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[67] FJ Bruggeman, B Teusink, R Steuer (2023) Trade-offs between the instantaneous growth rate and long-term fitness: consequences for microbial physiology and predictive computational models preprint/submitted
[66] R Steuer (2022) Fast‐growing phototrophic microorganisms and the productivity of phototrophic cultures Biotechnology and Bioengineering, 119, 2261– 2267.
[65] MA Köbis, A Bockmayr, R Steuer (2022) Time-Optimal Adaptation in Metabolic Network Models Front. Mol. Biosci. 9:866676.
[64] S Boecker, G Slaviero, T Schramm, W Szymanski, R Steuer, H Link, S Klamt (2021) Deciphering the physiological response of Escherichia coli under high ATP demand Molecular systems biology 17 (12), e10504
[63] Sharma S and Steuer R (2019) Modeling microbial communities using biochemical resource allocation analysis. J. R. Soc. Interface 16: 20190474.
[62] Faizi M and Steuer R (2019) Optimal proteome allocation strategies for phototrophic growth in a light-limited chemostat. Microb Cell Fact 18, 165
[61] Tomáš Zavřel(*), Marjan Faizi, Cristina Loureiro, Gereon Poschmann, Kai Stühler, Maria Sinetova, Anna Zorina, Ralf Steuer(*), Jan Červený (2019) Quantitative insights into the cyanobacterial cell economy. eLife 2019;8:e42508 [* corresponding author]
[60] Janasch M, Asplund-Samuelsson J, Steuer R, Hudson EP. (2019) Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation. J Exp Bot. doi: 10.1093/jxb/ery382.
[59] K Keil, J Dierenbach, UM Tillich, R Steuer, M Frohme (2019) An improved open-source software platform for high-throughput cultivation of phototrophic microorganisms and its application for salt tolerance experiments Journal of Cellular Biotechnology 5 (2), 103-114
[58] Beck C, Knoop H, Steuer R (2018) Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes. PLoS Genet 14(3): e1007239. https://doi.org/10.1371/journal.pgen.1007239
[57] Faizi M, Zavrel T, Loureiro C, Cerveny J, Steuer R (2018) A model of optimal protein allocation during phototrophic growth. Biosystems 166, 26-36. doi: 10.1016/j.biosystems.2018.02.004.
[56] Lippi L, Bähr L, Wüstenberg A, Wilde A, Steuer R (2018) Exploring the potential of high-density cultivation of cyanobacteria for the production of cyanophycin. Algal Research 31, 363–366. https://doi.org/10.1016/j.algal.2018.02.028
[55] Fuhr L, El-Athman R, Scrima R, Cela O, Carbone A, Knoop H, Li Y, Hoffmann K, Laukkanen MO, Corcione F, Steuer R, Meyer TF, Mazzoccoli G, Capitanio N, Relógio A. (2018) The Circadian Clock Regulates Metabolic Phenotype Rewiring Via HKDC1 and Modulates Tumor Progression and Drug Response in Colorectal Cancer. EBioMedicine pii: S2352-3964(18)30241-X. doi: 10.1016/j.ebiom.2018.07.002
[54] Reimers AM, Knoop H, Bockmayr A, Steuer R. (2017) Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. Proc Natl Acad Sci U S A. pii: 201617508. doi: 10.1073/pnas.1617508114.
[53] Marianne Gründel, Henning Knoop, Ralf Steuer (2017) Activity and functional properties of the isocitrate lyase in the cyanobacterium Cyanothece sp. PCC 7424 Microbiology. doi: 10.1099/mic.0.000459
[52] Malatinszky D, Steuer R, Jones PR. (2017) A comprehensively curated genome-scale two-cell model for the cyanobacterium Anabaena sp. PCC 7120. Plant Physiol. 173(1):509-523. doi: 10.1104/pp.16.01487
[51] Westermark S and Steuer R (2016) Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. Front. Bioeng. Biotechnol. 4:95. doi: 10.3389/fbioe.2016.00095
[50] Baum K, Politi AZ, Kofahl B, Steuer R, Wolf J. (2016) Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations. PLoS Comput Biol. 2016 Dec 27;12(12):e1005298
[49] Zavřel T, Červený J, Knoop H, Steuer R (2016) Optimizing cyanobacterial product synthesis: Meeting the challenges. Bioengineered. 2016 Jul 15:1-7.
[48] Zavřel T, Knoop H, Steuer R, Jones PR, Červený J, Trtílek M. (2016) A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry. Bioresour Technol. 202:142-51. doi: 10.1016/j.biortech.2015.11.062.
[47] Muller S, Regensburger G, Steuer R. (2015) Resource allocation in metabolic networks: kinetic optimization and approximations by FBA. Biochem Soc Trans. 2015 Dec 1;43(6):1195-200. doi: 10.1042/BST20150156. Review.
[46] Ruegen M, Bockmayr A, Steuer R. (2015) Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA Sci Rep. 2015 Oct 26;5:15247. doi: 10.1038/srep15247.
[45] Erdrich P, Steuer R, Klamt S. (2015) An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Syst Biol. 2015 Aug 19;9:48. doi: 10.1186/s12918-015-0191-x.
[44] Knoop H, Steuer R. (2015) A computational analysis of stoichiometric constraints and trade-offs in cyanobacterial biofuel production. Front Bioeng Biotechnol. 3:47. doi: 10.3389/fbioe.2015.00047.
[43] Klemke F, Baier A, Knoop H, Kern R, Jablonsky J, Beyer G, Volkmer T, Steuer R, Lockau W, Hagemann M. (2015) Identification of the light-independent phosphoserine pathway as additional source for serine in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology. 2015 Feb 20. pii: mic.0.000055. doi: 10.1099/mic.0.000055.
[42] Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R. (2014) Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS One. 9(9):e106453.
[41] Erdrich P, Knoop H, Steuer R, Klamt S. (2014) Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microb Cell Fact. 2014 Sep 19;13(1):128.
[40] Müller S, Regensburger G, Steuer R. (2014) Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes. J Theor Biol. 347:182-90. doi: 10.1016/j.jtbi.2013.11.015.
[39] Gottstein W, Müller S, Herzel H, Steuer R. (2014) Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution. Biosystems. 117:68-76. doi: 10.1016/j.biosystems.2013.12.006.
[38] Klement M, Děd T, Šafránek D, Červený J, Müller S, Steuer R. (2014) Biochemical Space: A Framework for Systemic Annotation of Biological Models. Electronic Notes in Theoretical Computer Science, Volume 306, 2014, Pages 31-44, ISSN 1571-0661, https://doi.org/10.1016/j.entcs.2014.06.013.
[37] H. Knoop, M. Gruendel, Y. Zilliges, R. Lehmann, S. Hoffmann, W. Lockau, R. Steuer. (2013) Flux Balance Analysis of Cyanobacterial Metabolism: The metabolic network of Synechocystis sp. PCC 6803. PLoS Comput Biol 9(6): e1003081. doi:10.1371/journal.pcbi.1003081
[36] R. Lehmann, R. Machne, J. Georg , M. Benary, I. M. Axmann, R. Steuer (2013) How cyanobacteria pose new problems to old methods: Challenges in microarray time series analysis. BMC Bioinformatics 14:133. doi: 10.1186/1471-2105-14-133.
[35] Klement M, Šafránek D, Děd T, Pejznoch A, Nedbal L, Steuer R, Červený J, Müller S (2013) A Comprehensive Web-based Platform For Domain-Specific Biological Models. Electronic Notes in Theoretical Computer Science, Volume 299, 2013, Pages 61-67, ISSN 1571-0661, https://doi.org/10.1016/j.entcs.2013.11.006.
[34] Kämäräinen J, Knoop H, Stanford NJ, Guerrero F, Akhtar MK, Aro EM, Steuer R, Jones PR. (2012) Physiological tolerance and stoichiometric potential of cyanobacteria for hydrocarbon fuel production. J Biotechnol. 162(1):67-74. doi: 10.1016/j.jbiotec.2012.07.193.
[33] R. Steuer, H. Knoop, R. Machne (2012) Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth. Journal of Experimental Botany 63(6):2259-74. doi:10.1093/jxb/ers018
[32] C. Beck, H. Knoop, IM Axmann, R. Steuer (2012) The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics. 13(1):56.
[31] Steuer R, Waldherr S, Sourjik V, Kollmann M (2011) Robust Signal Processing in Living Cells. PLoS Comput Biol 7(11): e1002218. doi:10.1371/journal.pcbi.1002218
[30] E. Murabito, K. Smallbone, J. Swinton, H. V. Westerhoff, R. Steuer (2011) A probabilistic approach to identify putative drug targets in biochemical networks. J R Soc Interface. 8(59):880-95.
[29] R. Steuer (2011) Exploring the Dynamics of Large-Scale Biochemical Networks: A Computational Perspective. The Open Bioinformatics Journal Vol. 5, pp.4-15
[28] H. Koeppl, S. Andreozzi, and R. Steuer (2011) Guaranteed and Randomized Methods for Stability Analysis of Uncertain Metabolic Networks. Lecture Notes in Control and Information Sciences, Volume 407, 297-307
[27] H. Knoop, Y. Zilliges, W. Lockau and R. Steuer (2010) The metabolic network of Synechocystis sp. PCC 6803: Systemic properties of autotrophic growth. Plant Physiol. 154(1):410-22.
[26] P. D. Kourdis, Ralf Steuer, and D. A. Goussis (2010) Physical understanding of complex multiscale biochemical models via algorithmic simplification: Glycolysis in Saccharomyces cerevisiae. Physica D Vol. 239, Issue 18, pp. 1798-1817
[25] R. Steuer and B. H. Junker (2009) Computational Models of Metabolism: Stability and Regulation in Metabolic Networks. Advances in Chemical Physics, Volume 142. Rice, Stuart A. (editor), ISBN-10: 0-470-46499-2 ISBN-13: 978-0-470-46499-1 - John Wiley & Sons (2009)
[24] SV Albers, NK Birkeland, AJ Driessen et al. (2009) SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochem Soc Trans. 37(Pt 1):58-64
[23] J. Schmiedel and R. Steuer (2008) From minimal to full-scale models of yeast glycolysis: The role of feedback mechanisms in maintaining stability. in: Proceedings of the 5th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg 22-23, 2008. R. Gauges, U. Kummer, J. Pahle and P. Willy (editors). Logos Verlag Berlin. ISBN 978-3-8325-1993-3.
[22] R. Steuer and G. Zamora-Lopez (2008) Global Properties of Networks (Review) , in: Junker BH and Schreiber F (eds.). Analysis of Biological Networks. Wiley Series on Bioinformatics: Computational Techniques and Engineering. Print ISBN: 9780470041444, Online ISBN: 9780470253489 (2008).
[21] D. Stiefs, T. Gross, R. Steuer, U. Feudel (2008) Computation and Visualization of Bifurcation Surfaces Intern. J. of Bifurcation and Chaos (IJBC), Vol. 18, No. 8, pp. 2191-2206
[20] Grimbs S, Selbig J, Bulik S, Holzhütter HG, and Steuer R (2007) The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks Molecular Systems Biology 3 Article number: 146 doi:10.1038/msb4100186
[19] Steuer R. (2007) Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 68(16-18):2139-51, doi:10.1016/j.phytochem.2007.04.041
[18] Steuer R, Nunes Nesi A, Fernie AR, Gross T, Blasius B, Selbig J. (2007) From Structure to Dynamics of Metabolic Pathways: Application to the Plant Mitochondrial TCA Cycle. Bioinformatics 23(11):1378-85, doi:10.1093/bioinformatics/btm065
[17] Steuer R, Morgenthal K, Weckwerth W, Selbig J. (2007) A gentle guide to the analysis of metabolomic data. Methods Mol Biol. 358:105-26.
[16] Steuer R, Gross T, Selbig J, Blasius B. (2006) Structural kinetic modeling of metabolic networks Proc Natl Acad Sci U S A. 103(32):11868-73.
[15] Morgenthal K., Weckwerth W., Steuer R. (2006) Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation. Biosystems. 83(2-3):108-17.
[14] Steuer R, Humburg P, Selbig J. (2006) Validation and functional annotation of expression-based clusters based on gene ontology. BMC Bioinformatics. 15;7:380.
[13] Steuer, R. (2006) On the analysis and interpretation of correlations in metabolomic data. Brief Bioinform. 7(2):151-8.
[12] W. Weckwerth and R. Steuer (2005) From Experiment to Biological Interpretation: Metabolic Networks from a Systems Perspective In: Metabolome Analyses: Strategies for Systems Biology. S. Vaidyanathan (Editor), G. G. Harrigan (Editor), R. Goodacre (Editor). Chapter 15, pp. 265-290. Springer; 1 edition
[11] Ralf Steuer (2004) Effects of stochasticity in models of the cell cycle: From quantized cycle times to noise-induced oscillations. J Theor Biol. 228(3):293-301.
[10] C. O. Daub, R. Steuer. S. Kloska, J. Selbig (2004) Improving estimates of mutual information using B-spline functions. BMC Bioinformatics. 5: 118, doi: 10.1186/1471-2105-5-118.
[9] R. Steuer, C. O. Daub, J. Selbig and J. Kurths (2004) Measuring Distances between Variables by Mutual Information. in: Proceedings of the 27th annual conference of the Gfkl, D. Baier and K.-D. Wernecke (eds) ,Springer-Verlag
[8] R. Steuer, W. Ebeling, T. Bengner, C. Dehnicke, H. Haettig and H.-J. Meencke (2004) Entropy and complexity analysis of intracranially recorded EEG. International Journal of Bifurcation and Chaos, Vol. 14, No. 2, pp. 815-823
[7] R. Steuer, J. Kurths, O. Fiehn and W. Weckwerth (2003) Observing and interpreting correlations in metabolomic networks. Bioinformatics, Vol. 19 (8), 1019-1026
[6] R. Steuer and C. Zhou and J. Kurths (2003) Constructive effects of fluctuations in genetic and biochemical regulatory systems. BioSystems, Vol. 72, 241-251
[5] R. Steuer, J. Kurths, O. Fiehn and W. Weckwerth (2003) Interpreting correlations in metabolomic networks. Biochemical Society Transactions, Vol. 31 (6), 1476-1478
[4] R. Steuer, J. Kurths, C. O. Daub, J. Weise and J. Selbig (2002) The Mutual Information: Detecting and evaluating dependencies between variables. Bioinformatics, Vol. 18 (Suppl. 2), S231-S240
[3] R. Steuer, W. Ebeling, D. F. Russell, S. Bahar, A. Neiman and F. Moss (2001) Entropy and local uncertainty of data from sensory neurons. Phys. Rev. E 64, 061911
[2] W. Ebeling, R. Steuer and M. R. Titchener (2001) Partition-based entropies of deterministic and stochastic maps. Stochastics and Dynamics, Vol. 1 (1), 45-61
[1] R. Steuer, L. Molgedey, W. Ebeling and M. A. Jimenez-Montano (2001) Entropy and optimal partition for data analysis. Eur. Phys. J. B 19, 265-269