Curriculum Vitae

Research Interests


  • Understanding gene regulation dynamics through the study of epigenetic modifications, mainly DNA methylation.
  • Understanding contributors to cancer relapse following immunotherapy and how alternative immunotherapies can slow or prevent relapse.

Education


University of California, Los Angeles, Los Angeles, California

Ph.D., Human Genetics, August 2016 - Spring 2021

  • Advisor: Prof. Matteo Pellegrini
  • Thesis Topic: Assessing human health using DNA methylation based predictive models
  • Thesis Committee: Matteo Pellegrini, Xia Yang, Jae-Hoon Sul, Aldons J. Lusis
  • Supported by NIH T32 CA201160-01 Biomedical Big Data (2018 - 2019)

University of Utah, Salt Lake City, Utah

M.P.H., Public Health, August 2011 - June 2013

  • Advisors: Professors Lisa Gren and David Sundwall
  • Practicum: Disconcerting headache practice patterns in academic primary care.

University of Utah, Salt Lake City, Utah

B.S., Chemistry, August 2006 - December 2010

Experience


University of California, Los Angeles Graduate Student Researcher, Pellegrini Lab, August 2016 – Current

  • Designed an integrated measure of type two diabetes and fit a DNA methylation based predictive model to this measure
  • Built a high performance bisulfite sequencing processing platform written in C, C++, and Python
  • Developed a novel statistical model of epigenetic aging to model non-linear epigenetic aging and open sourced the model as a Python package
  • Built an analysis pipeline to assess inactivation of CAR T-cell therapy vectors following product infusion using DNA methylation and vector integration location
  • Designed a targeted bisulfite sequencing method and implemented an optimized analysis pipeline
  • Collaborated with researches, clinicians, and support staff to implement research projects and meet project goals
  • Managed several parallel research projects, completing simultaneous tasks and delegating appropriate tasks to assistants
  • Carried out large scale data processing on high performance computing clusters and AWS
  • Instituted lab wide version control best practice to ease collaboration and foster reproducibility

University of Utah School of Medicine Lab Specialist, Phillips Lab, February 2014 – Current**

  • Analyzed sequencing data to identify causative genetic variants in clinical cases diagnosed with iron homeostasis and heme synthesis disorders
  • Integrated PacBio, Oxford Nanopore, and Illumina sequencing data to assemble a high quality reference genome for the Babraham pig breed with intact T-Cell Receptor loci for vaccine development
  • Performed CRISPR KO analysis to identify ligands targeted by a ubiquitous cancer killing T-Cell line

Open Source Software Tools


BSBolt (Python, C, C++) – High performance bisulfite sequencing processing platform; bsbolt.readthedocs.io Epigenetic Pacemaker (Python) – Evolutionary model of epigenetic aging; epigeneticpacemaker.readthedocs.io

Computer Skills


  • Languages
    • Proficient - Python
    • Competent - C, C++, R, Bash
  • Unit Testing
  • System - Linux/UNIX, MacOS
  • Tools - Git, Jupyter, SGE, AWS, SLURM, Anaconda, Vim

Teaching


Research Immersion Laboratory in Genomic Biology at UCLA(Spring 2018, Spring 2019) Instructed laboratory class for upper division molecular biology students at UCLA. In the laboratory class I introduced bioinformatics tools and workflow utilized to perform a quarter long genome annotation project. (Review available upon request)

Mentoring


  • Huling Huang (Bruins In Genomics Undergraduate Researcher, Summer 2018): Modeled non-linear epigenetic aging trends in publicly available datasets and compared epigenetic aging trends across distinct populations.
  • Maria Malikwa (Santa Monica College Summer Scholars, Summer 2018): Designed a DNA methylation based predictor of folic acid levels in pregnant women.
  • Ibrahime Wone (Santa Monica College Summer Scholars, Summer 2019): Built a non-linear DNA methylation based predictive model for type two diabetes progression.
  • Adewale Oytetunde (UCLA-CSUN Stem Cell Bridges Program, August 2018 - August 2019): Modeled methylation dynamics during cellular differentiation and how the DNA methylation landscape is altered by induced pluripotency.
  • Kalsuda Lapborisuth (UCLA Undergraduate Research Fellow, August 2018 - Present) Developing a simulation framework for modeling epigenetic age acceleration in response to physiological stress and is validating the framework using publicly available methylation datasets.

Publications



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