James Bray

JamesBrayBioinformatics Postdoctoral Research Scientist

Contact
E-mail: james.bray@zoo.ox.ac.uk

About me

I am responsible for assembling high-throughput DNA sequencing results for the Campylobacter, Neisseria and Multi-species research projects within the Maiden Group. As a result, I have developed an automated de novo genome assembly pipeline and I manage the exchange of large amounts of data between sequencing centres, different labs and the ENA Sequence Read Archive (SRA). The assembled genomes are accessible on the PubMLST website (pubmlst.org) for bacterial population studies, pathogen surveillance and gene-by-gene analysis.

As part of the Patho-NGen-Trace project, I have contributed towards a RESTful interface for selected aspects of the PubMLST website. This interface provides MLST sequence definitions and profiles for all bacterial species hosted by PubMLST using the Microbial Typing Ontology (TypOn).

My research interests include:

  • Pathogen strain identification
  • Bacterial genome annotation and protein structure/function prediction
  • Knowledge-based structural genomics target selection

Selected Publications

Bacterial Genomics

van Tonder AJ, Bray JE, Roalfe L, White R, Zancolli M, Quirk SJ, Haraldsson G, Jolley KA, Maiden MC, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Goldblatt D, Brueggemann AB. (2015) Genomics reveals the worldwide distribution of multidrug-resistant serotype 6E pneumococci. Journal of Clinical Microbiology  PMID: 25972423

Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK. (2015) Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. PMID: 25888688

van Tonder AJ, Mistry S, Bray JE, Hill DM, Cody AJ, Farmer CL, Klugman KP, von Gottberg A, Bentley SD, Parkhill J, Jolley KA, Maiden MC, Brueggemann AB. (2014) Defining the estimated core genome of bacterial populations using a Bayesian decision model. PLoS Computational Biology 10(8):e1003788. PMID: 25144616

Bull MJ, Jolley KA, Bray JE, Aerts M, Vandamme P, Maiden MC, Marchesi JR, Mahenthiralingam E. (2014) The domestication of the probiotic bacterium Lactobacillus acidophilus. Science Reports 4:7202. PMID: 25425319

Vaz C, Francisco AP, Silva M, Jolley KA, Bray JE, Pouseele H, Rothganger J, Ramirez M, Carriço JA. (2014) TypOn: the microbial typing ontology. Journal of Biomedical Semantics.  5(1):43. PMID: 25584183

Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nature Reviews Microbiology 11(10):728-36. PMID: 23979428

Structural Genomics

Bray JE. (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 WW, Rose NR, Ng SS, Gileadi C, Loenarz C, Bello SH, Bray JE, 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 JE, Cooper CD, Marsden BD, Mahajan P, Burgess-Brown NA, 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 JE, Marsden BD, 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 BM, Bray JE, et al. (2008) Protein production and purification. Nature Methods. 5(2):135-46. PMID: 18235434

Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BM, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U. (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature. 448(7149):87-91. PMID: 17589501

Krogan NJ, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440(7084):637-43. PMID: 16554755

Dobrovetsky E, Lu ML, Andorn-Broza R, Khutoreskaya G, Bray JE, Savchenko A, Arrowsmith CH, Edwards AM, Koth CM. (2005) High-throughput production of prokaryotic membrane proteins. Journal of Structural and Functional Genomics. 6(1):33-50. PMID:15909233

Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA. (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 DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Research. 31(1):469-73. PMID: 12520054

Bray JE, Todd AE, Pearl FM, Thornton JM, Orengo CA. (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 CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L and Thornton JM (1999) The CATH database provides insights into protein structure/function relationships. Nucleic Acids Research, 27 (1), 275-279. PMID: 9847200