Excel Que

Experience

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  USDA-ARS

  Mar 2015 - Dec 2016

  Biological Science Technician - Physiology Support Staff

  Responsible for a variety of physiological and biological specimen laboratory support tasks in human metabolomic research center.Experience with human specimen processing including breath, urine, fecal, and blood processing. Skilled in the operation, maintenance, and calibration of physiologic testing equipment, including the ParvoMedic TrueOne 2400 Metabolic Cart, Respironics activity monitor, SDI Spirometer, Quintron Breath Analyzer and Itamar Endothelial Patography system.Experienced in the administration of cognitive testing protocols, as well as diet and nutrition recall questionnaires.General laboratory skills include centrifugation, pipetting, sample labeling/cataloging, proper handling and transport of bio-hazardous material and safe laboratory practices. General duties: basic anthropometry and vitals collection, coordination of glucose tolerance and meal challenge testing, food preparation and delivery, spreadsheet and database management of metabolic and physiologic data, training of interns and coworkers, and routine study participant communication. Show less

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  University of California, Davis - Department of Nutrition

  Dec 2016 - May 2019

  Acts as Bennett Laboratory’s resource for R and Shell script, HPC incorporation, workflowautomation, and analytical pipeline creation/maintenance.Performs statistical analysis and reporting on multi-omics, microbiome, and clinical data.Improves analysis efficiency and reproducibility through the creation of custom functions or thewrapping of existing functions to fit project needs.Documents work in R Markdown, simplifying the presentation and reporting of code, methods,results, and visualizations.Contributes to the writing of manuscripts, abstracts, and scientific posters.*See attached resume for the different R pipelines I've developed for different research center projects Show less Responsible for the recruitment, screening, scheduling, and testing of women with insulin resistance/elevated lipid profiles for a 9-week cardio-metabolic clinical trial.Directed task assignment of study team and coordination between Human Studies Management and Support Laboratories.Managed the collection, cleaning, and quality control of large phenotypic databases.Oversaw study inventory, nursing invoices, off-center analyses, and participant disbursements.Performed clinical outcome specimen analyses utilizing colorimetric and multiplex assays.Operated whole room calorimeter using Sable Systems gas analyzer and Expedata analysis software.Interpreted clinical pathology laboratory reports for study inclusion purposes.Composed scientific posters, grant abstracts, manuscript sections, literature reviews, and data analysis reports Show less

  • Junior Specialist - Bioinformatic Analyst

    Oct 2017 - May 2019

  • Clinical Study Coordinator

    Dec 2016 - Oct 2017
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  US Department of Agriculture (USDA) Agricultural Research Service (ARS)

  May 2019 - Apr 2020

  Biological Technician - Bioinformatics Analyst

  - Manages laboratory’s High Performance Computing resources- Establishes and maintains bioinformatics infrastructure on local machines and HPC partitions- Creates and curates repositories for robust analytical tools and methodologies in R and bash- Proofreads and edits manuscripts and grant proposals- Instructs graduate students and colleagues in the use of R, bash, and HPC for research- Performs specialized RNA-seq alignment and quantification for multiparent mouse models- Builds front-end interfaces for lab-generated results and tools in R Shiny- Develops and/or improves computational research methods within and across laboratories Show less

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  Q² Solutions

  Apr 2020 - Apr 2022

  Bioinformaticist - Translational Genomics

  Bioinformatics software developer, pipeline architect, and subject matter expert.Develops novel bioinformatics and data visualization algorithms. Constructs bioinformatics pipelines using Nextflow DSL2 for High Performance Computing systems, implementing the following technologies:- Containerized process environments built from best-practice dockerfiles- Custom scripts in R, python, and bash- Process-specific logging- Command line control of within-pipeline software arguments- Azure Dev Ops continuous integration for containers and unit testing- Structured output directory- Publication quality visualizations Show less

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  IQVIA Laboratories

  Apr 2022 - now

  Senior Bioinformaticist - Translational Genomics

  Product owner, subject matter expert, and developer of bioinformatics software.Areas of Focus: - Viral Strain Identification/Vaccine Development- Certified Scrum Product Ownership- Software Development Team Leadership- CAP-CLIA/GCP/RUO pipeline development and validation of user requirements - Nextflow DSL2 Pipeline Development- Docker/Kubernetes Development- SLURM/HPC Cluster Expertise- Azure DevOps Artifact Development and Continuous Integration/Deployment- Advanced R/Java/Python/Bash software development- Anaconda Environment Management- Tableau Dashboard and Oracle Database Deployment - Illumina/PacBio/ThermoSequencing TechnologyProjects:- Influenza Strain Identification and Database Curation for Seasonal Vaccines - Golden Helix CAP-CLIA Variant Reporting- Structural Variant Identification Pipeline Development - CAR T-Cell Vector Detection- Automated DNA/RNA Assay Validation- Software Development and Product Feasibility Testing for Viral Genotyping and Variant Detection (SARS-CoV2, HPV, HBV, HCV, RSV)- Bacterial and Viral Classification Database Development- Copy Number Variant Detection- Complex Variant Detection in Human CancersSide Projects:- Customizable short read sequence simulation (wgsim)- Human genome feature annotation pipeline (featureCounts)- Kmer Uncertainty Visualizer (Kraken2)- Custom annotation build-call-annotate pipeline (bwa/lofreq3/snpEff)- Variant Truth file generation pipeline (Minimap2/Freebayes)- Iterative downsampling variant caller (seqtk)- Entrez fetch cluster quality control (UCLUST)- Primer binding localization and visualization pipeline (bowtie2) Show less