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The University of Southampton
Biological Sciences

Dr Joe Parker DPhil, BSc (Hons.), ARCS

Research Fellow in Real-time phylogenomics, National Biofilms Innovation Centre (NBIC)

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Realtime phylogenomics

Dr. Parker joined the National Biofilms Innovation Centre’s Southampton University group in 2018 shortly after its formation. He is developing lab techniques, statistical methods, and software to exploit portable, real-time DNA sequencing for biofilm microbial community analyses. These will enable non-experts with minimal equipment to explore these ubiquitous microcosms’ composition, evolution and ecology, rapidly, anywhere on the planet.

Previously he has held an independent Early-Career Research Fellowship at the Royal Botanic Gardens, Kew (where he published the first-ever demonstration of congeneric species ID by genome-scale DNA sequencing in the field), and Queen Mary, University of London, where he published the first-ever detection of adaptive molecular convergent evolution (in Nature).

He is a Fellow of the Software Sustainability Institute, and Stipendiary Lecturer in Statistics and Modelling at St Hilda’s College, Oxford.

Career history

2018: Postdoctoral bioinformatician, Dunn School of Pathology, Oxford University.

2015-2018: Early-Career Research Fellow in Phylogenomics, Royal Botanic Gardens, Kew.

2011-2015: Postdoctoral Researcher, Queen Mary, University of London

2009-2011: Postdoctoral Researcher, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford.

Academic qualifications

2004-2009: DPhil in evolutionary virology, Linacre College, Oxford, UK.

2001-2004: BSc (Hons.) in biology, Imperial College, University of London, UK.


Research interests

The DNA of living things is everywhere, and tells us about the identity, ecology, and even past evolutionary history of organisms from blue whales to viruses. This is especially true of biofilms – ubiquitous communities of microscopic organisms responsible for infection, contamination, and biofouling.. which also serve vital functions cycling nutrients in the ecosystem.

Modern technology can put the power of portable DNA sequencing and cloud-based high-performance computing into the hands of every doctor, nurse, engineer, farmer, or schoolchild on the planet. But to realise the massive potential of this technology we need simplified lab methods and DNA analysis apps, driven by statistical algorithms optimised for massive, real-time, noisy datasets.

At the National Biofilms Innovation Centre (NBIC), I am developing these tools to investigate biofilms. I conduct basic research into biofilm evolutionary ecology and comparative genome statistics (phylogenomics); and we are trialling these in clinical and industrial settings with stakeholders.

Research group

National Biofilms Innovation Centre

Affiliate research groups

Institute for Life Sciences (IfLS), Microbiology

External teaching: Stipendiary Lecturer (Statistics & Modelling), St. Hilda’s College, Oxford.

Bioinformatician: Kitson Consulting Ltd., Bristol.

Reviewer: NERC; Nature Sci. Rep; Meth. Ecol. Evol.; Syst. Biol.; Plant Ecol. Div.; Axios; Int. J. Plant Sci.; J. Exp. Z.; Mol. Ecol. Res.; Ecol. & Evol.

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Dr Joe Parker
School of Biological Sciences
Faculty of Environmental and Life Sciences
Life Sciences Building 85
University of Southampton
Highfield Campus
SO17 1BJ

Room Number: 85/4041

Dr Joe Parker's personal home page
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