Title Bacterial molecular networks : methods and protocols / edited by Jacques van Helden and Ariane Toussaint, Denis Thieffry

Published New York, NY : Humana Press, ©2012

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Description 1 online resource (xi, 546 pages) Series Methods in molecular biology, 1064-3745 ; 804 Methods in molecular biology ; 804. 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 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 Analysis Life sciences Microbiology Bacteriology bacteriologie groeiregulatoren growth regulators genetische regulatie genetic regulation genomen genomes Microbiology (General) Microbiologie (algemeen) Notes Includes index Bibliography Includes bibliographical references and index Notes English Subject Bacterial genetics -- Laboratory manuals Cell interaction -- Laboratory manuals Gene regulatory networks. Bacteria -- genetics Gene Regulatory Networks Systems Biology -- methods Gene regulatory networks Bacterial genetics Cell interaction Genre/Form Laboratory manuals Laboratory manuals. Manuels de laboratoire. Form Electronic book Author Helden, Jacques van Toussaint, Ariane Thieffry, Denis. ISBN 9781617793615 1617793612 1617793604 9781617793608

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