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Why optimal states recruit fewer reactions in metabolic networks
1. | Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, United States |
2. | Department of Mathematics, Clarkson University, Potsdam, NY 13699, United States |
3. | Department of Physics & Astronomy and Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, United States |
References:
[1] |
U. Alon, "An Introduction to Systems Biology: Design Principles of Biological Circuits," Chapman & Hall/CRC Mathematical and Computational Biology Series, Chapman & Hall/CRC, Boca Raton, FL, 2007. |
[2] |
A.-L. Barabási and Z. N. Oltvai, Network biology: Understanding the cell's functional organization, Nat. Rev. Genet., 5 (2004), 101-113. |
[3] |
S. D. Becker, et al., Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox, Nat. Protoc., 2 (2007), 727-738.
doi: 10.1038/nprot.2007.99. |
[4] |
M. J. Best and K. Ritter, "Linear Programming: Active Set Analysis and Computer Programs," Prentice-Hall, Engelwood Cliffs, NJ, 1985. |
[5] |
L. M. Blank, L. Kuepfer and U. Sauer, Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast, Genome Biol., 6 (2005), R49.
doi: 10.1186/gb-2005-6-6-r49. |
[6] |
H. P. J. Bonarius, G. Schmid and J. Tramper, Flux analysis of underdetermined metabolic networks: The quest for the missing constraints, Trends Biotechnol., 15 (1997), 308-314.
doi: 10.1016/S0167-7799(97)01067-6. |
[7] |
S. P. Cornelius, J. S. Lee and A. E. Motter, Dispensability of Escherichia coli's latent pathways, Proc. Natl. Acad. Sci. USA, 108 (2011), 3124-3129.
doi: 10.1073/pnas.1009772108. |
[8] |
N. C. Duarte, et al., Global reconstruction of the human metabolic network based on genomic and bibliomic data, Proc. Natl. Acad. Sci. USA, 104 (2007), 1777-1782.
doi: 10.1073/pnas.0610772104. |
[9] |
S. S. Fong, A. R. Joyce and B. Ø. Palsson, Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states, Genome. Res., 15 (2005), 1365-1372.
doi: 10.1101/gr.3832305. |
[10] |
S. S. Fong, A. Nanchen, B. Ø. Palsson and U. Sauer, Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes, J. Biol. Chem., 281 (2006), 8024-8033.
doi: 10.1074/jbc.M510016200. |
[11] |
, ILOG CPLEX (Version 10.2.0)., Available from: \url{http://www.ilog.com/products/cplex/}., ().
|
[12] |
D. E. Kaufman and R. L. Smith, Direction choice for accelerated convergence in hit-and-run sampling, Oper. Res., 46 (1998), 84-95.
doi: 10.1287/opre.46.1.84. |
[13] |
D.-H. Kim and A. E. Motter, Slave nodes and the controllability of metabolic networks, New J. Phys., 11 (2009), 113047.
doi: 10.1088/1367-2630/11/11/113047. |
[14] |
M. V. Kritz, M. T. dos Santos, S. Urrutia and J.-M. Schwartz, Organising metabolic networks: Cycles in flux distributions, J. Theo. Biol., 265 (2010), 250-260.
doi: 10.1016/j.jtbi.2010.04.026. |
[15] |
O. L. Mangasarian, Uniqueness of solution in linear programming, Linear Algebra Appl., 25 (1979), 151-162.
doi: 10.1016/0024-3795(79)90014-4. |
[16] |
A. E. Motter, Improved network performance via antagonism: From synthetic rescues to multi-drug combinations, BioEssays, 32 (2010), 236-245.
doi: 10.1002/bies.200900128. |
[17] |
A. E. Motter, N. Gulbahce, E. Almaas and A.-L. Barabási, Predicting synthetic rescues in metabolic networks, Mol. Syst. Biol., 4 (2008), 168.
doi: 10.1038/msb.2008.1. |
[18] |
T. Nishikawa, N. Gulbahce and A. E. Motter, Spontaneous reaction silencing in metabolic optimization, PLoS Comput. Biol., 4 (2008), e1000236.
doi: 10.1371/journal.pcbi.1000236. |
[19] |
B. Papp, C. Pál and L. D. Hurst, Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast, Nature, 429 (2004), 661-664.
doi: 10.1038/nature02636. |
[20] |
B. Ø. Palsson, "Systems Biology: Properties of Reconstructed Networks," Cambridge University Press, Cambridge, UK, 2006. |
[21] |
E. Ravasz, A. Somera, D. Mongru, Z. Oltvai and A.-L. Barabási, Hierarchical organization of modularity in metabolic networks, Science, 297 (2002), 1551-1555.
doi: 10.1126/science.1073374. |
[22] |
J. L. Reed, T. D. Vo, C. H. Schilling and B. Ø. Palsson, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR), Genome Biol., 4 (2003), R54.
doi: 10.1186/gb-2003-4-9-r54. |
[23] |
W. Rudin, "Real and Complex Analysis,'' Third edition, McGraw-Hill Book Co., New York, 1987. |
[24] |
R. Schuetz, L. Kuepfer and U. Sauer, Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli, Mol. Syst. Biol., 3 (2007), 119.
doi: 10.1038/msb4100162. |
[25] |
T. Shlomi, T. Benyamini, E. Gottlieb, R. Sharan and E. Ruppin, Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect, PLoS Comput. Biol., 7 (2011), e1002018.
doi: 10.1371/journal.pcbi.1002018. |
[26] |
R. L. Smith, Efficient Monte Carlo procedures for generating points uniformly distributed over bounded regions, Oper. Res., 32 (1984), 1296-1308.
doi: 10.1287/opre.32.6.1296. |
[27] |
V. Spirin and L. A. Mirny, Protein complexes and functional modules in molecular networks, Proc. Natl. Acad. Sci. USA, 100 (2003), 12123-12128.
doi: 10.1073/pnas.2032324100. |
[28] |
P. Szilágyi, On the uniqueness of the optimal solution in linear programming, Rev. Anal. Numér. Théor. Approx., 35 (2006), 225-244. |
[29] |
A. Varma and B. Ø. Palsson, Metabolic flux balancing: Basic concepts, scientific and practical use, Nat. Biotechnol., 12 (1994), 994-998.
doi: 10.1038/nbt1094-994. |
show all references
References:
[1] |
U. Alon, "An Introduction to Systems Biology: Design Principles of Biological Circuits," Chapman & Hall/CRC Mathematical and Computational Biology Series, Chapman & Hall/CRC, Boca Raton, FL, 2007. |
[2] |
A.-L. Barabási and Z. N. Oltvai, Network biology: Understanding the cell's functional organization, Nat. Rev. Genet., 5 (2004), 101-113. |
[3] |
S. D. Becker, et al., Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox, Nat. Protoc., 2 (2007), 727-738.
doi: 10.1038/nprot.2007.99. |
[4] |
M. J. Best and K. Ritter, "Linear Programming: Active Set Analysis and Computer Programs," Prentice-Hall, Engelwood Cliffs, NJ, 1985. |
[5] |
L. M. Blank, L. Kuepfer and U. Sauer, Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast, Genome Biol., 6 (2005), R49.
doi: 10.1186/gb-2005-6-6-r49. |
[6] |
H. P. J. Bonarius, G. Schmid and J. Tramper, Flux analysis of underdetermined metabolic networks: The quest for the missing constraints, Trends Biotechnol., 15 (1997), 308-314.
doi: 10.1016/S0167-7799(97)01067-6. |
[7] |
S. P. Cornelius, J. S. Lee and A. E. Motter, Dispensability of Escherichia coli's latent pathways, Proc. Natl. Acad. Sci. USA, 108 (2011), 3124-3129.
doi: 10.1073/pnas.1009772108. |
[8] |
N. C. Duarte, et al., Global reconstruction of the human metabolic network based on genomic and bibliomic data, Proc. Natl. Acad. Sci. USA, 104 (2007), 1777-1782.
doi: 10.1073/pnas.0610772104. |
[9] |
S. S. Fong, A. R. Joyce and B. Ø. Palsson, Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states, Genome. Res., 15 (2005), 1365-1372.
doi: 10.1101/gr.3832305. |
[10] |
S. S. Fong, A. Nanchen, B. Ø. Palsson and U. Sauer, Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes, J. Biol. Chem., 281 (2006), 8024-8033.
doi: 10.1074/jbc.M510016200. |
[11] |
, ILOG CPLEX (Version 10.2.0)., Available from: \url{http://www.ilog.com/products/cplex/}., ().
|
[12] |
D. E. Kaufman and R. L. Smith, Direction choice for accelerated convergence in hit-and-run sampling, Oper. Res., 46 (1998), 84-95.
doi: 10.1287/opre.46.1.84. |
[13] |
D.-H. Kim and A. E. Motter, Slave nodes and the controllability of metabolic networks, New J. Phys., 11 (2009), 113047.
doi: 10.1088/1367-2630/11/11/113047. |
[14] |
M. V. Kritz, M. T. dos Santos, S. Urrutia and J.-M. Schwartz, Organising metabolic networks: Cycles in flux distributions, J. Theo. Biol., 265 (2010), 250-260.
doi: 10.1016/j.jtbi.2010.04.026. |
[15] |
O. L. Mangasarian, Uniqueness of solution in linear programming, Linear Algebra Appl., 25 (1979), 151-162.
doi: 10.1016/0024-3795(79)90014-4. |
[16] |
A. E. Motter, Improved network performance via antagonism: From synthetic rescues to multi-drug combinations, BioEssays, 32 (2010), 236-245.
doi: 10.1002/bies.200900128. |
[17] |
A. E. Motter, N. Gulbahce, E. Almaas and A.-L. Barabási, Predicting synthetic rescues in metabolic networks, Mol. Syst. Biol., 4 (2008), 168.
doi: 10.1038/msb.2008.1. |
[18] |
T. Nishikawa, N. Gulbahce and A. E. Motter, Spontaneous reaction silencing in metabolic optimization, PLoS Comput. Biol., 4 (2008), e1000236.
doi: 10.1371/journal.pcbi.1000236. |
[19] |
B. Papp, C. Pál and L. D. Hurst, Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast, Nature, 429 (2004), 661-664.
doi: 10.1038/nature02636. |
[20] |
B. Ø. Palsson, "Systems Biology: Properties of Reconstructed Networks," Cambridge University Press, Cambridge, UK, 2006. |
[21] |
E. Ravasz, A. Somera, D. Mongru, Z. Oltvai and A.-L. Barabási, Hierarchical organization of modularity in metabolic networks, Science, 297 (2002), 1551-1555.
doi: 10.1126/science.1073374. |
[22] |
J. L. Reed, T. D. Vo, C. H. Schilling and B. Ø. Palsson, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR), Genome Biol., 4 (2003), R54.
doi: 10.1186/gb-2003-4-9-r54. |
[23] |
W. Rudin, "Real and Complex Analysis,'' Third edition, McGraw-Hill Book Co., New York, 1987. |
[24] |
R. Schuetz, L. Kuepfer and U. Sauer, Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli, Mol. Syst. Biol., 3 (2007), 119.
doi: 10.1038/msb4100162. |
[25] |
T. Shlomi, T. Benyamini, E. Gottlieb, R. Sharan and E. Ruppin, Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect, PLoS Comput. Biol., 7 (2011), e1002018.
doi: 10.1371/journal.pcbi.1002018. |
[26] |
R. L. Smith, Efficient Monte Carlo procedures for generating points uniformly distributed over bounded regions, Oper. Res., 32 (1984), 1296-1308.
doi: 10.1287/opre.32.6.1296. |
[27] |
V. Spirin and L. A. Mirny, Protein complexes and functional modules in molecular networks, Proc. Natl. Acad. Sci. USA, 100 (2003), 12123-12128.
doi: 10.1073/pnas.2032324100. |
[28] |
P. Szilágyi, On the uniqueness of the optimal solution in linear programming, Rev. Anal. Numér. Théor. Approx., 35 (2006), 225-244. |
[29] |
A. Varma and B. Ø. Palsson, Metabolic flux balancing: Basic concepts, scientific and practical use, Nat. Biotechnol., 12 (1994), 994-998.
doi: 10.1038/nbt1094-994. |
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