Bacterial Molecular Networks: Methods and Protocols

ISBN-13: 9781617793608 / Angielski / Twarda / 2011 / 546 str.

Denis Thieffry; Jacques Van Helden; Ariane Toussaint

Opis

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.

Spis treści

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

            Denis Thieffry, Ariane Toussaint, and Jacques van Helden

 

Part I. Experimental and in silico approaches to unravel network components

 

2. Bacterial Interactomes: From Interactions to Networks

            Emmanuelle Bouveret and Christine Brun

 

3. From Bacterial to Microbial Ecosystems (Metagenomics)

            Shannon J. Williamson and Shibu Yooseph

 

4. Prokaryote Genome Fluidity: Towards a System Approach of the Mobilome

            Ariane Toussaint and Mick Chandler

 

5. Reticulate Classification of Mosaic Microbial Genomes using NeAT Website

            Gipsi Lima-Mendez

 

6. From Metabolic Reactions to Networks and Pathways

            Masanori Arita

 

7. Predicting Metabolic Pathways by Subnetwork Extraction

            Karoline Faust and Jacques van Helden

 

8. Directed Module Detection in a Large-scale Expression Compendium

            Qiang Fu, Karen Lemmens, Aminael Sanchez-Rodriguez, Inge M. Thijs, Pieter Meysman, Hong Sun, Ana Carolina Fierro, Kristof Engelen, and Kathleen Marchal

 

9. Using Phylogenetic Profiles to Predict Functional Relationships

            Matteo Pellegrini

 

10. Extracting Regulatory Networks of Escherichia coli from RegulonDB

            Heladia Salgado, Irma Martínez-Flores, Alejandra López-Fuentes, Jair Santiago García-Sotelo, Liliana Porrón-Sotelo, Hilda Solano, Luis Muniz-Rascado, and Julio Collado-Vides

 

11. Browsing Metabolic and Regulatory Networks with BioCyc

            Mario Latendresse, Suzanne Paley, and Peter D. Karp

 

Part II. Topological analysis of bacterial networks

 

12. Algorithms for Systematic Identification of Small Sub-graphs

            Joseph Geraci, Geoffrey Liu, and Igor Jurisica

 

13. The Degree Distribution of Networks: Statistical Model Selection

            William P. Kelly, Piers J. Ingram, and Michael P. H. Stumpf

 

14. MAVisto: A Tool for Biological Network Motif Analysis

            Henning Schwöbbermeyer and Röbbe Wünschiers

 

15. Using MCL to Extract Clusters from Networks

            Stijn van Dongen and Cei Abreu-Goodger

 

16. Protein Complex Prediction with RNSC (Method)

            Andrew D. King, Nataša Pržulj, and Igor Jurisica

 

17. Network Analysis and Protein Function Prediction with the PRODISTIN Web Site

            Anaïs Baudot, Ouissem Souiai and Christine Brun

 

18. Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Networks to Clusters

            Sylvain Brohée

 

19. Analyzing Biological Data Using R: Methods for Graphs and Networks

            Nolwenn Le Meur and Robert Gentleman

 

Part III. Dynamical Modelling

 

20. Detecting Structural Invariants in Biological Reaction Networks

            Jörn Behre, Luís Filipe de Figueiredo, Stefan Schuster, and Christoph Kaleta

 

21. Petri nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks

            Wolfgang Marwan, Christian Rohr, and Monika Heiner

 

22. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks

            Grégory Batt, Bruno Besson, Pierre-Emmanuel Ciron, Hidde de Jong, Estelle Dumas, Johannes Geiselmann, Regis Monte, Pedro T. Monteiro, Michel Page, François Rechenmann, and Delphine Ropers

 

23. Logical Modelling of Gene Regulatory Networks with GINsim

            Claudine Chaouiya, Aurélien Naldi, and Denis Thieffry

 

24. Modelling the Evolution of Mutualistic Symbioses

            Maren L. Friesen and Emily L. Jones

 

25. Modelling the Onset of Virulence in Pathogenic Bacteria

            Wilfred D. Kepseu, Frédérique Van Gijsegem, and Jacques-Alexandre Sepulchre

 

26. Spatial Stochastic Cellular Modeling with the Smoldyn Simulator

            Steven S. Andrews