BIOINFORMATICS SCIENTIST III | Thermo Fisher Scientific - Life Sciences Group, Microarray Business Unit
February 2020 - Current
- Design, development, maintenance, and testing of software tools and pipelines to assist with microarray bioinformatics data processing and delivery.
- Biobank Pipeline: Implementation and improvement of a pipeline to improve genotyping results for data with >20k samples. (Python)
- Imputation Pipeline: Leveraging AWS to pipeline scripts for imputing markers & calculating coverage to assist in GWAS grid selection. (Python & R)
- Developing new methods, algorithms, and tools for problem solving
- Ratio Alternate Allele Frequency Tool - Algorithm design and implementation of a tool to assess consistency of genotyping results
- Intermediate SSP Generation Tool - Algorithm design and implementation of a tool to assist in improving genotyping results for <20k samples.
- Copy Number Consensus Tool and various format checking tools to assist in troubleshooting and streamlining processes.
- Working directly with customers and/or field scientists to analyze data, address and solve customer complaints and unexpected genotyping results.
GRADUATE STUDENT RESEARCHER | Laboratory for Pathogenesis of Clinical Drug Resistance & Persistence
December 2017-December 2019
- Development of a novel software pipeline and test suite to identify, score, and visualize non-B DNA structures and analyze their clinical implications using Pacific Biosciences (PacBio) SMRT sequencing long reads & kinetic information.
- Leveraging existing bioinformatics software and pipelines for assembly and annotation of PacBio SMRT long read sequencing data of Mycobacterium Tuberculosis (MTB) genomes.
- Genome-Wide Association Study (GWAS) of Isoniazid and Pyrazinamide resistance in MTB and the roles of mutations in drug resistance. Applying genome-wide association methods, drug susceptibility profiles, and drug mechanisms of action to investigate mutations that could be responsible for drug resistance.
WEB DEVELOPER | University of Washington (UW) Health Sciences
December 2014-August 2017
- Collaboration with researchers, physicians, and stakeholders at UW, UW Medicine and UW School of Medicine to create and maintain accessible data visualization and websites on many platforms including WordPress, Drupal, Joomla, and SharePoint using PHP, HTML, CSS, and JavaScript.
WEB APPLICATION DEVELOPER | Wittwer Lab for DNA Analysis - University of Utah Pathology
June 2011-July 2013
- Design, development, testing, and documentation of web applications for use in research and clinical environments working with diverse stakeholders in biochemistry, mechanical engineering, and algorithm development.