Collado-Vides, J., Hofestadt, R., Mavrovouniotis, M.L., and Michal, G.. "Modeling and simulation of gene regulation and metabolic pathways." Biosystems. 49
(1).
1999.
pp. 79-82.
[ .pdf ] [ PubMed ]
Keywords: *Gene Expression Regulation ; *Metabolism ; *Models Genetic
Hofestadt, R., Mavrovouniotis, M.L., Collado-Vides, J., and Loffler, M.. "Modeling and simulation of metabolic pathways, gene regulation and cell differentiation. October 22-27, 1995. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany." Bioessays. 18
(4).
1996.
pp. 333-5.
[ PubMed ]
Keywords: Cell Differentiation ; *Computer Simulation ; Gene Expression Regulation ; Information Systems ; Metabolism ; *Models Biological
Mavrovouniotis, M.L.. "Identification of localized and distributed bottlenecks in metabolic pathways." Proc Int Conf Intell Syst Mol Biol.
vol. 1.
1993.
pp. 275-83.
[ PubMed ]
The usual thermodynamic evaluation, based solely on the Standard Gibbs Energy of reaction, does not take into account the permissible ranges of concentrations of metabolites, and it faces further difficulties when, instead of isolated reactions, we are examining whole pathways. For pathways, we seek not only to decide whether they are feasible but also to pinpoint the pathway segment that causes any thermodynamic difficulties. We define a set of scaled quantities which reformulate the thermodynamic-feasibility problem for the whole pathway. We present an algorithm which analyzes individual reactions and selective construction of larger subpathways and uncovers localized and distributed thermodynamic bottlenecks of the biotransformation. This type of thermodynamic treatment contributes to the effort to include more physical, chemical, and biological factors in the computer-aided analysis of metabolic pathways.
Keywords: *Algorithms ; *Computer Simulation ; Glycolysis ; *Metabolism ; *Models Biological ; *Thermodynamics
Mavrovouniotis, M.L.. "Describing multiple levels of abstraction in the metabolism." Proc Int Conf Intell Syst Mol Biol.
vol. 2.
1994.
pp. 294-302.
[ PubMed ]
We discuss some central issues that arise in the computer representation of the metabolism and its subsystems. We provide a framework for the representation of metabolites and bioreactions at multiple levels of detail. The framework is based on defining an explicit linear mapping of metabolites and reactions from one level of detail to another. A simple reaction mechanism serves as an illustration and shows the emergence of the concept of a catalyst from metabolic abstraction levels.
Keywords: Catalysis ; *Computer Simulation ; *Metabolism
Reddy, V.N., Liebman, M.N., and Mavrovouniotis, M.L.. "Qualitative analysis of biochemical reaction systems." Comput Biol Med. 26
(1).
1996.
pp. 9-24.
[ PubMed ]
The qualitative analysis of biochemical reaction systems is presented. A discrete event systems approach is used to represent and analyze bioreaction pathways. The approach is based on Petri nets, which are particularly suited to modeling stoichiometric transformations, i.e. the inter-conversion of metabolites in fixed proportions. The properties and methods for the analysis of Petri nets, along with their interpretation for biochemical systems, are presented. As an example, the combined glycolytic and pentose phosphate pathway of the erythrocyte cell is presented to illustrate the concepts of the methodology.
Keywords: Biochemistry ; *Computer Simulation ; Erythrocytes_*physiology ; Glycolysis_*physiology ; Human ; Models Theoretical ; Pentosephosphate Pathway_*physiology
Reddy, V.N., Mavrovouniotis, M.L., and Liebman, M.N.. "Petri net representations in metabolic pathways." Proc Int Conf Intell Syst Mol Biol.
vol. 1.
1993.
pp. 328-36.
[ PubMed ]
The present methods for representing metabolic pathways are limited in their ability to handle complex systems, incorporate new information, and to provide for drawing qualitative conclusions from the structure of pathways. The theory of Petri nets is introduced as a tool for computer-implementable representation of pathways. Petri nets have the potential to overcome the present limitations, and through a multitude of properties, enable the preliminary qualitative analysis of pathways.
Keywords: *Computer Simulation ; Fructose_metabolism ; Liver_metabolism ; *Metabolism ; *Models Biological