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Bacterial Molecular Networks

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Cover of 'Bacterial Molecular Networks'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling.
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    Chapter 2 Bacterial Interactomes: From Interactions to Networks
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    Chapter 3 Bacterial Molecular Networks
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    Chapter 4 Prokaryote genome fluidity: toward a system approach of the mobilome.
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    Chapter 5 Reticulate Classification of Mosaic Microbial Genomes Using NeAT Website
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    Chapter 6 From Metabolic Reactions to Networks and Pathways
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    Chapter 7 Predicting Metabolic Pathways by Sub-network Extraction
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    Chapter 8 Directed Module Detection in a Large-Scale Expression Compendium
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    Chapter 9 Using Phylogenetic Profiles to Predict Functional Relationships
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    Chapter 10 Extracting Regulatory Networks of Escherichia coli from RegulonDB
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    Chapter 11 Browsing Metabolic and Regulatory Networks with BioCyc
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    Chapter 12 Algorithms for Systematic Identification of Small Subgraphs
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    Chapter 13 The Degree Distribution of Networks: Statistical Model Selection
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    Chapter 14 MAVisto: A Tool for Biological Network Motif Analysis
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    Chapter 15 Using MCL to Extract Clusters from Networks
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    Chapter 16 Protein Complex Prediction with RNSC
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    Chapter 17 Network Analysis and Protein Function Prediction with the PRODISTIN Web Site
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    Chapter 18 Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Network to Clusters
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    Chapter 19 Analyzing Biological Data Using R: Methods for Graphs and Networks
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    Chapter 20 Detecting Structural Invariants in Biological Reaction Networks
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    Chapter 21 Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks
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    Chapter 22 Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks
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    Chapter 23 Logical Modelling of Gene Regulatory Networks with GINsim.
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    Chapter 24 Modelling the Evolution of Mutualistic Symbioses
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    Chapter 25 Modelling the Onset of Virulence in Pathogenic Bacteria
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    Chapter 26 Spatial and Stochastic Cellular Modeling with the Smoldyn Simulator
Attention for Chapter 23: Logical Modelling of Gene Regulatory Networks with GINsim.
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Chapter title
Logical Modelling of Gene Regulatory Networks with GINsim.
Chapter number 23
Book title
Bacterial Molecular Networks
Published in
Methods in molecular biology, December 2011
DOI 10.1007/978-1-61779-361-5_23
Pubmed ID
Book ISBNs
978-1-61779-360-8, 978-1-61779-361-5

Chaouiya C, Naldi A, Thieffry D, Claudine Chaouiya, Aurélien Naldi, Denis Thieffry


Discrete mathematical formalisms are well adapted to model large biological networks, for which detailed kinetic data are scarce. This chapter introduces the reader to a well-established qualitative (logical) framework for the modelling of regulatory networks. Relying on GINsim, a software implementing this logical formalism, we guide the reader step by step towards the definition and the analysis of a simple model of the lysis-lysogeny decision in the bacteriophage λ.

Mendeley readers

The data shown below were compiled from readership statistics for 70 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 3 4%
Italy 1 1%
Portugal 1 1%
Unknown 65 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 29%
Researcher 19 27%
Student > Master 12 17%
Professor 4 6%
Professor > Associate Professor 4 6%
Other 8 11%
Unknown 3 4%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 36%
Biochemistry, Genetics and Molecular Biology 11 16%
Computer Science 11 16%
Engineering 4 6%
Neuroscience 3 4%
Other 7 10%
Unknown 9 13%

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