Bacterial Molecular Networks Methods and Protocols

About this book

Network-based representations have become pervasive in most fields in biology. "Bacterial Molecular Networks: Methods and Protocols" provides authoritative descriptions of various experimental and computational methods enabling the characterization and analysis of molecular interaction networks, with a focus on bacteria. Divided into three convenient sections, this volume provides extensive coverage of various experimental and in silico approaches aiming at the characterization of network components, addresses the presentation of computational approaches to analyze the topology of molecular networks, and further introduces a variety of methods and tools enabling scientists to generate qualitative or quantitative dynamical models of molecular processes in bacteria.

Written in the highly successful "Methods in Molecular Biology" series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, "Bacterial Molecular Networks: Methods and Protocols" is intended primarily for post-graduate students and researchers working in the field of experimental and computational microbiology and provides a combination of up-to-date reviews along with detailed protocols written by the developers of bioinformatics resources, such as databases and software tools.

Contents

1. Bacterial Molecular Networks: Bridging the Gap Between Functional Genomics and Dynamical Modeling

Part I. Experimental and in silico approaches to unravel network components
2. Bacterial Interactomes: From Interactions to Networks
3. From Bacterial to Microbial Ecosystems (Metagenomics)
4. Prokaryote Genome Fluidity: Towards a System Approach of the Mobilome
5. Reticulate Classification of Mosaic Microbial Genomes using NeAT Website
6. From Metabolic Reactions to Networks and Pathways
7. Predicting Metabolic Pathways by Subnetwork Extraction
8. Directed Module Detection in a Large-scale Expression Compendium
9. Using Phylogenetic Profiles to Predict Functional Relationships
10. Extracting Regulatory Networks of Escherichia coli from RegulonDB
11. Browsing Metabolic and Regulatory Networks with BioCyc

Part II. Topological analysis of bacterial networks
12. Algorithms for Systematic Identification of Small Sub-graphs
13. The Degree Distribution of Networks: Statistical Model Selection
14. MAVisto: A Tool for Biological Network Motif Analysis
15. Using MCL to Extract Clusters from Networks
16. Protein Complex Prediction with RNSC (Method)
17. Network Analysis and Protein Function Prediction with the PRODISTIN Web Site
18. Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Networks to Clusters
19. Analyzing Biological Data Using R: Methods for Graphs and Networks

Part III. Dynamical Modelling
20. Detecting Structural Invariants in Biological Reaction Networks
21. Petri nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks
22. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks
23. Logical Modelling of Gene Regulatory Networks with GINsim
24. Modelling the Evolution of Mutualistic Symbioses
25. Modelling the Onset of Virulence in Pathogenic Bacteria
26. Spatial Stochastic Cellular Modeling with the Smoldyn Simulator

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