Biomedical research is at a critical juncture in which vast amounts of information on molecules and molecular interactions have been collected, but methods to integrate and analyze these data are still in their infancy. The sheer number and variety of technologies is staggering. In terms of molecules, global mRNA profiles are obtained using DNA microarrays 178 or next-generation sequencing 179, while changes in protein abundance 180, protein phosphorylation state 181 and metabolite concentrations 182 are quantified with mass spectrometry, NMR and other advanced techniques. In terms of molecular interactions, protein-protein binding is measured using yeast-two-hybrid assays 183,184,185,186,187,188,189,190, LUMIER 191, affinity purification coupled to mass spectrometry 192,193,194, or kinase-substrate arrays 195. Protein-DNA and protein-RNA binding are measured with technologies such as chIP-chip 196,197,198, chIP-PET 199,200, DAM-ID 201, double-stranded DNA arrays 202, yeastone- hybrid 203,204, or RIP-chip 205. There has also been an explosion in techniques for mapping genetic networks, including Synthetic Genetic Arrays 206, dSLAM 207, EMAP 208, high-throughput liquid culture assays 209, and combinatorial RNAi 210, which rapidly identify epistatic relationships such as synthetic lethality or suppression in an automated fashion. Large networks are generated by functional genomic studies, involving panels of gene knock-outs 211,212,213,214,215 or analysis of expression Quantitative Trait Loci (eQTL) 216,217,218,219. Alternatively, networks are being defined using functional inter-relationships, such as linking two proteins that are co-expressed or that are given the same protein functional annotation 220. This enormous collection of measurement types necessitates a bioinformatic framework to integrate, filter, and interpret the resulting data. The Mission of the Network Assembly Core is to provide tools for integration and visualization of network level and other genome-scale data, assembly of these data into biological networks in which functional network modules can be identified, and storage and dissemination of data and resulting models. The director, Dr. Ideker is an established leader in the area of bioinformatics dedicated to developing such methods.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center (P50)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-CBCB-2)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
La Jolla
United States
Zip Code
Bean, Gordon J; Jaeger, Philipp A; Bahr, Sondra et al. (2014) Development of ultra-high-density screening tools for microbial "omics". PLoS One 9:e85177
Nazarko, Taras Y; Ozeki, Katharine; Till, Andreas et al. (2014) Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy. J Cell Biol 204:541-57
Hossain, Munshi Azad; Johnson, Tracy L (2014) Using yeast genetics to study splicing mechanisms. Methods Mol Biol 1126:285-98
Hui, Ashley; Pinter-Wollman, Noa (2014) Individual variation in exploratory behaviour improves speed and accuracy of collective nest selection by Argentine ants. Anim Behav 93:261-266
Tsimring, Lev S (2014) Noise in biology. Rep Prog Phys 77:026601
Mather, William; Hasty, Jeff; Tsimring, Lev S (2014) Synchronization of degrade-and-fire oscillations via a common activator. Phys Rev Lett 113:128102
Bouslimani, Amina; Sanchez, Laura M; Garg, Neha et al. (2014) Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 31:718-29
Gorkin, David U; Leung, Danny; Ren, Bing (2014) The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14:762-75
Lee, KiYoung; Sung, Min-Kyung; Kim, Jihyun et al. (2014) Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A 111:E3157-66
Caldwell, Andrew B; Cheng, Zhang; Vargas, Jesse D et al. (2014) Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev 28:2120-33

Showing the most recent 10 out of 69 publications