Bacterial Molecular Networks

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.