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Bacterial Molecular Networks: Methods and Protocols
Paperback
Series: Methods in Molecular Biology, Book 804
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ISBN13: 9781493961566
Publisher: Humana
Published: Aug 23 2016
Pages: 546
Weight: 2.11
Height: 1.14 Width: 7.01 Depth: 10.00
Language: English
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 MartÃnez-Flores, Alejandra López-Fuentes, Jair Santiago GarcÃa-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, Natasa Przulj, 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, LuÃs 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
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