| [1] | Kholodenko BN (2006) Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 7: 165–176.
|
| [2] | Kumar D, Srikanth R, Ahlfors H, Lahesmaa R, Rao KV (2007) Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol Syst Biol 3: 150.
|
| [3] | Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283: 381–387.
|
| [4] | Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47–52.
|
| [5] | Helikar T, Konvalina J, Heidel J, Rogers JA (2008) Emergent decision-making in biological signal transduction networks. Proc Natl Acad Sci U S A 105: 1913–1918.
|
| [6] | Strogatz SH (2001) Exploring complex networks. Nature 410: 268–276.
|
| [7] | Weng G, Bhalla US, Iyengar R (1999) Complexity in biological signaling systems. Science 284: 92–96.
|
| [8] | Williams JW, Cui X, Levchenko A, Stevens AM (2008) Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops. Mol Syst Biol 4: 234.
|
| [9] | Justman QA, Serber Z, Ferrell JE Jr, El-Samad H, Shokat KM (2009) Tuning the activation threshold of a kinase network by nested feedback loops. Science 324: 509–512.
|
| [10] | Brandman O, Ferrell JE Jr, Li R, Meyer T (2005) Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 310: 496–498.
|
| [11] | Brandman O, Meyer T (2008) Feedback loops shape cellular signals in space and time. Science 322: 390–395.
|
| [12] | Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450–461.
|
| [13] | Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980–11985.
|
| [14] | Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA (2006) Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 75: 655–680.
|
| [15] | Ma W, Trusina A, El-Samad H, Lim WA, Tang C (2009) Defining network topologies that can achieve biochemical adaptation. Cell 138: 760–773.
|
| [16] | Chaudhri VK, Kumar D, Misra M, Dua R, Rao KV (2009) Integration of a phosphatase cascade with the Mitogen Activated Protein Kinase pathway provides for a novel signal processing function. J Biol Chem.
|
| [17] | Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, et al. (2005) Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 309: 1078–1083.
|
| [18] | Ferrell JE Jr, Bhatt RR (1997) Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J Biol Chem 272: 19008–19016.
|
| [19] | Orton RJ, Sturm OE, Vyshemirsky V, Calder M, Gilbert DR, et al. (2005) Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. Biochem J 392: 249–261.
|
| [20] | Eungdamrong NJ, Iyengar R (2007) Compartment-specific feedback loop and regulated trafficking can result in sustained activation of Ras at the Golgi. Biophys J 92: 808–815.
|
| [21] | Qiao L, Nachbar RB, Kevrekidis IG, Shvartsman SY (2007) Bistability and oscillations in the Huang-Ferrell model of MAPK signaling. PLoS Comput Biol 3: 1819–1826.
|
| [22] | Das J, Ho M, Zikherman J, Govern C, Yang M, et al. (2009) Digital signaling and hysteresis characterize ras activation in lymphoid cells. Cell 136: 337–351.
|
| [23] | Kholodenko BN (2000) Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem 267: 1583–1588.
|
| [24] | Levchenko A, Bruck J, Sternberg PW (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc Natl Acad Sci U S A 97: 5818–5823.
|
| [25] | Bhalla US, Ram PT, Iyengar R (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297: 1018–1023.
|
| [26] | Martinez LA, Chen Y, Fischer SM, Conti CJ (1999) Coordinated changes in cell cycle machinery occur during keratinocyte terminal differentiation. Oncogene 18: 397–406.
|
| [27] | Downward J (2001) The ins and outs of signalling. Nature 411: 759–762.
|
| [28] | Yen HC, Xu Q, Chou DM, Zhao Z, Elledge SJ (2008) Global protein stability profiling in mammalian cells. Science 322: 918–923.
|
| [29] | Bissell MJ, Radisky D (2001) Putting tumours in context. Nat Rev Cancer 1: 46–54.
|
| [30] | Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, et al. (2007) A map of human cancer signaling. Mol Syst Biol 3: 152.
|
| [31] | Bar-Yam Y, Epstein IR (2004) Response of complex networks to stimuli. Proc Natl Acad Sci U S A 101: 4341–4345.
|
| [32] | Bruggeman FJ, Bluthgen N, Westerhoff HV (2009) Noise management by molecular networks. PLoS Comput Biol 5: e1000506.
|
