Research

Cores

Functional Genomics
The Functional Genomics Core provides cutting-edge innovative technologies for the functional characterization of the genome in a reliable, reproducible and cost-efficient manner. We provide combinatorial genetic knockout by CRISPR, CRISPRi and CRISPRa, mass spectrometry characterization, and expertise in data processing for these experimental platforms. This core is partnered with two well established facilities: the Thermo Fisher Scientific Proteomics Facility for Disease Target Discovery located at the J. David Gladstone Institutes and the UCSD Institute for Genomic Medicine Genomics Center sequencing facility. We are also creating a new CRISPR screening core that leverages our foundational expertise in genome engineering.

Bioinformatics Infrastructure and Services
The Bioinformatics Infrastructure and Services Core provides support to all three CCMI projects at all stages of research and publication. The Core is made up of three major components: Cytoscape and the Cytoscape Cyberinfrastructure (CI); the Network Data Exchange (NDEx); and the CCMI Data and Analysis Portal. Cytoscape provides a range of tools for the analysis and visualization of biological networks. NDEx provides the database infrastructure to support the sharing, review and dissemination of network data and models. It also enables a consolidated access point to public biological network resources for use by CCMI investigators. Finally, the CCMI Data and Analysis Portal provides a common access point for software tools and pipelines and for their associated data. This component will be supported by GenePattern Notebooks, which will facilitate the development of workflow pipelines and the sharing and reproducibility of analyses.