Bibliography of: Metabolism

  1. 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


  2. Hofestadt, R. and Meineke, F.. "Interactive modelling and simulation of biochemical networks." Comput Biol Med. 25 (3). 1995. pp. 321-34.
    [ PubMed ]

    The analysis of biochemical processes can be supported using methods of modelling and simulation. New methods of computer science are discussed in this field of research. This paper presents a new method which allows the modelling and analysis of complex metabolic networks. Moreover, our simulation shell is based on this formalization and represents the first tool for the interactive simulation of metabolic processes.

    Keywords: *Biochemistry ; Cell Communication_physiology ; Databases Factual ; Enzymes_physiology ; Gene Expression_physiology ; Genes Regulator_physiology ; Genetic Diseases Inborn_enzymology ; Genetic Diseases Inborn_genetics ; Genetic Diseases Inborn_metabolism ; *Metabolism ; *Models Chemical ; *Models Genetic ; Probability ; *Software


  3. 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


  4. Hofestadt, R.. "Grammatical formalization of metabolic processes." Proc Int Conf Intell Syst Mol Biol. vol. 1. 1993. pp. 181-9.
    [ PubMed ]

    In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.

    Keywords: *Computer Simulation ; *Expert Systems ; Gene Expression ; *Metabolism ; *Models Biological ; Programming Languages


  5. Karp, P.D., Riley, M., Paley, S.M., and Pellegrini-Toole, A.. "The MetaCyc Database." Nucleic Acids Res. 30 (1). 2002. pp. 59-61.
    [ .pdf ] [ PubMed ]

    MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates information from multiple literature sources. The pathways in MetaCyc were determined experimentally and are labeled with the species in which they are known to occur based on literature references examined to date. MetaCyc contains extensive commentary and literature citations. Applications of MetaCyc include pathway analysis of genomes, metabolic engineering and biochemistry education. MetaCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. MetaCyc is available via the World Wide Web at http://ecocyc.org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info

    Keywords: Comparative Study ; Database Management Systems ; *Databases Protein ; Enzymes_chemistry ; Enzymes_*metabolism ; Genome ; Human ; Information Storage and Retrieval ; Internet ; *Metabolism


  6. 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


  7. 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


  8. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.. "KEGG: Kyoto Encyclopedia of Genes and Genomes." Nucleic Acids Res. 27 (1). 1999. pp. 29-34.
    [ .pdf ] [ PubMed ]

    Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).

    Keywords: Computational Biology ; *Databases Factual ; Gene Expression ; *Genes ; *Genome ; Ligands ; Metabolism ; Sequence Homology


  9. 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


  10. Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., and Dandekar, T.. "Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae." Bioinformatics. 18 (2). 2002. pp. 351-61.
    [ PubMed ] [ WebSite ]

    MOTIVATION: Reconstructing and analyzing the metabolic map of microorganisms is an important challenge in bioinformatics. Pathway analysis of large metabolic networks meets with the problem of combinatorial explosion of pathways. Therefore, appropriate algorithms for an automated decomposition of these networks into smaller subsystems are needed. RESULTS: A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented. Interrelations of this algorithm with alternative methods proposed in the literature and the theory of small world networks are discussed. The applicability of our method is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae, which is an organism of considerable medical interest. The decomposition gives rise to 19 subnetworks. Three of these are here discussed in biochemical terms: arginine degradation, the tetrahydrofolate system, and nucleotide metabolism. The interrelations of pathway analysis of biochemical networks with Petri net theory are outlined.

    Keywords: Algorithms ; Arginine_metabolism ; Computational Biology ; *Metabolism ; Models Biological ; Mycoplasma pneumoniae_*metabolism ; Nucleotides_metabolism ; *Software