A BetaWB Model for the NFkB Pathway

[1] Thoma D Gilmore. The Rel/NF-B signal transduction pathway: intro- duction. Oncogene, 19(49):6842–6844, 1999. [2] Albensi BS and Mattson MP. Evidence for the involvement of TNF and NF-kappaB in hippocampal synaptic plasticity. Synapse, 35(2):151–159, 2000. [3] Michael Karin, Yumi Yamamoto, and Q.May Wang. The IKK NF-B system: a treasure trove for drug development. Nature, 3(1):17–26, 2004. [4] Ghosh S, May MJ, and Kopp EB. NF-kappa B and Rel proteins: evolu- tionarily conserved mediators of immune responses. Annu. Rev. Immunol., 16:225–260, 1998. [5] Alexander Hoffmann, Andre Levchenko, Martin L. Scott, and David Bal- timore. The IB−NF Signaling Module: Temporal Control and Selective Gene Activation. Science, 298(5596):1241–1254, 2002. [6] A.E.C. Ihekwaba, D.S. Broomhead, R.L. Grimley, N. Benson, and D.B. Kell. Sensitivity analysis of parameters controlling oscillatory signalling in the nf-kappab pathway: the roles of ikk and ikappabalpha. Syst Biol (Stevenage), 1(1):93–103, 2004. [7] Karin M and Ben-Neriah Y. Phosphorylation meets ubiquitination: the control of nf-b activity. Annu. Rev. Immunol., 18:6680–6684, 2000. [8] Lorenzo Demmat´e, Corrado Priami, and Alessandro Romanel. BetaWB: modelling and simulating biological processes. In SCSC 2007, pages 777– 784, 2007. [9] Corrado Priami and Paola Quaglia. Beta binders for biological interactions. In CMSB, Lecture Notes in Computer Science, pages 20–33, 2004. [10] P. Degano, D. Prandi, C. Priami, and P. Quaglia. Beta-binders for biolog- ical quantitative experiments. Electronic Notes in Theoretical Computer Science, 164(3):101–117, October 2006. [11] Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, and al. COPASI−a COmplex PAthway SImulator. Bioinformatics, 22(24):3067–3074, 2006. [12] Hoffmann A, Levchenko, Scott ML, and Baltimore D. Ib-nf-b signal- ing module: temporal control and selective gene activation, supplementary material. Science Magazine, 298(5596):1241–1245, 2002. 41 42 BIBLIOGRAPHY [13] Corrado Priami and Paola Quaglia. Operational patterns in beta-binders. volume 1 of Lecture Notes in Computer Science, pages 50–65, 2005. [14] Ralf Steuer. Effects of stochasticity in models of the cell cycle: from quantized cycle times to noise-induced oscillations. Theoretical Biology, 228(3):293–301, 2004. [15] Raymond Cheong, Adriel Bergmann, Shannon L. Werner, Joshua Rega, Alexander Hoffmann, and Andre Levchenko. Transient IB Kinase Activity Mediates Temporal NF-B Dynamics in Response to a Wide Range of Tumor Necrosis Factor- Doses Formula. J. Biol. Chem, 281(5):2945–2950, 2006.