Core L - Scientific inquiry and public health are being fundamentally changed by immense volumes of complex data, and modern computational techniques that are able to mine these data for pattern discovery and inference. The field of HIV research is no exception, and many innovative discoveries have been facilitated or validated by sophisticated modeling and data analyses. Traditional biostatistics services are neither designed to handle gigantic volumes of complex data, nor are these new data types (e.g., next generation sequencing data) a natural fit for current computational biology and informatics applications. The purpose of the Bioinformatics and Information Technologies (BIT) is to handle CFAR investigator demand for storing, managing, analyzing, interpreting, and disseminating large and complex data sets, especially those containing viral and host molecular sequences. Based on ongoing and anticipated future needs of CFAR members, in the next five years, the BIT Core is structured as three interlinked units that will: (1) provide bioinformatics support for CFAR researchers by leveraging world-class expertise in bioinformatics and computational biology available at UCSD to offer a comprehensive spectrum of services and consultations related to computational analyses of data collected by CFAR investigators;(2) supply content management systems, web services for biomedical data, and computational infrastructure;and (3) provide training in bioinformatics and information technology. The BIT Core is uniquely positioned to provide these innovative services to CFAR members by drawing upon cutting edge in-house methodological research, modern sequencing and biomedical technologies offered by other CFAR Cores (e.g. GS, PEP, Flow Cytometry Cores), and professional software development and support expertise of its programming team. The CFAR External Advisory Committee reviewed our Center in February, 2012 and noted the following about the BIT Core in their final report:

Public Health Relevance

The mission of the Bioinformatics and Information Technologies (BIT) Core is to provide accessible, affordable, reliable, flexible, and timely services and facilities for biomedical data management, computational analysis and interpretation of complex biomedical (especially sequence) data, and to train CFAR members in relevant computational and informatics techniques.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Center Core Grants (P30)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-UKS-A (J1))
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
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

Showing the most recent 10 out of 522 publications