Biography

Gord began his career as a programmer when Fortran was still cool and the Internet hadn’t yet been invented. After working in telecommunications for several years, he moved into computational biology in 1998, and now spends his time striving to transmute the base metal of high-throughput sequencing data into research gold.

After completing his PhD, he moved to the CRUK Cambridge Institute, initially as a post-doc researcher under Duncan Odom working on the evolution of gene regulatory regions. He then moved to Jason Carroll’s group, working as a computational analyst, primarily on breast cancer. He now works as part of the Bioinformatics Core, primarily on automating the analysis of high-throughput sequencing data, especially RNA-seq and small RNA data sets.

He believes passionately in the ubiquitous use of revision control systems (for example Subversion, Git).

Skills

Programming languages: C, C++, R, Ruby, Java, Python, and a few others he won’t admit to knowing

Analysis methods: experienced with ChIP-seq, RNA-seq, and small RNA analysis

Software: experienced with many widely used computational biology tools: BLAST, RepeatMasker, Clustal, Phred/Phrap/Consed, Staden, Velvet, widely used alignment software such as BWA and BowTie, various BioConductor packages. Also familiar with the usual document production tools (LaTeX, FrameMaker, etc).

Education

Ph.D., University of Victoria, March 2008

  • department: Computer Science
  • supervisors: Dr. V. King (computer science) and Dr. B. Koop (biology)
  • research areas: automation of sequence analysis, molecular evolution, evolution of salmonids
  • dissertation: “Analysis of salmonid RNA sequences and implications for salmonid evolution”

Publications (first author)

Serandour AA, Brown GD, Cohen JD, Carroll JS. “Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties”. Genome Biology 14:R147 (2013 Dec 27).

Kutter C, Brown GD, Goncalves A, Wilson MD, Watt S, Brazma A, White RG, Odom, DT. “Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes”, Nature Genetics 43(10): 948-955 (2011 August 28).

Selected Other Publications (contributing author)

Holmes KA, Brown GD, Carroll JS. “Chromatin Immunoprecipitation-Sequencing (ChIP-seq) for Mapping of Estrogen Receptor-Chromatin Interactions in Breast Cancer”, in Methods in Molecular Biology 1366, 79–98 (Springer New York, 2016).

Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS. “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer”. Nature 481(7381):389–393 (2012 Jan 19). Available online 2012 Jan 04.

Ross-Innes CS, Brown GD, Carroll JS. “A co-ordinated interaction between CTCF and ER in breast cancer cells”. BMC Genomics 12:593 (2011 Dec 5).

Gord contributes to various software projects, including:

  • DiffBind– a Bioconductor package for the analysis of differential binding in ChIPseq and similar experiments
  • GreyListChIP– a Bioconductor package for identifying regions of high read density in input lanes, which might cause artefacts in ChIP analysis
  • a few Redmineplugins:
    • Project State– adds a layer of state more coarse-grained than status, and provides some reports for identifying issues that require attention
    • Custom Projects– provides a per-user editable list of projects, so if your Redmine instance has a lot of projects, you can see just the few you routinely need easily
    • Resolved Reminder– to remind users that there are issues assigned to them in the “Resolved” state, which should be checked and closed, or returned to an open status and reassigned to whoever still needs to work on them