Gene network dynamics

Busch, H., Camacho-Trullio, D., Rogon, Z. et al. 2008. Gene network dynamics controlling keratinocyte... 

Agrawal A. and Mittal A. (2005). A dynamic time-lagged correlation based method to learn multi-time delay gene networks. Transactions on Engineering, Computing and Technology. 9, pp 167-174. 

Edwards R. (2001). Chaos in neural and gene networks with hard switching. Differential Equations and Dynamical Systems. 9, pp 187-220. 

Kim S. Y., Imoto S. and Miyano S. (2003). Inferring gene networks from time series microarray data using dynamic Bayesian networks. Briefings in Bioinformatics. 4, pp 228-235. 

Perrin B. E., Ralaivola L., Mazurie A., Bottani S., Mallet J. and dAlche-Buc F. (2003). Gene network inference using dynamic Bayesian networks. Bioinformatics. 19, pp 138-142. 

Even though Eq. (5) is more realistic than Eq. (3) as a model for biological systems, this equation still is highly oversimplified. Yet this equation has remarkable mathematical properties that facilitate theoretical analysis. Moreover, there is an expectation, demonstrated in some simple examples like those discussed above, that the qualitative dynamics in the model system wiU be preserved in more realistic versions, for example when the discontinuous step functions are replaced by continuous sigmoidal functions [33, 34, 37]. As mentioned above, synthetic gene networks have been created that show some of the simple types of dynamical behavior found in our class of networks—in particular, bistability (two fixed points) [26] and oscillation in an inhibitory loop [27]. 

Tegner, J., M. K. S. Yeung, J. Hasty, and J. J. Collins. 2003. Reverse engineering gene networks Integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci USA 100 5944-9. 

Metivier R, Reid G, Gannon F 2006 Transcription in four dimensions nuclear receptor-directed initiation of gene expression. EMBO Rep 7 161-167 Nilsson R, Bajic V, Katayama S et al 2006 Transcriptional network dynamics in macrophage activation. Genomics 88 133-142... 

Anthony M. Lowman, Thomas D. Dziubla, Petr Bures, and Nicholas A. Peppas, Structural and Dynamic Response of Neutral and Intelligent Networks in Biomedical Environments F. Kurds Kasper and Antonios G. Mikos, Biomaterials and Gene Therapy Balaji Narasimhan and Matt J. Kipper, Surface-Erodible Biomaterials for Drug Delivery... 

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