We study the effect of extrinsic noise in metabolic networks. We introduce external random fluctuations at the kinetic level, and show how these lead to a stochastic generalization of standard metabolic control analysis. While summation and connectivity theorems hold true in the presence of extrinsic noise, control coefficients incorporate its effect through an explicit dependency on the noise ...

Biological databases contain a large amount of data about metabolic pathways, in particular about similar pathways in different species. Biologists are familiar with visual representations of metabolic pathways. Pathway diagrams help them to understand the complex relationships between the components of the pathways, to extract information from the data, and to compare pathways between differen...

Flux balance analysis (FBA) is a standard optimization model that is used to study the metabolisms of cells that are in a steady state of optimal growth. The model optimizes a biologically defined objective while assuming (1) equilibria of a linear system of ordinary differential equations, and (2) deterministic data. However, the steady state assumption is imperfect from a biological point of ...

networks (or graphs) consist of nodes and links between them. The number of links per node, which we call the class of the node, may vary between nodes, but in a homogeneous network the statistical distribution of links will be the same from region to region across the network. Classically, the distinction amongst homogeneous networks has been made between fully ordered networks, in which the n...

This work enriches the visualization of complex graphs from the biomedical domain called metabolic pathways by means of interactive linked views in 2D and 3D. Due to the high degree of complexity of pathways biologists are restrained by currently available systems in the process of hypothesis generation and validation. We propose an interactive visual data mining process that is supported by th...

The products of hexavalent chromium [Cr(VI)] reduction by glutathione (GSH) alone or in the presence of equimolar quantities of aspartate (Asp) and/or glutamate (Glu) and a chromium-containing material extracted from bovine liver were studied by ultraviolet-visible spectrum (UV-vis) studies, electrospray mass spectrometry (ES-MS), electron paramagnetic resonance (EPR), and nuclear magnetic reso...

Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of downstream targets in a network. Here, we develop an analytic framework to investigate the phenomenon of noise correlation in molecular networks. Specifically, w...