Resume

Skills

Technologies

I like to build things

  • C++

    Boost, STL

  • Java

    Eclipse, Maven, Spring Boot, Tomcat

  • Mathematical

    MATLAB, R

  • Python

    Django, Matplotlib, Pandas, Scikit-learn, Seaborn

  • Scripting

    BASH

  • Web Development

    Astro, Javascript, Next, React, Typescript

  • Amazon Web Services

    API Gateway, CloudFront, EC2, Lambda, Route 53, S3

  • Databases

    MySQL/MariaDB, Postgresql, Sqlite3

Experience

  • Senior Developer

    Institute for Cancer Genetics Columbia University New York

    2015 - Present

    I develop specialized full stack applications for analyzing and visualizing high throughput sequence data for cancer genetics research.

    • Develop a web based modular genomic data analysis suite to support research biologists. This runs on Amazon Web Services and is a React/Typescript web app connected to Golang microservices backed by Postgresql databases.
    • AWS administrator leading project to move lab to based cloud infrastructure due to the lab transitioning from purely wet biology to a mixed biology and computational group. This reduced storage and data costs by 50% from in house solutions.
    • Managed the complete redesign of the Institute for Cancer Genetic's web site as a JAMStack application using React and Gatsby in less than 6 months. This modernized and optimized the site to be performant as well as offering a solution tailored to the institute's need. It resulted in a saving of $40,000 by eliminating the reliance on Drupal and an external provider to manage it.

  • Associate Research Scientist

    Institute for Cancer Genetics Columbia University New York

    2012 - 2015

    I analyze next generation sequencing data and provide bioinformatics support for the world renowned Dalla-Favera research lab.

    • Lead bioinformatician managing all lab next generation sequencing projects focused on cancer genetics.
    • Focused on bringing data analysis in house and standardizing processes and methods to reduce data analysis time on many projects from days to hours.
    • Developed a suite of open source applications in Java for biological data analysis with easy to use interfaces to allow non computational scientists to do common tasks including performing statistical analysis and visualizing large data sets.

  • Postdoctoral Scientist

    Institute for Cancer Genetics Columbia University New York

    2009 - 2012

    I design data pipelines for processing single cell RNA-seq data as well as specialized biology application development, database administration, and REST based web application development.

    • Implemented data pipelines to process and analyze next generation sequencing data including microarray, SNP 6.0, RNA-seq, Chip-seq, and single cell genomic data.
    • My work resulted resulted in the publication of more than 16 research papers in journals including Nature, Cell, Blood, and the New England Journal of Medicine, primary focussed on B-cell development and genetic lesions associated with development.

Volunteer Work

  • Team Leader

    New York Cares

    2017 - Present

    • Manage a small team of volunteers and act as a liaison between New York Cares and partner organizations.
    • Talk with clients to understand their tax situation and prepare all relevant federal and state forms.
    • Annually save clients $100,000 in tax preparation fees.
    • Quality review tax returns for accuracy. I oversee work prepared by junior volunteers.

Education

  • School

    Places I've studied

    Ph.D in Mathematical Biology

    University of Warwick, UK

    • Understanding morphogenesis in myxobacteria from a theoretical and experimental perspective.

  • M.Sc in Computer Science

    University of Warwick, UK

  • B.Sc in Computer Science

    University of Warwick, UK

    • First-class honours.