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.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee I - Transistion to Independence (NCI)
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Duke University
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Wu, Mengxi; Huang, Po-Hsun; Zhang, Rui et al. (2018) Circulating Tumor Cell Phenotyping via High-Throughput Acoustic Separation. Small 14:e1801131
Vlahovic, Gordana; Meadows, Kellen L; Hatch, Ace J et al. (2018) A Phase I Trial of the IGF-1R Antibody Ganitumab (AMG 479) in Combination with Everolimus (RAD001) and Panitumumab in Patients with Advanced Cancer. Oncologist 23:782-790
Xu, Yinghui; Liu, Hongliang; Liu, Shun et al. (2018) Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer. Int J Cancer 143:2400-2408
Feng, Yun; Wang, Yanru; Liu, Hongliang et al. (2018) Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. Mol Carcinog 57:216-224
Naqvi, Ibtehaj; Gunaratne, Ruwan; McDade, Jessica E et al. (2018) Polymer-Mediated Inhibition of Pro-invasive Nucleic Acid DAMPs and Microvesicles Limits Pancreatic Cancer Metastasis. Mol Ther 26:1020-1031
Wen, Juyi; Liu, Hongliang; Wang, Lili et al. (2018) Potentially Functional Variants of ATG16L2 Predict Radiation Pneumonitis and Outcomes in Patients with Non-Small Cell Lung Cancer after Definitive Radiotherapy. J Thorac Oncol 13:660-675
Li, Bo; Wang, Yanru; Xu, Yinghui et al. (2018) Genetic variants in RORA and DNMT1 associated with cutaneous melanoma survival. Int J Cancer 142:2303-2312
Gearhart-Serna, Larisa M; Jayasundara, Nishad; Tacam Jr, Moises et al. (2018) Assessing Cancer Risk Associated with Aquatic Polycyclic Aromatic Hydrocarbon Pollution Reveals Dietary Routes of Exposure and Vulnerable Populations. J Environ Public Health 2018:5610462
Bakthavatsalam, Subha; Sleeper, Mark L; Dharani, Azim et al. (2018) Leveraging ?-Glutamyl Transferase To Direct Cytotoxicity of Copper Dithiocarbamates against Prostate Cancer Cells. Angew Chem Int Ed Engl 57:12780-12784
Dai, Ziwei; Mentch, Samantha J; Gao, Xia et al. (2018) Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width. Nat Commun 9:1955

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