Using nonlinear stochastic evolutionary game strategy to model an evolutionary biological network of organ carcinogenesis under a natural selection scheme

Evolutionary Bioinformatics

Volumn 11, Issue , 2015, Pages 155-178

  Chen, Bor Sen ^a   Tsai, Kun Wei ^a   Li, Cheng Wei ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Carcinogenesis; Global linearization; Hamilton Jacobi inequality; LMI; Natural selection; Network evolution; Network phenotype robustness criterion; Stochastic evolutionary game strategy

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; CALCULATION; CANCER STAGING; CARCINOGENESIS; COMPUTER MODEL; EPIGENETICS; GENETIC TRAIT; GENETIC VARIABILITY; HERITABILITY; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; NATURAL SELECTION; NEGATIVE FEEDBACK; NONLINEAR SYSTEM; PHENOTYPIC VARIATION; PREDICTION; STATISTICAL ANALYSIS;

EID: 84937416292     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S26195     Document Type: Article

References (53)

1. Kaern M, Blake WJ, Collins JJ. The engineering of gene regulatory networks. Annu Rev Biomed Eng. 2003; 5: 179-206.
2. Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet. 2005; 6(6): 451-64.
3. Chu LH, Chen BS. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. BMC Syst Biol. 2008; 2: 56.
4. Ao P. Laws in Darwinian evolutionary theory. Phys Life Rev. 2005; 2(2): 117-56.
5. Carter AJ, Hermisson J, Hansen TF. The role of epistatic gene interactions in the response to selection and the evolution of evolvability. Theor Popul Biol. 2005; 68(3): 179-96.
6. Bloom JD, Labthavikul ST, Otey CR, Arnold FH. Protein stability promotes evolvability. Proc Natl Acad Sci U S A. 2006; 103(15): 5869-74.
7. Aldana M, Balleza E, Kauffman S, Resendiz O. Robustness and evolvability in genetic regulatory networks. J Theor Biol. 2007; 245(3): 433-48.
8. Felix MA, Wagner A. Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity. 2008; 100(2): 132-40.
9. Chen BS, Lin YP. A unifying mathematical framework for genetic robustness, environmental robustness, network robustness and their trade-off on phenotype robustness in biological networks part I: gene regulatory networks in systems and evolutionary biology. Evol Bioinform Online. 2013; 9: 43-68.
10. Chen BS, Lin YP. A unifying mathematical framework for genetic robustness, environmental robustness, network robustness and their tradeoff on phenotype robustness in biological networks part II: ecological networks. Evol Bioinform Online. 2013; 9: 69-85.
11. Chen BS, Lin YP. A unifying mathematical framework for genetic robustness, environmental robustness, network robustness and their trade-offs on phenotype robustness in biological networks. Part III: synthetic gene networks in synthetic biology. Evol Bioinform Online. 2013; 9: 87-109.
12. Kitano H. Biological robustness. Nat Rev Genet. 2004; 5(11): 826-37.
13. Wagner A. Robustness and evolvability: a paradox resolved. Proc Biol Sci. 2008; 275(1630): 91-100.
14. Chen BS, Wu WS, Wu WS, Li WH. On the adaptive design rules of biochemical networks in evolution. Evol Bioinform Online. 2007; 3: 27-39.
15. Draghi JA, Parsons TL, Wagner GP, Plotkin JB. Mutational robustness can facilitate adaptation. Nature. 2010; 463(7279): 353-55.
16. Chen B-S, Lin Y-P. On the interplay between the evolvability and network robustness in an evolutionary biological network: a systems biology approach. Evol Bioinform Online. 2011; 7: 201.
17. Barillot E. Computational Systems Biology of Cancer. Boca Raton, FL: CRC Press; 2013.
18. Wong YH, Chen RH, Chen BS. Core and specific network markers of carcinogenesis from multiple cancer samples. J Theor Biol. 2014; 362: 17-34.
19. Tawfik DS. Messy biology and the origins of evolutionary innovations. Nat Chem Biol. 2010; 6(10): 692-6.
20. Ao P, Galas D, Hood L, Zhu X. Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution. Med Hypotheses. 2008; 70(3): 678-84.
21. Weinberg RA. The Biology of Cancer. New York: Taylor & Francis Group; 2006.
22. Murgia C, Pritchard JK, Kim SY, Fassati A, Weiss RA. Clonal origin and evolution of a transmissible cancer. Cell. 2006; 126(3): 477-87.
23. Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nat Med. 2004; 10(8): 789-99.
24. Nagy JD. Competition and natural selection in a mathematical model of cancer. Bull Math Biol. 2004; 66(4): 663-87.
25. Kitano H. Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer. 2004; 4(3): 227-35.
26. Kitano H. Cancer robustness: tumour tactics. Nature. 2003; 426(6963): 125-5.
27. Lobov IB, Brooks PC, Lang RA. Angiopoietin-2 displays VEGF-dependent modulation of capillary structure and endothelial cell survival in vivo. Proc Natl Acad Sci USA. 2002; 99(17): 11205-10.
28. Yancopoulos GD, Davis S, Gale NW, Rudge JS, Wiegand SJ, Holash J. Vascular-specific growth factors and blood vessel formation. Nature. 2000; 407(6801): 242-8.
29. Greaves MF. Cancer: The Evolutionary Legacy. Oxford: Oxford University Press; 2000.
30. Carmeliet P, Jain RK. Angiogenesis in cancer and other diseases. Nature. 2000; 407(6801): 249-57.
31. Weibel ER. The Pathway for Oxygen: Structure and Function in the Mammalian Respiratory System. Cambridge, Mass: Harvard University Press; 1984.
32. Chen BS, Ho SJ. The stochastic evolutionary game for a population of biological networks under natural selection. Evol Bioinform Online. 2014; 10: 17-38.
33. Gardner WA. Introduction to Random Processes: With Applications to Signals and Systems. Vol 31. New York: McGraw-Hill; 1990.
34. Chen B-S, Uang H-J, Tseng C-S. Robust tracking enhancement of robot systems including motor dynamics: a fuzzy-based dynamic game approach. IEEE Trans Fuzzy Syst. 1998; 6(4): 538-52.
35. Chen B-S, Tseng C-S, Uang H-J. Fuzzy differential games for nonlinear stochastic systems: suboptimal approach. IEEE Trans Fuzzy Syst. 2002; 10(2): 222-33.
36. de Visser JA, Hermisson J, Wagner GP, et al. Perspective: evolution and detection of genetic robustness. Evolution. 2003; 57(9): 1959-72.
37. Vincent TL, Brown JS. Evolutionary Game Theory, Natural Selection, and Darwinian Dynamics. Cambridge, UK: Cambridge University Press; 2005.
38. Chen BS, Chang CH, Lee HC. Robust synthetic biology design: stochastic game theory approach. Bioinformatics. 2009; 25(14): 1822-30.
39. Chen BS, Hsu CY, Liou JJ. Robust design of biological circuits: evolutionary systems biology approach. J Biomed Biotechnol. 2011; 2011: 304236.
40. Boyd SP. Linear Matrix Inequalities in System and Control Theory. Philadelphia: Society for Industrial and Applied Mathematics; 1994.
41. Chen B-S, Zhang W. Stochastic H 2/H∞ control with state-dependent noise. IEEE Trans Autom Control. 2004; 49(1): 45-57.
42. Zhang W, Chen B-S. State feedback H-∞ control for a class of nonlinear stochastic systems. Ser Intell Control Intell Autom. 2006; 44(6): 1973-91.
43. Wang YC, Chen BS. A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med Genomics. 2011; 4: 2.
44. Chen W-H, Chen B-S. Robust stabilization design for nonlinear stochastic system with Poisson noise via fuzzy interpolation method. Fuzzy Set Syst. 2013; 217(0): 41-61.
45. Tomasetti C, Vogelstein B. Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science. 2015; 347(6217): 78-81.
46. Shukla S, Meeran SM. Epigenetics of cancer stem cells: pathways and therapeutics. Biochim Biophys Acta. 2014; 1840(12): 3494-502.
47. Kozielski J, Kaczmarczyk G, Porębska I, Szmygin-Milanowska K, Gołecki M. Lung cancer in patients under the age of 40 years. Contemp Oncol (Pozn). 2012; 16: 413-5.
48. Crespi B, Summers K. Evolutionary biology of cancer. Trends Ecol Evol. 2005; 20(10): 545-52.
49. Campisi J. Aging, tumor suppression and cancer: high wire-act! Mech Ageing Dev. 2005; 126(1): 51-8.
50. Waddington CH. Canalization of development and the inheritance of acquired characters. Nature. 1942; 150: 563-5.
51. Voit EO, Ferreira AEN. Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists. Cambridge: Cambridge University Press; 2000.
52. Hasty J, Dolnik M, Rottschafer V, Collins JJ. Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett. 2002; 88(14): 148101.
53. Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci U S A. 2003; 100(13): 7714-9.