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Bacterial Molecular Networks

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Jacques Helden

    1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium

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  2. Ariane Toussaint

    1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium

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  3. Denis Thieffry

    1. INSERM 1024, Institut de Biologie de l'Ecole Normale, Paris, France

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 804)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xi
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  2. Bacterial Molecular Networks: Bridging the Gap Between Functional Genomics and Dynamical Modelling

    • Jacques van Helden, Ariane Toussaint, Denis Thieffry
    Pages 1-11

  3. Experimental and In Silico Approaches to Unravel Network Components

    1. Front Matter

      Pages 13-13
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  4. Experimental and in silico approaches to unravel network components

    1. Bacterial Interactomes: From Interactions to Networks

      • Emmanuelle Bouveret, Christine Brun
      Pages 15-33

    2. From Bacterial to Microbial Ecosystems (Metagenomics)

      • Shannon J. Williamson, Shibu Yooseph
      Pages 35-55

    3. Prokaryote Genome Fluidity: Toward a System Approach of the Mobilome

      • Ariane Toussaint, Mick Chandler
      Pages 57-80

    4. Reticulate Classification of Mosaic Microbial Genomes Using NeAT Website

      • Gipsi Lima-Mendez
      Pages 81-91

    5. From Metabolic Reactions to Networks and Pathways

      • Masanori Arita
      Pages 93-106

    6. Predicting Metabolic Pathways by Sub-network Extraction

      • Karoline Faust, Jacques van Helden
      Pages 107-130

    7. Directed Module Detection in a Large-Scale Expression Compendium

      • Qiang Fu, Karen Lemmens, Aminael Sanchez-Rodriguez, Inge M. Thijs, Pieter Meysman, Hong Sun et al.
      Pages 131-165

    8. Using Phylogenetic Profiles to Predict Functional Relationships

      • Matteo Pellegrini
      Pages 167-177

    9. 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 et al.
      Pages 179-195

    10. Browsing Metabolic and Regulatory Networks with BioCyc

      • Mario Latendresse, Suzanne Paley, Peter D. Karp
      Pages 197-216

  5. Topological Analysis of Bacterial Networks

    1. Front Matter

      Pages 217-217
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  6. Topological analysis of bacterial networks

    1. Algorithms for Systematic Identification of Small Subgraphs

      • Joseph Geraci, Geoffrey Liu, Igor Jurisica
      Pages 219-244

    2. The Degree Distribution of Networks: Statistical Model Selection

      • William P. Kelly, Piers J. Ingram, Michael P. H. Stumpf
      Pages 245-262

    3. MAVisto: A Tool for Biological Network Motif Analysis

      • Henning Schwöbbermeyer, Röbbe Wünschiers
      Pages 263-280

    4. Using MCL to Extract Clusters from Networks

      • Stijn van Dongen, Cei Abreu-Goodger
      Pages 281-295

    5. Protein Complex Prediction with RNSC

      • Andrew D. King, Nataša Pržulj, Igor Jurisica
      Pages 297-312

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

      • Anaïs Baudot, Ouissem Souiai, Christine Brun
      Pages 313-326
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Keywords

About this book

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.

Editors and Affiliations

  • Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium

    Jacques Helden, Ariane Toussaint

  • INSERM 1024, Institut de Biologie de l'Ecole Normale, Paris, France

    Denis Thieffry

Bibliographic Information

  • Book Title: Bacterial Molecular Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Jacques Helden, Ariane Toussaint, Denis Thieffry

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-361-5

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2012

  • Hardcover ISBN: 978-1-61779-360-8Published: 06 December 2011

  • Softcover ISBN: 978-1-4939-6156-6Published: 23 August 2016

  • eBook ISBN: 978-1-61779-361-5Published: 07 December 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 546

  • Topics: Microbiology, Bacteriology

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