Joe Parker

Joe Parker
University of Southampton · National Biofilms Innovation Centre (NBIC)

DPhil, BSc (Hons.)

About

36
Publications
3,512
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Introduction
Joe Parker currently works at the National Biofilms Innovation Centre (NBIC), University of Southampton. Joe does research in Bioinformatics, Evolutionary Biology and Molecular Ecology using real-time phylogenomics, field-based DNA sequencing (MinION) and cloud-based compute platforms.
Additional affiliations
April 2011 - February 2015
Queen Mary, University of London
Position
  • PostDoc Position

Publications

Publications (36)
Article
Full-text available
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species' capacities to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has a...
Preprint
Full-text available
The impact of human mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species' capacity to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has als...
Preprint
Full-text available
The versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. In fact, the distinction between fieldwork and the laboratory is becoming blurred since genome-scale data can now be collected in challenging conditions in a...
Preprint
Full-text available
The versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonic...
Article
Full-text available
Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation o...
Preprint
Full-text available
Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored 1,2 . Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere 3–5 . However, th...
Article
Full-text available
The known genetic diversity of the hepaciviruses and pegiviruses has increased greatly in recent years through the discovery of viruses related to hepatitis C virus and human pegivirus in bats, bovines, equines, primates and rodents. Analysis of these new species is important for research into animal models of hepatitis C virus infection and into t...
Article
Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups [1, 2], yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) [3-6]. Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are p...
Article
Full-text available
Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon i...
Data
Neutralizing antibody responses against Tier 1 pseudoviruses. Percentage neutralization of individual rabbits as tested against Tier 1 viruses belonging to subtype B (SF162 and Bx08), subtype C (MW965.26) and CRF02_AG (DJ263.8) are given. The data is color coded: Green represents between 50 and 69% neutralization, yellow represents between 70 and 8...
Data
PBMC neutralization data and correlation with end-point binding titers. (A) Neutralization of SF162 virus using IgG (at a final concentration of 125 µg/ml) isolated from week 14 sera of rabbits immunized with 100 µg/dose trimeric gp140 in the presence of CAF01. Note that using Bx08 only 20 µg/dose was used. Each dot represents one rabbit. Horizonta...
Data
Mean end-point binding titers and neutralizing antibody responses. Results for all groups receiving trimeric gp140 and the group receiving monomeric gp120 of UG_A is given. The TZMbl neutralization data (SF162) were obtained using IgG at 250 µg/ml. MT: overall mean titer. SEM: standard error of the mean. (XLSX)
Article
Full-text available
Ten to 30% of HIV-1 infected subjects develop broadly neutralizing antibodies (bNAbs) during chronic infection. We hypothesized that immunizing rabbits with viral envelope glycoproteins (Envs) from these patients may induce bNAbs, when formulated as a trimeric protein and in the presence of an adjuvant. Based on in vitro neutralizing activity in se...
Article
Elicitation of Neutralising Antibodies Using Patient-Derived gp140 Immunogens from a Long-Term Non-Progressor E.J. Bowles1, J. Parker1, L. Heyndrickx2, B. Grevstad3, M. Jansson4, G. Vanham2, G. Stewart-Jones1 1Oxford University, Oxford, United Kingdom (Great Britain); 2Institute of Tropical Medicine, Antwerp, Belgium; 3Statens Serum Institut, Copen...
Data
Full-text available
Figure S1: The G/C content at each codon position for three datasets. Three separate data sets are shown: among host subtype 1a (green), among host subtype 1b (blue) and within-host (red). Separate parameters were estimated for each of 21 partitions spanning the HCV coding region (see genome schematic and partition numbering at top of Figure). The...
Data
Table S1: Accession numbers and dates of sampling. Accession numbers and isolate sampling dates of all sequences used in this study.
Data
Full-text available
Figure S2: Absolute rates for the 1st+2nd versus 3rd codon positions for each partition. Three separate data sets are shown: among host subtype 1a (green), among host subtype 1b (blue) and within-host (red). Squares represent the rate of the 1st+2nd positions, circles the 3rd position. The symbols are offset within each partition for visual clarity...
Article
Full-text available
Hepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus' public health importance and a wealth of sequence data, basic aspects of HCV molecular evolution remain poorly understood. Here we investigate three sets of whole HCV genomes in order to directly compare the evolution of whole H...
Article
Full-text available
Canine parvovirus type 2 (CPV-2) is a severe enteric pathogen of dogs, causing high mortality in unvaccinated dogs. After emerging, CPV-2 spread rapidly worldwide. However, there is now some evidence to suggest that international transmission appears to be more restricted. In order to investigate the transmission and evolution of CPV-2 both nationa...
Data
Empirical cumulative density functions (eCDF) of p-values for positively-selected amino-acid substitutions. The eCDF is a binning function that scores the proportion of total data points (vertical axis) of equal or lesser p with increasing values of p from 0 to 1 (horizontal axis). Low-valued (significant p) data sets are expected to plateau early,...
Data
Positive and negative selection in SIV env. (0.15 MB DOC)
Data
Epistasis in SIV env. (0.09 MB DOC)
Data
CD4+ T cells in macaques after SIVmac239 infection. Kinetic analyses of peripheral blood CD4+ T cells during SIVmac239 infection. CD4 counts are depicted longitudinally for each animal (LC; green, TC; blue and NC; red). Tenofovir treatment period is indicated by shaded area. (0.41 MB TIF)
Data
Heterologous neutralization of HIV-2. Purified IgG obtained from plasma samples 14 months post-inoculation were titrated and analyzed for neutralization of HIV-2 1812 (A) and HIV-2 1682 (B). Neutralization profiles of NC (animal 3, red) and TC (animals 1, 5, 8, 11 blue) as well as LC (animals 2, 4, 6, 7, 9, 10, 12, green) are shown. Values are mean...
Data
Number of env sequences obtained from plasma samples and re-isolated virus for macaques 1–12. (0.04 MB DOC)
Data
Sequence positions of mutations in re-isolates from NC3. Env sequences from virus re-isolated from macaques 3 at 4.5 months p.i. were compared with that of SIVmac239 in order to identify escape mutations that could account for the observed changes in neutralization sensitivity. NC3 sequences displayed a number of sequence changes including V67M, A4...
Data
Phylogeny reconstruction and arrival times of significant positively-selected codon substitutions. Phylogeny reconstruction: Maximum clade credibility (MCC) tree of 281 SIV env sequences (12 hosts) plus inoculate (SIVmac239). MCC tree resolved from posterior set of 9000 trees (PST) sampled from the posterior distribution in BEAST. Sequences from ea...
Article
Full-text available
Neutralizing antibodies (NAb) able to react to heterologous viruses are generated during natural HIV-1 infection in some individuals. Further knowledge is required in order to understand the factors contributing to induction of cross-reactive NAb responses. Here a well-established model of experimental pathogenic infection in cynomolgus macaques, w...
Article
Full-text available
Although major inroads into making antiretroviral therapy available in resource-poor countries have been made, there is an urgent need for an effective vaccine administered shortly after birth, which would protect infants from acquiring human immunodeficiency virus type 1 (HIV-1) through breast-feeding. Bacillus Calmette-Guérin (BCG) is given to mo...
Article
Full-text available
Hepatitis C virus subtype 3a is a highly prevalent and globally distributed strain that is often associated with infection via injection drug use. This subtype exhibits particular phenotypic characteristics. In spite of this, detailed genetic analysis of this subtype has rarely been performed. We performed full-length viral sequence analysis in 18...
Article
Full-text available
Hepatitis C virus subtype 3a is a highly prevalent and globally distributed strain that is often associated with infection via injection drug use. This subtype exhibits particular phenotypic characteristics. In spite of this, detailed genetic analysis of this subtype has rarely been performed. We performed full-length viral sequence analysis in 18...
Article
HIV is capable of frequent genetic exchange through recombination. Despite the pandemic spread of HIV-1 recombinants, their times of origin are not well understood. We investigate the epidemic history of a HIV-1 circulating recombinant form (CRF) by estimating the time of the recombination event that lead to the emergence of CRF33_01B, a recently d...
Article
Many recent studies have sought to quantify the degree to which viral phenotypic characters (such as epidemiological risk group, geographic location, cell tropism, drug resistance state, etc.) are correlated with shared ancestry, as represented by a viral phylogenetic tree. Here, we present a new Bayesian Markov-Chain Monte Carlo approach to the in...

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