Experience

Basepaws
• United States
• Biotechnology Research
• 1 - 100 Employee
• Senior Bioinformatics Scientist

  • May 2022 - Present

Personal Genome Diagnostics (PGDx)
• United States
• Biotechnology Research
• 1 - 100 Employee
• Senior Bioinformatics Scientist

  • Nov 2021 - May 2022


Arc Bio

• United States
• Biotechnology
• 1 - 100 Employee

• Bioinformatics Scientist II

  • Feb 2019 - Jul 2021

  • Authored deep-learning based software for thresholding and visualizing NGS-derived metagenomic data. • Led project to integrate LIMS system with bioinformatics tools, pipelines and laboratory SOP's. • Collaborated on the continual updating and validation of custom-designed NGS pipelines running on AWS instances (EC2, S3, RDS). • Developed analysis pipeline targeted at ancient/degraded genetic samples. • Worked closely with lab scientists to flexibly analyze and interpret the results of experiments. Show less



University of California, Santa Cruz

• United States
• Higher Education
• 700 & Above Employee

• Postdoctoral Scholar

  • Jul 2017 - Dec 2018

  • Led ancient DNA-focused investigation into the ancestry of South American populations, involving extraction and library preparation of ancient samples as well as population genetic analysis. • Authored pipeline in Python to process and perform statistical analysis on large WGS data sets by integrating: BWA, samtools, MALT, mia, SeqPrep2, Kraken, bcftools, bedtools, EIGENSTRAT, plink, ADMIXTOOLS, PMDTools. • Designed scripts for automated calling of mitochondrial and Y chromosomal haplogroups, phylogenetic tree construction, imputation, analysis and automation of ADMIXTURE runs. • Developed software for performing population genetic analyses on NGS data. • Created tools for assessing accuracy of NGS reads in metagenome analysis. Show less



Santa Clara University

• United States
• Higher Education
• 700 & Above Employee

• Lecturer, Independent Researcher

  • Sep 2009 - Jul 2018

  • Created Imputor software for phylogenetically-aware imputation of NGS data. Collaborated on investigation of human Y chromosomal dataset and published the results in Genome Biology and Evolution. • Designed Plexus software involving use of Gibbs sampling and model selection using Bayesian statistics. • Presented to both academic and non-academic audiences on human genetics and genomics. • Designed and taught five courses annually for the Department of Anthropology focused primarily on biological anthropology and evolution. Show less



Stanford University

• United States
• Higher Education
• 700 & Above Employee

• Lecturer, Independent Reseacher

  • Jan 2008 - Jun 2011

  • Created rejection algorithm software Rejector to track rare HLA allele in human population and collaborated to test hypothesis of human/Neandertal/Denisovan introgression, publishing the results in Science. • Designed and taught three courses for the Department of Anthropology and three courses for the Stanford Continuing Studies Program focused on human evolution • Created rejection algorithm software Rejector to track rare HLA allele in human population and collaborated to test hypothesis of human/Neandertal/Denisovan introgression, publishing the results in Science. • Designed and taught three courses for the Department of Anthropology and three courses for the Stanford Continuing Studies Program focused on human evolution