Research Support

We gratefully acknowledge support from the following agencies. For more information on specific research projects, please click on project titles with associated links.

National Resource for Network Biology (NRNB)
P41 GM103504-04

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.

As of July 2015, we're pleased to announce that the NIGMS has renewed funding for the NRNB for another five years (2016-2020) -- see the NRNB web site for information.

Crowdsourcing Network Biology using the Cytoscape AppStore
P41 GM103504-03S1 (new#) 

Building upon the strengths of the current Cytoscape platform, we have the opportunity to dramatically accelerate the development and distribution of Cytoscape Apps through an innovative crowdsourcing system we are calling the Cytoscape AppStore. This supplement will be jointly utilized by collaborator Alexander Pico (UCSF Gladstone Institute).

San Diego Center for Systems Biology 
P50 GM085764-04 

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.

A systems approach to mapping the DNA damage response
R01 ES014811-08 

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 Richard Kolodner at UCSD.

Cytoscape: A modeling platform for biomolecular networks
R01 GM070743-10

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.

Comparative physical and genetic interaction mapping in yeasts
R01 GM084279-04

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.

GenomeSpace: A community web environment for integrative genomic analysis
P01 HG005062-03
Under the leadership of Dr. Jill Mesirov (Broad Institute), GenomeSpace is integrating features from leading bioinformatics platforms into an interoperable web-based framework to be hosted at Broad/MIT. These include GenePattern, UCSC GenomeBrowser, Cytoscape, and several others.

Chronic HIV infection and Aging in NeuroAIDS (CHAIN) Center
P30 MH062261
CHAIN is a multi-disciplinary center supporting biomedical research relevant to neurological AIDS. This subcontract aims to develop a suite of bioinformatics tools to help CHAIN scientists refine the extraction of pathway models from molecular interaction networks and better characterize their complex neuropathology.

NDEx – The Network Data Exchange A Network Commons for BiologistsPast Funding
U24 CA184427
The Network Data Exchange is a collaborative web resource that captures knowledge of the structure and function of molecular networks giving rise to cancer. This system, NDEx, the Network Data Exchange, will be comprised of (1) a freely available, open-source server platform and (2) a public website built on that platform. Cancer researchers will use NDEx to access, share, and publish biological knowledge in multiple network formats.

Cancer Center Support Grant




The CCSG provides support for the center’s 6 research programs, 6 shared resources, the clinical trials office, and developmental initiatives to foster collaboration and translation of research discoveries into patient care.