Core E - The principal objective of the Genomics and Sequencing (GS) Core of the Center for AIDS research (CFAR) at the University of California San Diego (UCSD) is to facilitate the research of HIV/AIDS investigators by providing cost-effective access to cutting-edge genomics and sequencing technologies. The GS Core will help investigators realize the enormous potential of these approaches to assist basic and applied research into the role of host and viral genes in HIV infection and pathogenesis, leading to new insights and treatments. Support for developmental projects and investigators new to HIV research is an area of special emphasis.
The specific aims of the GS Core are: (1) to develop and provide molecular tools and resources to HIV researchers for the determination of host and viral mechanisms of pathogenesis, (2) to guide HIV researchers in the value, use, and interpretation of genetic information and gene expression data, and (3) to facilitate education and training in genomics and sequencing technologies for CFAR investigators, students, staff, and other researchers. The GS Core will achieve these aims by providing: (1) assays for gene expression, viral detection and quantitation for research purposes, genetic variation, tools for functional genomics (e.g., siRNA expressing vectors), sequencing and/or deep sequencing of virus, host, transcriptome, or small RNAs, and provision of useful reagents to researchers, (2) analysis of gene expression and genetic variation, help with open source and proprietary tools for alignment and comparison of sequences, and collaboration with the Bioinformatics and Information Technologies (BIT) Core in molecular phylogeny studies, application-specific high throughput sequencing (HTS) pipelines, or more advanced data analysis, and (3) seminars, workshops, and individual training for graduate students and fellows, web resources, and mentoring of undergraduate independent study students. The GS Core will serve as an important resource for basic and translational HIV-related research, as best exemplified by 129 publications and 211 investigators supported by the combined services of the Genomics and Molecular Biology Cores since the last renewal. All evidence indicates the GS Core will be a valuable, productive, and popular basic science core for the UCSD CFAR.

Public Health Relevance

The Genomics and Sequencing (GS) Core of the Center for AIDS Research at UCSD provides HIV/AIDS researchers with access to the latest genomics technologies and sequencing applications for their research. The services performed by the GS Core provide information on the host and viral mechanisms of HIV associated disease. This in turn will lead to new treatments and interventions for HIV-infected individuals

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Center Core Grants (P30)
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Special Emphasis Panel (ZAI1-UKS-A (J1))
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University of California San Diego
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Heaton, Robert K; Franklin Jr, Donald R; Deutsch, Reena et al. (2015) Neurocognitive change in the era of HIV combination antiretroviral therapy: the longitudinal CHARTER study. Clin Infect Dis 60:473-80
Hepler, N Lance; Scheffler, Konrad; Weaver, Steven et al. (2014) IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Comput Biol 10:e1003842
Szumowski, Suzannah C; Botts, Michael R; Popovich, John J et al. (2014) The small GTPase RAB-11 directs polarized exocytosis of the intracellular pathogen N. parisii for fecal-oral transmission from C. elegans. Proc Natl Acad Sci U S A 111:8215-20
Murrell, Ben; Murrell, Daniel; Murrell, Hugh (2014) R2-equitability is satisfiable. Proc Natl Acad Sci U S A 111:E2160
Grant, Igor; Franklin Jr, Donald R; Deutsch, Reena et al. (2014) Asymptomatic HIV-associated neurocognitive impairment increases risk for symptomatic decline. Neurology 82:2055-62
Blattner, Claudia; Lee, Jeong Hyun; Sliepen, Kwinten et al. (2014) Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers. Immunity 40:669-80
Cachay, Edward R (2014) The forgotten component in the staging and management of HIV/hepatitis C virus-coinfected patients. Clin Infect Dis 59:320-1
Jeong, Su Jin; Kim, Min Hyung; Song, Je Eun et al. (2014) Short communication: prospective comparison of qualitative versus quantitative polymerase chain reaction for monitoring virologic treatment failure in HIV-infected patients. AIDS Res Hum Retroviruses 30:827-9
Wang, Cathy X; Sather, Blythe D; Wang, Xuefeng et al. (2014) Rapamycin relieves lentiviral vector transduction resistance in human and mouse hematopoietic stem cells. Blood 124:913-23
Scheffler, Konrad; Murrell, Ben; Kosakovsky Pond, Sergei L (2014) On the validity of evolutionary models with site-specific parameters. PLoS One 9:e94534

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