Network Biology Methods and Applications

About this book

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.

Network Biology: Methods and Applications 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.

Contents

1. Analysis of Protein-Protein Interactions Using High-throughput Yeast Two-Hybrid Screens Seesandra V. Rajagopala and Peter Uetz
2. Identification of Mammalian Protein Complexes by Lentiviral-Based Affinity Purification and Mass Spectrometry Zuyao Ni, Jonathan B. Olsen, Andrew Emili, and Jack F. Greenblatt
3. 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, and David J. O'Connell
4. Identification and Relative Quantification of Native and Proteolytically Generated Protein C-termini from Complex Proteomes: C-terminome Analysis Oliver Schilling, Pitter F. Huesgen, Olivier Barre, and Christopher M. Overall
5. Construction of Protein Interaction Networks Based on the Label Free Quantitative Proteomics Mihaela E. Sardiu and Michael P. Washburn
6. Studying Binding Specificities of Peptide Recognition Modules by High-Throughput Phage Display Selections Haiming Huang and Sachdev S. Sidhu
7. Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli Mohan Babu, Alla Gagarinova, and Andrew Emili
8. Advanced Methods for High-Throughput Microscopy Screening of Genetically Modified Yeast Libraries Yifat Cohen and Maya Schuldiner
9. Pooled Lentiviral shRNA Screening for Functional Genomics in Mammalian Cells Kim Blakely, Troy Ketela, and Jason Moffat
10. Plant DNA Sequencing for Phylogenetic Analyses: From Plants to Sequences Susana S. Neves and Laura L. Forrest
11. Using Coevolution to Predict Protein-Protein Interactions Gregory W. Clark, Vaqaar-un-Nisa Dar, Alexandr Bezginov, Jinhao M. Yang, Robert L. Charlebois, and Elisabeth R.M. Tillier
12. Visualizing Gene-Set Enrichment Results Using the Cytoscape Plugin Enrichment Map Daniele Merico, Ruth Isserlin, and Gary D. Bader
13. Quality Control Methodology for High-Throughput Protein-Protein Interaction Screening Alexei Vazquez, Jean-Francois Rual, and Kavitha Venkatesan
14. Filtering and Interpreting Large-Scale Experimental Protein-Protein Interaction Data Gabriel Musso, Andrew Emili, and Zhaolei Zhang
15. 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, and Marc R. Wilkins
16. Statistical Analysis of Dynamic Transcriptional Regulatory Network Structure Jennifer J. Smith, Ramsey A. Saleem, and John D. Aitchison
17. Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs Colm Ryan, Gerard Cagney, Nevan Krogan, Padraig Cunningham, and Derek Greene
18. Displaying Chemical Information on a Biological Network Using Cytoscape Iain M. Wallace, Gary D. Bader, Guri Giaever, and Corey Nislow
19. 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, Javier Velazquez-Muriel, Daniel Russel, and Andrej Sali
20. Predicting Node Characteristics from Molecular Networks Sara Mostafavi, Anna Goldenberg, and Quaid Morris
21. Mathematical Modeling of Biomolecular Network Dynamics Alexander V. Ratushny, Stephen A. Ramsey, and John D. Aitchison

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