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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
Authors

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

Abstract

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

Mendeley readers

The data shown below were compiled from readership statistics for 86 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 3 3%
Italy 1 1%
Portugal 1 1%
Unknown 81 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 22 26%
Researcher 22 26%
Student > Master 16 19%
Student > Bachelor 4 5%
Professor 4 5%
Other 11 13%
Unknown 7 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 29%
Biochemistry, Genetics and Molecular Biology 20 23%
Computer Science 11 13%
Engineering 5 6%
Immunology and Microbiology 3 3%
Other 9 10%
Unknown 13 15%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 15 December 2014.
All research outputs
#20,246,428
of 22,774,233 outputs
Outputs from Methods in molecular biology
#9,866
of 13,091 outputs
Outputs of similar age
#219,304
of 241,158 outputs
Outputs of similar age from Methods in molecular biology
#410
of 463 outputs
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So far Altmetric has tracked 13,091 research outputs from this source. They receive a mean Attention Score of 3.3. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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We're also able to compare this research output to 463 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.