackermann, M., Benz, M., Dormann, J., & Hardt, W-D. (2011). The cost of virulence: retarded growth of Salmonella Typhimurium cells expressing type III secretion system 1. PLoS Pathogens, 7(7), Article 1002143.
Milias-Argeitis, A., Summers, S., Stewart-Ornstein, J., Zuleta, I., Pincus, D., El-Samad, H., Khammash, M., & 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), Article 165102.


Kotte, O., Zaugg, J. B., & Heinemann, M. (2010). Bacterial adaptation through distributed sensing of metabolic fluxes. Molecular Systems Biology, 82(9), 1492-1493. Article 355.
Kummel, A., Ewald, J. C., Fendt, S-M., Jol, S. J., Picotti, P., Aebersold, R., Sauer, U., Zamboni, N., & Heinemann, M. (2010). Differential glucose repression in common yeast strains in response to HXK2 deletion. Fems Yeast Research, 10(3), 322-332.
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.
Heinemann, M., & Sauer, U. (2010). Systems biology of microbial metabolism. Current Opinion in Microbiology, 13(3), 337-343.
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.
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). Article 5717307


Kotte, O., & Heinemann, M. (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4), 519-525.
Lee, S. S., Vizcarra, I. A., Lee, L. P., & Heinemann, M. (2009). Long-term monitoring of yeast cell division via elastic micro-pad. In Proceedings of Conference, MicroTAS 2009 - The 13th International Conference on Miniaturized Systems for Chemistry and Life Sciences (pp. 478-480). Chemical and Biological Microsystems Society .
Graaf, A. A. D., Freidig, A. P., Roos, B. D., Jamshidi, N., Heinemann, M., Rullmann, J. A. C., Hall, K. D., Adiels, M., & Ommen, B. V. (2009). Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology. PLoS Computational Biology, 5(11), Article 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.
Heinemann, M., & Panke, S. (2009). Synthetic Biology: Putting Engineering into Bioengineering. In P. Fu, & S. Panke (Eds.), Systems Biology and Synthetic Biology (pp. 387-409). Wiley.
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).


Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Novère, N. L., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., ... Kell, D. B. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26(10), 1155-1160.
Zamboni, N., Kümmel, A., & Heinemann, M. (2008). anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. Bmc Bioinformatics, 9(199), Article 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.
Cinquemani, E., Milias-Argeitis, A., & Lygeros, J. (2008). Identification of genetic regulatory networks: A stochastic hybrid approach. In Proceedings of the 17th World Congress, International Federation of Automatic Control, IFAC (IFAC Proceedings Volumes (IFAC-PapersOnline); Vol. 17, No. 1 PART 1). Elsevier.
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.


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.
Sauer, U., Heinemann, M., & Zamboni, N. (2007). Genetics - Getting closer to the whole picture. Science, 316(5824), 550-551.
Hübscher, J., Jansen, A., Kotte, O., Schäfer, J., Majcherczyk, P. A., Harris, L. G., Bierbaum, G., Heinemann, M., & Berger-Bächi, B. (2007). Living with an imperfect cell wall: compensation of femAB inactivation in Staphylococcus aureus. BMC Genomics, 8, Article 307.


Seggewib, J., Becker, K., Kotte, O., Eisenacher, M., Khoschkhoi Yazdi, M. R., Fischer, A., McNamara, P., Proctor, R. A., Peters, G., Heinemann, M., & 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., 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.
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., McNamara, P., Laham, N. A., Proctor, R., Peters, G., Heinemann, M., & 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.
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.
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.
Heinemann, M., & Panke, S. (2006). Synthetic biology--putting engineering into biology. Bioinformatics, 22(22), 2790-2799.
Kümmel, A., Panke, S., & Heinemann, M. (2006). Systematic assignment of thermodynamic constraints in metabolic network models. Bmc Bioinformatics, 7(512).,


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.
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.
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.
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.
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.
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.


Panke, S., Kümmel, A., Schümperli, M., & Heinemann, M. (2004). Industrial multi-step biotransformations. Chimica Oggi-Chemistry Today, 22(9), 44-47.
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.
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., 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:09 June 2023 8.36 p.m.