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Systems Genetics and Bioinformatics

Research Interests

My research interests focus on developing and implementing systems genetics statistical models to complex traits. Currently in the lab we are working on several different projects:

  1. Methods for qualitative and quantitative analysis of transcripts (non-coding and coding) from RNA-Seq data
  2. Network analyses of RNA expression analysis
  3. Quantitative Trait Loci (QTL) analysis of behavioral, physiologic, and molecular traits (e.g., RNA expression)
  4. Analysis of quantitative proteomics analyses
  5. Pharmacogenetics/Pharmacokinetics
  6. Visualization of system genetics analysis results
  7. Integration of multiple types of ‘omics data

Most of my research has been studying genetic predisposition to alcohol dependence in rodent models, specifically in recombinant inbred panels of mice and rats. Much of the data produced and analysis results are available on the PhenoGen website​ as simple downloads or as interactive graphics.

Ongoing Projects

Ongoing funded projects within the lab include:

  1. Identification of genetic pathways related to alcohol metabolism in the HXB/BXH recombinant inbred panel (NIH-NIAAA R24 AA013162)
  2. Applying Bayesian Network models to RNA expression levels from RNA-Seq and DNA sequence information to build predictive models (NIH-NIAAA R24 AA013162)
  3. Integrating miRNA and mRNA expression data in the LXS panel to investigate genetic determinates of alcohol dependence related endophenotypes (NIH-NIAAA R01 AA021131; PI – Katerina Kechris)
  4. Identification of genes and gene networks involved in regulating the stochastic determination of R7 photoreceptor cell fate within the Drosophila Genetic Reference Panel (NIH-NEI R21 EY024413; PI – Steve Britt)
  5. Elucidating the role of genetics in mast cell responses to engineered nanomaterial exposure using genome wide association analysis and transcriptomics with a hybrid mouse diversity panel (NIH-NIEHS R01 ES019311; PI – Jared Brown)
  6. Using RNA-Seq to identify genetic pathways associated with neuronal excitability in epileptic tissue (SSPPS ADR Pilot Grant with Molly Huntsman and Brent O’Neill)
  7. Identification of genetic predictors of cardiac allograft vasculopathy following cardiac transplantation (SSPPS ADR Pilot with Christina Aquilante and Robert Page)