Experience

Invitae

• United States
• Biotechnology Research
• 700 & Above Employee

• Technical Lead, Content Platform

  • Aug 2022 - Present

• Engineering Manager (interim), Content Platform

  • May 2022 - Aug 2022

  * Supported team of 10 engineers during our manager's paternity leave

• Technical Lead, Content Platform

  • Nov 2021 - May 2022



Helix

• United States
• Hospitals and Health Care
• 200 - 300 Employee

• Senior Bioinformatics Engineer

  • Jan 2021 - Oct 2021

  • Led engineering efforts to build Helix’s automated COVID-19 qPCR pipeline (concept, architecture, development) • Implemented novel read filtering algorithm to increase analytical performance of production variant calling pipeline • Performed ad-hoc analyses and developed tools to support CLIA certification, CAP accreditation, and various validations • Interfaced with internal and external partners to collect requirements and coordinate deployment activities • Developed custom… Show more • Led engineering efforts to build Helix’s automated COVID-19 qPCR pipeline (concept, architecture, development) • Implemented novel read filtering algorithm to increase analytical performance of production variant calling pipeline • Performed ad-hoc analyses and developed tools to support CLIA certification, CAP accreditation, and various validations • Interfaced with internal and external partners to collect requirements and coordinate deployment activities • Developed custom Python-based tools to support Production and R&D laboratory operations • Validated software by generating and executing test plans and documenting results • Created tools to augment and automate LIMS capabilities and workflows • Collaborated with Quality Assurance to document and perform validation/verification, change controls, etc. • Ran annual bioinformatics training course to help CLS personnel earn CGMBS licenses • Regularly contributed to code reviews, planning sessions, best-practices discussions, etc.

• Senior Bioinformatics Scientist

  • Jan 2020 - Jan 2021



Verogen

• United States
• Biotechnology Research
• 1 - 100 Employee

• Senior Bioinformatics Scientist

  • Nov 2017 - Jan 2020

  • Design novel bioinformatic algorithms to address the needs of the forensics community • Lead development of bioinformatics behind ForenSeq™ mtDNA Control Region and Whole Genome Solutions • Create Python and R-based pipelines to aid R&D in QC and assay design • Collaborate with assay and software teams to create integrated workflows and meaningful statistical metrics • Apply Bayesian and machine learning techniques in mathematical models to gain further insights from NGS data •… Show more • Design novel bioinformatic algorithms to address the needs of the forensics community • Lead development of bioinformatics behind ForenSeq™ mtDNA Control Region and Whole Genome Solutions • Create Python and R-based pipelines to aid R&D in QC and assay design • Collaborate with assay and software teams to create integrated workflows and meaningful statistical metrics • Apply Bayesian and machine learning techniques in mathematical models to gain further insights from NGS data • Develop performant analysis software in C# while expanding upon Illumina codebase • Characterize bioinformatics requirements with Chief Scientific Officer, subject matter experts, and customers • Propose timelines, resource requirements, and risk mitigation strategies for each project phase • Oversee execution of projects and development of junior staff through brainstorming sessions, code review, etc. • Represent bioinformatics in Core Team meetings and present project updates to senior leadership • Provide solutions to escalated customer support questions and document necessary software changes • Developed multiplexed primer design pipeline with off-target screening, dimer reduction, and target optimization • Automated analysis job submission, enabling assay scientists to analyze their experiments independently Show less • Design novel bioinformatic algorithms to address the needs of the forensics community • Lead development of bioinformatics behind ForenSeq™ mtDNA Control Region and Whole Genome Solutions • Create Python and R-based pipelines to aid R&D in QC and assay design • Collaborate with assay and software teams to create integrated workflows and meaningful statistical metrics • Apply Bayesian and machine learning techniques in mathematical models to gain further insights from NGS data •… Show more • Design novel bioinformatic algorithms to address the needs of the forensics community • Lead development of bioinformatics behind ForenSeq™ mtDNA Control Region and Whole Genome Solutions • Create Python and R-based pipelines to aid R&D in QC and assay design • Collaborate with assay and software teams to create integrated workflows and meaningful statistical metrics • Apply Bayesian and machine learning techniques in mathematical models to gain further insights from NGS data • Develop performant analysis software in C# while expanding upon Illumina codebase • Characterize bioinformatics requirements with Chief Scientific Officer, subject matter experts, and customers • Propose timelines, resource requirements, and risk mitigation strategies for each project phase • Oversee execution of projects and development of junior staff through brainstorming sessions, code review, etc. • Represent bioinformatics in Core Team meetings and present project updates to senior leadership • Provide solutions to escalated customer support questions and document necessary software changes • Developed multiplexed primer design pipeline with off-target screening, dimer reduction, and target optimization • Automated analysis job submission, enabling assay scientists to analyze their experiments independently Show less



University of Colorado Anschutz Medical Campus

• United States
• Higher Education
• 700 & Above Employee

• Professional Research Assistant

  • Jun 2012 - Nov 2017

  • Built and utilized automated pipelines to explore NGS datasets and communicate results to colleagues/researchers • Called and classified genetic variants in clinical samples and curated public datasets • Explored drug target biology and gene regulation in xenograft studies via gene expression analysis, differential exon usage/transcript variant characterization, gene set enrichment, and pathway analysis of RNA-Seq data • Generated data summaries/visualizations and interactive web… Show more • Built and utilized automated pipelines to explore NGS datasets and communicate results to colleagues/researchers • Called and classified genetic variants in clinical samples and curated public datasets • Explored drug target biology and gene regulation in xenograft studies via gene expression analysis, differential exon usage/transcript variant characterization, gene set enrichment, and pathway analysis of RNA-Seq data • Generated data summaries/visualizations and interactive web applications using R Shiny • Analyzed immunome data to describe T-cell receptor repertoires in humanized patient-derived xenografts • Collaborated closely in a cross-functional environment with bench scientists and medical fellows to aid in design, implementation, and interpretation of research project results • Identified novel gene fusion events in salivary gland cancer tumors • Trained new laboratory members in NGS techniques • Developed GATK-based WES variant calling pipeline to detect somatic variants in matched tumor and blood samples • Authored and published review of MEK1/2 inhibitors in BRAF V600-mutant melanoma • Performed survival and descriptive analyses for Otolaryngology and Radiation Oncology department clinical studies Show less • Built and utilized automated pipelines to explore NGS datasets and communicate results to colleagues/researchers • Called and classified genetic variants in clinical samples and curated public datasets • Explored drug target biology and gene regulation in xenograft studies via gene expression analysis, differential exon usage/transcript variant characterization, gene set enrichment, and pathway analysis of RNA-Seq data • Generated data summaries/visualizations and interactive web… Show more • Built and utilized automated pipelines to explore NGS datasets and communicate results to colleagues/researchers • Called and classified genetic variants in clinical samples and curated public datasets • Explored drug target biology and gene regulation in xenograft studies via gene expression analysis, differential exon usage/transcript variant characterization, gene set enrichment, and pathway analysis of RNA-Seq data • Generated data summaries/visualizations and interactive web applications using R Shiny • Analyzed immunome data to describe T-cell receptor repertoires in humanized patient-derived xenografts • Collaborated closely in a cross-functional environment with bench scientists and medical fellows to aid in design, implementation, and interpretation of research project results • Identified novel gene fusion events in salivary gland cancer tumors • Trained new laboratory members in NGS techniques • Developed GATK-based WES variant calling pipeline to detect somatic variants in matched tumor and blood samples • Authored and published review of MEK1/2 inhibitors in BRAF V600-mutant melanoma • Performed survival and descriptive analyses for Otolaryngology and Radiation Oncology department clinical studies Show less



University of Colorado Boulder

• United States
• Higher Education
• 700 & Above Employee

• Undergraduate Researcher

  • Jun 2010 - May 2012

  • Worked closely with graduate students, primary investigator, and other members of research team on genetics-related research projects through the utilization of computational and laboratory techniques • Performed basic microbiome analysis using QIIME • Implemented individual research projects involving collection, purification, amplification, and quantification of DNA as well as analysis of findings from DNA sequencing

• Undergraduate Mentor/Researcher

  • Feb 2011 - Aug 2011

  • Trained undergraduates in many research methods and applications, in addition to data analysis techniques • Developed project devoted to novel cancer research by utilizing quantitative PCR to compare the expression of selected genes extracted from tumor cells to expression in normal tissue