~~NOTOC~~ ====== Publications 2001 - now ====== ** This page is no longer maintained. Please visit: https://research.uni-leipzig.de/physics-of-evolution/ ** see also [[https://scholar.google.de/citations?user=9Cxz-pQAAAAJ&view_op=list_works&sortby=pubdate|google scholar]] for an up to date list ====Publications 2023==== [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 ---- ====Publications 2022==== [66] R Steuer (2022) **[[https://doi.org/10.1002/bit.28123|Fast‐growing phototrophic microorganisms and the productivity of phototrophic cultures]]** Biotechnology and Bioengineering, 119, 2261– 2267. [65] MA Köbis, A Bockmayr, R Steuer (2022) **[[https://doi.org/10.3389/fmolb.2022.866676|Time-Optimal Adaptation in Metabolic Network Models]]** Front. Mol. Biosci. 9:866676. ---- ====Publications 2021==== [64] S Boecker, G Slaviero, T Schramm, W Szymanski, R Steuer, H Link, S Klamt (2021) **[[https://www.embopress.org/doi/full/10.15252/msb.202110504|Deciphering the physiological response of Escherichia coli under high ATP demand]]** Molecular systems biology 17 (12), e10504 ---- ====Publications 2019==== [63] Sharma S and Steuer R (2019) **[[http://dx.doi.org/10.1098/rsif.2019.0474|Modeling microbial communities using biochemical resource allocation analysis.]]** J. R. Soc. Interface 16: 20190474. [62] Faizi M and Steuer R (2019) **[[https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-019-1209-7|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) **[[https://elifesciences.org/articles/42508|Quantitative insights into the cyanobacterial cell economy.]]** eLife 2019;8:e42508 [* corresponding author] [60] Janasch M, Asplund-Samuelsson J, Steuer R, Hudson EP. (2019) **[[https://academic.oup.com/jxb/article/70/3/973/5145700|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) **[[https://content.iospress.com/articles/journal-of-cellular-biotechnology/jcb199002|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 ---- ====Publications 2018==== [58] Beck C, Knoop H, Steuer R (2018) **[[http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007239|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) **[[https://www.ncbi.nlm.nih.gov/pubmed/29476802|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) **[[https://www.sciencedirect.com/science/article/pii/S2211926418300055|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) **[[https://www.ncbi.nlm.nih.gov/pubmed/30005951|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 ---- ====Publications 2017==== [54] Reimers AM, Knoop H, Bockmayr A, Steuer R.​ (2017) **[[https://www.ncbi.nlm.nih.gov/pubmed/28720699|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) **[[http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000459|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/27899536|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 ---- ====Publications 2016==== [51] Westermark S and Steuer R (2016) **[[http://journal.frontiersin.org/article/10.3389/fbioe.2016.00095/|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) **[[https://www.ncbi.nlm.nih.gov/pubmed/28027301|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/27420605|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/ 26708481|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. ---- ====Publications 2015==== [47] Muller S, Regensburger G, Steuer R. (2015) **[[http://www.ncbi.nlm.nih.gov/pubmed/26614660|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/26496972|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/26286864|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/25941672|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/25701735|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. ---- ====Publications 2014==== [42] Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R. (2014) **[[http://www.ncbi.nlm.nih.gov/pubmed/25268481|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/25323065|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/24295962|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/24440082|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) **[[http://www.sciencedirect.com/science/article/pii/S1571066114000590|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. ---- ====Publications 2013==== [37] H. Knoop, M. Gruendel, Y. Zilliges, R. Lehmann, S. Hoffmann, W. Lockau, R. Steuer. (2013) **[[http://www.ncbi.nlm.nih.gov/pubmed/23843751|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/23601192|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) **[[http://www.sciencedirect.com/science/article/pii/S1571066113000777|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. ---- ====Publications 2012==== [34] Kämäräinen J, Knoop H, Stanford NJ, Guerrero F, Akhtar MK, Aro EM, Steuer R, Jones PR. (2012) **[[http://www.ncbi.nlm.nih.gov/pubmed/22954891|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/22450165|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/22300633|The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms.]]** BMC Genomics. 13(1):56. ---- ====Publications 2011==== [31] Steuer R, Waldherr S, Sourjik V, Kollmann M (2011) **[[http://www.ncbi.nlm.nih.gov/pubmed/22215991|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/21123256|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 ---- ====Publications 2010==== [27] H. Knoop, Y. Zilliges, W. Lockau and R. Steuer (2010) **[[http://www.ncbi.nlm.nih.gov/pubmed/20616194|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 ---- ====Publications 2009==== [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) [[http://www.ncbi.nlm.nih.gov/pubmed/19143602|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 ---- ====Publications 2008==== [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 ---- ====Publications 2007==== [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) **[[http://www.sciencedirect.com/science/article/pii/S0031942207002919| 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) **[[https://www.ncbi.nlm.nih.gov/pubmed/17344242|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. ---- ====Publications 2006==== [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. ---- ====Publications 2005==== [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 ---- ====Publications 2004==== [11] Ralf Steuer (2004) **[[http://www.ncbi.nlm.nih.gov/pubmed/15135028|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) **[[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-118|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) **[[http://www.worldscientific.com/doi/abs/10.1142/S021812740400948X|Entropy and complexity analysis of intracranially recorded EEG.]]** International Journal of Bifurcation and Chaos, Vol. 14, No. 2, pp. 815-823 ---- ====Publications 2003==== [7] R. Steuer, J. Kurths, O. Fiehn and W. Weckwerth (2003) **[[http://www.ncbi.nlm.nih.gov/pubmed/12761066|Observing and interpreting correlations in metabolomic networks.]]** Bioinformatics, Vol. 19 (8), 1019-1026 [6] R. Steuer and C. Zhou and J. Kurths (2003) **[[http://www.ncbi.nlm.nih.gov/pubmed/14643492|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) **[[http://www.ncbi.nlm.nih.gov/pubmed/14641093|Interpreting correlations in metabolomic networks.]]** Biochemical Society Transactions, Vol. 31 (6), 1476-1478 ---- ====Publications 2002==== [4] R. Steuer, J. Kurths, C. O. Daub, J. Weise and J. Selbig (2002) **[[http://www.ncbi.nlm.nih.gov/pubmed/12386007|The Mutual Information: Detecting and evaluating dependencies between variables.]]** Bioinformatics, Vol. 18 (Suppl. 2), S231-S240 ---- ====Publications 2001==== [3] R. Steuer, W. Ebeling, D. F. Russell, S. Bahar, A. Neiman and F. Moss (2001) **[[http://www.ncbi.nlm.nih.gov/pubmed/11736214|Entropy and local uncertainty of data from sensory neurons.]]** Phys. Rev. E 64, 061911 [2] W. Ebeling, R. Steuer and M. R. Titchener (2001) **[[http://www.worldscientific.com/doi/abs/10.1142/S0219493701000047|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) **[[http://epjb.epj.org/articles/epjb/abs/2001/02/b0426/b0426.html|Entropy and optimal partition for data analysis.]]** Eur. Phys. J. B 19, 265-269 ----