==== Metabolic Network Analysis − Publications ====

**Publications 2016**

[47] 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. 

[46] 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**

[45] 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.

[44] 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.

[43] 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.

[42] 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. 2015 Apr 20;3:47. doi: 10.3389/fbioe.2015.00047. eCollection 2015.

[41] 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**

[40] 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.  

[39] 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. 

[38] 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.

[37] 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. 

**Publications 2013**

[36] 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

[35] 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. 

**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)
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.  

**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)
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 

**Publications 2003**

[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  

**Publications 2002**

[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 

**Publications 2001**

[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  

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