Scientific challenges in systems biology

Introduction to Systems Biology

Volumn , Issue , 2007, Pages 3-13

  Kitano, Hiroaki ^a,b  

^a SONY COMPUTER SCIENCE LABORATORIES INC   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

robustness; Systems biology; technology platforms; trade offs

Indexed keywords

EID: 84871364629     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-59745-531-2_1     Document Type: Chapter

References (53)

1. Kitano H. Systems biology: a brief overview. Science 2002;295(5560):1662- 1664.
2. Kitano H. Computational systems biology. Nature 2002;420(6912):206-210.
3. Cannon WB. The Wisdom of the Body, 2nd edition. New York: W.W. Norton; 1939.
4. Wiener N. Cybernetics: Or Control and Communication in the Animal and the Machine. Cambridge: The MIT Press; 1948.
5. Bertalanffy LV. General System Theory. New York: George Braziller; 1968.
6. Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature 2002; 420(6912):224-230.
7. Guelzim N, Bottani S, Bourgine P, et al. Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002;31(1):60-63.
8. Ideker T, Ozier O, Schwikowski B, et al. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002;18 Suppl 1: S233-S240.
9. Ideker T, Thorsson V, Ranish JA, et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001; 292(5518):929-934.
10. Ihmels J, Friedlander G, Bergmann S, et al. Revealing modular organization in the yeast transcriptional network. Nat Genet 2002;31(4):370-377.
11. Ferrell JE, Jr. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 2002; 14(2):140-148.
12. Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Science 1999;283(5400):381-387.
13. Tyson JJ, Chen K, Novak B. Network dynamics and cell physiology. Nat Rev Mol Cell Biol 2001;2(12):908-916.
14. Chen KC, Calzone L, Csikasz-Nagy A, et al. Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 2004;15(8):3841-3462.
15. Kitano H. Biological robustness. Nat Rev Genet 2004;5(11):826-837.
16. Little JW, Shepley DP, Wert DW. Robustness of a gene regulatory circuit. EMBO J 1999;18(15):4299-4307.
17. Alon U, Surette MG, Barkai N, et al. Robustness in bacterial chemotaxis. Nature 1999;397(6715):168-171.
18. Barkai N, Leibler S. Robustness in simple biochemical networks. Nature 1997;387(6636):913-917.
19. Yi TM, Huang Y, Simon MI, et al. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 2000;97(9):4649-4653.
20. von Dassow G, Meir E, Munro EM, Odell GM. The segment polarity network is a robust developmental module. Nature 2000;406(6792):188-192.
21. Kitano H. Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer 2004;4(3):227-235.
22. Kitano H. Cancer robustness: tumour tactics. Nature 2003;426(6963):125.
23. Wagner GP, Altenberg L. Complex adaptations and the evolution of evolvability. Evolution 1996;50(3):967-976.
24. Rutherford SL. Between genotype and phenotype: protein chaperones and evolvability. Nat Rev Genet 2003;4(4):263-274.
25. de Visser J, Hermission J, Wagner GP, et al. Evolution and Detection of Genetics Robustness. Evolution 2003;57(9):1959-1972.
26. Agrawal AA. Phenotypic plasticity in the interactions and evolution of species. Science 2001;294(5541):321-326.
27. Schlichting C, Pigliucci M. Phenotypic Evolution: A Reaction Norm Perspective. Sunderland: Sinauer Associates, Inc.; 1998.
28. Eldar A, Dorfman R, Weiss D, et al. Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature 2002;419(6904):304-308.
29. Meir E, von Dassow G, Munro E, et al. Robustness, flexibility, and the role of lateral inhibition in the neurogenic network. Curr Biol 2002;12(10): 778-786.
30. Schlosser G, Wagner G. Modularity in Development and Evolution. Chicago: The University of Chicago Press; 2004.
31. Rutherford SL, Lindquist S. Hsp90 as a capacitor for morphological evolution. Nature 1998;396(6709):336-342.
32. Queitsch C, Sangster TA, Lindquist S. Hsp90 as a capacitor of phenotypic variation. Nature 2002;417(6889):618-624.
33. Siegal ML, Bergman A. Waddington's canalization revisited: developmental stability and evolution. Proc Natl Acad Sci USA 2002;99(16):10528-10532.
34. Waddington CH. The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology. New York: Macmillan; 1957.
35. Csete ME, Doyle J. Bow ties, metabolism and disease. Trends Biotechnol 2004;22(9):446-450.
36. Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003;19(11):1423-1430.
37. Oda K, Kitano H. A comprehensive pathway map of toll-like receptor signaling network. Mol Syst Biol 2:2006.0015. Epub 2006 Apr 18.
38. Oda K, Matsuoka Y, Funahashi, et al. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 2005;1:E1-17.
39. Kitano H, Oda K. Self-extending symbiosis: a mechanism for increasing robustness through evolution. Biol Theory 2006;1(1):61-66.
40. Kirschner M, Gerhart J. Evolvability. Proc Natl Acad Sci USA 1998;95(15): 8420-8427.
41. Carlson JM, Doyle J. Highly optimized tolerance: a mechanism for power laws in designed systems. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1999;60(2 Pt A):1412-4127.
42. Carlson JM, Doyle J. Complexity and robustness. Proc Natl Acad Sci USA 2002;99 Suppl 1:2538-2545.
43. Bak P, Tang C, Wiesenfeld K. Self-organized criticality. Phys Rev A 1988; 38(1):364-374.
44. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004;5(2):101-113.
45. Kitano H, Kimura T, Oda K, et al. Metabolic syndrome and robustness tradeoffs. diabetes. 2004;53(Supplment 3):S1-S10.
46. Harris AL. Hypoxia-a key regulatory factor in tumour growth. Nat Rev Cancer 2002;2(1):38-47.
47. Sharp FR, Bernaudin M. HIF1 and oxygen sensing in the brain. Nat Rev Neurosci 2004;5(6):437-448.
48. Kitano H, Oda K. Robustness trade-offs and host-microbial symbiosis in the immune system. Mol Syst Biol 2006;doi:10.1038/msb4100039.
49. Kitano H. A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 2007;6(3):202-210.
50. Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003;19(4):524-531.
51. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle J, Kitano H. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Pac Symp Biocomput 2002: 450-461.
52. Kitano H. Computational Cellular Dynamics: A Network-Physics Integral. Nat Rev Mol Cell Biol 2006;7:163.
53. Balagadde FK, You L, Hansen CL, Arnold FH, Quake SR. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 2005;309(5731):137-140.