Mapping of genetic and molecular networks across species, diseases and cell states. The Ideker lab has long promoted strategies to experimentally map and analyze the molecular networks that encode biological function. This interest began during Dr. Ideker’s PhD, at which time Leroy Hood and Dr. Ideker outlined the “Systems Biology” approach to the study of biological systems by “perturbing them systematically; monitoring the global response at multiple levels (gene, protein, metabolite); and formulating network models that describe the structure of the system and its response to perturbation” [2a below]. Network mapping has continually driven the research agenda of the Ideker laboratory via our interest in complementary approaches, especially in mapping protein interaction networks with affinity purification mass spectrometry or yeast-two-hybrid [2b] or mapping epistatic genetic interactions by combinatorial gene knockout [2c,d]. Recently, we have participated in large team efforts to map the physical interaction landscapes of multiple cancer types and SARS-CoV-2. We are also making exciting progress with integrating protein interaction networks with protein immunofluorescent images to reconstruct most human cell components and chart new ones.
(Figure 2) Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network: Perturbation matrix.