Experience and Skills
Data Analysis
- Developing deep learning (computer vision) methods to support photo-based dietary assessment for use with human research studies
- Collaborating on development of database of monosaccharides of foods commonly consumed by adults and for toddlers
- Assessed utility of portable near-infrared spectrometer to distinguish between visually-similar foods
- Random forest classifiers achieved 100% accuracy on test data
- Collaborated on project to develop and validate computer-assisted database matching methods to match foods between different food and nutrient databases:
- resulted in over 90% reduction in time to obtain food matches
- resulted in over 90% reduction in time to obtain food matches
- Adapted phylogenetic tree-based methods to visualize and analyze food intake so diet diversity can be calculated like microbial diversity
- Experience with dietary intake data: determining association of lactase persistence genetics with dairy consumption from dietary data and other markers of health using a variety of statistical analyses
- Assisted with quality control (QC) of dual-energy x-ray absorptiometry (DEXA) for a large, cross-sectional human nutrition study
- QC’d short chain fatty acid (SCFA) data and evaluated the relationship with respect to stool pH, DEXA variables, and dietary fiber and calcium intake. The results contributed to the decision making for extraction and analysis of additional SCFA samples
- Manipulation, analysis, integration and biological interpretation of “Big Data” (transcriptomic, proteomic, and metabolomic data) to track metabolism changes in diseased plants
- “Big Data” statistical analyses included: univariate and multivariate (both supervised, unsupervised) statistical methods, performed data pre-processing and transformation prior to analysis, and multidimensional data visualization
Computational
- Fluent in the statistical programming language R
- Regularly uses Python and Jupyter Notebooks
- Experience with scikit, Tensorflow, pandas, scipy
- Use of shell scripting with a compute cluster (UC Davis FARM) and cloud computing servings (Amazon Web Services) for RNA-seq analysis
- Experience implementing software on Unix and HPC using SLURM submission scheduling
- Documenting work and organizing scripts with Git/GitHub and R Markdown
Communication
- Led and organized an “Intro to R” mini-workshop series for lab meetings. Workshop will be expanded to include all USDA Davis, CA area employees
- Supervised undergraduate researchers conducting quality control of dietary data. Taught undergraduate students basic techniques for data management and writing reproducible code
- Experienced with scientific manuscript preparation for peer-reviewed journals
- Shared research findings to citrus growers, academic and government scientists, and industry members through oral and poster presentations at scientific meetings during Ph.D.
- Translated complex scientific ideas to citrus growing community by writing lay articles and designing accompanying graphics for the magazine Citrograph
- Independently contracted by a USDA lab to design non-technical flyers to share the findings from a study that evaluated the nutritional quality and consumer acceptability of persimmons. Flyers were distributed to persimmon growers, producers, and consumers
Laboratory
- Planned and conducted experiments in small greenhouse and large field settings
- Protocol development: non-hazardous, low waste polar metabolite extraction protocol; RNA extraction protocol from citrus leaves; rapid, automated assay for evaluation of antimicrobial efficacy
- Operation of 600 MHz NMR and targeted and untargeted analysis of 1H NMR spectra
- Antioxidant evaluation of various food using HPLC, GC-MS, Oxygen Radical Absorbance Capacity (ORAC), and Trolox equivalent assay
Research Positions
USDA | Davis, CA…………………………………………………………………………………2019 - Present
Computational Biologist Research Associate | Laboratory of Danielle Lemay, Ph.D.
UC Davis Genome Center | Davis, CA………………………………………………………….2018 – 2019
Postdoctoral Researcher | Laboratory of Danielle Lemay, Ph.D.
UC Davis Food Science and Technology | Davis, CA
Postdoctoral Researcher | Laboratory of Carolyn Slupsky, Ph.D……………………….2017 – 2018
Graduate Student Researcher | Laboratory of Carolyn Slupsky, Ph.D…………………2012 – 2017
PepsiCo | Valhalla, NY……………………………………………………………………………2011
Research and Development Intern | Supervised by Richard Smith, Ph.D.
The Hershey Co. | Hershey, PA………………………………………………………………….2010
Research and Development Intern | Supervised by Dan Sweigart, Ph.D.
Virginia Tech Food Science Department | Blacksburg, VA…………………………………..2008 - 2011
Undergraduate Research Assistant | Laboratory by Sean O’Keefe, Ph.D.
Education
Ph.D. in Food Science and Technology | University of California, Davis………………….August 2017
Dissertation: Changes in Citrus Metabolism During Candidatus Liberibacter asiaticus Infection
Advisor: Carolyn Slupsky, Ph.D.
B.S. in Food Science and Technology & Biological Sciences | Virginia Tech……………. 2008 – 2012
Minor: Chemistry