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, Natasa Przulj, 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

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