Dr. Cooper joined HudsonAlpha in 2010 from the University of Washington in Seattle, where she was a postdoctoral research fellow. Dr. Cooper received her graduate degree in Genetics from Stanford University in 2006.
The Cooper Lab is interested in using metabolomics in combination with other high-throughput technologies to understand human biology. Metabolomics focuses on the comprehensive quantitation of small molecules in biological samples. The lab divides its time between developing methods for reproducible, high-throughput mass spectrometry assays, developing data analysis tools and completing experiments at the bench that applies these methods.
Current research areas in the Cooper Lab include :
• Development of two-dimensional gas chromatography with time-of-flight mass spectrometry for metabolomics assays. The Cooper Lab has developed methods for analyzing microbial extracts, human blood, urine and tissue samples. The Cooper Lab also develops analysis tools to maximize identification of metabolites and improve quantification accuracy.
• Identification of biomarkers for human health and disease. Using the methods we have developed, we are generating metabolic profiles for individuals of various disease states including looking for profiles useful for the diagnostic or prognostic applications in pancreatic cancer. Related work has led us to quantify metabolite profiles associated with environmental exposures such as BMI, diet and smoking.
• Identification of genetic variants in the human population that contribute to alterations in metabolic profiles. Preliminary studies have identified a few genetic variants that correlate with changes in metabolite levels. The lab is conducting further study to characterize additional loci
that affect metabolism.
• A new area of study in the Cooper Lab is soil metagenomics. The lab has just begun collecting nucleic acids from soil samples with the goal of uncovering new gene functions and characterizing alterations in bacterial populations associated with exposure to common industrial chemicals.
Selected recent publications
Fowler, D. M. et al. (2011). Suppression of statin effectiveness by copper and zinc in yeast and human cells. Mol. Biosyst. 7: 533–544.
Cooper, S. J. et al. (2010). High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. Genome Res. 20: 1288–1296.
Cooper, S. J., Trinklein, N. D., Nguyen, L., and Myers, R. M. (2007). Serum response factor binding sites differ in three human cell types. Genome Res. 17: 136–144.
Cooper, S. J., Trinklein, N. D., Anton, E. D., Nguyen, L., and Myers, R. M. (2006). Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 16: 1–10.