Employment History

 

 

  • Facility Manager, Bioinformatics Support Unit
    • 2011 - present, Newcastle University
  • Bioinformatics Support Scientist
    • 2005 - 2011, Newcastle University

The Bioinformatics Support Unit is a cross-faculty, University-wide resource. The Unit employs posts specialising in transcriptomics and proteomics. We are involved in many aspects of medical and environmental research and currently support over 100 researchers as well as having a significant involvement with major systems biology and neuroinformatics programs.

 

Education

 

 

  • MRes Bioinformatics and Computational Biology, University of Leeds
    • 2004 - 2005, awarded with distinction

Project – Validating protein-protein interaction predictions made using distant conservation of sequence patterns and structure relationships. (Supervisor, Dr. R. Jackson)

  • PhD Genetics, Leicester University
    • 1999 - 2004

Project – Aplip1, a potential scaffold protein of Drosophila melanogaster may be involved in facilitating signal transduction. (Supervisor, Dr. F. Tata)

  • BSc (Hons) Biochemistry and Genetics, University of Nottingham
    • 1996 - 1999, 2(i)

Honours project - Identification of a novel TFIIS-like factor. (Supervisor - Dr. G Morgan)

 

Skills

 

 

Proteomics

Extensive experience handling raw and processed data from 2D- GE and LC-MS experiments. Experience of major 2D-GE analysis platforms (Progenesis (Nonlinear Dynamics), Delta2D (Decodon Gmbh), DeCyder (GE Healthcare)).

Sequencing

Experience with ChIP-Seq data from the Illumina platform. Use of major software packages: MACS, PeakFinder, PeakRanger, BEDTools.

Data Integration

Ondex, Cytoscape, Taverna, Ingenuity Pathway Analysis

Technical

Programming – Python, R, PHP , Perl, Java, SQL (MySQL & PostgreSQL), shell scripting. Linux systems administration, virtualization (VirtualBox, KVM), web services (REST, SOAP). Frameworks – Wordpress, Django. Tools – Subversion, Git, Mercurial, Apache Maven, Apache Lucene.

Management

Supervision of postgraduate students (Masters and Doctoral level).

Training

Invited lecturer on a number of Masters courses (Newcastle University and Sunderland University), and an undergraduate course. Development of bespoke bioinformatics training for researchers.