• deterministic • stochastic • hybrid Ventura, B. D., Lemerle, C., Michalodimitrakis, K. & Serrano, L. From in vivo to in silico biology and back. Nature 443, 527–533 (2006). No space!!!
Borisov, N. et al. Systems-level interactions between insulin–EGF networks amplify mitogenic signaling. Mol Syst Biol 5, (2009). 3 years of life Kiselev, V. Y. Computational Study of Electrostatic Contribution to Membrane Dynamics. My thesis 1–124 (2011). Diffusion of a pentapeptide on cell membrane
papers ! • includes more than1900 experimentally observed parameters ‘This is potentially the new Human Genome Project. It's going to take a really large community effort to get close to a human model.’ J.R. Karr et al. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell 150, 389–401 (2012) First Author - J. Karr
1,000-fold higher than others 44% discrepancy between total energy usage and production ‘If growth is limited by nutrients other than energy, however, bacteria can spill ATP in reactions that cannot be readily categorized as maintenance per se. Recent work indicated that bacteria utilize futile cycles of ions through the cell membrane as a means of hydrolyzing ATP’ Russel, J.B. et al. Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol. Rev. vol. 59, №1, p. 48-62, (1995).
more closely related species The higher consistency reflects novel insights into M. genitalium biology Gene disruption strains reveal discrepancy between the model and experimental data