Bacterial molecular networks : methods and protocols /

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Bibliographic Details
Imprint:	New York, NY : Humana Press, ©2012.
Description:	1 online resource (xi, 546 pages)
Language:	English
Series:	Methods in molecular biology, 1064-3745 ; 804 Methods in molecular biology ; 804.
Subject:	Bacterial genetics -- Laboratory manuals. Cell interaction -- Laboratory manuals. Bacteria -- genetics. Gene Regulatory Networks. Systems Biology -- methods. Bacterial genetics. Cell interaction. Laboratory Manual. Laboratory manuals.
Format:	E-Resource Book
URL for this record:	http://pi.lib.uchicago.edu/1001/cat/bib/11122548

Hidden Bibliographic Details
Other authors / contributors:	Helden, Jacques van. Toussaint, Ariane. Thieffry, Denis.
ISBN:	9781617793615 1617793612 1617793604 9781617793608 9781617793608
Notes:	Includes index. Includes bibliographical references and index. English.
Summary:	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
Other form:	Print version: Bacterial molecular networks. New York, NY : Humana Press, ©2012
Standard no.:	10.1007/978-1-61779-361-5.

Table of 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.

Bacterial molecular networks : methods and protocols /

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