? BIOINFORMATICS SHARED RESOURCE The Bioinformatics (BIn) shared resource, a core function of the Duke Cancer Institute (DCI), serves as a centralized resource for expertise in applied and theoretical cancer bioinformatics, genomics, computational biology, machine learning and statistical genetics. The faculty and staff members of this shared resource support DCI members across the continuum of research, including experimental and statistical design for genomic studies, complex genomic data management, integration of diverse data sets, computing and statistical analysis, and machine learning. The shared resource provides support for investigator-generated data as well as retrospective data from research databases (e.g., GDC [large datasets like TCGA] or dbGAP). The resource?s mission is to provide high-quality, service-oriented, coordinated and cost-efficient bioinformatics support and infrastructure for DCI members. Emphasis is placed on facilitating increased collaborations across DCI programs and other DCI shared resources. The mission of this shared resource is addressed within the framework of adherence to 3 principles: 1- sound data provenance and statistical principles, 2- literate programming, and 3- reproducible analysis. The BIn shared resource provides and runs standardized genomic analysis pipelines (e.g., germline, tumor and cell-free DNA-Seq, bulk and single-cell RNA-Seq, CHiP-Seq, and sequencing of T-Cell Receptor repertoire and microbiome). These pipelines are constructed on the basis of state-of-the-art published tools, maintained under strict source code version control and designed to be extensible and deployable in a scalable fashion on local servers and cloud services. The philosophy of the BIn shared resource is that the scope of scientific discovery and rigor should neither be limited nor compromised due to lack of appropriate and adequate statistical methodology or computational tools. When needed and appropriate, the faculty and staff of the shared resource extend or revise existing or develop de novo methods and computational tools to enable DCI members to address scientific questions with requisite rigor and efficiency. In addition to computing and analysis support, the shared resource provides extensive support for writing of scientific abstracts and manuscripts, as well as grant proposals. The BIn shared resource also serves as a liaison and facilitator between DCI members and other DCI shared resources (e.g., the Biostatistics, Functional Genomics, Information Systems, and BioRepository and Precision Pathology Center Shared Resources). The research support, services and resources of the BIn shared resource are provided exclusively to DCI members. In 2018, the BIn shared resource provided services to 53 investigators, 100% of whom were DCI members, accounting for 100% of total usage, from all 8 DCI Research Programs. Use of this shared resource by DCI members contributed to 178 publications over the project period, 41 of which were in high impact journals, demonstrating the value of services offered by the resource.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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Subcommittee I - Transistion to Independence (NCI)
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Duke University
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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
Powell Gray, Bethany; Kelly, Linsley; Ahrens, Douglas P et al. (2018) Tunable cytotoxic aptamer-drug conjugates for the treatment of prostate cancer. Proc Natl Acad Sci U S A 115:4761-4766
Abdi, Khadar; Lai, Chun-Hsiang; Paez-Gonzalez, Patricia et al. (2018) Uncovering inherent cellular plasticity of multiciliated ependyma leading to ventricular wall transformation and hydrocephalus. Nat Commun 9:1655
Hudson, Kathryn E; Rizzieri, David; Thomas, Samantha M et al. (2018) Dose-intense chemoimmunotherapy plus radioimmunotherapy in high-risk diffuse large B-cell lymphoma and mantle cell lymphoma: a phase II study. Br J Haematol :

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