Systems biology is becoming an emerging field, as systems science is demonstrated as an essential tool in untangling biocomplexity. While various steady-state-based methods have been developed for study of metabolic networks, the study of the network dynamics is a less explored area, as it is inherently related to the regulatory network. The difficulty of regulatory network inference opens up t...

SUMMARY MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. It allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out t...

Thermodynamic-based constraints on biochemical fluxes and concentrations are applied in concert with mass balance of fluxes in glycogenesis and glycogenolysis in a model of hepatic cell metabolism. Constraint-based modeling methods that facilitate predictions of reactant concentrations, reaction potentials, and enzyme activities are introduced to identify putative regulatory and control sites i...

Biological pathways information has accumulated along with Genomic sequence data. These metabolic pathways help us in understanding network robustness and complex reaction networks. They also provide a framework for improved understanding of microbial physiology and for antimicrobial drug discovery. This article is an attempt to understand the local and global properties of metabolic networks i...

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising fro...

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlyin...

for Patterns of Dynamics 2016 Contributed talk ∗ Electronic Address: [email protected] † Electronic Address: [email protected] 1 Free University of Berlin Sensitivity of metabolic reaction networks Bernhard Brehm1∗, Bernold Fiedler1† We study the influence of rate perturbations on reaction fluxes, at steady state, in general metabolic networks. In particular, we establish transit...

Orthologous proteins descend from a common ancestral protein via a speciation event and often keep their ancestral functions. Therefore, orthology assignment is often applied to identify gene content and functions in newly sequenced species. No commonly accepted gold standard exists so far for orthology assignment. One reason for this is a preference of different evolutionary mechanisms in diff...