Networks reconstruction

H. Ma, A. Sorokin, A. Mazein, A. Selkov, E. Selkov, O. Demin, and I. Goryanin, The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Syst. Biol. 3, 135 (2007). 

H. Ma and I. Goryanin, Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov. Today 13(9 10), 402 408 (2008). 

R. Schwarz, C. Liang, C. Kaleta, M. Kiihnel, E. Hoffmann, S. Kuznetsov, M. Hecker, G. Griffiths, S. Schuster, and T. Dandekar, Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 8, 313 (2007). 

Applying mass-balance and thermodynamic constraints typically leaves one without a precisely defined (unique) solution for reaction fluxes and reactant concentration, but instead with a mathematically constrained feasible space for these variables. Exploration of this feasible space is the purview of constraint-based analysis. It has so far been left unstated that any application in this area starts with the determination of the reactions in a system, from which the stoichiometric matrix arises. This first step, network reconstruction, integrates genomic and proteomic data to determine carefully the enzymes present in an organism, cell, or subcellular compartment. The network reconstruction process is described elsewhere [107]. 

Large-scale regulatory network reconstructions can be converted to in silico models that allow systematic analysis of network behavior in response to changes in environmental conditions. These models can be combined further with genome-scale metabolic models to build integrated models of cellular function including both metabolism and its regulation [41]. 

Getting, P.A. 1983. Mechanisms of pattern generation underlying swimming in Tritonia. II. Network reconstruction. J. Neurophysiol. 46 64-79. 

Bolten, C.J., Heinzle, E., Muller, R., and Wittmann, C. (2009) Investigation of the central carbon metabolism of Sorangium cellulosum metabolic network reconstruction and quantification of pathway fluxes. /. Microbiol. Biotechnol, 19 (1), 23-36. 

Zak et al. have argued that inferring the GRN structure from expression data alone is impossible. However, promising results come from more recent work showing that properly designed perturbation experiments do permit network reconstruction (see Stark et al., Husmeier, de La Fuente et al., Kholodenko et al., and Gardner et al. ). Two papers " extended ideas from metabolic control analysis to suggest perturbation experiments... 

A more investigative approach to functional analysis applies network reconstruction algorithms, which leverage comprehensive databases of molecular interactions (protein-protein, compound-protein, protein-gene, protein-enzyme, etc.) to... 

Mccloskey, D., Palsson, B. O., Feist, A. M. (2013). Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Molecular Systems Biology, 9,661. 

MUne C, Eddy J, Raju R, Ardekani S, Kim P-J, Senger R, Jin Y-S, Blaschek H, Price N. (2011). Metabohc network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst Biol, 5,130. 

Haggart CR, Bartell JA, Saucerman JJ, Papin JA (2011) Whole-genome metabolic network reconstruction and constraint-based modeling. Methods Enzymol 500 411 33. Elsevier Inc... 

Molnar, 1., Lopez, D., Wisecaver, J.H., Devarenne, T.P., Weiss, T.L., Pellegrini, M., and Hackett, ).D. (2012) Bio-crude transcriptomics gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome... 

Fourmigue M, Auban-Senzier P (2008) Anionic laytaed networks reconstructed liom [Cd (SCN)3]oo chains in pseudo one-dimensional ctmducting salts of halogenaled tetra-thialiilvalenes. Inorg Chem 47 9979-9986... 

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