In 2001 I quit my high-paying senior software engineering position with Walmart.com to apply my engineering background to medical research. For the next four years I was a full-time student at CSU Chico, doing contract software work during my summer breaks. My Masters thesis project involved using classical genetic recombination mapping techniques to find genes that underlie the mechanism of action of the insect repellent DEET (N,N-Diethyl-metatoluamide). DEET is considered a front-line defense against mosquitoes that carry malaria and other diseases, but is also highly toxic, thus the development of alternatives is an active area of research. I used both classically mapping techniques and recently developed quantitative trait loci (QTL) mapping software to map the trait to a specific region of the X chromosome. My poster presentation of this work won the departmental "Outstanding Student Researcher" award in 2005 and my written thesis won "Outstanding Masters Thesis" at Chico State in 2006. I also completed advanced courses in immunology, physiology, and molecular biology.
In my PhD work at UC Davis (2007-2013) I studied MUTYH, a base excision repair glycosylase that removes adenine mis-incorporated opposite OG, thereby preventing accumulation of G:C to T:A caused by reactive oxygen species. Lack of proper repair of this lesion due to inherited mutations in MUTYH causes excessive genome-wide somatic mutations, including in APC, KRAS and p53, leading to cancer. My primary thesis project involved developing a novel assay in mammalian cells to measure the MUTYH-mediated repair of DNA with a synthetic OG:A lesion. Additionally, I discovered a previously unnoticed three cysteine motif in MUTYH that is highly conserved within vertebrate animals, and this was verified experimentally to be a zinc-binding domain within the critical interdomain connector region of MUTYH.
After graduating, I was awarded a NIH T32 postdoctoral fellowship with Priscilla Cooper at Lawrence Berkeley National Laboratory. I investigated the expression of pathogenic XPG protein variants in primary human fibroblasts from Xeroderma Pigmentosum (XP) patients as part of a larger project to understand the function of the XPG catalytic domain. I then worked over two years at Ingenuity (now Qiagen Bioinformatics) as a bioinformatics developer. I was responsible for developing and maintaining software to map mutations curated from scientific papers in HGVS standardized format to genomic coordinates that align these mutations to the human genome sequence. This software automated error detection from human-curated mutations to ensure accuracy of the final data used by customers (doctors and clinicians) who submit clinical whole genome sequencing data via the Ingenuity Clinical Insight product. I was also responsible for developing a data pipeline to map the entire ensembl.org database (transcripts and proteins) to the Ingenuity Pathway Analysis (IPA) product. Previous to my work, IPA only supported RefSeq (NCBI) transcripts and proteins, and many customers had RNA-seq data mapped to Ensembl. Thus, my work greatly expanded the utility of the IPA product for many researchers doing gene expression analysis across many fields.
Returning to academic work with my PhD mentor Sheila David at UC Davis in a postdoctoral position, I published further cellular and biochemical evidence that MUTYH enhances the toxicity of alkylating agents via MUTYH interactions with AP sites and the downstream partner APE1 endonuclease. I have also begun to design and develop better methods to produce GFP reporter vectors with synthetic lesions needed for cellular assay of MUTYH OG:A repair, and published a review paper of MUTYH function and its role in cancer.
My next postdoc in the laboratory of Jeremy Chien at UC Davis Medical Center leveraged my bioinformatics and software development background to analyze of RNASeq expression data in ovarian cancer cell lines treated with experimental drugs and in cell lines with CRISPR gene deletions. We also used high-content imaging to do statistical analysis of single-cell immunofluoresce data.