Joe Parker

My work

I work on convergent evolution at the genome level in the Rossiter Group within the School of Biological Sciences at Queen Mary College, University of London.

The main focus of my research is high-throughput phylogenomics: marrying large public datasets (including next-generation sequencing; NGS) with high-performance computing approaches to empirically determine the nature of evolutionary processes at the scale of the genome.

Other links

Research group: Rossiter Group

Host Department: School of Biological and Chemical Sciences

Academic profile: Academia.edu

Academic profile: Linkedin

Academic profile: Mendeley

Academic profile: Google Citations

Personal blog: lonelyjoeparker.com

Biographical Information

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. Experimental design will be more focused on biological questions and less limited by data availability or computational constraints.

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.

Publications, talks and other research outputs

List coming soon. In the meantime see here (14 May 2012.)

Joe Parker, Georgia Tsagkogeorga, James A Cotton, Yuan Liu, Paolo Provero, Elia Stupka, Stephen J Rossiter (2013). Genome-wide signatures of convergent evolution in echolocating mammals. Nature 502:228-231 Google Scholar | doi:10.1038/nature12511 | See more...

Leo Heyndrickx, Guillaume Stewart-Jones, Marianne Jansson, Hanneke Schuitemaker, Emma Bowles, Luigi Buonaguro, Berit Grevstad, Lasse Vinner, Katleen Vereecken, Joe Parker, Meghna Ramaswamy, Priscilla Biswas, Guido Vanham, Gabriella Scarlatti, Anders Fomsgaard, NGIN Consortium (2013). Selected HIV-1 Env Trimeric Formulations Act as Potent Immunogens in a Rabbit Vaccination Model. PloS one 8:e74552 Google Scholar | doi:10.1371/journal.pone.0074552 | See more...

Joe Parker, Georgia Tsagkogeorga, James A. Cotton, Elia Stupka & Stephen J. Rossiter (2012). Signatures of genome-wide convergent molecular evolution: initial results.. Poster presented at SMBE 2012, Dublin, June 23-26 2012: : Google Scholar

EJ Bowles, J Parker, L Heyndrickx, B Grevstad, M Jansson, G Vanham, G Stewart-Jones (2011). Elicitation of Neutralising Antibodies Using Patient-Derived gp140 Immunogens from a Long-Term Non-Progressor. 27:A48-A48 Google Scholar | doi:full/10.1089/aid.2011.1502 | See more...

Rebecca Gray, Joe Parker, Philippe Lemey, Marco Salemi, Aris Katzourakis, Oliver Pybus (2011). The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131 Google Scholar | See more...

SR Clegg, KP Coyne, J Parker, S Dawson, SA Godsall, G Pinchbeck, PJ Cripps, RM Gaskell, AD Radford (2011). Molecular epidemiology and phylogeny reveals complex spatial dynamics of endemic canine parvovirus. Journal of virology :JVI. 01576-10v1 Google Scholar | See more...

Gül?en Özkaya ?ahin, Emma J Bowles, Joe Parker, Hannes Uchtenhagen, Enas Sheik-Khalil, Stephen Taylor, Oliver G Pybus, Barbro Mäkitalo, Lilian Walther-Jallow, Mats Spångberg, Rigmor Thorstensson, Adnane Achour, Eva Maria Fenyö, Guillaume BE Stewart-Jones, Anna-Lena Spetz (2010). Generation of Neutralizing Antibodies and Divergence of SIVmac239 in Cynomolgus Macaques Following Short-Term Early Antiretroviral Therapy. PLoS pathogens 6:e1001084 Google Scholar | doi:10.1371/journal.ppat.1001084 | See more...

Maximillian Rosario, John Fulkerson, Shamit Soneji, Joe Parker, Eung-Jun Im, Nicola Borthwick, Anne Bridgeman, Charles Bourne, Joan Joseph, Jerald C Sadoff, Tomas Hanke (2010). Safety and immunogenicity of novel recombinant BCG and modified vaccinia virus Ankara vaccines in neonate rhesus macaques. Journal of virology 84:7815 Google Scholar

Isla Humphreys, Vicki Fleming, Paolo Fabris, Joe Parker, Bodo Schulenberg, Anthony Brown, Charis Demetriou, Silvana Gaudieri, Katja Pfafferott, Michaela Lucas, Jane Collier, Kuan-Hsiang Gary Huang, Oliver G Pybus, Paul Klenerman, Eleanor Barnes (2010). Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection. Journal of Virology 84:1664 Google Scholar | See more...

Kok Keng Tee, Oliver G Pybus, Joe Parker, Kee Peng Ng, Adeeba Kamarulzaman, Yutaka Takebe (2009). Estimating the date of origin of an HIV-1 circulating recombinant form. Virology 387:229-234 Google Scholar

Joe Parker, Andrew Rambaut, Oliver G Pybus (2008). Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics and Evolution 8:239-246 Google Scholar | See more...

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