Intracellular signaling: Spatial and temporal control

Physiology

Volumn 20, Issue 3, 2005, Pages 169-179

  Moraru, Ion I ^a   Loew, Leslie M ^a  

^a UNIVERSITY OF CONNECTICUT SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; CYCLIC AMP;

ANIMAL; BIOLOGICAL MODEL; CELL FUNCTION; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; COMPUTER SIMULATION; CYTOLOGY; EUKARYOTIC CELL; GENE EXPRESSION; HUMAN; MAMMAL; MOLECULAR INTERACTION; PHYSIOLOGY; REVIEW; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SIMULATION;

ANIMALS; COMPUTER SIMULATION; EUKARYOTIC CELLS; HUMANS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION;

EID: 20444384349     PISSN: 15489213     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiol.00052.2004     Document Type: Review

References (63)

1. Alon U. Biological networks: the tinkerer as an engineer. Science 301: 1866-1867, 2003.
2. Bhalla US. Use of Kinetikit and GENESIS for modeling signaling pathways. Methods Enzymol 345: 3-23, 2002.
3. Bhalla US. Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways. Biophys J 87: 733-744, 2004.
4. Bhalla US. Signaling in small subcellular volumes. II. Effects on synaptic network properties. Biophys J 87: 745-753, 2004.
5. Bhalla US and lyengar R. Emergent properties of networks of biological signaling pathways. Science 283: 381-387, 1999.
6. Bray D. Reductionism for biochemists - how to survive the protein jungle. Trends Biochem Sci 22: 325-326, 1997.
7. Bray D. Molecular networks: the top-down view. Science 301: 1864-1865, 2003.
8. Cao Y, Li H, and Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J Chem Phys 121: 4059-4067, 2004.
9. Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, and Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 15: 3841-3862, 2004.
10. Csete ME and Doyle JC. Reverse engineering of biological complexity. Science 295: 1664-1669, 2002.
11. Csete M and Doyle J. Bow ties, metabolism and disease. Trends Biotechnol 22: 446-450, 2004.
12. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338, 2000.
13. Endy D and Brent R. Modelling cellular behaviour. Nature 409: 391-395, 2001.
14. 2+ wave along the cell surface in a model of the Xenopus egg. J Theor Biol 231: 487-496, 2004.
15. Fell DA. Understanding the Control of Metabolism. London: Portland, 1997.
16. Fink CC, Slepchenko B, Moraru II, Schaff J, Watras J, and Loew LM. Morphological control of inositol-1,4,5-trisphosphate-dependent signals. J Cell Biol 147: 929-935, 1999.
17. Finney A and Hucka M. Systems biology markup language: level 2 and beyond. Biochem Soc Trans 31: 6-7, 2003.
18. Friedman N. Inferring cellular networks using probabilistic graphical methods. Science 303: 799-805, 2004.
19. Gardner TS, Cantor CR, and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342, 2000.
20. Gardner TS, di Bernardo D, Lorenz D, and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105, 2003.
21. Gibson M and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104: 1876-1889, 2000.
22. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361, 1977.
23. 2+ release. Biophys J 83: 2918-2945, 2002.
24. Hartwell LH, Hopfield JJ, Leibler S, and Murray AW. From molecular to modular cell biology. Nature 402: C47-C52, 1999.
25. Hasty J, McMillen D, and Collins JJ. Engineered gene circuits. Nature 420: 224-230, 2002.
26. Haugh JM, Schooler K, Wells A, Wiley HS, and Lauffenburger DA. Effect of epidermal growth factor internalization on regulation of the phospholipase C-γ1 signaling pathway. J Biol Chem 27: 8958-8965, 1999.
27. Hood L, Heath JR, Phelps ME, and Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science 306: 640-643, 2004.
28. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, and Wang J; SBML Forum. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531, 2003.
29. Ideker T, Galitski T, and Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2: 343-372, 2001.
30. Ideker T and Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 21: 255-262, 2003.
31. Jordan MI. Learning in Graphical Models. Cambridge, MA: MIT Press, 1998.
32. Kholodenko BN. Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors. J Exp Biol 206: 2073-2082, 2003.
33. Kitano H. Systems biology: a brief overview. Science 295: 1662-1664, 2002.
34. Lander E. Array of hope. Nat Genet 21: 3-4, 1999.
35. Lazebnik Y. Can a biologist fix a radio? Or, what I learned while studying apoptosis. Cancer Cell 2: 179-182, 2002.
36. Loew LM and Schaff JC. The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol 19: 401-406, 2001.
37. Lloyd CM, Halstead MD, and Nielsen PF. Cell ML: its future, present and past. Prog Biophys Mol Biol 85: 433-450, 2004.
38. Mannella CA, Pfeiffer DR, Bradshaw PC, Moraru II, Slepchenko B, Loew LM, Hsieh C, Buttle K, and Marko M. Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications. IUBMB Life 52: 93-100, 2001.
39. McAdams HH and Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 15: 65-69, 1999.
40. McAdams HH and Shapiro L. A bacterial cell-cycle regulatory network operating in time and space. Science 301: 1874-1877, 2003.
41. Mellman I and Misteli T. Computational cell biology. J Cell Biol 161: 463-464, 2003.
42. Mendes P. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem Sci 22: 361-363, 1997.
43. Mohler WA and White JG. Multiphoton imaging of embryonic development. In: Imaging Neurons: A Laboratory Manual, edited by Yuste R, Lanni F, and Konnerth A. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 2000, sect. 3, chapt. 21, p. 21.11-21.21.
44. Nachman I, Regev A, and Friedman N. Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20: i248-i256, 2004.
45. Neves SR and Iyengar R. Modeling of signaling networks. Bioessays 24: 1110-1117, 2002.
46. Noble D. Modeling the heart. Physiology 19: 191-197, 2004.
47. Novak B and Tyson JJ. Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. J Cell Sci 106: 1153-1168, 1993.
48. Peletier MA, Westerhoff HV, and Kholodenko BN. Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J Theor Biol 225: 477-487, 2003.
49. Phair RD and Misteli T. Kinetic modeling approaches to in vivo imaging. Nat Rev Mol Cell Biol 2: 898-907, 2001.
50. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, and Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555, 2002.
51. Resat H, Ewald JA, Dixon DA, and Wiley HS. An integrated model of epidermal growth factor receptor trafficking and signal transduction. Biophys J 85: 730-743, 2003.
52. 2+ release in the functional unit of the cardiac diadic space. Biophys J 77: 1871-1884, 1999.
53. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, and Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176, 2003.
54. Selinger DW, Wright MA, and Church GM. On the complete determination of biological systems. Trends Biotechnol 21: 251-254, 2003.
55. Slepchenko BM, Schaff JC, Carson JH, and Loew LM. Computational cell biology: spatiotemporal simulation of cellular events. Annu Rev Biophys Biomol Struct 31: 423-441, 2002.
56. Slepchenko BM, Schaff JC, Macara I, and Loew LM. Quantitative cell biology with the Virtual Cell. Trends Cell Biol 13: 570-576, 2003.
57. Sourjik V. Receptor clustering and signal processing in E. coli chemotaxis. Trends Microbiol 12: 569-576, 2004.
58. Stelling J, Sauer U, Szallasi Z, Doyle FJ, and Doyle J. Robustness of cellular functions. Cell 118: 675-685, 2004.
59. Stiles JR and Bartol TM. Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: Computational Neuroscience: Realistic Modeling for Experimentalists, edited by De Schutter E. Boca Raton, FL: CRC, 2001, p. 87-127.
60. Tyson JJ, Chen KC, and Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221-231. 2003.
61. 2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support. Cell Calcium 35: 433-447, 2004.
62. Wiley HS, Shvartsman SY, and Lauffenburger DA. Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol 13: 43-50, 2003.
63. Wolf DM and Arkin AP. Motifs, modules and games in bacteria. Curr Opin Microbiol 6: 125-134, 2003.