Nick Nunley Cancer researcher, bioinformatician, molecular biologist, musician, mathematics enthusiast, board game enthusiast, and surfer

CV

Biomedical researcher passionate about applying mathematical theory and developing software to solve problems in biology

Experience

Staff Research Associate

University of California Los Angeles (2022 - present)

  • Conducted research in two labs investigating metabolic and transcriptional reprogramming across prostate cancer disease states:
  • Led two distinct research projects in parallel and developed a third open-source software project
  • Hands-on experience in culturing and performing experiments with ~8 different prostate cancer model systems:
    • Lentiviral transductions
    • Immunoblotting
    • Metabolic tracing assays
    • Viability assays
  • Developed and applied computational pipelines for transcriptional analysis
  • Developed an R datasets package containing processed transcriptional data from over 200 samples across seven different studies at release:
    • Performed data curation and quality assessment where I detected and corrected sample swaps in external datasets
    • Developed an object-oriented dataset class using the S4 system to enable easy access to metadata, sample information, and analysis methods
    • Added gene set enrichment analysis and meta-analysis features
    • Implemented a gene identifier mapping system to enable cross-species analysis without relying on external databases
    • Resolved graphics-rendering failures caused by memory limits and label collisions in enrichment and volcano plots using custom downsampling and cartesian coordinate offsetting algorithms
    • Extended the default lattice axes labeling system to support logarithmic axes
    • Implemented a custom colour-mapping engine based on deriving and using an affine RGB transformation matrix, enabling continuous two-colour gradients and three-colour (diverging) schemes
  • Developed RAGToolBox: a modular python package for Retrieval-Augmented Generation (RAG) prototyping
    • Engineered 9 modules with 4 CLI entrypoints for loading, indexing, retrieval, and augmentation
    • Shipped v0.1.0 with tagged release and changelog
    • Implemented 3 CI/CD workflows via GitHub Actions
    • Published package to PyPI
    • Implemented continuous unit and integration testing with ~83% coverage

Lead K-12 Mathematics Instructor

Mathnasium, LLC (2019 - 2021)

  • Provided one-on-one and group tutoring in foundational mathematics (e.g. algebra, geometry, trigonometry, calculus) and other general science courses
  • Managed learning center operations on weekends:
    • Administered assessments to new students
    • Managed student learning plans
    • Followed up with leads
    • Scheduled and matched instructors with students

Education

BS: Biochemistry

University of California Los Angeles (2020-2022)

  • Conducted biomedical research while completing undergraduate coursework
  • Completed a graduate-level course in mass spectrometry proteomics, and upper-division electives in mathematics and machine learning

AA (honors): Social and Behavioral Science

Santa Monica College (2015-2020)

  • Explored multiple academic tracks before transitioning to STEM
  • Worked part-time in service roles and as a peer tutor for foundational science and math courses