Visualizing regulatory interactions in metabolic networks

Modules in the metabolic network of E.coli with regulatory interactions

We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E. coli. We introduce novel clustering algorithm and compare it with mainstream module detection method based on simulated annealing. Both methods identify the similar modular core. Slight but significant increase in modularity is ...

DataViz: Visualizing Metabolic Pathways

Tools for visualization of biological data focus more on the algorithms behind data processing than on the needs of their biologist users. Scientists in the field of biology and bioinformatics require software that is more versatile, yet simple to use. This has become a necessity as the depth of information scientists have to organize becomes more and more complex. Disparities between the progr...

Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context

DNA microarrays are used to measure the expression levels of thousands of genes simultaneously. In a time series experiment, the gene expressions are measured as a function of time. We present an application for integrated visualization of genome expression and network dynamics in both regulatory networks and metabolic pathways. Integration of these two levels of cellular processes is necessary...

Metabolic interlock. Regulatory interactions exerted between biochemical pathways.

Estimating Hidden Influences in Metabolic and Gene Regulatory Networks

We address the applicability of blind source separation (BSS) methods for the estimation of hidden influences in biological dynamic systems such as metabolic or gene regulatory networks. In simple processes obeying mass action kinetics, we find the emergence of linear mixture models. More complex situations as well as hidden influences in regulatory systems with sigmoidal input functions howeve...