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 proteinprotein 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)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-BB-M)
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
Xiao, Yinghong; Rouzine, Igor M; Bianco, Simone et al. (2016) RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell Host Microbe 19:493-503
Webb, Benjamin; Sali, Andrej (2016) Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics 54:5.6.1-5.6.37
Cimermancic, Peter; Weinkam, Patrick; Rettenmaier, T Justin et al. (2016) CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol 428:709-19
Whitfield, Zachary J; Andino, Raul (2016) Characterization of Viral Populations by Using Circular Sequencing. J Virol 90:8950-3
Verschueren, Erik; Von Dollen, John; Cimermancic, Peter et al. (2015) Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics 49:8.19.1-16
Ramage, Holly R; Kumar, G Renuka; Verschueren, Erik et al. (2015) A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Mol Cell 57:329-40
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
Schulte, Michael B; Draghi, Jeremy A; Plotkin, Joshua B et al. (2015) Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses. Elife 4:
Costa, Helio A; Leitner, Michael G; Sos, Martin L et al. (2015) Discovery and functional characterization of a neomorphic PTEN mutation. Proc Natl Acad Sci U S A 112:13976-81
Shah, Priya S; Wojcechowskyj, Jason A; Eckhardt, Manon et al. (2015) Comparative mapping of host-pathogen protein-protein interactions. Curr Opin Microbiol 27:62-8

Showing the most recent 10 out of 41 publications