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.
|Duan, Hongliang; Arora, Daleep; Li, Yu et al. (2016) Identification of 1,2,3-triazole derivatives that protect pancreatic Î² cells against endoplasmic reticulum stress-mediated dysfunction and death through the inhibition of C/EBP-homologous protein expression. Bioorg Med Chem 24:2621-30|
|Borgogno, MarÃa V; Monti, Mariela R; Zhao, Weixing et al. (2016) Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange. J Biol Chem 291:4928-38|
|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|
|Griffin, Timothy M; Humphries, Kenneth M; Kinter, Michael et al. (2016) Nutrient sensing and utilization: Getting to the heart of metabolic flexibility. Biochimie 124:74-83|
|Duan, Hongliang; Lee, Jae Wook; Moon, Sung Won et al. (2016) Discovery, Synthesis, and Evaluation of 2,4-Diaminoquinazolines as a Novel Class of Pancreatic Î²-Cell-Protective Agents against Endoplasmic Reticulum (ER) Stress. J Med Chem 59:7783-800|
|Siefert, Joseph C; Clowdus, Emily A; Sansam, Christopher L (2015) Cell cycle control in the early embryonic development of aquatic animal species. Comp Biochem Physiol C Toxicol Pharmacol 178:8-15|
|Larabee, Chelsea M; Georgescu, Constantin; Wren, Jonathan D et al. (2015) Expression profiling of the ubiquitin conjugating enzyme UbcM2 in murine brain reveals modest age-dependent decreases in specific neurons. BMC Neurosci 16:76|
|Dozmorov, Mikhail G; Adrianto, Indra; Giles, Cory B et al. (2015) Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. BMC Bioinformatics 16 Suppl 13:S10|
|Pezza, Roberto J (2015) Mechanisms of chromosome segregation in meiosis--new views on the old problem of aneuploidy. FEBS J 282:2424-5|
|Lee, Chih-Ying; Horn, Henning F; Stewart, Colin L et al. (2015) Mechanism and regulation of rapid telomere prophase movements in mouse meiotic chromosomes. Cell Rep 11:551-63|
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