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Joe Parker

  • Postdoctoral Research Assistant
  • School of Biological and Chemcial Sciences, Queen Mary, University of London
  • 8PublicationsNumber of items in Joe's My Publications folder on Mendeley.
  • 5Followers


I want to make the power of bioinformatics more widely available and more robustly applied. I believe that one day we will visualise and analyse molecular and genetic data as easily as earlier naturalists watched a flock of birds or measured a field of wheat. History: I studied general biology at Imperial College, University of London (2001-2004), gaining first-class honours partly on the strength of my final-year research into bioinformatic pipelines for the detection of endogenous retroviruses (ERVs) in genomic data. Subsequently I completed a D.Phil at Linacre College, University of Oxford, based in the Zoology department under Andrew Rambaut and Oliver G. Pybus (2004-2008). I developed novel phylogenetic strategies and bioinformatic pipelines for the analysis of measurably evolving pathogens’ evolution. I focused particularly on methods for the detection of trait-phylogeny association (e.g. viral quasispecies compartmentalization or geographical segregation) and disparate between- and within-host evolutionary dynamics in hepatitis C virus (HCV) and human immunodeficiency virus (HIV). I also convened a graduate course in science and media communication and gave tutorial and practical support to undergraduate courses in multivariate statistics, population genetics and evolution at the Zoology Department. From 2009 I worked at the Weatherall Institute of Molecular Medicine (John Radcliffe Hospital: Univ. Oxford / Medical Research Council (UK)), mainly on phylogenetic and machine-learning methods for the detection of correlates between antigenicity and sequence evolution. This work has integrated clinical, structural, evolutionary and population genetic data leading to immunogen design and assessment in silico, now trialling in vivo for the Europe-wide NGIN vaccine consortium. Present: Since April 2011 I have been engaged in a large-scale genomics project to look for markers of molecular convergence in mammals, with bats as the focal taxonomic group. This work (in the Rossiter Lab, Queen Mary, University of London) involves the de novo sequencing, assembly and annotation of several bat genomes. We have developed a comprehensive analysis pipeline based on a novel Java API (developed in-house) that is able to analyse data orders of magnitude faster than manual techniques, and auto-optimize parameters on-the-fly. I have also been involved in several other international research collaborations and training seminars at undergraduate level and beyond, usually delivered through Kitson Consulting, a bioinformatics consultancy. I am available for research collaborations requiring phylogenetic, statistical or bioinformatic support, undergraduate lectures, and technical seminars and training.

Recent publications

  • Estimating the date of origin of an HIV-1 circulating recombinant form.

    • Tee K
    • Pybus O
    • Parker J
    • et al.
  • Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection

    • Humphreys I
    • Fleming V
    • Fabris P
    • et al.

Professional experience

Postdoctoral Research Assistant

School of Biological and Chemcial Sciences, Queen Mary, University of London

April 2011 - Present

Director / Consultant Bioinformatician

Kitson Consulting Ltd.

February 2009 - Present

Postdoctoral Research Assistant

Weatherall Institute of Molecular Medicine

March 2010 - December 2010(9 months)



Department of Zoology, University of Oxford

September 2004 - January 2009(4 years)

BSc (Hons)

Department of Life Sciences, Imperial College

September 2001 - June 2004(3 years)


Followers (5)

Following (7)

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