Metabolic networks

Biological Networks

Volumn , Issue , 2007, Pages 163-197

  Fell, David A ^a  

^a OXFORD BROOKES UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84858865463     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789812772367_0006     Document Type: Chapter

References (69)

1. Huynen, M.A., Dandekar, T. and Bork P. (1999). Variation and evolution of the citric acid cycle: A genomic perspective. Trends Microbiol. 7, 281-291.
2. Arita, M. (2004). The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci U.S.A. 101, 1543-1547.
3. Rahman, S.A., Advani, P., Schunk, R., Schrader, R. and Schomburg, D. (2005). Metabolic pathway analysis web service (pathway hunter tool at CUBIC). Bioinformatics. 21, 1189-1193.
4. Croes, D., Couche, F., Wodak, S.J. and Van Helden, J. (2006). Metabolic PathFinding: Inferring relevant pathways in biochemical networks. J Mol Biol. 356, 222-236.
5. Fell, D.A. (1997). Understanding the Control of Metabolism. Portland Press, London.
6. Goldberg, R.N., Tewari, Y.B. and Bhat, T.N. (2004). Thermodynamics of enzyme- catalyzed reactions - a database for quantitative biochemistry. Bioinformatics. 20, 2874-2877.
7. Forsythe, R.G., Karp, P.D. and Mavrovouniotis, M.L. (1997). Estimation of equilibrium constants using automated group contribution methods. Comput Appl Biosci. 13, 537-543.
8. Cornish-Bowden, A. and Cárdenas, M.L. (2001). Information transfer in metabolic pathways. Effects of irreversible steps in computer models. Eur J Biochem. 268, 6616-6624.
9. Cornish-Bowden, A. (1995). Fundamentals of Enzyme Kinetics. Portland Press, London, 2nd edn.
10. Voss, K., Heiner, M. and Koch, I. (2003). Steady state analysis of metabolic pathways using Petri nets. In Silico Biol. 3, 367-387.
11. Edwards, J.S. and Palsson, B.O. (1999). Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem. 274, 17410-17416.
12. Edwards, J.S. and Palsson, B.O. (2000). The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics and capabilities. Proc Natl Acad Sci U.S.A. 97, 5528-5533.
13. Borodina, I., Krabben, P. and Nielsen, J. (2005). Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 15, 820-829.
14. Francke, C., Siezen, J.S. and Teusink, B. (2005). Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 13, 550-558.
15. Poolman, M.G., Bonde, B.K., Gevorgyan, A., Patel, H.H. and Fell, D.A. (2006). Challenges to be faced in the reconstruction of metabolic networks from public databases. IEEE Proc. Syst Biol. 153, 379-384.
16. Horne, A.B., Hodgman, T.C., Spence, H.D. and Dalby, A.R. (2004) Constructing an enzyme-centric view of metabolism. Bioinformatics. 20, 2050-2055.
17. Dandekar, T., Schuster, S., Snel, B., Huynen, M. and Bork, P. (1999). Pathway alignment: Application to the comparative analysis of glycolytic enzymes. Biochem J. 343, 115-124.
18. Romero, P., Wagg, J., Green, M.L., Kaiser, D., Krummenacker, M. and Karp, P.D. (2004). Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 6, R2, 1-13.
19. Sirava, M., Schäfer Eigisperger, M., Kaufmann, M., Kohlbacher, O., Bornberg-Bauer, E. and Lenhof, H.P. (2002). BioMiner - modelling, analyzing and visualizing biochemical pathways and networks. Bioinformatics. 18, S219-S230.
20. Pinney, J.M., Shirley, M.W., McConkey, G.A. and Westhead, D.R. (2005). MetaSHARK: Software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res. 33, 1399-1409.
21. Von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005). STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433-D437.
22. Knuth, D.E. (1981). Seminumerical Algorithms, vol. 2 of The Art of Computer Programming. Addison-Wesley, Reading, second edn.
23. Schuster, S., Dandekar, T. and Fell, D.A. (1999). Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17, 53-60.
24. Schuster, S., Fell, D.A. and Dandekar, T. (2000). A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol. 18, 326-332.
25. Schilling, C.H., Schuster, S., Palsson, B. and Heinrich, R. (1999). Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era. Biotechnol Prog. 15, 296-303.
26. Papin, J.A., Price, N.D., Wiback, S.J., Fell, D.A. and Palsson, B.O. (2003). Metabolic pathways in the post-genome era. Trends BiochemSci. 28, 250-258.
27. Papoutsakis, E.T. (1984). Equations and calculations for fermentations of butyric- acid bacteria. Biotechnol Bioeng. 26, 174-187.
28. Watson M.R. (1986). A discrete model of bacterial metabolism. CABIOS. 2, 23-27.
29. Fell, D.A. and Small, J.R. (1986). Fat synthesis in adipose tissue: an examination of stoichiometric constraints. Biochem J. 238, 781-786.
30. Varma, A. and Palsson, B.O. (1993a). Metabolic capabilities of Escherichia coli. 1. synthesis of biosynthetic precursors and cofactors. J Theor Biol. 165, 477-502.
31. Varma, A. and Palsson, B.O. (1993b). Metabolic capabilities of Escherichia coli. 2. optimal growth patterns. J Theor Biol. 165, 503-522.
32. Reder, C. (1988). Metabolic control theory: a structural approach. J Theor Biol. 135, 175-201.
33. Leiser, J. and Blum, J.J. (1987). On the analysis of substrate cycles in large metabolic systems. Cell Biophysics. 11, 123-138.
34. Mavrovouniotis, M.L. and Stephanopoulos, G. (1990). Computer-aided synthesis of biochemical pathways. Biotech Bioeng. 36, 1119-1132.
35. Mavrovouniotis, M.L. and Stephanopoulos, G. (1992). Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 2. A synthesis approach in the context of simple examples. Ind Eng Chem Res. 31, 1625-1637.
36. Ingraham, J.L., Maaloe, O.E. and Neidhardt, F.C. (1983) Growth of the Bacterial Cell. Sinauer Associates Inc, Sunderland, MA.
37. Holmes, W.H. (1986) The central metabolic pathways of Escherichia coli:Relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. Curr Top Cellul Regul. 28, 69-105.
38. Kauffman, S.A. (1967) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol. 22, 437-467.
39. Kauffman, S.A. (1993) The Origins of Order. Oxford University Press, Oxford.
40. Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N. and Barabási, A.L. (2000) The large- scale organization of metabolic networks. Nature. 407, 651-654.
41. Wagner, A.and Fell, D.A. (2001) The small world inside large metabolic networks. Proc Roy Soc (London) Series B. 268, 1803-1810.
42. Watts, D.J. (1997) The Structure and Dynamics of Small-World Systems. Ph.D. thesis, Cornell University.
43. Watts, D.J. and Strogatz, S.H. (1998) Collective dynamics of ‘small-world’ networks. Nature. 393, 440-442.
44. Gleis, P.M., Stadler, P.F., Wagner, A.and Fell, D.A. (2001) Relevant cycles in chemical reaction networks. Adv Complex Syst. 4, 207-226.
45. Zhu, D. and Qin, Z.S. (2005) Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics. 6, 8, 1-12.
46. Barabási, A.L. (2002) Linked. Perseus Publishing, Cambridge, Massachusetts.
47. Csete, M. and Doyle, J (2004) Bow ties, metabolism and disease. Trends Biotechnol. 22, 446-450.
48. Pfieffer, T., Soyer, O.S. and Bonhoeffer, S. (2005) The evolution of connectivity in metabolic networks. PLOS Biology. 3, 1269-1275.
49. Meléndez-Hevia, E. and Isidoro, A. (1985) The game of the pentose phosphate cycle. J Theor Biol. 117, 251-263.
50. Meléndez-Hevia, E., Waddell, T.G. and Cascante, M. (1996) The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions and opportunism in the design of metabolic pathways during evolution. J Mol Evol. 43, 293-303.
51. Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I. and Dandekar, T. (2002) Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics. 18, 351-361.
52. Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N. and Barabási, A.L. (2002) Hierarchical organization of modularity in metabolic networks. Science. 297, 1551-1555.
53. Ma, H.W. and Zeng, A.P. (2003) The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics. 19, 1423-1430.
54. Tanaka, R. (2005) Scale-rich metabolic networks. Phys Rev Lett. 94, 168101-1-168101-4.
55. Barabási, A.L. and Albert, R. (1999) Emergence of scaling in random networks. Science. 286, 509-512.
56. Morowitz, H.J. (1992) Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. Yale University Press, New Haven.
57. Morowitz, H.J. (1999) A theory of biochemical organization, metabolic pathways and evolution. Complexity. 4, 39-53.
58. Light, S., Kraulis, P. and Elofsson, A. (2005) Preferential attachment in the evolution of metabolic networks. BMC Genomics. 6, 159.
59. Lemke, N., Herédia, F., Barcellos, C.K., Dos Reis, A.N. and Mombach, J.C.M. (2004) Essentiality and damage in metabolic networks. Bioinformatics. 20, 115-119.
60. Thatcher, J.W., Shaw, J.M. and Dickinson, W.J. (1998) Marginal fitness contributions of nonessential genes in yeast. Proc Natl Acad Sci U.S.A. 95, 253-257.
61. Yeh, I., Hanekamp, T., Tsoka, S., Karp, P.D. and Altman, R.B. (2004) Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery. Genome Res. 14, 917-924.
62. Papin, J.A., Price, N.D., Edwards, J.S. and Palsso, B.O. (2002) The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J theor Biol. 215, 67-82.
63. Wilhelm, T., Behre, J. and Schuster, S. (2004) Analysis of structural robustness of metabolic networks. Syst Biol. 1, 114-120.
64. Klamt, S. and Gilles, E.D. (2004) Minimal cut sets in biochemical reaction networks. Bioinformatics. 20, 226-234.
65. Mulquiney, P.J. and Kuchel, P.W. (1999) Model of 2, 3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations:Equations and parameter refinement. Biochem J. 342, 581-596.
66. Chassagnole, C., Fell, D.A., Rais, B., Kudla, B. and Mazat, J.P. (2001) Control of the threonine-synthesis pathway in Escherichia coli: A theoretical and experimental approach. Biochem J. 356, 433-444.
67. Olivier, B.G. and Snoep, J.L. (2004) Web-based kinetic modelling using JWS online. Bioinformatics. 20, 2143-2144.
68. Novère, N.L., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J.L. and Hucka, M. (2006) BioModels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, 689-691.
69. Almaas, E., Kovács, B., Vicsek, T., Oltvai, Z.N. and Barabási, A.L. (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature. 427, 839-843.