Biological networks

Nikolsky Y, Nikolskaya T, Bugrim A. Biological networks and analysis of experimental data in drug discovery. Drug Discov Today 2005 10 653-62. 

Ghazalpour A, Doss S, Yang X, Aten J, Toomey EM, Van Nas A, et al. Thematic review series The pathogenesis of atherosclerosis. Toward a biological network for atherosclerosis. J Lipid Res 2004 45 1793-805. 

Hu Z, Mellor J, Wu J, Yamada T, Holloway D, Delisi C. VisANT data-integrating visual framework for biological networks and modules. Nucleic... 

Chen H, Sharp BM. Content-rich biological network constructed by mining. BMC Bioinformatics 2004 5 147. 

Glass, L. (1975). Classification of biological networks by their qualitative dynamics. J. Theor. Biol. 54 85-107. 

R. Steuer and G. Zamora Lopez, Global network properties. Analysis of Biological Networks, Wiley Series on Bioinformatics Computational Techniques and Engineering. B. H. Junker and F. Schreiber, eds., John Wiley Sons, Inc. 2008. 

Barsky, A., Gardy, J.L., Hancock, R.E. and Munzner, T. (2007) Cerebral A Cyto-scape Plugin for Layout of and Interaction with Biological Networks Using Subcellular Localization Annotation. Bioinformaties, 23, 1040-1042. 

Universite Libre de Bruxelles Toolbox for the analysis of biological networks, clusters, classes, and pathways (http //rsat.bigre.ulb.ac.be/rsat/index neat. html)... 

VisANT Boston University Integrative visual analysis tool for biological networks and pathways (http //visant.bu.edu/)... 

Taylor R, Singhal M (2009) Biological network inference and analysis using SEBINI and CABIN. Methods Mol Biol 541 551-576... 

The need for multiscale modeling of biological networks in zero-dimensional (well mixed) systems has been emphasized in Rao et al. (2002). The multiscale nature of stochastic simulation for well-mixed systems arises from separation of time scales, either disparity in rate constants or population sizes. In particular, the disparity in species concentrations is commonplace in biological networks. The disparity in population sizes of biological systems was in fact recognized early on by Stephanopoulos and Fredrickson (1981). This disparity in time scales creates slow and fast events. Conventional KMC samples only fast events and cannot reach long times. 

This equation is valid only in the linear region, which may be rare in biology. Equation (11.194) may be used for the evolution of all biological networks, which can be characterized by thermodynamic considerations. Equation (11.194) is valid for both linear and nonlinear constitutive relations, and can be used for quasi-equilibrium and far-from-equilibrium regions of the thermodynamic branch. 

The symmetry of coupled membrane transport holds in a wide range of network structure applications and for the general behavior of biological networks. 

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