Title | Bacterial Molecular Networks [electronic resource] : Methods and Protocols / edited by Jacques van Helden, Ariane Toussaint, Denis Thieffry |
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Imprint | New York, NY : Springer New York, 2012 |
Connect to | http://dx.doi.org/10.1007/978-1-61779-361-5 |
Descript | XI, 546 p. 206 illus., 1 illus. in color. online resource |
Bacterial Molecular Networks: Bridging the Gap Between Functional Genomics and Dynamical Modeling -- Bacterial Interactomes: From Interactions to Networks -- From Bacterial to Microbial Ecosystems (Metagenomics) -- Prokaryote Genome Fluidity: Towards a System Approach of the Mobilome -- Reticulate Classification of Mosaic Microbial Genomes using NeAT Website -- From Metabolic Reactions to Networks and Pathways -- Predicting Metabolic Pathways by Subnetwork Extraction -- Directed Module Detection in a Large-scale Expression Compendium -- Using Phylogenetic Profiles to Predict Functional Relationships -- Extracting Regulatory Networks of Escherichia coli from RegulonDB -- Browsing Metabolic and Regulatory Networks with BioCyc -- Algorithms for Systematic Identification of Small Sub-graphs -- The Degree Distribution of Networks: Statistical Model Selection -- MAVisto: A Tool for Biological Network Motif Analysis -- Using MCL to Extract Clusters from Networks -- Protein Complex Prediction with RNSC (Method) -- Network Analysis and Protein Function Prediction with the PRODISTIN Web Site -- Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Networks to Clusters -- Analyzing Biological Data Using R: Methods for Graphs and Networks -- Detecting Structural Invariants in Biological Reaction Networks -- Petri nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks -- Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks -- Logical Modelling of Gene Regulatory Networks with GINsim -- Modelling the Evolution of Mutualistic Symbioses -- Modelling the Onset of Virulence in Pathogenic Bacteria -- Spatial Stochastic Cellular Modeling with the Smoldyn Simulator