The Bioinformatics and Pathways Core (BPC) will analyze microarray and proteomics high-throughput data for COBRE Junior Investigators. The BPC assembles and coordinates bioinformatics and statistics experts into a central core facility to help with experimental design and analysis, which entails both the use of standard/commercial bioinformatics and statistical software such as MatLab and Ingenuity Pathways Analysis, as well as novel in-house developed methods for predicting gene functions, disease associations, and phenotypes. The BPC also has developed software for large-scale literature analysis (IRIDESCENT) that enables both inference of novel relationships for genes as well as commonalities for gene sets derived from high-throughput data such as microarrays and proteomics (GAMMA). The BPC will be directed by Dr. Jonathan Wren, a well-known bioinformatician, and staffed by Dr. Mikhail Dozmorov, a Senior Research Associate with seven years of bioinformatics experience, and Chee Paul Lin, a MS-level biostatistician. Together, they will work with each ofthe investigators to meet their bioinformatics needs according to the following Specific Aims:
Aim 1) Provide complete bioinformatics analysis and biological interpretation of high-throughput data.
Aim 2) Identify key genes and biomarkers involved in processes of interest and predict gene functions, phenotypes and disease relevance.
Aim 3) Create a sustainable core facility that can be used institution-wide.
|Siefert, Joseph C; Georgescu, Constantin; Wren, Jonathan D et al. (2017) DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation. Genome Res 27:1406-1416|
|de Castro, Rodrigo O; Previato, Luciana; Goitea, Victor et al. (2017) The chromatin-remodeling subunit Baf200 promotes homology-directed DNA repair and regulates distinct chromatin-remodeling complexes. J Biol Chem 292:8459-8471|
|Duan, Hongliang; Li, Yu; Arora, Daleep et al. (2017) Discovery of a Benzamide Derivative That Protects Pancreatic ?-Cells against Endoplasmic Reticulum Stress. J Med Chem 60:6191-6204|
|He, Chaoyong; Medley, Shayna C; Kim, Jang et al. (2017) STAT1 modulates tissue wasting or overgrowth downstream from PDGFR?. Genes Dev 31:1666-1678|
|Sun, Chengyi; Berry, William L; Olson, Lorin E (2017) PDGFR? controls the balance of stromal and adipogenic cells during adipose tissue organogenesis. Development 144:83-94|
|Jordan, Philip W; Eyster, Craig; Chen, Jingrong et al. (2017) Sororin is enriched at the central region of synapsed meiotic chromosomes. Chromosome Res 25:115-128|
|Rao, H B D Prasada; Qiao, Huanyu; Bhatt, Shubhang K et al. (2017) A SUMO-ubiquitin relay recruits proteasomes to chromosome axes to regulate meiotic recombination. Science 355:403-407|
|Tipton, Aaron R; Wren, Jonathan D; Daum, John R et al. (2017) GTSE1 regulates spindle microtubule dynamics to control Aurora B kinase and Kif4A chromokinesin on chromosome arms. J Cell Biol 216:3117-3132|
|Duan, Hongliang; Arora, Daleep; Li, Yu et al. (2016) Identification of 1,2,3-triazole derivatives that protect pancreatic ? cells against endoplasmic reticulum stress-mediated dysfunction and death through the inhibition of C/EBP-homologous protein expression. Bioorg Med Chem 24:2621-30|
|Tsou, Pei-Suen; Wren, Jonathan D; Amin, M Asif et al. (2016) Histone Deacetylase 5 Is Overexpressed in Scleroderma Endothelial Cells and Impairs Angiogenesis via Repression of Proangiogenic Factors. Arthritis Rheumatol 68:2975-2985|
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