About Me

I'm an experienced bioinformatician with a passion for my field and a keen interest in genomics and data science. I hold a master's in bioinformatics, and I have been working as a bioinformatician for a number of years with a focus on genomic pipeline development for commercial testing, research translation, as well as process and data infrastructure.

I have strong data analysis and software development skills using R and Python, as well as workflow automation using Snakemake and Nextflow. I also have strong expertise in molecular biology and genomics, including cancer genomics and current NGS technologies.

I consider myself a lifelong learner with an aptitude for problem-solving. I'm largely self-taught in most of my computational and data analysis skills. I'm most passionate about applying this skill to achieving a meaningful goal, advancing human health, and improving lives where possible.

Skills

Bioinformatics

  • DNA

    Domain knowledge in genomics and cell biology as well as current NGS technologies.

  • D

    Software development in R and Python.

  • D

    Bash scripting fluency.

  • D

    Snakemake workflow language.

  • DEV

    Data analysis and visualisation.

  • D

    Expertise working in a Linux environment.

  • a

    Experience with Github, Gitlab, and Jira.

  • Version control and other good development practices.

Other Skills

  • Experience working in a scrum agile environment.
  • Working well as part of a team, managing interests, expectations, and development goals.
  • Experience with project planning, scoping, and management.

Experience

Feb 2021 - Present

Zinto Ltd

Operational Bioinformatician

  • Driving force behind introduction & implementation of the LIMS system; current project owner.
  • Led the overhauling of existing bioinformatics workflow into a standardised form based on Snakemake; involved an almost total rewrite & implementation of several key upgrades.
  • Ongoing Linux server optimization & management.
  • Translation of research outputs into bioinformatic analysis workflows as part of product development.
  • Devising and implementing novel solutions for genetic testing process and data infrastructure.
  • Overhauling & management of the genetic database.

Oct 2020 - Feb 2021

Enfer Group

Laboratory Data Analyst

  • Implementing data analysis skills and strong working knowledge of molecular biology to analyse RT-PCR results data.
  • Application of quality control pipelines to ensure integrity of results.
  • Co-ordinating within the Data Analytics department to make decisions that impact lab operations, informed by best clinical practice and the public health context.

May 2018 - Aug 2019

BMS

Lab Services Associate

  • Bioreactor cleaning, assembly, and maintenance.
  • Downstream buffer preparation and supply management.
  • Pipette verification and maintenance.

Professional Projects

Genetic Analysis Workflow

  • Initiated & led the development of a genotype data analysis workflow using Snakemake.
  • Effective rewrite of existing ad hoc workflow to a standardised & maintainable form as well as key workflow upgrades.
  • This included an upgrade of the genetic database to the latest Equine genome build and accompanying workflow adjustments.

LIMS

  • Identified the requirement for a new LIMS system and accompanying update to lab processes.
  • Took ownership of the introduction and implementation of the LIMS system & development of a middleware application for the transfer of lab results data.
  • Played a pivotal role in designing an upgraded lab testing process centred around LIMS.
  • Also involved gathering, cleaning, and migration of all historical Equine sample and results data to create a central source of truth on LIMS.

Data Engineering Platform

  • Development of a data engineering solution in the form of a Flask web app.
  • Designed to manage total data quality and flow between LIMS and other internal software platforms for greater leveraging and quality of the Equine sample testing database.
  • Built with a Flask and SQLAlchemy backend, and a minimal frontend using HTML and Ajax.

Masters Research Project (University of Galway)

An analysis of the overlap between DNA methylation and gene expression patterns during maternal immune activation
  • Investigated the relationship between gene expression and DNA methylation patterns in a mouse model of maternal immune activation.
  • Methods included differential expression andmethylation analysis, functional enrichment, and expression-weighted cell type enrichment based on published single-cell RNA-seq reference data.

Undergraduate Research Project (Dublin City University)

RNA-seq analysis of Peyer’s patches tissue from mice infected with Fasciola hepatica
  • RNA-seq analysis of immunological samples taken from mice infected with Fasciola hepatica.

Personal Projects

Copernicus

An app for exploring sunrise and sunset times globally, as well as astronomical positions. It's now live, you can try it out here.

Custom UI for gget

An app designed to be a custom UI for the brilliant package gget developed by Laura Luebbert with Pachter Labs.

Self-hosting

This app has been built using a Flask backend and a frontend adapted from the Strata template by HTML5UP.
It is hosted on my own server along with my other projects. Over this year I've been managing this server including networking and security in my spare time.

Education

2019 - 2020

MSc. in Bioinformatics

First Class Honours
University of Galway

2014 - 2018

BSc. in Genetics & Cell Biology

Second Class Honours
Dublin City University

Publications

2022

RNA-seq analysis of peyer’s patches at 6 and 18 hours in mice infected with Fasciola hepatica metacecariae.

Connick K., Lalor R., Murphy A., GlasgowA., Breen C., Malfait Z., Harold D., and O’Neill S.M.
Vet Parasitol 2022, doi:10.1016/j.vetpar.2021.109643.

Get In Touch

If you'd like to get in touch with me for any reason, you can fill in the form
below and I'd be very happy to hear from you.

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