Buch, Englisch, Band 804, 546 Seiten, Previously published in hardcover, Format (B × H): 178 mm x 254 mm, Gewicht: 1040 g
Reihe: Methods in Molecular Biology
Methods and Protocols
Buch, Englisch, Band 804, 546 Seiten, Previously published in hardcover, Format (B × H): 178 mm x 254 mm, Gewicht: 1040 g
Reihe: Methods in Molecular Biology
ISBN: 978-1-4939-6156-6
Verlag: Humana Press
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.
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Weitere Infos & Material
1. Bacterial Molecular Networks: Bridging the Gap Between Functional Genomics and Dynamical Modeling
Denis Thieffry, Ariane Toussaint, and Jacques van Helden
Part I. Experimental and in silico approaches to unravel network components
2. Bacterial Interactomes: From Interactions to Networks
Emmanuelle Bouveret and Christine Brun
3. From Bacterial to Microbial Ecosystems (Metagenomics)
Shannon J. Williamson and Shibu Yooseph
4. Prokaryote Genome Fluidity: Towards a System Approach of the Mobilome
Ariane Toussaint and Mick Chandler
5. Reticulate Classification of Mosaic Microbial Genomes using NeAT Website
Gipsi Lima-Mendez
6. From Metabolic Reactions to Networks and Pathways
Masanori Arita
7. Predicting Metabolic Pathways by Subnetwork Extraction
Karoline Faust and Jacques van Helden
8. Directed Module Detection in a Large-scale Expression Compendium
Qiang Fu, Karen Lemmens, Aminael Sanchez-Rodriguez, Inge M. Thijs, Pieter Meysman, Hong Sun, Ana Carolina Fierro, Kristof Engelen, and Kathleen Marchal
9. Using Phylogenetic Profiles to Predict Functional Relationships
Matteo Pellegrini
10. 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, Luis Muniz-Rascado, and Julio Collado-Vides
11. Browsing Metabolic and Regulatory Networks with BioCyc
Mario Latendresse, Suzanne Paley, and Peter D. Karp
Part II. Topological analysis of bacterial networks
12. Algorithms for Systematic Identification of Small Sub-graphs
Joseph Geraci, Geoffrey Liu, and Igor Jurisica
13. The Degree Distribution of Networks: Statistical Model Selection
William P. Kelly, Piers J. Ingram, and Michael P. H. Stumpf
14. MAVisto: A Tool for Biological Network Motif Analysis
Henning Schwöbbermeyer and Röbbe Wünschiers
15. Using MCL to Extract Clusters from Networks
Stijn van Dongen and Cei Abreu-Goodger
16. Protein Complex Prediction with RNSC (Method)
Andrew D. King, Nataša Pržulj, and Igor Jurisica
17. Network Analysis and Protein Function Prediction with the PRODISTIN Web Site
Anaïs Baudot, Ouissem Souiai and Christine Brun
18. Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Networks to Clusters
Sylvain Brohée
19. Analyzing Biological Data Using R: Methods for Graphs and Networks
Nolwenn Le Meur and Robert Gentleman
Part III. Dynamical Modelling
20. Detecting Structural Invariants in Biological Reaction Networks
Jörn Behre, Luís Filipe de Figueiredo, Stefan Schuster, and Christoph Kaleta
21. 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
22. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks
Grégory Batt, Bruno Besson, Pierre-Emmanuel Ciron, Hidde de Jong, Estelle Dumas, Johannes Geiselmann, Regis Monte, Pedro T. Monteiro, Michel Page, François Rechenmann, and Delphine Ropers
23. Logical Modelling of Gene Regulatory Networks with GINsim
Claudine Chaouiya, Aurélien Naldi, and Denis Thieffry
24. Modelling the Evolution of Mutualistic Symbioses
Maren L. Friesen and Emily L. Jones
25. Modelling the Onset of Virulence in Pathogenic Bacteria
Wilfred D. Kepseu, Frédérique Van Gijsegem, and Jacques-Alexandre Sepulchre
26. Spatial Stochastic Cellular Modeling with the Smoldyn Simulator
Steven S. Andrews
