Dr James Bray
I am a bioinformatics scientist working in the bacterial genomics field.
Bacterial species identification using ribosomal multilocus sequence typing (rMLST)
I curate the ribosomal multilocus sequence typing (rMLST) scheme and associated databases. The goal of rMLST is the accurate taxonomic classification of all bacterial isolates using the DNA sequences found within the ribosomal protein-encoding genes (pubmlst.org/species-id).
My research involves applying rMLST in three ways:
1. Performing phylogenetic analysis for taxonomic investigations
2. Defining ribosomal sequence types for the rapid species identification of bacterial isolates
3. Developing and maintaining a 'one-click' species identification server
Large-scale bacterial genomics projects
I am responsible for assembling high-throughput DNA sequencing data for the large-scale genomic projects with the Maiden Group (with a focus on Campylobacter, Neisseria and Streptococcus). As a result, I manage the exchange of large amounts of data between sequencing centres, different labs and the ENA Sequence Read Archive (SRA).
Assembled genomes are accessible on the PubMLST website (pubmlst.org) for bacterial population studies, pathogen surveillance and gene-by-gene analysis.
My research interests include:
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Pathogen strain identification
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Bacterial genome annotation and protein structure/function prediction
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Knowledge-based structural genomics target selection
Bacterial Genomics
Mulhall R, Bennett D, Bratcher H, Jolley K, Bray J, O'Lorcain P, Cotter S, Maiden M, Cunney R. (2019) cgMLST characterisation of invasive Neisseria meningitidis serogroup C and W strains associated with increasing disease incidence in the Republic of Ireland. PLoS One. 14 (5). e0216771. PMID: 31141820
van Tonder A, Bray J, Jolley K, Jansen van Rensburg M, Quirk S, Haraldsson G, Maiden M, Bentley S, Haraldsson Á, Erlendsdóttir H, Kristinsson K, Brueggemann A. (2019) Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions. Frontiers in Microbiology. 10:317. PMID: 30858837
Jolley A, Bray J, Maiden M. (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research. 3:124. PMID: 30345391
Cody A, Bray J, Jolley K, McCarthy N, Maiden M (2017) Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates. Journal of Clinical Microbiology. 55 (7), 2086-2097. PMID: 28446571
Sharp C, Bray J, Housden N, Maiden M, Kleanthous C (2017) Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. PLoS Computational Biology. 13 (7), e1005652. PMID: 28715501
Hill D, Lucidarme J, Gray S, Newbold L, Ure R, Brehony C, Harrison O, Bray J, Jolley K, Bratcher H, Parkhill J, Tang C, Borrow R, Maiden M. (2015) Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. The Lancet Infectious Diseases. 15 (12), 1420-1428. PMID: 26515523
Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson T, Rolo J, Lamble S, Bray J, Jolley K, Hanage W, Bowden R, Maiden M, Mack D, de Lencastre H, Feil E, Corander J, Sheppard S. (2015) Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. PMID: 25888688
Bull M, Jolley K, Bray J, Aerts M, Vandamme P, Maiden M, Marchesi J, Mahenthiralingam E. (2014) The domestication of the probiotic bacterium Lactobacillus acidophilus. Science Reports 4:7202. PMID: 25425319
Vaz C, Francisco A, Silva M, Jolley K, Bray J, Pouseele H, Rothganger J, Ramirez M, Carriço J. (2014) TypOn: the microbial typing ontology. Journal of Biomedical Semantics. 5(1):43. PMID: 25584183
Maiden M, Jansen van Rensburg M, Bray J, Earle S, Ford S, Jolley A, McCarthy N (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nature Reviews Microbiology 11(10):728-36. PMID: 23979428
Structural Genomics
Bray J. (2012) Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. Journal of Structural and Functional Genomics. 13(1):37-46. PMID: 22354707
Hillringhaus L, Yue W, Rose N, Ng S, Gileadi C, Loenarz C, Bello S, Bray J, Schofield CJ, Oppermann U. (2011) Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family. Journal of Biological Chemistry. 286(48):41616-25. PMID: 21914792
Savitsky P, Bray J, Cooper C, Marsden B, Mahajan P, Burgess-Brown N, Gileadi O. (2010) High-throughput production of human proteins for crystallization: the SGC experience. Journal of Structural Biology. 172(1):3-13. PMID: 20541610
Bray J, Marsden B, Oppermann U. (2009) The human short-chain dehydrogenase/reductase (SDR) superfamily: a bioinformatics summary. Chemico-Biological Interactions 178(1-3):99-109. PMID: 19061874
Gräslund S Nordlund P, Weigelt J, Hallberg B, Bray J, et al. (2008) Protein production and purification. Nature Methods. 5(2):135-46. PMID: 18235434
Ng S, Kavanagh K, McDonough M, Butler D, Pilka E, Lienard B, Bray J, Savitsky P, Gileadi O, von Delft F, Rose N, Offer J, Scheinost J, Borowski T, Sundstrom M, Schofield C, Oppermann U. (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature. 448(7149):87-91. PMID: 17589501
Krogan J, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440(7084):637-43. PMID: 16554755
Dobrovetsky E, Lu M, Andorn-Broza R, Khutoreskaya G, Bray J, Savchenko A, Arrowsmith CH, Edwards A, Koth C. (2005) High-throughput production of prokaryotic membrane proteins. Journal of Structural and Functional Genomics. 6(1):33-50. PMID:15909233
Bray J, Marsden R, Rison S, Savchenko A, Edwards A, Thornton J, Orengo C. (2004) A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics. 20(14):2288-95. PMID: 15201178
Protein Structure & Function Resources
Buchan D, Rison S, Bray J, Lee D, Pearl F, Thornton J, Orengo C. (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Research. 31(1):469-73. PMID: 12520054
Bray J, Todd A, Pearl F, Thornton J, Orengo C. (2000) The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. Protein Engineering. 13(3):153-65. PMID: 10775657
Orengo C, Pearl F, Bray J, Todd A, Martin A, Lo Conte L and Thornton J (1999) The CATH database provides insights into protein structure/function relationships. Nucleic Acids Research, 27 (1), 275-279. PMID: 9847200