The CATH Database provides insights into protein structure/function relationships. - Christine A. Orengo; Frances M. G. Pearl; James E. Bray; Annabel E. Todd; A. C. Martin; Loredana Lo Conte; Janet M. Thornton (Nucleic Acids Res., 1999)

Assigning genomic sequences to CATH. - Frances M. G. Pearl; David A. Lee; James E. Bray; Ian Sillitoe; Annabel E. Todd; Andrew P. Harrison; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2000)

A rapid classification protocol for the CATH Domain Database to support structural genomics. - Frances M. G. Pearl; Nigel J. Martin 001; James E. Bray; Daniel W. A. Buchan; Andrew P. Harrison; David A. Lee; Gabrielle A. Reeves; Adrian J. Shepherd; Ian Sillitoe; Annabel E. Todd; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2001)

Gene3D: structural assignments for the biologist and bioinformaticist alike. - Daniel W. A. Buchan; Stuart C. G. Rison; James E. Bray; David A. Lee; Frances M. G. Pearl; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2003)

The CATH database: an extended protein family resource for structural and functional genomics. - Frances M. G. Pearl; C. F. Bennett; James E. Bray; Andrew P. Harrison; Nigel J. Martin 001; Adrian J. Shepherd; Ian Sillitoe; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2003)

A practical and robust sequence search strategy for structural genomics target selection. - James E. Bray; Russell L. Marsden; Stuart C. G. Rison; Alexei Savchenko; Aled M. Edwards; Janet M. Thornton; Christine A. Orengo (Bioinform., 2004)

TypOn: the microbial typing ontology. - Cátia Vaz; Alexandre P. Francisco; Mickael Silva; Keith A. Jolley; James E. Bray; Hannes Pouseele; Jörg Rothgänger; Mário Ramirez; João A. Carriço (J. Biomed. Semant., 2014)

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model. - Andries J. van Tonder; Shilan Mistry; James E. Bray; Dorothea M. C. Hill; Alison J. Cody; Chris L. Farmer; Keith P. Klugman; Anne von Gottberg; Stephen D. Bentley; Julian Parkhill; Keith A. Jolley; Martin C. J. Maiden; et al. (PLoS Comput. Biol., 2014)

A RESTful application programming interface for the PubMLST molecular typing and genome databases. - Keith A. Jolley; James E. Bray; Martin C. J. Maiden (Database J. Biol. Databases Curation, 2017)

Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. - Connor Sharp; James E. Bray; Nicholas G. Housden; Martin C. J. Maiden; Colin Kleanthous (PLoS Comput. Biol., 2017)

Visual Analytics Exploration of PubMLST Meningitis Genomic Data. - Margaret J. Varga; Holly B. Bratcher; Keith A. Jolley; Odile B. Harrison; James E. Bray; Martin C. J. Maiden (BIBM, 2022)