Automated construction and analysis of the design space for biochemical systems

Bioinformatics

Volumn 26, Issue 20, 2010, Pages 2601-2609

  Fasani, Rick A ^a   Savageau, Michael A ^a  

^a University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; BIOCHEMISTRY; BIOLOGICAL MODEL; BIOLOGY; METHODOLOGY; PHENOTYPE; SYSTEMS BIOLOGY;

AUTOMATION; BIOCHEMICAL PHENOMENA; COMPUTATIONAL BIOLOGY; MODELS, BIOLOGICAL; PHENOTYPE; SYSTEMS BIOLOGY;

EID: 77957765858     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq479     Document Type: Article

References (30)

1. Atkinson,M.R. et al. (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell, 113, 597-607.
2. Avis,D. and Fukuda,K. (1992) A pivoting algorithm for convex hulls and vertex enumeration of arrangements and polyhedra. Discrete Comput. Geom., 8, 295-313.
3. Avis,D. et al. (1997) How good are convex hull algorithms? Comput. Geom.,7,265-301.
4. Boyd,S.P. and Vandenberghe,L. (2004) Convex Optimization. Cambridge University Press, Cambridge, UK.
5. Coelho,P.M. et al. (2009) Quantifying global tolerance of biochemical systems: design implications for moiety-transfer cycles. PLoS Comput. Biol., 5, e1000319.
6. Dantzig,G.B. (1963) Linear Programming and Extensions. Princeton University Press, Princeton, NJ.
7. Hlavacek,W.S. and Savageau,M.A. (1995) Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. J. Mol. Biol., 248, 739-755.
8. Hlavacek,W.S. and Savageau,M.A. (1996) Rules for coupled expression of regulator and effector genes in inducible circuits. J. Mol. Biol., 255, 121-139.
9. Lander,E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
10. Mehlhorn,K. and Sagraloff,M. (2009) Isolating real roots of real polynomials. In Proceedings of the 2009 International Symposium on Symbolic and Algebraic Computation. ACM, Seoul, Republic of Korea, pp. 247-254.
11. Metzker,M.L. (2010) Sequencing technologies the next generation. Nat. Rev. Genet., 11, 31-46.
12. Mourrain,B. and Pavone,J.P. (2009) Subdivision methods for solving polynomial equations. J. Symbolic Comput., 44, 292-306.
13. Pan,V.Y. (1997) Solving a polynomial equation: some history and recent progress. SIAM Rev., 39, 187-220.
14. Pan,V.Y. (2001) Univariate polynomials: nearly optimal algorithms for factorization and rootfinding. In Proceedings of the 2001 International Symposium on Symbolic and Algebraic Computation. ACM, London, Ontario, Canada, pp. 253-267.
15. Sanger,F. et al. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
16. Savageau,M.A. (1971a) Concepts relating the behavior of biochemical systems to their underlying molecular properties. Arch. Biochem. Biophys., 145, 612-621.
17. Savageau,M.A. (1971b) Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature, 229, 542-544.
18. Savageau,M.A. (1974) Comparison of classical and autogenous systems of regulation in inducible operons. Nature, 252, 546-549.
19. Savageau,M.A. (1975) Optimal design of feedback control by inhibition. J. Mol. Evol., 5, 199-222.
20. Savageau,M.A. (2001) Design principles for elementary gene circuits: elements, methods, and examples. Chaos, 11, 142-159.
21. Savageau,M.A. (2002) Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation. Math. Biosci., 180, 237-253.
22. Savageau,M.A. (2009) Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Reprint of the original edition published byAddison-Wesley, Reading, MA, 1976.
23. Savageau,M.A. and Fasani,R.A. (2009) Qualitatively distinct phenotypes in the design space of biochemical systems. FEBS Lett., 583, 3914-3922.
24. Savageau,M.A. and Voit,E.O. (1987) Recasting nonlinear differential equations as S-systems: a canonical nonlinear form. Math. Biosci., 87, 83-115.
25. Savageau,M.A. et al. (2009) Phenotypes and tolerances in the design space of biochemical systems. Proc. Natl Acad. Sci. USA, 106, 6435-6440.
26. Shendure,J. and Ji,H. (2008) Next-generation DNA sequencing. Nat. Biotechnol., 26, 1135-1145.
27. Vanderbei,R.J. (2008) Linear Programming: Foundations and Extensions. Springer, New York.
28. Venter,J.C. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
29. Yamamura,K. and Fujioka,T. (2003) Finding all solutions of nonlinear equations using the dual simplex method. J. Comput. Appl. Math., 152, 587-595.
30. Yamamura,K. et al. (2009) LP narrowing: a new strategy for finding all solutions of nonlinear equations. Appl. Math. Comput., 215, 405-413.