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The Regulation of Cellular Systems
The basic equations of metabolic control analysis are rewritten in terms of co-response coefficients and internal response coefficients to describe the interaction of optimization methods and the interrelation with evolution.
ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE
It is shown that for systems in which all flux- have fixed signs, all elementary modes are given by the generating vectors of a convex cone and can, thus, be computed by an existing algorithm.
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
This work analyzes the interplay between the pentose phosphate pathway (PPP) and glycolysis to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes.
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.
Metabolic network structure determines key aspects of functionality and regulation
A theoretical method for simultaneously predicting key aspects of network functionality, robustness and gene regulation from network structure alone is devised by determining and analysing the non-decomposable pathways able to operate coherently at steady state (elementary flux modes).
METATOOL: for studying metabolic networks
- T. Pfeiffer, I. Sánchez-Valdenebro, J. C. Nuño, F. Montero, S. Schuster
- 1 March 1999
Algorithms for computing the convex basis and elementary modes developed earlier are briefly reviewed, and a newly developed algorithm for detecting all enzyme subsets in a given network is presented.
Metatool 5.0: fast and flexible elementary modes analysis
The performance of Metatool has been significantly increased and the new version 5.0 can now be run inside the GNU octave or Matlab environments to allow more flexible usage and integration with other tools.
Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism
- S. Schuster, C. Hilgetag, J. H. Woods, D. Fell
- Computer ScienceJournal of mathematical biology
- 1 August 2002
It is formally proved that this algorithm will exclusively generate all the elementary flux modes of an arbitrary network containing reversible or irreversible reactions or both.
Comparison of network-based pathway analysis methods.
Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling.
This review provides a comparative overview of recent developments in the modelling of cellular calcium oscillations and suggests suggestions concerning the physiological significance of oscillatory behaviour in intra- and intercellular signalling.