Bibliography of: Computational Biology_methods

  1. Goss, P.J. and Peccoud, J.. "Analysis of the stabilizing effect of Rom on the genetic network controlling ColE1 plasmid replication." Pac Symp Biocomput. 1999. pp. 65-76.
    [ .pdf ] [ PubMed ]

    A stochastic model of ColE1 plasmid replication is presented. It is implemented by using UltraSAN, a simulation tool based on an extension of stochastic Petri nets (SPNs). It allows an exploration of the variation in plasmid number per bacterium, which is not possible using a deterministic model. In particular, the rate at which plasmid-free bacteria arise during bacterial division is explored in some detail since spontaneous plasmid loss is a widely observed empirical phenomenon. The rate of spontaneous plasmid loss provides an evolutionary explanation for the maintainance of Rom protein. The presence of Rom acts to reduce variance in plasmid copy number, thereby reducing the rate of plasmid loss at bacterial division. The ability of stochastic models to link biochemical function with evolutionary considerations is discussed.

    Keywords: Cell Division ; Computational Biology_*methods ; *DNA Replication ; Escherichia coli_*genetics ; Escherichia coli_growth and development ; *Models Genetic ; *Plasmids ; Stochastic Processes


  2. Kuffner, R., Zimmer, R., and Lengauer, T.. "Pathway analysis in metabolic databases via differential metabolic display (DMD)." Bioinformatics. 16 (9). 2000. pp. 825-36.
    [ .pdf ] [ PubMed ] [ WebSite ]

    MOTIVATION: A number of metabolic databases are available electronically, some with features for querying and visualizing metabolic pathways and regulatory networks. We present a unifying, systematic approach based on PETRI nets for storing, displaying, comparing, searching and simulating such nets from a number of different sources. RESULTS: Information from each data source is extracted and compiled into a PETRI net. Such PETRI nets then allow to investigate the (differential) content in metabolic databases, to map and integrate genomic information and functional annotations, to compare sequence and metabolic databases with respect to their functional annotations, and to define, generate and search paths and pathways in nets. We present an algorithm to systematically generate all pathways satisfying additional constraints in such PETRI nets. Finally, based on the set of valid pathways, so-called differential metabolic displays (DMDs) are introduced to exhibit specific differences between biological systems, i.e. different developmental states, disease states, or different organisms, on the level of paths and pathways. DMDs will be useful for target finding and function prediction, especially in the context of the interpretation of expression data.

    Keywords: *Algorithms ; Catalysis ; Computational Biology_*methods ; Computer Simulation ; *Data Display ; *Databases Factual ; Enzymes_genetics ; Enzymes_metabolism ; Glycolysis ; Metabolism_*physiology ; Mycoplasma_metabolism ; Yeasts_metabolism