COMPUTATIONAL SCIENCES The JAX Computational Sciences (CS) Shared Resource is central to the achievement of the JAX Cancer Center's (JAXCC) scientific program objectives. As cancer research has become increasingly data intensive, it is vital that investigators be capable of interpreting and leveraging vast data sets, both publicly available and internally generated, to understand tumor biology. Such data analysis requires access to a dynamic suite of analytical tools; infrastructure supporting those tools; computational, bioinformatic and statistical expertise to mine and analyze the data; and quantitative analysts and software engineers to develop and build queries and algorithms. Established in 1998, CS has been operating as a shared resource within the JAXCC since 2001 but was dramatically expanded in 2013. The 41 member CS group addresses faculty needs by providing in-depth expertise to JAXCC members in support of their independent research projects. This includes guidance in experimental design; support for the integration of multi-platform data sets, data analysis software applications and database development; development and application of computational procedures, statistical methods and scientific software; and project management. CS also provides training and mentorship opportunities in computational cancer research approaches and manages a plethora of analysis pipelines essential for cancer genomic research conducted by JAXCC members. Staff include a multi-disciplinary mix of computational biologists, computer scientists, statisticians, bioinformatics software engineers, and research project managers, who bring significant depth of expertise in cancer genomics, metabolomics, biostatistics, software development, machine learning, single cell genomics and integrative analysis, consistent with the needs of JAXCC members. CS' three operational groups (Statistics and Analysis, Scientific Computing, Research Project Management) are housed on the Bar Harbor, ME and Farmington, CT campuses, and each supports JAXCC members on both campuses. Functioning in a modular manner, PIs can access the right mix of experienced expertise tailored to their scientific needs.
The Specific Aims for CS are: 1) To support JAXCC members in developing cutting-edge analytical procedures for emerging problems in cancer genomics, and to carry out integrative analysis in fundamental and translational cancer research; 2) To develop bioinformatics applications, maintain scientific analysis workflows, and provide data architecture and software engineering expertise for the development and management of scientific data portals pertaining to specific scientific questions addressed by JAXCC members; and 3) To assist in resource planning for and management of complex computational projects and long-term information technology and data science development for JAXCC members.
|Dominguez, Pilar M; Ghamlouch, Hussein; Rosikiewicz, Wojciech et al. (2018) TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis. Cancer Discov 8:1632-1653|
|Paigen, Kenneth; Petkov, Petko M (2018) PRDM9 and Its Role in Genetic Recombination. Trends Genet 34:291-300|
|Schloss, Jennifer; Ali, Riyasat; Racine, Jeremy J et al. (2018) HLA-B*39:06 Efficiently Mediates Type 1 Diabetes in a Mouse Model Incorporating Reduced Thymic Insulin Expression. J Immunol 200:3353-3363|
|Nakatsuji, Teruaki; Chen, Tiffany H; Butcher, Anna M et al. (2018) A commensal strain of Staphylococcus epidermidis protects against skin neoplasia. Sci Adv 4:eaao4502|
|Racine, Jeremy J; Stewart, Isabel; Ratiu, Jeremy et al. (2018) Improved Murine MHC-Deficient HLA Transgenic NOD Mouse Models for Type 1 Diabetes Therapy Development. Diabetes 67:923-935|
|Ye, Fengdan; Jia, Dongya; Lu, Mingyang et al. (2018) Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma. Oncotarget 9:15015-15026|
|Kong, Yang; Zhao, Lihong; Charette, Jeremy R et al. (2018) An FRMD4B variant suppresses dysplastic photoreceptor lesions in models of enhanced S-cone syndrome and of Nrl deficiency. Hum Mol Genet 27:3340-3352|
|Wu, Te-Chia; Xu, Kangling; Martinek, Jan et al. (2018) IL1 Receptor Antagonist Controls Transcriptional Signature of Inflammation in Patients with Metastatic Breast Cancer. Cancer Res 78:5243-5258|
|Muscat, Andrea M; Wong, Nicholas C; Drummond, Katharine J et al. (2018) The evolutionary pattern of mutations in glioblastoma reveals therapy-mediated selection. Oncotarget 9:7844-7858|
|Kohar, Vivek; Lu, Mingyang (2018) Role of noise and parametric variation in the dynamics of gene regulatory circuits. NPJ Syst Biol Appl 4:40|
Showing the most recent 10 out of 1156 publications