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members:steuer:publicationssteuer [2014/04/10 13:45] – steuermembers:steuer:publicationssteuer [2016/09/21 09:26] (current) – steuer
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-==== Ralf Steuer − Publications ====+==== 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 [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) [35] 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. +**[[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 ===+**Publications 2012**
  
 [34] Kämäräinen J, Knoop H, Stanford NJ, Guerrero F, Akhtar MK, Aro EM, Steuer R, Jones PR. (2012)  [34] Kämäräinen J, Knoop H, Stanford NJ, Guerrero F, Akhtar MK, Aro EM, Steuer R, Jones PR. (2012) 
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 BMC Genomics. 13(1):56. BMC Genomics. 13(1):56.
  
-=== Publications 2011 ===+**Publications 2011**
  
 [31] Steuer R, Waldherr S, Sourjik V, Kollmann M (2011) [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 +**[[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) [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. +**[[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) [29] R. Steuer (2011)
-Exploring the Dynamics of Large-Scale Biochemical Networks: A Computational Perspective. The Open Bioinformatics Journal Vol. 5, pp.4-15+**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) [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 Guaranteed and Randomized Methods for Stability Analysis of Uncertain Metabolic Networks. Lecture Notes in Control and Information Sciences, Volume 407, 297-307
  
-=== Publications 2010 ===+**Publications 2010** 
  
 [27] H. Knoop, Y. Zilliges, W. Lockau and R. Steuer (2010) [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. +**[[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) [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 +**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 ===+**Publications 2009**
  
 [25] R. Steuer and B. H. Junker (2009) [25] R. Steuer and B. H. Junker (2009)
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 [24] SV Albers, NK Birkeland, AJ Driessen et al. (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 +[[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) [23] J. Schmiedel and R. Steuer (2008)
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 [21] D. Stiefs, T. Gross, R. Steuer, U. Feudel (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  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) [20] Grimbs S, Selbig J, Bulik S, Holzhütter HG, and Steuer R (2007)
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 [17] Steuer R, Morgenthal K, Weckwerth W, Selbig J. (2007) [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.   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) [16] Steuer R, Gross T, Selbig J, Blasius B. (2006)
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 [13] Steuer, R.  (2006) [13] Steuer, R.  (2006)
 On the analysis and interpretation of correlations in metabolomic data. Brief Bioinform. 7(2):151-8.  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) [12] W. Weckwerth and R. Steuer (2005)
 From Experiment to Biological Interpretation: Metabolic Networks from a Systems Perspective  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  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) [11] Ralf Steuer (2004)
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 [8] R. Steuer, W. Ebeling, T. Bengner, C. Dehnicke, H. Haettig and H.-J. Meencke (2004) [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  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) [7] R. Steuer, J. Kurths, O. Fiehn and W. Weckwerth (2003)
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 [5] R. Steuer, J. Kurths, O. Fiehn and W. Weckwerth (2003) [5] R. Steuer, J. Kurths, O. Fiehn and W. Weckwerth (2003)
 Interpreting correlations in metabolomic networks. Biochemical Society Transactions, Vol. 31 (6), 1476-1478   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) [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  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) [3] R. Steuer, W. Ebeling, D. F. Russell, S. Bahar, A. Neiman and F. Moss (2001)
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 Entropy and optimal partition for data analysis. Eur. Phys. J. B 19, 265-269   Entropy and optimal partition for data analysis. Eur. Phys. J. B 19, 265-269  
  
 +-----
  
  
-===== in revision ===== 
  
-E. Murabito, M. Verma, M. Bekker, D. Bellomo, H. V. Westerhoff, B. Teusink, R. Steuer. Probabilistic Modeling of the Central Carbon Metabolism of Lactococcus lactis: Insights into Metabolic Regulation. First submission January 2013. 
  
-W. Gottstein, S. Müller, H. Herzel and R. Steuer. Elucidating the temporal coordination of metabolic pathways using in-silico evolution. BioSystems. In revision. 
  
-S. Müller, G. Regensburger, R. Steuer. Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes. arXiv:1308.0510 [q-bio.MN]