The High-Throughput Functional Genomics, Proteomics, and Computational Core (referred to as "Core B") of this program project proposal has four distinct research support goals that are designed to enable the Individual objectives as described In each project. These research roles are as follows. First, Core B will provide high-throughput mass spectrometry services for the purpose of establishing viral and host protein-protein Interaction maps. Second, Core B will provide advanced computational research support, by bringing modern bioinformatic approaches to protein sequence, structure, and function analysis to bear on the expected deluge of functional data this proposal will generate. Third, Core B will provide leading-edge ultra deep sequencing support to the program project. A major focus of the proposal is the analysis of viral diversity, population structure and plasticity, especially with respect to the evolution of quasi-specles. Ultra deep sequencing (such as that provided by lllumina Solexa technology) allows quantitative and precise measurements of genome-wide genetic dynamics at a depth and accuracy that was unthinkable just a few years ago. The field of deep sequencing, which Includes the methodologies for library generation, the actual sequencing, and the downstream sequence analysis, are rapidly changing. This section of the core will actively research and optimize approaches and Informatics associated with sequencing to support the goals of the program project. Fourth, Core B will provide high-throughput RNAi screening support to the program. In conjunction with the Chandra and Young labs, personnel of Core B will work closely with the Chandra and Young labs for the generation of RNAi libraries and the actual screening.

Public Health Relevance

Enteroviruses are a major threat to public health. The High-Throughput Functional Genomics, Proteomics, and Computational Core (Core B) of this program project seeks to provide leading-edge technologies and approaches to support the overall goals of characterizing and dissecting enterovirus diversity, evolution, and pathogenesis.

National Institute of Health (NIH)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
San Francisco
United States
Zip Code
Davis, Zoe H; Verschueren, Erik; Jang, Gwendolyn M et al. (2015) Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell 57:349-60
Stern, Adi; Bianco, Simone; Yeh, Ming Te et al. (2014) Costs and benefits of mutational robustness in RNA viruses. Cell Rep 8:1026-36
Acevedo, Ashley; Andino, Raul (2014) Library preparation for highly accurate population sequencing of RNA viruses. Nat Protoc 9:1760-9
Morris, John H; Knudsen, Giselle M; Verschueren, Erik et al. (2014) Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 9:2539-54
Acevedo, Ashley; Brodsky, Leonid; Andino, Raul (2014) Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 505:686-90
Hagai, Tzachi; Azia, Ariel; Babu, M Madan et al. (2014) Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions. Cell Rep 7:1729-39
Pechmann, Sebastian; Frydman, Judith (2014) Interplay between chaperones and protein disorder promotes the evolution of protein networks. PLoS Comput Biol 10:e1003674
Fraser, James S; Gross, John D; Krogan, Nevan J (2013) From systems to structure: bridging networks and mechanism. Mol Cell 49:222-31
Geller, Ron; Andino, Raul; Frydman, Judith (2013) Hsp90 inhibitors exhibit resistance-free antiviral activity against respiratory syncytial virus. PLoS One 8:e56762
Roguev, Assen; Talbot, Dale; Negri, Gian Luca et al. (2013) Quantitative genetic-interaction mapping in mammalian cells. Nat Methods 10:432-7

Showing the most recent 10 out of 17 publications