Bookedited by Jacques van Helden and Ariane Toussaint, Denis Thieffry.
Contents:
Bacterial molecular networks : bridging the gap between functional genomics and dynamical modelling / Jacques van Helden, Ariane Toussaint, and Denis Thieffry
Bacterial interactomes : from interactions to networks / Emmanuelle Bouveret and Christine Brun
From bacterial to microbial ecosystems (metagenomics) / Shannon J. Williamson and Shibu Yooseph
Prokaryote genome fluidity : toward a system approach of the mobilome / Ariane Toussaint and Mick Chandler
Reticulate classification of mosaic microbial genomes using NeAT website / Gipsi Lima-Mendez
From metabolic reactions to networks and pathways / Masanori Arita
Predicting metabolic pathways by sub-network extraction / Karoline Faust and Jacques van Helden
Directed module detection in a large-scale expression compendium / Qiang Fu [and others]
Using phylogenetic profiles to predict functional relationships / Matteo Pellegrini
Extracting regulatory networks of Escherichia coli from RegulonDB / Heladia Salgado [and others]
Browsing metabolic and regulatory networks with BioCyc / Mario Latendresse, Suzanne Paley, and Peter D. Karp
Algorithms for systematic identification of small subgraphs / Joseph Geraci, Geoffrey Liu, and Igor Jurisica
The degree distribution of ntworks : statistical model selection / William P. Kelly, Piers J. Ingram, and Michael P.H. Stumpf
MAVisto : a tool for biological network motif analysis / Henning Schwöbbermeyer and Röbbe Wünschiers
Using MCL to extract clusters from networks / Stijn van Dongen and Cei Abreu-Goodger
Protein complex prediction with RNSC / Andrew D. King, Nataša Pržulj, and Igor Jurisica
Network analysis and protein function prediction with the PRODISTIN web site / Anaïs Baudot, Ouissem Souiai, and Christine Brun
Using NeAT Toolbox to compare networks to networks, clusters to clusters, and network to clusters / Sylvain Brohée
Analyzing biological data using R : methods for graphs and networks / Nolwenn Le Meur and Robert Gentleman
Detecting structural invariants in biological reaction networks / Jörn Behre [and others]
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
Genetic Network Analyzer : a tool for the qualitative modeling and simulation of bacterial regulatory networks / Grégory Batt [and others]
Logical modelling of gene regulatory networks with GINsim / Claudine Chaouiya, Aurélien Naldi, and Denis Thieffry
Modelling the evolution of mutualistic symbioses / Maren L. Friesen and Emily I. Jones
Modelling the onset of virulence in pthogenic bacteria / Wilfred D. Kepseu [and others]
Spatial and stochastic cellular modeling with the Smoldyn Simulator / Steven S. Andrews.