Network Biology: Methods and Applications

While extremely large datasets describing gene sequences, mRNA transcripts, protein abundance, and metabolite concentrations are increasingly commonplace, these represent only starting ‘parts lists’ that are usually insufficient to unlock mechanistic insights on their own right.  Fortunately, as Network Biology: Methods and Applications examines, concepts emerging from the study of biological entities such as networks (e.g. functional interactions linking genes, proteins, metabolites, etc.) suggest that order rather than chaos prevails, with such principles as modular and hierarchical organization, reactive information-driven causal-response behaviours, systems robustness, co-evolution, and self-organization guiding the way.  This volume presents detailed, practical descriptions of the experimental and computational approaches currently prevalent in network biology as written by practiced experts in the field.  Written in the highly successful Methods in Molecular Biology™ series format, relevant chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.   Comprehensive and accessible, Network Biology: Methods and Applications provides an ensemble of procedures that will be of great value to a broad assortment of readers, ranging from graduate students to seasoned professionals looking to polish their skill sets.

Table of Contents:
Analysis of Protein–Protein Interactions Using High-throughput Yeast Two-Hybrid Screens.- Identification of Mammalian Protein Complexes by Lentiviral-Based Affinity Purification and Mass Spectrometry.- Protein Networks Involved in Vesicle Fusion, Transport, and Storage Revealed by Array-Based Proteomics.- Identification and Relative Quantification of Native and Proteolytically Generated Protein C-termini from Complex Proteomes: C-terminome Analysis.- Construction of Protein Interaction Networks Based on the Label Free Quantitative Proteomics.- Studying Binding Specificities of Peptide Recognition Modules by High-Throughput Phage Display Selections.- Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli.- Advanced Methods for High-Throughput Microscopy Screening of Genetically Modified Yeast Libraries.- Pooled Lentiviral shRNA Screening for Functional Genomics in Mammalian Cells.- Plant DNA Sequencing for Phylogenetic Analyses: From Plants to Sequences.- Using Coevolution to Predict Protein-Protein Interactions.- Visualizing Gene-Set Enrichment Results Using the Cytoscape Plugin Enrichment Map.- Quality Control Methodology for High-Throughput Protein-Protein Interaction Screening.- Filtering and Interpreting Large-Scale Experimental Protein-Protein Interaction Data.- Classification of Cancer Patients Using Pathway Analysis and Network Clustering.- Statistical Analysis of Dynamic Transcriptional Regulatory Network Structure.- Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs.- Displaying Chemical Information on a Biological Network Using Cytoscape.- Modeling of Proteins and TheirAssemblies with the Integrative Modeling Platform.- Predicting Node Characteristics from Molecular Networks.- Mathematical Modeling of Biomolecular Network Dynamics.