Identification of intra-cellular feedback loops by intermittent step perturbation method

IFAC Proceedings Volumes (IFAC-PapersOnline)

Volumn 17, Issue 1 PART 1, 2008, Pages

  Dong, Chaoyi ^a   Cho, Kwang Hyun ^a   Yoon, Tae Woong ^a  

^a NONE

Author keywords

Control in system biology

Indexed keywords

BIO-MOLECULAR; CELLULAR PROCESS; FEED-BACK LOOP; GENE TRANSCRIPTIONS; IDENTIFICATION METHOD; PERTURBATION METHOD; REGULATION AND CONTROL; REGULATORY MECHANISM; REGULATORY NETWORK; SIGNAL TRANSDUCTION PATHWAYS; STATISTICAL ALGORITHM; STOCHASTIC FUNCTIONS; TIME-SERIES DATA;

BACTERIOPHAGES; IDENTIFICATION (CONTROL SYSTEMS); LAWS AND LEGISLATION; MOLECULAR BIOLOGY; PERTURBATION TECHNIQUES; SIGNAL TRANSDUCTION; TRANSCRIPTION;

FEEDBACK;

EID: 79961019580     PISSN: 14746670     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.3182/20080706-5-KR-1001.1224     Document Type: Conference Paper

References (22)

1. A.Arkin, J.Ross (1995). Statistical construction of chemicalreaction mechanisms from measured time-series. J. Phys. Chem., vol.99, pp. 970?979.
2. A.R.Sedaghat, A.Sherman and M.J.Quon (2002). A mathematical model of metabolic insulin signaling pathways. Am. J. Physiol Endocrinol Metab., vol.283, pp. 1084-1101.
3. H.Eisen, P.Brachet, L.Pereira da Silva and F.Jacob (1967). Regulation of repressor inhibition in lambda. Proc. Natl. Acad. Sci., vol.66, pp. 855?862.
4. J.E.T.Corrie, Y.Katayama, G.P.Reid, M.Anson, D.R. Trentham (1992). The development and application of photosensitive caged compounds to aid time-resolved structure determination of macromolecules. Philos. Trans. R. Soc. London Ser., A vol. 340, pp. 233-243.
5. J.J.Rice, Y.H.Tu and G.Stolovitzky (2005). Reconstructing biological networks using conditional correlation analysis. Bioinformatics, vol.21, N. 6, pp. 765-773.
6. J.M.Nerbonne (1986). Design and application of photolabile intracellular probes. Soc. Gen. Physiol. Ser., vol.40, pp. 417-445
7. J.Wolf and R.Heinrich (2000). Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation. Biochem J., vol.345, pp. 321-334.
8. K.DeFea and R.A.Roth (1997). Protein kinase C modulation of insulin receptor substrate-1 tyrosine phosphorylation requires serine 612. Biochemistry, vol.36, pp. 12939?12947.
9. K.-H.Cho, J.-R.Kim, S.Baek, H.-S.Choi, and S.-M.Choo (2006). Inferring Biomolecular Regulatory Networks from Phase Portraits of Time-Series Expression profiles. FEBS Letters, vol.580, pp. 3511-3518.
10. K.Paz, Y.F.Liu, H.Shorer, R.Hemi, D.LeRoith, M.Quon, H.Kanety, R.Seger and Y.Zick (1999). Phosphorylation of insulin receptor substrate-1 (IRS-1) by protein kinase B positively regulates IRS-1 function. J. Biol. Chem., vol.274, pp. 28816?28822.
11. L.V.Ravichandran, H.Chen, Y.Li, and M.J.Quon (2001a). Phosphorylation of PTP1B at Ser(50) by Akt impairs its ability to dephosphorylate the insulin receptor. Mol. Endocrinol, vol.15, pp. 1768?1780.
12. L.V.Ravichandran, D.L.Esposito, J.Chen, and M.J.Quon (2001b). Protein kinase C-phosphorylates insulin receptor substrate-1 and impairs its ability to activate phosphatidylinositol 3-kinase in response to insulin. J. Biol. Chem., vol.276, pp. 3543?3549.
13. L.Wolpert and J.H.Lewis (1975). Towards a theory of development. Fed. Proc., vol.34, pp. 14?20.
14. M.B.Eisen, P.T.Spellman, P.O.Brown and D.Botstein (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, vol.95, pp. 14863? 14868.
15. M.Maeda, Lu.Sijie, G.Shaulsky, Y.Miyazaki, H.Kuwayama, Y.Tanaka, A.Kuspa and W.F.Loomis (2004). Periodic signaling controlled by an oscillatory circuit that includes protein kinase ERK2 and PKA. Science, vol.304, pp. 875- 878.
16. M.T.Laub and W.F.Loomis (1998). A molecular network that produces spontaneous oscillations in excitable cells of dictyostelium. Molecular Biology of the Cell, vol.9, pp. 3521-3532.
17. R.Thomas and M.Kaufman (2001). Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chao, vol.11, pp. 170-179.
18. S.H.Strogatz (2000). From Kuramoto to Crawford: Exploring the onset of synchronization in populations of coupled oscillations. Physica D., vol.143, pp. 1-20.
19. S.R.Adams and R.Y.Tsien (1993). Controlling cell chemistry with caged compounds. Annu. Rev. Physiol. , vol.55, pp. 755-784
20. T.E.Hull, and A.R.Dobell (1962). Random Number Generater Soc. Indust. Appl. Math. Rev., vol.4, pp. 230-254.
21. W.Vance, A.Arkin, J.Ross (2002). Determination of causal connectivities of biomolecular species in reaction networks. Proc. Natl. Acad. Sci. USA, vol.99, pp. 5816?5821.
22. P.E. Caines and C.W. Chan, (1975). Feedback between stationary stochastic processes. IEEE Trans AC. vol.20, pp. 498-508.