Bacterial Molecular Networks

Methods and Protocols

  • Jacques van Helden
  • Ariane Toussaint
  • Denis Thieffry

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

Table of contents

  1. Front Matter
    Pages i-xi
  2. 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
    2. Emmanuelle Bouveret, Christine Brun
      Pages 15-33
    3. Shannon J. Williamson, Shibu Yooseph
      Pages 35-55
    4. Ariane Toussaint, Mick Chandler
      Pages 57-80
    5. Karoline Faust, Jacques van Helden
      Pages 107-130
    6. Qiang Fu, Karen Lemmens, Aminael Sanchez-Rodriguez, Inge M. Thijs, Pieter Meysman, Hong Sun et al.
      Pages 131-165
    7. Heladia Salgado, Irma Martínez-Flores, Alejandra López-Fuentes, Jair Santiago García-Sotelo, Liliana Porrón-Sotelo, Hilda Solano et al.
      Pages 179-195
    8. Mario Latendresse, Suzanne Paley, Peter D. Karp
      Pages 197-216
  4. Topological Analysis of Bacterial Networks

    1. Front Matter
      Pages 217-217
    2. Joseph Geraci, Geoffrey Liu, Igor Jurisica
      Pages 219-244
    3. William P. Kelly, Piers J. Ingram, Michael P. H. Stumpf
      Pages 245-262
    4. Henning Schwöbbermeyer, Röbbe Wünschiers
      Pages 263-280
    5. Stijn van Dongen, Cei Abreu-Goodger
      Pages 281-295
    6. Andrew D. King, Nataša Pržulj, Igor Jurisica
      Pages 297-312
    7. Anaïs Baudot, Ouissem Souiai, Christine Brun
      Pages 313-326
    8. Nolwenn Le Meur, Robert Gentleman
      Pages 343-373
  5. Dynamical Modelling

    1. Front Matter
      Pages 375-375
    2. Jörn Behre, Luís Filipe de Figueiredo, Stefan Schuster, Christoph Kaleta
      Pages 377-407
    3. Grégory Batt, Bruno Besson, Pierre-Emmanuel Ciron, Hidde de Jong, Estelle Dumas, Johannes Geiselmann et al.
      Pages 439-462
    4. Claudine Chaouiya, Aurélien Naldi, Denis Thieffry
      Pages 463-479
    5. Maren L. Friesen, Emily I. Jones
      Pages 481-499
    6. Wilfred D. Kepseu, Frédérique Van Gijsegem, Jacques-Alexandre Sepulchre
      Pages 501-517
  6. Back Matter
    Pages 543-546

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.


bacterial interactomes gene regulatory networks mosaic microbial genomes pathogenic bacteria prokaryote genomes

Editors and affiliations

  • Jacques van Helden
    • 1
  • Ariane Toussaint
    • 2
  • Denis Thieffry
    • 3
  1. 1.Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe)Université Libre de BruxellesBruxellesBelgium
  2. 2.Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe)Université Libre de BruxellesBruxellesBelgium
  3. 3.INSERM 1024Institut de Biologie de l'Ecole NormaleParisFrance

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC 2012
  • Publisher Name Springer, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-61779-360-8
  • Online ISBN 978-1-61779-361-5
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site