Network Biology

Chapter 1 Analysis of protein-protein interactions using high-throughput yeast two-hybrid screens.

Chapter 2 Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry.

Chapter 3 Protein networks involved in vesicle fusion, transport, and storage revealed by array-based proteomics.

Chapter 4 Identification and relative quantification of native and proteolytically generated protein C-termini from complex proteomes: C-terminome analysis.

Chapter 5 Construction of protein interaction networks based on the label-free quantitative proteomics.

Chapter 6 Studying binding specificities of peptide recognition modules by high-throughput phage display selections.

Chapter 7 Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Chapter 9 Pooled lentiviral shRNA screening for functional genomics in mammalian cells.

Chapter 10 Plant DNA sequencing for phylogenetic analyses: from plants to sequences.

Chapter 11 Using coevolution to predict protein-protein interactions.

Chapter 12 Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map.

Chapter 13 Quality control methodology for high-throughput protein-protein interaction screening.

Chapter 14 Filtering and interpreting large-scale experimental protein-protein interaction data.

Chapter 15 Classification of Cancer Patients Using Pathway Analysis and Network Clustering

Chapter 16 Statistical analysis of dynamic transcriptional regulatory network structure.

Chapter 17 Imputing and predicting quantitative genetic interactions in epistatic MAPs.

Chapter 18 Displaying chemical information on a biological network using Cytoscape.

Chapter 19 Modeling of proteins and their assemblies with the integrative modeling platform.

Chapter 20 Predicting node characteristics from molecular networks.

Chapter 21 Mathematical modeling of biomolecular network dynamics.