From the determination of complex reaction mechanisms to systems biology

Annual Review of Biochemistry

Volumn 77, Issue , 2008, Pages 479-494

  Ross, John ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Causal connectivity; Correlation functions; Genetic algorithms

Indexed keywords

BELUZOV ZHABOTINSKY REACTION; CITRIC ACID CYCLE; CORRELATION FUNCTION; GENETIC ALGORITHM; GLYCOLYSIS; MICHAELIS MENTEN KINETICS; NUTRIENT; PRIORITY JOURNAL; REACTION ANALYSIS; REVIEW; SYSTEMS BIOLOGY; ALGORITHM; ANIMAL; BIOCHEMISTRY; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; GENE REGULATORY NETWORK; HUMAN; METHODOLOGY; OSCILLOMETRY; THEORETICAL MODEL;

ALPHA-GLYCEROPHOSPHORIC ACID; GLYCEROPHOSPHATE;

ALGORITHMS; ANIMALS; BIOCHEMISTRY; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; GLYCEROPHOSPHATES; HUMANS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR CONFORMATION; OSCILLOMETRY; SYSTEMS BIOLOGY;

EID: 50649101988     PISSN: 00664154     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biochem.77.102507.115132     Document Type: Review

References (48)

1. Ross J, Schreiber I, Vlad MO. 2006. Determination of Complex Reaction Mechanisms: Analysis of Chemical, Biological, and Genetic Networks. New York: Oxford Univ. Press. 230 pp.
2. Ross J. 2003. Acc. Chem. Res. 36:839-47
3. Ross J, Schreiber I, Vlad MO. 2006. Computations by means of macroscopic chemical kinetics. See Ref. 1, pp. 34-45
4. Hjelmfelt A, Weinberger ED, Ross J. 1992. Proc. Natl. Acad. Sci. USA 89:383-87
5. Hjelmfelt A, Schneider FW, Ross J. 1993. Science 260:335-37
6. Hjelmfelt A, Ross J. 1995. Physica D 84:180-93
7. Laplante JP, Pemberton M, Hjelmfelt A, Ross J. 1995. J. Phys. Chem. 99:10063-65
8. Hauri DC, Shen P, Arkin AP, Ross J. 1997. J. Phys. Chem. B 101:3872-76
9. Arkin A, Ross J. 1994. Biophys. J. 67:560-78
10. Arkin A, Ross J. 1995. J. Phys. Chem. 99:970-79
11. Arkin A, Shen P, Ross J. 1997. Science 277:1275-79
12. Samoilov M, Arkin A, Ross J. 2001. Chaos 11:108-14
13. Schmitt WM Jr, Raab RM, Stephanopoulos G. 2004. Genome Res. 14:1654-63
14. Remondini D, O'Connell B, Intrator N, Sedivy JM, Neretti N, et al. 2005. Proc. Natl. Acad. Sci. USA 102:6902-6
15. Steuer R, Kurths J, Fiehn O, Weckwerth W. 2003. Bioinformatics 19:1019-26
16. Kaufmann KJ, Pajerowski JD, Jamshidi N, Paulson BO, Edwards JS. 2002. Biophys. J. 83:646-62
17. Vance W, Arkin A, Ross J. 2002. Proc. Natl. Acad. Sci. USA 99:5816-21
18. Tyson JJ. 1975. J. Chem. Phys. 62:1010-15
19. Luo Y, Epstein IR. 1990. Adv. Chem. Phys. 79:269-99
20. Chevalier T, Schreiber I, Ross J. 1993. J. Phys. Chem. 97:6776-87
21. Sanchez-Torralba A, Yu K, Shen P, Oefner PJ, Ross J. 2003. Proc. Natl. Acad. Sci. USA 100:1494-98
22. Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB. 2002. Proc. Natl. Acad. Sci. USA 99:12841-46
23. Santos SDM, Verveer PJ, Bastiaens PIH. 2007. Nat. Cell Biol. 9(11):324-30
24. Ross J, Schreiber I, Vlad MO. 2006. Lifetime and transit time distributions and response experiments in chemical kinetics. See Ref. 1, pp. 170-206
25. Vlad MO, Moran F, Rodriguez Y, Ross J. 2002. Int. J. Bifurc. Chaos 12:2599-618
26. Morán F, Vlad MO, Bustos M, Triviño JC, Ross J. 2007. J. Phys. Chem. A 110:1844-51
27. Chance B, Pye EK, Ghosh AK, Hess B, eds. 1973. Biological and Biochemical Oscillators. New York: Academic
28. Pigolotti S, Krishna S, Jensen MH. 2007. Proc. Natl. Acad. Sci. USA 104:6533-37
29. Eiswirth M, Freund A, Ross J. 1991. Adv. Chem. Phys. 90:127-99
30. Stemwedel JD, Schreiber I, Ross J. 1995. Adv. Chem. Phys. 89:327-88
31. Schreiber I, Ross J. 2003. J. Phys. Chem. A 107:9846-59
32. Mitchell M. 1996. An Introduction to Genetic Algorithms. Cambridge: MIT Press
33. Gilman A, Ross J. 1995. Biophys. J. 69:1321-33
34. Tsuchiya M, Ross J. 2003. Proc. Natl. Acad. Sci. USA 100:9691-95
35. Termonia Y, Ross J. 1981. Proc. Natl. Acad. Sci. USA 78:2952-56
36. Termonia Y, Ross J. 1982. Proc. Natl. Acad. Sci. USA 79:2878-81
37. Lazar JG, Ross J. 1990. Science 247:189-92
38. Lazar JG, Ross J. 1990. J. Chem. Phys. 92:3579-89
39. Escher C, Ross J. 1985. J. Chem. Phys. 82:2453-56
40. Schram H, Schell M, Ross J. 1988. J. Chem. Phys. 88:2730-34
41. Kocks P, Ross J, Bjorkman O. 1995. J. Phys. Chem. 99:16483-89
42. Schell M, Kundu K, Ross J. 1987. Proc. Natl. Acad. Sci. USA 84:424-28
43. Leigh EG Jr, Paine RT, Quinn JF, Suchanek TH. 1987. Proc. Natl. Acad. Sci. USA 84:1314-18
44. Kitano H. 2002. Science 295:1662-64
45. Sauer U, Heinemann M, Zamboni N. 2007. Science 316:550-51
46. Alon U. 2007. An Introduction to Systems Biology: Design Principles of Biological Circuits. London: Chapman & Hall/CRC. 301 pp.
47. Palsson BO. 2007. Systems Biology: Properties of Reconstructed Networks. New York: Cambridge Univ. Press. 322 pp.
48. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, et al. 2007. Science 316:593-97