The Bioinformatics Core provides data management, communications systems, statistical analysis, and support for functional interpretation of high-throughput data as part of the systems biology approach to immunogenetics. Existing platforms will be leveraged to develop and maintain a sophisticated laboratory information management system (LIMS) to facilitate the tracking of information, the processing of raw data through computational pipelines, and communication between all U19 investigators. In addition, the Core will support the prioritization of key immune genes and pathways derived from expression quantitative trait loci (eQTL) and QTL analyses.
The Specific Aims of the Core are as follows:
Aim 1 : Develop and maintain a dedicated data management system with a Systems Immunogenetics Web Portal. The Core will define and implement a program-wide data communication plan that ensures the capture of all grant-generated sample information, data, and resources. Public access to grant-generated data, resources, and mouse line infomnation will also be provided through the Web portal.
Aim 2; Assist in the development of data processing pipelines that ensure data is high-quality, conforms to technical specifications for modeling, and is accessible to all U19 investigators. In collaboration with the Systems Immunogenetics Core, an existing infrastructure will be leveraged to develop and implement data processing pipelines for all high-throughput profiling data, including quality control protocols for microarray, next-generation sequencing, and proteomics.
Aim 3 : Provide analytical support for high-throughput data and the computational predictions generated by the Research Projects and Cores. Statistical, computational, and functional analysis support will be provided for the interpretation of data and results. In addition, the Core will provide analysis of next-generation sequencing data, including in-depth analysis of noncoding RNAs, and processing and interpretation of targeted proteomics studies allowing for a systems level view of key immune genes and pathways across a select set of mouse lines.
The analysis of genetic trait and gene expression data will provide a deeper understanding of the specific immune responses that contribute to viral disease. Communication of this information to the larger research community will help to foster the development of new antiviral therapies and improved vaccines.
|Gorman, Matthew J; Caine, Elizabeth A; Zaitsev, Konstantin et al. (2018) An Immunocompetent Mouse Model of Zika Virus Infection. Cell Host Microbe 23:672-685.e6|
|Baxter, Victoria K; Heise, Mark T (2018) Genetic control of alphavirus pathogenesis. Mamm Genome 29:408-424|
|Chow, Kwan T; Driscoll, Connor; Loo, Yueh-Ming et al. (2018) IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection. J Leukoc Biol :|
|Gralinski, Lisa E; Sheahan, Timothy P; Morrison, Thomas E et al. (2018) Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis. MBio 9:|
|Menachery, Vineet D; Gralinski, Lisa E; Mitchell, Hugh D et al. (2018) Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines. J Virol 92:|
|McMullan, Rachel C; Ferris, Martin T; Bell, Timothy A et al. (2018) CC002/Unc females are mouse models of exercise-induced paradoxical fat response. Physiol Rep 6:e13716|
|Menachery, Vineet D; Schäfer, Alexandra; Burnum-Johnson, Kristin E et al. (2018) MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proc Natl Acad Sci U S A 115:E1012-E1021|
|Adams Waldorf, Kristina M; Nelson, Branden R; Stencel-Baerenwald, Jennifer E et al. (2018) Congenital Zika virus infection as a silent pathology with loss of neurogenic output in the fetal brain. Nat Med 24:368-374|
|Hickman, Heather D; Suthar, Mehul S (2018) Editorial overview: Viral immunology: Generating immunity to diverse viral pathogens. Curr Opin Virol 28:viii-x|
|Chow, Kwan T; Wilkins, Courtney; Narita, Miwako et al. (2018) Differential and Overlapping Immune Programs Regulated by IRF3 and IRF5 in Plasmacytoid Dendritic Cells. J Immunol 201:3036-3050|
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