EDUCATION

Ph.D. Biology

2015 – Present. Stanford University. Stanford, CA.

Molecular, cellular and developmental with a strong computational component.

Advisors: Hunter Fraser, Ashby Morrison

B.Sc. Genomics

2009 – 2013. National Autonomous University of Mexico Mexico City, Mexico. With university honors.

Advisor: Jean-Philippe Vielle-Calzada

RESEARCH EXPERIENCE

Ph.D. thesis project

2015 – Present, Fraser and Morrison labs. Stanford University Stanford, CA.

Working on the application of evolution and population genomics to understand the mutational process in humans. Pioneering computational methods and techniques that leverage public genomic data to understand the somatic mutation landscape in the human healthy body. Integration of genomics, transcriptomics and phenotypic data to perform association analysis, which together have uncovered the molecular mechanisms underlying the acquisition of somatic mutations in the human body.

Research Assistant

2013 – 2015 Morrison Lab. Stanford University Stanford, CA

Worked on investigating how the three-dimensional structure of the genome influences genomic susceptibility to ultraviolet radiation. We developed a novel sequencing technique to map UV-induced DNA lesions. I was in charge of data processing and analysis. By integrating with melanoma mutation data and chromatin data from the roadmap epigenomics project, we were able to unravel the features defining the landscape of carcinogen (UV) susceptibility in the human genome.

B.Sc. thesis project

2012 – 2011 Vielle-Calzada Lab.National laboratory of genomics for biodiversity Irapuato, Mexico.

Worked on the application of functional genomics through computational biology to investigate sexual development in plants. I processed and analyzed small-RNA sequencing data obtained from plant ovules.

Research internship

2010 – 2011 National Autonomous University of Mexico Mexico City, Mexico.

Worked in the Esperanza Martinez’s lab at UNAM on the Mechanisms of Gram-negative bacteria competition.

SKILLS

Computational

  • Proficient in R and python
  • Proficient in snakemake
  • Experience in bash scripting
  • Use of high-performance clusters with SLURM or Torque
  • Development of pipelines to process and analyze sequencing data
  • Experience with analysis of FACS data in R
  • Experience with biological databases like GTEx, COSMIC, TCGA and roadmap epigenomics.
  • Strong statistical background

Experimental

  • Human tissue culture
  • Molecular techniques including, wester and slot blots, transfection and infection of cells, FACS, electrophoresis, and qPCR
  • Imaging techniques like DNA labelling and immunofluorescence
  • Classical and topo cloning

PUBLICATIONS

Garcia-Nieto PE, Morrison AJ, Fraser H. The landscape of somatic mutations in the human healthy body. Submitted

Beckwith SL, Schwartz EK, García-Nieto PE, King DA, Gowans GJ, Wong KM, Eckley TL, Paraschuk AP, Peltan EL, Lee LR, Yao W, Morrison AJ. The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation. PLoS Genet. 2018

Garcia-Nieto PE, Schwartz E, King DA, Paulsen J, Collas P, Herrera RE, Morrison AJ. Carcinogen susceptibility is regulated by genome architecture and dictates cancer mutagenesis. EMBO. 2017

Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ. Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons. Epigenetics. 2014

Martín GM, King DA Garcia-Nieto PE, Morrison AJ. Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression. Genomics Data. 2014

AWARDS, HONORS & FELLOWSHIPS

  • 2016 – Bio-X Ph.D. fellowship. Full funding for Ph.D. studies given to students with academic excellence and interdisciplinary projects

  • 2013 – Coca Cola fellowship for research abroad. Given to outstanding undergraduate students from Latin America to perform research in the USA or Europe

  • 2013 – Honors in B.Sc. thesis Given to students who achieved a GPA greater that 3.7, performed a research project and their committee assessed it as high-quality research.

  • 2010 – Gold Medal in the synthetic biology iGEM competition – MIT Given to excelling competitors that contribute with an impactful project in synthetic biology and develop molecular tools for the scientific community.