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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory Grants (P20)
Project #
5P20GM103636-02
Application #
8625778
Study Section
Special Emphasis Panel (ZGM1-TWD-B)
Project Start
Project End
Budget Start
2014-03-01
Budget End
2015-02-28
Support Year
2
Fiscal Year
2014
Total Cost
$168,000
Indirect Cost
$68,000
Name
Oklahoma Medical Research Foundation
Department
Type
DUNS #
077333797
City
Oklahoma City
State
OK
Country
United States
Zip Code
73104
Bhaskaran, Shylesh; Pharaoh, Gavin; Ranjit, Rojina et al. (2018) Loss of mitochondrial protease ClpP protects mice from diet-induced obesity and insulin resistance. EMBO Rep 19:
Siefert, Joseph C; Clowdus, Emily A; Goins, Duane et al. (2018) Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System. J Vis Exp :
Borga, Chiara; Park, Gilseung; Foster, Clay et al. (2018) Simultaneous B and T cell acute lymphoblastic leukemias in zebrafish driven by transgenic MYC: implications for oncogenesis and lymphopoiesis. Leukemia :
Wren, Jonathan D (2018) Algorithmically outsourcing the detection of statistical errors and other problems. EMBO J 37:
Georgescu, Constantin; Wren, Jonathan D (2018) Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values. Bioinformatics 34:1758-1766
Snider, Timothy A; Richardson, Arlan; Stoner, Julie A et al. (2018) The Geropathology Grading Platform demonstrates that mice null for Cu/Zn-superoxide dismutase show accelerated biological aging. Geroscience 40:97-103
Sansam, Courtney G; Pietrzak, Katarzyna; Majchrzycka, Blanka et al. (2018) A mechanism for epigenetic control of DNA replication. Genes Dev 32:224-229
Lee, Sunji; Bao, Hong; Ishikawa, Zachary et al. (2017) Cardiomyocyte Regulation of Systemic Lipid Metabolism by the Apolipoprotein B-Containing Lipoproteins in Drosophila. PLoS Genet 13:e1006555
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
Arriens, Cristina; Wren, Jonathan D; Munroe, Melissa E et al. (2017) Systemic lupus erythematosus biomarkers: the challenging quest. Rheumatology (Oxford) 56:i32-i45

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