The Bioinformatics Shared Resource, a core function of Duke Cancer Institute (DCI), supports the bioinformatics research needs of DCI investigators including their needs for complex genomic data management, data integration, computing and statistical analysis. Its mission is to provide a high-quality, service-oriented, coordinated and cost efficient bioinformatics infrastructure for DCI researchers, one which increases collaborations across DCI programs, and among the DCI, other Duke programs and external investigators. This mission is accomplished within the framework of adherence to sound data provenance and statistical principles, literate programming, and reproducible analysis. The Bioinformatics Shared Resource covers every facet of analysis of high-dimensional genomic data starting from the design stage to pre- processing (background, normalization and summarization of RNA microarrays; genotype and copy number calling from GWAS platforms; and alignment, normalization (RNA-seq) and SNV calling (DNA-seq) of next- generation sequencing [NGS] platforms), high-level association analyses with complex phenotypes, and genomic annotation of results. While traditionally focused on omics research, the shared resource plans to expand its reach into analysis of electronic health record (EHR) research as the -omics and EHR-based research intersect. Since August 2013, the DCI Bioinformatics Shared Resource has been under the leadership of Dr. Kouros Owzar. The shared resource is staffed by two bioinformaticians and two information technology analysts, and works closely with the DCI Biostatistics and Information Systems Shared Resources to support clinical and translation research at the DCI. Additionally, a cadre of four faculty members from Duke's Department of Biostatistics and Bioinformatics bring to the resource expertise in theoretical and applied statistics and computational biology. The Shared Resource's effort is allocated exclusively to DCI members and contributed to 111 publications during the funding period. Its current model is to contribute to DCI members' grant and contract development at no charge in order to build long-term collaborations in which the Resource faculty and staff have effort supported by those successful grants and/or contracts.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA014236-44
Application #
9404306
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2018-01-01
Budget End
2018-12-31
Support Year
44
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Duke University
Department
Type
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Galaz-Montoya, Monica; Wright, Sara J; Rodriguez, Gustavo J et al. (2017) ?2-Adrenergic receptor activation mobilizes intracellular calcium via a non-canonical cAMP-independent signaling pathway. J Biol Chem 292:9967-9974
Lanier, Megan L; Park, Hyeri; Mukherjee, Paramita et al. (2017) Formal Synthesis of (+)-Laurencin by Gold(I)-Catalyzed Intramolecular Dehydrative Alkoxylation. Chemistry 23:7180-7184
Shi, Qiong; Liu, Hongliang; Han, Peng et al. (2017) Genetic Variants in WNT2B and BTRC Predict Melanoma Survival. J Invest Dermatol 137:1749-1756
Woyach, Jennifer A; Ruppert, Amy S; Guinn, Daphne et al. (2017) BTKC481S-Mediated Resistance to Ibrutinib in Chronic Lymphocytic Leukemia. J Clin Oncol 35:1437-1443
Wang, Yanru; Freedman, Jennifer A; Liu, Hongliang et al. (2017) Associations between RNA splicing regulatory variants of stemness-related genes and racial disparities in susceptibility to prostate cancer. Int J Cancer 141:731-743
Fayanju, Oluwadamilola M; Hall, Carolyn S; Bauldry, Jessica Bowman et al. (2017) Body mass index mediates the prognostic significance of circulating tumor cells in inflammatory breast cancer. Am J Surg 214:666-671
Leu, David; Spasojevic, Ivan; Nguyen, Huy et al. (2017) CNS bioavailability and radiation protection of normal hippocampal neurogenesis by a lipophilic Mn porphyrin-based superoxide dismutase mimic, MnTnBuOE-2-PyP5. Redox Biol 12:864-871
Sauer, Scott J; Tarpley, Michael; Shah, Imran et al. (2017) Bisphenol A activates EGFR and ERK promoting proliferation, tumor spheroid formation and resistance to EGFR pathway inhibition in estrogen receptor-negative inflammatory breast cancer cells. Carcinogenesis 38:252-260
Pan, Yongchu; Liu, Hongliang; Wang, Yanru et al. (2017) Associations between genetic variants in mRNA splicing-related genes and risk of lung cancer: a pathway-based analysis from published GWASs. Sci Rep 7:44634
Yin, Jieyun; Liu, Hongliang; Liu, Zhensheng et al. (2017) Pathway-analysis of published genome-wide association studies of lung cancer: A potential role for the CYP4F3 locus. Mol Carcinog 56:1663-1672

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