Research Support

The Ideker Lab gratefully acknowledges active research support from the following agencies. For more information on specific research projects, please click on project titles with associated links.

The Cancer Cell Map Initiative (CCMI) was established to harness the tools of systems and computational biology with world-class cancer researchers to comprehensively discover and analyze the molecular networks of cancer. The major outcomes of our work will be a collection of comprehensive Cancer Cell Maps and Cancer Gene Ontologies, and the application of these resources to hypothesis-driven investigation and personalized, precision medicine.

NIH/NCI - U24 CA184427     
The Network Data Exchange (NDEx) Project provides an open-source framework where scientists and organizations can find, store, share and publish biological network knowledge. The project maintains a free Public Server and an informational website with technical documentation. Researchers will use NDEx to access, share, and publish biological knowledge in multiple network formats.

A systems approach to mapping the DNA damage response
NIH/NIEHS - R01 ES014811
The goal of this proposal is to elucidate the eukaryotic DNA damage response through an integrated experimental / computational approach leading to in-silico models of signaling and regulatory networks.  These studies are performed in collaboration with the laboratory of Co-I Robert Sobol at University of Alabama.

Cytoscape: A modeling platform for biomolecular networks
NIH/NIGMS - R01 GM070743
Cytoscape is an Open Source bioinformatics software environment for biological network analysis and modeling. This award funds continued development and maintenance of the existing functionality of Cytoscape as well as a pipeline for identification of network modules through integration with gene expression data and through evolutionary comparison.  Ideker collaborates in this work with Co-I Gary Bader’s lab at University of Toronto.

National Resource for Network Biology (NRNB)
NIH/NIGMS - 5 P41 GM103504
The National Resource for Network Biology is a Biomedical Technology Resource Center (BTRC) previously funded by NCRR and now funded by NIGMS. The aim of this resource is to provide a freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease.

San Diego Center for Systems Biology 
NIH/NIGMS - P50 GM085764
The San Diego Center for Systems Biology is a cross cutting initiative directed by Trey Ideker and involving investigators from UCSD, Salk, Scripps, and the Sanford/Burnham Institute.  Ideker is leading a genetic interaction-mapping project on stress responses in yeast, and he is also running the Bioinformatics Core, which provides broad bioinformatics support to dozens of Center investigators.

Comparative physical and genetic interaction mapping in yeasts
NIH/NIGMS - R01 GM084279
This grant funds work to generate high-density physical interaction maps (protein-DNA, protein-protein) and genetic interaction maps (synthetic lethals and epistasis) in the model organism Schizosaccharomyces pombe. These network data are providing a major resource for evolutionary comparison to existing interaction maps of Saccharomyces cerevisiae.  This proposal is jointly directed by Ideker and his collaborator, Nevan Krogan, at UCSF.

The goal is to design and prototype the Deep Translate strategy for biomedical data translation.

UC San Diego Clinical and Translational Research Institute
NIN/NCATS - 1UL1TR001442
The CTRI provides infrastructure support and educational opportunities related to clinical and translational research at UC San Diego and its affiliated institutions.