Gordon Blackshields Email & Phone Number

Dublin

County Meath, Ireland

I support molecular biology research into animal healthcare and productivity for the Irish Agriculture and Food Development Authority, implementing software and workflows for RNA gene expression analysis, variant detection, and the classification of diverse microbial communities (metagenomics / metatranscriptomics).

Ireland

Bioinformatics research fellow in the department of Histopathology and Morbid Anatomy, Trinity College Dublin. A major research theme is the analysis of genomic and transcriptomic changes in the context of in human cancers. I provide bioinformatic analysis of Next Generation Sequencing data for whole genome sequencing (WGS), whole exome sequencing (WES), RNA sequencing (RNASeq) and small RNA sequencing (miRNA-Seq) from a number of DNA sequencing platfroms (SOLiD, Illumina, IonTorrent) well as data from more traditional array-based gene expression platforms (Affymetrix, TaqMan). I advise and assist on computational aspects of research projects for in-house scientists as well as national and international collaborators. I also contribute to research papers, grant applications and program calls. As part of my work I have mentored several students on short-term research projects, as well as mentoring PhD students on the bioinformatics component of their theses.

Nottingham, United Lkingdom

I held the role of senior bioinformatician for a large UK-based commercial next-generation sequencing services firm, with sole responsibility for all bioinformatics activity within the company. I was responsible for the development and provision of bioinformatics services and data analysis workflows for a diverse range of next-generation sequencing (NGS) applications for both the Illumina GAIIx and HiSeq2000 platforms, as well as array-based technologies (Affymetrix), on contract research projects for clients from pharma-biotech, academic and healthcare industries. Analyses included full genomic DNA sequencing, total-exome targeted sequencing, RNA-Sequencing, ChIP-Sequencing and variation detection, from bacterial, plant and mammalian genomes. As a direct point of contact with clients, I offered tailored bioinformatic consultancy for custom projects, was heavily involved in customer relations and the business development of new bioinformatics services.

Ireland

Folowing the completion of my PhD I undertook a short post-doctoral position for the continuation of prior research into data embedding methods for clustering of large biological databases.

Thesis Title: Multiple Sequence Alignments in the Post-Genomic Era.Supervisor: Des HigginsContinuing advances in the sequencing of biological molecules means that public repositories store increasingly vast amounts of biological sequence data. Traditional approaches to analysing these data sets suffered from computational constraints, and available methods were limited to analysing a few thousand sequences at any one time. The most accurate methods were restricted to a hundred or so, and very slow to operate. This served to highlight the urgent need for enabling bioinformatics software to handle greater amounts of information and to do so in reasonable time. A key achievement in my PhD research was the development of a hybrid clustering algorithm based on multi-dimensional scaling that cold quickly identify similarities between very large sets of biological data. Critically, it allowed the most computationally expensive steps to be largely avoided, simultaneously causing a reduction in memory requirements and an increase in overall speed of the software. This algorithm was later modified and integrated into the popular bioinformatics software ClustalW. This work was funded by a Science Foundation Ireland Research Grant.

Phd, Bioinformatics

Activities and Societies: Judo Club, Climbing Club

Bsc, Biochemistry

Activities and Societies: Judo Club