Network Biology Methods and Applications 1st Edition by Seesandra V Rajagopala, Peter Uetz, Gerard Cagney, Andrew Emili ISBN 1617792764 9781617792762

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ISBN 10: 1617792764 
ISBN 13: 9781617792762
Author: Seesandra V Rajagopala, Peter Uetz, Gerard Cagney, Andrew Emili

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.

Network Biology Methods and Applications 1st Table of contents:

Analysis of Protein–Protein Interactions Using High-Throughput Yeast Two-Hybrid Screens
Seesandra V. Rajagopala, Peter Uetz
Pages 1-29
Identification of Mammalian Protein Complexes by Lentiviral-Based Affinity Purification and Mass Spectrometry
Zuyao Ni, Jonathan B. Olsen, Andrew Emili, Jack F. Greenblatt
Pages 31-45
Protein Networks Involved in Vesicle Fusion, Transport, and Storage Revealed by Array-Based Proteomics
Mikael Bauer, Magdalena Maj, Ludwig Wagner, Dolores J. Cahill, Sara Linse, David J. O’Connell
Pages 47-58
Identification and Relative Quantification of Native and Proteolytically Generated Protein C-Termini from Complex Proteomes: C-Terminome Analysis
Oliver Schilling, Pitter F. Huesgen, Olivier Barré, Christopher M. Overall
Pages 59-69
Construction of Protein Interaction Networks Based on the Label-Free Quantitative Proteomics
Mihaela E. Sardiu, Michael P. Washburn
Pages 71-85
Studying Binding Specificities of Peptide Recognition Modules by High-Throughput Phage Display Selections
Haiming Huang, Sachdev S. Sidhu
Pages 87-97
Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli
Mohan Babu, Alla Gagarinova, Andrew Emili
Pages 99-126
Advanced Methods for High-Throughput Microscopy Screening of Genetically Modified Yeast Libraries
Yifat Cohen, Maya Schuldiner
Pages 127-159
Pooled Lentiviral shRNA Screening for Functional Genomics in Mammalian Cells
Kim Blakely, Troy Ketela, Jason Moffat
Pages 161-182
Plant DNA Sequencing for Phylogenetic Analyses: From Plants to Sequences
Susana S. Neves, Laura L. Forrest
Pages 183-235
Using Coevolution to Predict Protein–Protein Interactions
Gregory W. Clark, Vaqaar-un-Nisa Dar, Alexandr Bezginov, Jinghao M. Yang, Robert L. Charlebois, Elisabeth R. M. Tillier
Pages 237-256
Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
Daniele Merico, Ruth Isserlin, Gary D. Bader
Pages 257-277
Quality Control Methodology for High-Throughput Protein–Protein Interaction Screening
Alexei Vazquez, Jean-François Rual, Kavitha Venkatesan
Pages 279-294
Filtering and Interpreting Large-Scale Experimental Protein–Protein Interaction Data
Gabriel Musso, Andrew Emili, Zhaolei Zhang
Pages 295-309
Classification of Cancer Patients Using Pathway Analysis and Network Clustering
David C. Y. Fung, Amy Lo, Lucy Jankova, Stephan J. Clarke, Mark Molloy, Graham R. Robertson et al.
Pages 311-336
Statistical Analysis of Dynamic Transcriptional Regulatory Network Structure
Jennifer J. Smith, Ramsey A. Saleem, John D. Aitchison
Pages 337-352
Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs
Colm Ryan, Gerard Cagney, Nevan Krogan, Pádraig Cunningham, Derek Greene
Pages 353-361
Displaying Chemical Information on a Biological Network Using Cytoscape
Iain M. Wallace, Gary D. Bader, Guri Giaever, Corey Nislow
Pages 363-376
Modeling of Proteins and Their Assemblies with the Integrative Modeling Platform
Benjamin Webb, Keren Lasker, Dina Schneidman-Duhovny, Elina Tjioe, Jeremy Phillips, Seung Joong Kim et al.
Pages 377-397

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Tags: Seesandra V Rajagopala, Peter Uetz, Gerard Cagney, Andrew Emili, Network Biology