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Justin Eagles

3rd

Previous positions

  • Professional Research Assistant at University of Colorado Anschutz Medical Campus
  • Undergraduate Researcher at University of Colorado Boulder

Education

University of Colorado Anschutz Medical Campus, Master of Science – MS, Biostatistics

192

Background

Experience

  • Senior Bioinformatics Scientist

    Verogen

    November 2017 – Present(1 year 11 months)Greater San Diego Area

    • Design novel bioinformatic algorithms to address the needs of the forensics community • Apply Bayesian and machine learning techniques in mathematical models to gain further insights from NGS data • Lead development of bioinformatics behind ForenSeq™ mtDNA Control Region and Whole Genome Solutions • Develop performant analysis software in C# while expanding upon illumina codebase • 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 • 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 • Automated analysis job submission, enabling assay scientists to analyze their experiments independently • Wrote multiplexed primer design pipeline that incorporates selection, off-target screening, and dimer filtering

  • Professional Research Assistant

    University of Colorado Anschutz Medical Campus

    June 2012 – November 2017(5 years 5 months)Jimeno Lab – Aurora, Colorado

    • Build 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

  • Undergraduate Researcher

    University of Colorado Boulder

    June 2010 – May 2012(1 year 11 months)Krauter Lab – Boulder, Colorado

    • 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

    University of Colorado Boulder

    February 2011 – August 2011(6 months)Klymkowsky Lab – Boulder, Colorado

    • Trained undergraduates in a multitude of research methods and applications, as well as data analysis • 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

Education

Publications

  • A patient tumor transplant model of squamous cell cancer identifies PI3K inhibitors as candidate therapeutics in defined molecular bins

    Molecular oncology

    August 2013

    Authors (1):
    • Justin Eagles
  • Hedgehog signaling alters reliance on EGF receptor signaling and mediates anti-EGFR therapeutic resistance in head and neck cancer

    Cancer research

    June 2013

    Authors (1):
    • Justin Eagles
  • FGFR1 expression levels predict BGJ398 sensitivity of FGFR1-dependent head and neck squamous cell cancers

    Clinical Cancer Research

    October 2015

    Authors (1):
    • Justin Eagles
  • XactMice: humanizing mouse bone marrow enables microenvironment reconstitution in a patient-derived xenograft model of head and neck cancer

    Oncogene

    January 2016

    Authors (1):
    • Justin Eagles
  • Hedgehog signaling drives radioresistance and stroma-driven tumor repopulation in head and neck squamous cancers

    Cancer Research

    December 2014

    Authors (1):
    • Justin Eagles
  • The dual pathway inhibitor rigosertib is effective in direct patient tumor xenografts of head and neck squamous cell carcinomas

    Molecular Cancer Therapeutics
    Authors (1):
    • Justin Eagles
  • A pilot study of cetuximab and the hedgehog inhibitor IPI-926 in recurrent/metastatic head and neck squamous cell carcinoma

    Oral Oncology

    February 2016

    Authors (1):
    • Justin Eagles
  • Regulation of head and neck squamous cancer stem cells by PI3K and SOX2

    JNCI: Journal of the National Cancer Institute

    January 2017

    Authors (1):
    • Justin Eagles
  • An inducible TGF-β2-TGFβR pathway modulates the sensitivity of HNSCC cells to tyrosine kinase inhibitors targeting dominant receptor tyrosine kinases

    PloS One

    June 2015

    Authors (1):
    • Justin Eagles
  • Cobimetinib: inhibiting MEK1/2 in BRAF V600-mutant melanoma

    Drugs of Today

    November 2016

    Authors (1):
    • Justin Eagles
  • Survival Impact of Local Therapy for Thyroid Carcinoma: A Surveillance, Epidemiology, and End Results Analysis

    International Journal of Radiation Oncology

    March 2016

    Authors (1):
    • Justin Eagles
  • Radiation dose uncertainty and correction for a mouse orthotopic and xenograft irradiation model

    International Journal of Radiation Biology

    January 2016

    Authors (1):
    • Justin Eagles
  • Radiation Dose Uncertainty in a Mouse Head and Neck Irradiation Model

    International Journal of Radiation Oncology

    September 2014

    Authors (1):
    • Justin Eagles
  • Hedgehog Pathway Mediates Head/Neck Radiation Resistance and Tumor Repopulation

    International Journal of Radiation Oncology

    February 2014

    Authors (1):
    • Justin Eagles
  • The Hedgehog Pathway Modulates Radiation Therapy Resistance in Head-and-Neck Cancer

    International Journal of Radiation Oncology

    October 2013

    Authors (1):
    • Justin Eagles
  • POSTER: Advances in MPS and Mitochondrial DNA Analysis

    2019 Green Mountain DNA Conference

    August 2019

    Walsh J*, Walichiewicz P, Eagles J, Daulo A, Didier M, Edwards C, Fleming K, Han Y, Hill T, Li S, Rensfield A, Sa D, Husbands J, Holt C, Stephens S. *Presenting author.

    Authors (1):
    • Justin Eagles
  • Salivary Gland Cancer Patient-Derived Xenografts Enable Characterization of Cancer Stem Cells and New Gene Events Associated with Tumor Progression

    Clinical Cancer Research

    June 2018

    Keysar SB*, Eagles JR*, Jackson BC, Reisinger J, Glogowska MJ, Tan AC, Reyland ME, Kechris KJ, Barón AE, Bowels DW, Jimeno A. *These authors contributed equally to this work.

    Authors (1):
    • Justin Eagles
  • Patterns of facial trauma before and after legalization of marijuana in Denver, Colorado: A joint study between two Denver hospitals

    The American Journal of Emergency Medicine

    May 2018

    Sokoya M, Eagles JR, Oakland T, Coughlin D, Dauber H, Greenlee C, Winker A.

    Authors (1):
    • Justin Eagles

Skills & Expertise

  • Statistics
  • RNA-Seq Analysis
  • Algorithms
  • Bioinformatics
  • Data Analysis
  • DNA Sequencing
  • GATK
  • C#
  • Unix
  • Time Series Analysis
  • Statistical Learning Methods
  • Python
  • Gene Expression
  • NGS
  • Microsoft Office
  • Data Mining
  • Machine Learning
  • Mac
  • Statistical Consulting
  • Linux
  • Jupyter Notebook
  • Survival Analysis
  • Exome-Seq Analysis
  • Amazon Web Services (AWS)
  • R
  • High Performance Computing (HPC)
  • Bayesian statistics
  • Pandas