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 Barré, 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-François 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, Pádraig 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 Velázquez-Muriel, Daniel Russel, and Andrej Sali
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