Bipolar linear algebra and yinyang-N-element cellular networks for equilibrium-based biosystem simulation and regulation

Journal of Biological Systems

Volumn 17, Issue 4, 2009, Pages 547-576

  Zhang, Wen Ran ^a   Zhang, Jane H ^a   Shi, Yong ^b,c   Chen, Su Shing ^d  

^a GEORGIA SOUTHERN UNIVERSITY   (United States)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c UNIVERSITY OF NEBRASKA AT OMAHA   (United States)

^d Chinese Academy of Sciences   (China)

Author keywords

Aging and Degeneration; Bipolar Linear Algebra; Equilibrium and Non Equilibrium Conditions; Repression and Activation; Simulation and Regulation; YinYang N Element Bipolar Cellular Networks

Indexed keywords

EID: 75149193123     PISSN: 02183390     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218339009002958     Document Type: Article

References (31)

1. Shi Y, Seto E, Chang L-S, Shenk T, Transcriptional repression by YY1, a human GLI-Kruppel-related protein, and relief of repression by adenovirus E1A protein, Cell 67:377-388, 1991.
2. Emran F, Florens L, Ma B, Swanson SK, Washburn MP, Hernandez N, A role for Yin Yang-1 (YY1) in the assembly of snRNA transcription complexes, Gene 1(377):96-108, 2006.
3. Kim JD, Faulk C, Kim J, Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1, Nucleic Acid Res 35(10):3442-3452, 2007.
4. Liu H, Schmidt-Supprian M, Shi Y, Hobeika E, Barteneva N, Jumaa H, Pelanda R, Reth M, Skok J, Rajewsky K, Shi Y, Yin Yang 1 is a critical regulator of B-cell development, Genes Dev 21:1179-1189, 2007.
5. Palko L, Bass HW, Beyrouthy MJ, Hurt MM, The Yin Yang-1 (YY1) protein undergoes a DNA-replication-associated switch in localization from the cytoplasm to the nucleus at the onset of S phase, J Cell Sci 117:465-476, 2004.
6. Park K, Atchison ML, Isolation of a candidate repressor/activator, NF-E1 (YY-1, delta), that binds to the immunoglobulin kappa 3′ enhancer and the immunoglobulin heavy-chain mu E1 site, Proc Natl Acad Sci USA 88(21):9804-9808, 1991.
7. Santiago FS, Ishii H, Shafi S, Khurana R, Kanellakis P, Bhindi R, Ramirez MJ, Bobik A, Martin JF, Chesterman CN, Zachary IC, Khachigian LM, Yin Yang-1 inhibits vascular smooth muscle cell growth and intimal, thickening by repressing p21WAF1/Cip1 transcription and p21WAF1/Cip1-Cdk4-Cyclin D1 assembly, Circ Res 101:146-155, 2007.
8. Vasudevan S, Tong Y, Steitz JA, Switching from repression to activation: MicroRNAs can up-regulate translation, Science 318(5858):1931-1934, 2007.
9. Wilkinson FH, Park K, Atchison ML, Polycomb recruitment to DNA in vivo by the YY1 REPO domain, Proc Natl Acad Sci USA 103:19296-19301, 2006.
10. Zhou Q, Yik JHN, The Yin and Yang of P-TEFb regulation: Implications for human immunodeficiency virus gene expression and global control of cell growth and differentiation, Microbiol Mol Biol Rev 70(3):646-659, 2006.
11. Alvarez-Ramirez J, Rodriguez E, Echeverria JC, Velasco-Hernandez JX, Equilibrium multiplicity in a cardiovascular system model, J Biol Syst 14(3):445-461, 2006.
12. Carotenuto L, Pace V, Bellizzi D, De Benedictis G, Equilibrium, stability and dynamical response in a model of the extrinsic apoptosis pathway, J Biol Syst 15(3):261-285, 2007.
13. Vakarelov II, Symmetry with the pinus mugo turra - An ecological approach, J Biol Syst 15(3):365-384, 2007.
14. Yin W, Voit EO, Construction and customization of stable oscillation models in biology, J Biol Syst 16(4):463-478, 2008.
15. McKelvey B, Toward a 0-super-th law of thermodynamics: Order-creation complexity dynamics from physics and biology to bioeconomics, J Bioecon 6(1):65-96, 2004.
16. Zhang W-R, Chen S, Bezdek JC, POOL2: A generic system for cognitive map development and decision analysis, IEEE T Syst Mon Cyb 19(1):31-39, 1989.
17. Zhang W-R, Chen S, Wang W, King R, A cognitive map based approach to the coordination of distributed cooperative agents, IEEE T Syst Mon Cyb 22(1):103-114, 1992.
18. Zhang W-R, NPN fuzzy sets and NPN qualitative algebra: A computational framework for bipolar cognitive modeling and multiagent decision analysis, IEEE T Syst Mon Cyb 16:561-574, 1996.
19. ZhangW-R, Equilibrium relations and bipolar cognitive mapping for online analytical processing with applications in international relations and strategic decision support, IEEE T Syst Mon Cyb 33(2):295-307, 2003.
20. Zhang W-R, Zhang L, YinYang bipolar logic and bipolar fuzzy logic, Inf Sci 165(3- 4):265-287, 2004.
21. Zhang W-R, YinYang bipolar lattices and L-sets for bipolar knowledge fusion, visualization, and decision, Int J Inf Tech Decis 4(4):621-645, 2005.
22. Zhang W-R, YinYang bipolar fuzzy sets and fuzzy equilibrium relations for bipolar clustering, optimization, and global regulation, Int J Inf Tech Decis 5(1):19-46, 2006.
23. Zhang W-R, Pandurangi A, Peace K, YinYang dynamic neurological modeling and diagnostic analysis of major depressive and bipolar disorders, IEEE T Biomed Eng 54(10):1729-1739, 2007.
24. Zhang W-R, YinYang Bipolar Universal Modus Ponens (BUMP) - A fundamental law of non-linear brain dynamics for emotional intelligence and mental health, in Proc of Walter J Freeman Workshop on Nonlinear Brain Dynamics (JCIS), July 2007, Salt Lake City, doi:10.1142/9789812709677 0014, 2007.
25. Zhang W-R, Six conjectures in quantum physics and computational neuroscience, in Proceedings of the Third International Conference on Quantum, Nano and Micro Technologies (ICQNM 2009), February 1-7, 2009, Cancun, Mexico, DOI 10.1109/ICQNM.2009.32.
26. Zhang W-R, YinYang bipolar dynamic logic (BDL) and equilibrium-based computational neuroscience, to appear in Proceedings of the International Joint Conference on Neural Networks (IJCNN 2009), Atlanta, 2009.
27. ZhangW-R, Chen SS, Equilibrium and non-equilibrium modeling of YinYangWuxing for diagnostic decision analysis in traditional chinese medicine, Int J Inf Tech Decis, Vol.8, No.3, September 2009 (in press).
28. Maciocia G, The Foundations of Chinese Medicine: A Comprehensive Text for Acupuncturists and Herbalists, Churchill Livingstone, 1989.
29. Li F, Functional structure mode of human body and Yinyang-Wuxing equations, Phys Scr 36:966-969, 1987.
30. Sengupta S, Toh S-A, Sellers LA, Skepper JN, Koolwijk P, Leung HW, Yeung H-W, Wong RNS, Sasisekharan R, Fan T-PD, Modulating angiogenesis: The Yin and the Yang in Ginseng, Circulation 110(10):1219-1225, 2004.
31. Olson D, Shi Y, Introduction to Business Data Mining, McGraw-Hill/Irwin, 2007.