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.
|Lim, Hui-Ying; Wang, Weidong; Chen, Jianming et al. (2014) ROS regulate cardiac function via a distinct paracrine mechanism. Cell Rep 7:35-44|
|Towner, Rheal A; Wren, Jonathan D (2014) Prioritizing uncharacterized genes in the search for glioma biomarkers. CNS Oncol 3:93-5|
|Dozmorov, Mikhail G; Wren, Jonathan D; Alarcon-Riquelme, Marta E (2014) Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes. Epigenetics 9:276-85|
|Bugreev, Dmitry V; Huang, Fei; Mazina, Olga M et al. (2014) HOP2-MND1 modulates RAD51 binding to nucleotides and DNA. Nat Commun 5:4198|
|Moktan, Hem; Guiraldelli, Michel F; Eyster, Craig A et al. (2014) Solution structure and DNA-binding properties of the winged helix domain of the meiotic recombination HOP2 protein. J Biol Chem 289:14682-91|
|Obeso, David; Pezza, Roberto J; Dawson, Dean (2014) Couples, pairs, and clusters: mechanisms and implications of centromere associations in meiosis. Chromosoma 123:43-55|
|Zhao, Weixing; Saro, Dorina; Hammel, Michal et al. (2014) Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res 42:906-17|
|Tran, Kim; Li, Yu; Duan, Hongliang et al. (2014) Identification of small molecules that protect pancreatic ? cells against endoplasmic reticulum stress-induced cell death. ACS Chem Biol 9:2796-806|
|Pezza, Roberto J; Voloshin, Oleg N; Volodin, Alexander A et al. (2014) The dual role of HOP2 in mammalian meiotic homologous recombination. Nucleic Acids Res 42:2346-57|
|Lessard, Christopher J; Li, He; Adrianto, Indra et al. (2013) Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome. Nat Genet 45:1284-92|
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