Works by Bray, James E.

Results: 26

Gene3D: structural assignments for the biologist and bioinformaticist alike.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 469, doi. 10.1093/nar/gkg051

By:

Buchan, Daniel W. A.;
Rison, Stuart C. G.;
Bray, James E.;
Lee, David;
Pearl, Frances;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

A rapid classification protocol for the CATH Domain Database to support structural genomics.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 223, doi. 10.1093/nar/29.1.223

By:

Pearl, Frances M. G.;
Martin, Nigel;
Bray, James E.;
Buchan, Daniel W. A.;
Harrison, Andrew P.;
Lee, David;
Reeves, Gabrielle A.;
Shepherd, Adrian J.;
Sillitoe, Ian;
Todd, Annabel E.;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

Assigning genomic sequences to CATH.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 277, doi. 10.1093/nar/28.1.277

By:

Pearl, Frances M. G.;
Lee, David;
Bray, James E.;
Sillitoe, Ian;
Todd, Annabel E.;
Harrison, Andrew P.;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46648-3

By:

Lin, Gu-Lung;
Drysdale, Simon B.;
Snape, Matthew D.;
O'Connor, Daniel;
Brown, Anthony;
MacIntyre-Cockett, George;
Mellado-Gomez, Esther;
de Cesare, Mariateresa;
Ansari, M. Azim;
Bonsall, David;
Bray, James E.;
Jolley, Keith A.;
Bowden, Rory;
Aerssens, Jeroen;
Bont, Louis;
Openshaw, Peter J. M.;
Martinon-Torres, Federico;
Nair, Harish;
Golubchik, Tanya;
Pollard, Andrew J.

Publication type:

Article

MLST revisited: the gene-by-gene approach to bacterial genomics.

Published in:

Nature Reviews Microbiology, 2013, v. 11, n. 10, p. 728, doi. 10.1038/nrmicro3093

By:

Maiden, Martin C. J.;
van Rensburg, Melissa J. Jansen;
Bray, James E.;
Earle, Sarah G.;
Ford, Suzanne A.;
Jolley, Keith A.;
McCarthy, Noel D.

Publication type:

Article

Screening Programs for SARS-CoV-2 Infections on a University Campus - Austin, Texas, September 30-November 30, 2020.

Published in:

2021

By:

Nerhood, Kayleigh J.;
James, Emily R.;
Hardin, Allen;
Bray, James E.;
Hines, Terrance S.;
Young, Amy E.;
Bhavnani, Darlene

Publication type:

journal article

Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 4, p. 830, doi. 10.1093/gbe/evx037

By:

Murray, Susan;
Pascoe, Ben;
Méric, Guillaume;
Mageiros, Leonardos;
Koji Yahara;
Hitchings, Matthew D.;
Friedmann, Yasmin;
Wilkinson, Thomas S.;
Gormley, Fraser J.;
Mack, Dietrich;
Bray, James E.;
Lamble, Sarah;
Bowden, Rory;
Jolley, Keith A.;
Maiden, Martin C. J.;
Wendlandt, Sarah;
Schwarz, Stefan;
Corander, Jukka;
Fitzgerald, J. Ross;
Sheppard, Samuel K.

Publication type:

Article

Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.

Published in:

Genome Biology & Evolution, 2015, v. 7, n. 5, p. 1313, doi. 10.1093/gbe/evv066

By:

Méric, Guillaume;
Miragaia, Maria;
de Been, Mark;
Koji Yahara;
Pascoe, Ben;
Mageiros, Leonardos;
Mikhail, Jane;
Harris, Llinos G.;
Wilkinson, Thomas S.;
Rolo, Joana;
Lamble, Sarah;
Bray, James E.;
Jolley, Keith A.;
Hanage, William P.;
Bowden, Rory;
Maiden, Martin C. J.;
Mack, Dietrich;
de Lencastre, Hermínia;
Feil, Edward J.;
Corander, Jukka

Publication type:

Article

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model.

Published in:

2014

By:

van Tonder, Andries J.;
Mistry, Shilan;
Bray, James E.;
Hill, Dorothea M. C.;
Cody, Alison J.;
Farmer, Chris L.;
Klugman, Keith P.;
von Gottberg, Anne;
Bentley, Stephen D.;
Parkhill, Julian;
Jolley, Keith A.;
Maiden, Martin C. J.;
Brueggemann, Angela B.

Publication type:

Case Study

The domestication of the probiotic bacterium Lactobacillus acidophilus.

Published in:

Scientific Reports, 2014, p. 1, doi. 10.1038/srep07202

By:

J. Bul, Matthew;
A. Jolley, Keith;
E. Bray, James;
Aerts, Maarten;
Vandamme, Peter;
Maiden, Martin C. J.;
Marchesi, Julian R.;
Mahenthiralingam, Eshwar

Publication type:

Article

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07368-7

By:

Méric, Guillaume;
Mageiros, Leonardos;
Pensar, Johan;
Laabei, Maisem;
Yahara, Koji;
Pascoe, Ben;
Kittiwan, Nattinee;
Tadee, Phacharaporn;
Post, Virginia;
Lamble, Sarah;
Bowden, Rory;
Bray, James E.;
Morgenstern, Mario;
Jolley, Keith A.;
Maiden, Martin C. J.;
Feil, Edward J.;
Didelot, Xavier;
Miragaia, Maria;
de Lencastre, Herminia;
Moriarty, T. Fintan

Publication type:

Article

Wild bird-associated C ampylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom.

Published in:

Environmental Microbiology Reports, 2015, v. 7, n. 5, p. 782, doi. 10.1111/1758-2229.12314

By:

Cody, Alison J.;
McCarthy, Noel D.;
Bray, James E.;
Wimalarathna, Helen M. L.;
Colles, Frances M.;
Jansen van Rensburg, Melissa J.;
Dingle, Kate E.;
Waldenström, Jonas;
Maiden, Martin C. J.

Publication type:

Article

cgMLST characterisation of invasive Neisseria meningitidis serogroup C and W strains associated with increasing disease incidence in the Republic of Ireland.

Published in:

PLoS ONE, 2019, v. 14, n. 5, p. 1, doi. 10.1371/journal.pone.0216771

By:

Mulhall, Robert M.;
Bennett, Desiree E.;
Bratcher, Holly B.;
Jolley, Keith A.;
Bray, James E.;
O’Lorcain, Piaras P.;
Cotter, Suzanne M.;
Maiden, Martin C. J.;
Cunney, Robert J.

Publication type:

Article

Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-59509-y

By:

Stenmark, Bianca;
Harrison, Odile B.;
Eriksson, Lorraine;
Anton, Brian P.;
Fomenkov, Alexey;
Roberts, Richard J.;
Tooming-Klunderud, Ave;
Bratcher, Holly B.;
Bray, James E.;
Thulin-Hedberg, Sara;
Maiden, Martin C. J.;
Mölling, Paula

Publication type:

Article

A practical and robust sequence search strategy for structural genomics target selection.

Published in:

Bioinformatics, 2004, v. 20, n. 14, p. 2288, doi. 10.1093/bioinformatics/bth240

By:

James E. Bray;
Russell L. Marsden;
Stuart C.G. Rison;
Alexei Savchenko;
Aled M. Edwards;
Janet M. Thornton;
Christine A. Orengo

Publication type:

Article

Genome-wide association of functional traits linked with C ampylobacter jejuni survival from farm to fork.

Published in:

Environmental Microbiology, 2017, v. 19, n. 1, p. 361, doi. 10.1111/1462-2920.13628

By:

Yahara, Koji;
Méric, Guillaume;
Taylor, Aidan J.;
de Vries, Stefan P. W.;
Murray, Susan;
Pascoe, Ben;
Mageiros, Leonardos;
Torralbo, Alicia;
Vidal, Ana;
Ridley, Anne;
Komukai, Sho;
Wimalarathna, Helen;
Cody, Alison J.;
Colles, Frances M.;
McCarthy, Noel;
Harris, David;
Bray, James E.;
Jolley, Keith A.;
Maiden, Martin C. J.;
Bentley, Stephen D.

Publication type:

Article

The CATH protein family database: A resource for structural and functional annotation of genomes.

Published in:

Proteomics, 2002, v. 2, n. 1, p. 11, doi. 10.1002/1615-9861(200201)2:1<11::AID-PROT11>3.0.CO;2-T

By:

Orengo, Christine A.;
Bray, James E.;
Buchan, Daniel W. A.;
Harrison, Andrew;
Lee, David;
Pearl, Frances M. G.;
Sillitoe, Ian;
Todd, Annabel E.;
Thornton, Janet M.

Publication type:

Article

Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.

Published in:

Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.00317

By:

van Tonder, Andries J.;
Bray, James E.;
Jolley, Keith A.;
Jansen van Rensburg, Melissa;
Quirk, Sigríður J.;
Haraldsson, Gunnsteinn;
Maiden, Martin C. J.;
Bentley, Stephen D.;
Haraldsson, Ásgeir;
Erlendsdóttir, Helga;
Kristinsson, Karl G.;
Brueggemann, Angela B.

Publication type:

Article

A RESTful application programming interface for the PubMLST molecular typing and genome databases.

Published in:

Database: The Journal of Biological Databases & Curation, 2017, v. 2017, n. 1, p. 1, doi. 10.1093/database/bax060

By:

Jolley, Keith A.;
Bray, James E.;
Maiden, Martin C. J.

Publication type:

Article

Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.

Published in:

Nature, 2007, v. 448, n. 7149, p. 87, doi. 10.1038/nature05971

By:

Ng, Stanley S.;
Kavanagh, Kathryn L.;
McDonough, Michael A.;
Butler, Danica;
Pilka, Ewa S.;
Lienard, Benoit M. R.;
Bray, James E.;
Savitsky, Pavel;
Gileadi, Opher;
von Delft, Frank;
Rose, Nathan R.;
Offer, John;
Scheinost, Johanna C.;
Borowski, Tomasz;
Sundstrom, Michael;
Schofield, Christopher J.;
Oppermann, Udo

Publication type:

Article

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Published in:

Nature, 2006, v. 440, n. 7084, p. 637, doi. 10.1038/nature04670

By:

Krogan, Nevan J.;
Cagney, Gerard;
Haiyuan Yu;
Gouqing Zhong;
Xinghua Guo;
Ignatchenko, Alexandr;
Li, Joyce;
Shuye Pu;
Datta, Nira;
Tikuisis, Aaron P.;
Punna, Thanuja;
Peregrín-Alvarez, José M.;
Shales, Michael;
Xin Zhang;
Davey, Michael;
Robinson, Mark D.;
Paccanaro, Alberto;
Bray, James E.;
Sheung, Anthony;
Beattie, Bryan

Publication type:

Article

Evolution of Sequence Type 4821 Clonal Complex Hyperinvasive and Quinolone-Resistant Meningococci.

Published in:

2021

By:

Chen, Mingliang;
Harrison, Odile B.;
Bratcher, Holly B.;
Zhiyan Bo;
Jolley, Keith A.;
Rodrigues, Charlene M. C.;
Bray, James E.;
Qinglan Guo;
Xi Zhang;
Min Chen;
Maiden, Martin C. J.;
Bo, Zhiyan;
Guo, Qinglan;
Zhang, Xi;
Chen, Min

Publication type:

journal article

Clonal Expansion of New Penicillin-Resistant Clade of Neisseria meningitidis Serogroup W Clonal Complex 11, Australia.

Published in:

2017

By:

Mowlaboccus, Shakeel;
Jolley, Keith A.;
Bray, James E.;
Stanley Pang;
Yung Thin Lee;
Bew, Jane D.;
Speers, David J.;
Keil, Anthony D.;
Coombs, Geoffrey W.;
Kahler, Charlene M.;
Pang, Stanley;
Lee, Yung Thin

Publication type:

journal article

Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3789-0

By:

Diallo, Kanny;
Gamougam, Kadija;
Daugla, Doumagoum M.;
Harrison, Odile B.;
Bray, James E.;
Caugant, Dominique A.;
Lucidarme, Jay;
Trotter, Caroline L.;
Hassan-King, Musa;
Stuart, James M.;
Manigart, Olivier;
Greenwood, Brian M.;
Maiden, Martin C. J.

Publication type:

Article

Distribution of class 1 integrons in historic and contemporary collections of human pathogenic Escherichia coli.

Published in:

PLoS ONE, 2020, v. 15, n. 6, p. 1, doi. 10.1371/journal.pone.0233315

By:

Sütterlin, Susanne;
Bray, James E.;
Maiden, Martin C. J.;
Tano, Eva

Publication type:

Article

The CATH extended protein-family database: Providing structural annotations for genome sequences.

Published in:

Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 2, p. 233, doi. 10.1110/ps.16802

By:

Pearl, Frances M.G.;
Lee, David;
Bray, James E.;
Buchan, Daniel W.A.;
Shepherd, Adrian J.;
Orengo, Christine A.

Publication type:

Article