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, Jinghao M. Yang, Robert L. Charlebois, and Elisabeth R.M. Tillier |
12. Visualizing gene-set enrichment results using the cytoscape plug-in 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, Karen Lasker, Dina Schneidman-Duhovny, Elina Tjioe, Jeremy Phillips, Seung Joong Kim, Javier Velázquez-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. Ramsay, and John D. Aitchison |
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 |