Publications

BµG@S microarrays have contributed to 138 publications to date:
 

2012
 
Dale A.G., Hinds J., Mann J., Taylor P.W. and Neidle S. (2012)
Symmetric bis-benzimidazoles are potent anti-Staphylococcal agents with dual inhibitory mechanisms against DNA gyrase. Biochemistry. Jul 12. [Epub ahead of print]
PubMed
 
Kudirkienė E., Cohn M.T., Stabler R.A., Strong P.C., Sernienė L., Wren B.W., Nielsen E.M., Malakauskas M. and Brøndsted L. (2012)
Phenotypic and genotypic characterizations of Campylobacter jejuni isolated from the broiler meat production process. Curr Microbiol. Jun 27. [Epub ahead of print]
PubMed
 
Scott J.R., Hinds J., Gould K.A., Millar E.V., Reid R., Santosham M., O'Brien K.L. and Hanage W.P. (2012)
Nontypeable pneumococcal isolates among Navajo and White Mountain Apache communities: Are these really a cause of invasive disease? J Infect Dis. 206(1):73-80.
PubMed
 
Salter S.J., Hinds J., Gould K.A., Lambertsen L. Hanage W.P., Antonio M., Turner P., Hermans P.W., Bootsma H.J., O'Brien K.L. and Bentley S.D. (2012)
Variation at the capsule locus, cps, of mistyped and non-typeable Streptococcus pneumoniae isolates. Microbiology. 158(6):1560-9.
PubMed
 
Riedel C.T., Cohn M.T., Stabler R.A., Wren B. and Brøndsted L. (2012)
Cellular response of Campylobacter jejuni to trisodium phosphate. Appl Environ Microbiol. 78(5):1411-5.
PubMed
 
Valente C., Hinds J., Pinto F., Brugger S.D., Gould K., Mühlemann K., de Lencastre H. and Sá-Leão R. (2012)
Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine. PLoS One. 7(1):e30235.
PubMed
 
Scott J.R., Hanage W.P., Lipsitch M., Millar E.V., Moulton L.H., Hinds J., Reid R., Santosham M. and O'Brien .KL. (2012)
Pneumococcal sequence type replacement among American Indian children: a comparison of pre- and routine-PCV7 eras. Vaccine. 30(13):2376-81.
PubMed
 

2011
 
Witney A.A., Waldron D.E., Brooks L.A., Tyler R.H., Withers M., Stoker N.G., Wren B.W., Butcher P.D. and Hinds J. (2011)
BµG@Sbase - a microbial gene expression and comparative genomic database. Nucleic Acids Res. 40:D605-9.
PubMed
 
McCarthy A.J., Witney A.A., Gould K.A., Moodley A., Guardabassi L., Voss A., Denis O., Broens E.M., Hinds J. and Lindsay J.A. (2011)
The distribution of mobile genetic elements (MGEs) in MRSA CC398 is associated with both host and country. Genome Biol Evol. 3:1164-74.
PubMed
 
Donkor E.S., Bishop C.J., Gould K.A., Hinds J., Antonio M., Wren B. and Hanage W.P. (2011)
High levels of recombination among Streptococcus pneumoniae isolates from the Gambia. MBio 2(3):e00040-11.
PubMed
 
Botella H., Peyron P., Levillain F., Poincloux R., Poquet Y., Brandli I., Wang C., Tailleux L., Tilleul S., Charrière G.M., Waddell S.J., Foti M., Lugo-Villarino G., Gao Q., Maridonneau-Parini I., Butcher P.D., Castagnoli P.R., Gicquel B., de Chastellier C. and Neyrolles O. (2011)
Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages. Cell Host Microbe 10(3):248-59.
PubMed
 
Ligowska M., Cohn M.T., Stabler R.A., Wren B.W. and Brøndsted L. (2011)
Effect of chicken meat environment on gene expression of Campylobacter jejuni and its relevance to survival in food. Int J Food Microbiol. 145(Suppl 1):S111-5.
PubMed
 
Gundogdu O., Mills D.C., Elmi A., Martin M.J., Wren B.W. and Dorrell N. (2011)
The Campylobacter jejuni transcriptional regulator Cj1556 plays a role in the oxidative and aerobic stress response and is important for bacterial survival in vivo. J Bacteriol. 193(16):4238-49.
PubMed
 
Trappetti C., Ogunniyi A.D., Oggioni M.R. and Paton J.C. (2011)
Extracellular matrix formation enhances the ability of Streptococcus pneumoniae to cause invasive disease. PLoS One. 6(5):e19844.
PubMed
 
Newton R., Hinds J. and Wernisch L. (2011)
Empirical Bayesian models for analyzing molecular serotyping microarrays. BMC Bioinformatics. 12:88.
PubMed
 
Hepworth P.J., Ashelford K.E., Hinds J., Gould K.A., Witney A.A., Williams N.J., Leatherbarrow H., French N.P., Birtles R.J., Mendonca C., Dorrell N., Wren B.W., Wigley P., Hall N. and Winstanley C. (2011)
Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ Microbiol. 13(6):1549-60.
PubMed
 
Harvey R.M., Stroeher U.H., Ogunniyi A.D., Smith-Vaughan H.C., Leach A.J. and Paton J.C. (2011)
A variable region within the genome of Streptococcus pneumoniae contributes to strain-strain variation in virulence. PLoS One. 6(5):e19650.
PubMed
 
Overton I.M., Graham S., Gould K.A., Hinds J., Botting C.H., Shirran S., Barton G.J. and Coote P.J. (2011)
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. BMC Syst Biol. 5:68.
PubMed
 
Turner P., Hinds J., Turner C., Jankhot A., Gould K., Bentley S.D., Nosten F. and Goldblatt D. (2011)
Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray. J Clin Microbiol. 49(5):1784-9.
PubMed
 
Rosado H., Rahman K.M., Feuerbaum E.A., Hinds J., Thurston D.E., Taylor P.W. (2011)
The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother. 66(5):985-96.
PubMed
 
Lemmens N., van Wamel W., Snijders S., Lesse A.J., Faden H. and van Belkum A. (2011)
Genomic comparisons of USA300 Staphylococcus aureus colonizating the nose and rectum of children with skin abscesses. Microb Pathog. 50(3-4):192-9.
PubMed
 
Carpaij N., Willems R.J., Rice T.W., Weinstein R.A., Hinds J., Witney A.A., Lindsay J.A., Bonten M.J. and Fluit A.C. (2011)
Genetic variation in spatio-temporal confined USA300 community-associated MRSA isolates: a shift from clonal dispersion to genetic evolution? PLoS One. 6(2):e16419.
PubMed
 
Tessema G.T., Møretrø T., Snipen L., Axelsson L. and Naterstad K. (2011)
Global transcriptional analysis of spontaneous sakacin P-resistant mutant strains of Listeria monocytogenes during growth on different sugars. PLoS One. 6(1):e16192.
PubMed
 

2010
 
McCallum N., Hinds J., Ender M., Berger-Bächi B. and Stutzmann Meier P. (2010)
Transcriptional profiling of XdrA, a new regulator of spa transcription in Staphylococcus aureus. J Bacteriol. 192(19):5151-64.
PubMed
 
Estorninho M., Smith H., Thole J., Harders-Westerveen J., Kierzek A., Butler R.E., Neyrolles O. and Stewart G.R. (2010)
ClgR regulation of chaperone and protease systems is essential for Mycobacterium tuberculosis parasitism of the macrophage. Microbiology. 156(11):3445-55.
PubMed
 
Fivian-Hughes A.S. and Davis E.O. (2010)
Analyzing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. J Bacteriol. 192(17):4348-56.
PubMed
 
Tudo G, Laing K, Mitchison DA, Butcher PD and Waddell SJ (2010).
Examining the basis of isoniazid tolerance in non-replicating Mycobacterium tuberculosis using transcriptional profiling. Future Med Chem; 2(8):1371-1383.
PubMed
 
Estorninho M, Smith H, Thole J, Harders-Westerveen J, Kierzek A, Butler RE, Neyrolles O, Stewart GR (2010)
ClgR regulation of chaperone and protease systems is essential for Mycobacterium tuberculosis parasitism of the macrophage. Microbiology. 2010 Nov;156(Pt 11):3445-55. Epub 2010 Aug 5.
PubMed
 
McCallum N., Hinds J., Ender M., Berger-Bächi B. and Stutzmann Meier P. (2010)
Transcriptional profiling of XdrA, a new regulator of spa transcription in Staphylococcus aureus. J Bacteriol. 192(19):5151-64.
PubMed
 
Ogunniyi AD, Mahdi LK, Jennings MP, McEwan AG, McDevitt CA, Van der Hoek MB, Bagley CJ, Hoffmann P, Gould KA and Paton JC. (2010)
Central Role of Manganese in Regulation of Stress Responses, Physiology and Metabolism in Streptococcus pneumoniae. J Bacteriol. 2010 Sep;192(17):4489-97.
PubMed
 
Mendoza Lopez P, Golby P, Wooff E, Nunez Garcia J, Garcia Pelayo MC, Conlon K, Camacho AG, Hewinson RG, Polaina J, Suárez García A, Gordon SV (2010)
Characterization of the transcriptional regulator Rv3124 of Mycobacterium tuberculosis identifies it as a positive regulator of molybdopterin biosynthesis and defines the functional consequences of a non-synonymous SNP in the Mycobacterium bovis BCG orthologue. Microbiology 156(Pt 7):2112-23. Epub
PubMed
 
Johnston C., Hinds J., Smith A., van der Linden M., van Eldere J. and Mitchell T.J. (2010)
Detection of large numbers of pneumococcal virulence genes in Streptococci of the Mitis group. J Clin Microbiol. 48(8):2762-9.
PubMed
 
Brugger S.D., Frey P., Aebi S., Hinds J. and Mühlemann K. (2010)
Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine. PLoS One. 5(7):e11638.
PubMed
 
Guinane C.M., Ben Zakour N.L., Tormo-Mas M.A., Weinert L.A., Lowder B.V., Cartwright R.A., Smyth D.S., Smyth C.J., Lindsay J.A., Gould K.A., Witney A., Hinds J., Bollback J.P., Rambaut A., Penadés J.R. and Fitzgerald J.R. (2010)
Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biol Evol. 2:454-66.
PubMed
 
Bernal P., Lemaire S., Pinho M.G., Mobashery S., Hinds J. and Taylor P.W. (2010)
Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2A-mediated {beta}-lactam resistance by delocalizing PBP2. J Biol Chem. 285(31):24055-65.
PubMed
 
Stegger M., Lindsay J.A., Sørum M., Gould K.A. and Skov R. (2010)
Genetic diversity in CC398 methicillin-resistant Staphylococcus aureus of different geographic origin. Clin Microbiol Infect. 16(7):1017-9.
PubMed
 
Li A.H., Waddell S.J., Hinds J., Malloff C.A., Bains M., Hancock R.E., Lam W.L., Butcher P.D. and Stokes R.W. (2010)
Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages. PLoS One. 5(6):e11066.
PubMed
 
Douillard F.P., Ryan K.A., Lane M.C., Caly D.L., Moore S.A., Penn C.W., Hinds J., O'Toole P.W. (2010)
The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori. BMC Microbiol. 10:106.
PubMed
 
Smith K., Gould K.A., Ramage G., Gemmell C.G., Hinds J. and Lang S. (2010)
Influence of tigecycline on expression of virulence factors in biofilm-associated cells of methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother. 54(1):380-7.
PubMed

2009
 
Bull T.J., Linedale R., Hinds J. and Hermon-Taylor J. (2009)
A rhodanine agent active against non-replicating intracellular Mycobacterium avium subspecies paratuberculosis. Gut Pathog. 1:25.
PubMed
 
Bortoni M.E., Terra V.S., Hinds J., Andrew P.W., and Yesilkaya H. (2009)
The pneumococcal response to oxidative stress includes a role for Rgg. Microbiology. 155(12):4123-34.
PubMed
 
Larsen A.R., Goering R., Stegger M., Lindsay J.A., Gould K.A., Hinds J., Sørum M., Westh H., Boye K. and Skov R. (2009)
Two distinct clones of methicillin-resistant Staphylococcus aureus (MRSA) with the same USA300 pulsed-field gel electrophoresis profile: a potential pitfall for identification of USA300 community-associated MRSA. J Clin Microbiol. 47(11):3765-8.
PubMed
 
Goldstone R.M., Goonesekera S.D., Bloom B.R. and Sampson SL. (2009)
The transcriptional regulator Rv0485 modulates the expression of a pe/ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect Immun. 77(10):4654-67.
PubMed
 
Vautor E., Cockfield J., Le Marechal C., Le Loir Y., Chevalier M., Robinson D.A., Thiery R. and Lindsay J. (2009)
Difference in virulence between Staphylococcus aureus isolates causing gangrenous mastitis versus subclinical mastitis in a dairy sheep flock. Vet Res. 40(6):56.
PubMed
 
O'Dwyer C.A., Li M.S., Langford P.R. and Kroll J.S. (2009)
Meningococcal biofilm growth on an abiotic surface - a model for epithelial colonization? Microbiology.155(6):1940-52.
PubMed
 
Douillard F.P., Ryan K.A., Hinds J. and O'Toole P.W. (2009)
Effect of FliK mutation on the transcriptional activity of the σ54 sigma factor RpoN in Helicobacter pylori. Microbiology. 155(6):1901-11.
PubMed
 
Corcionivoschi N., Clyne M., Lyons A., Elmi A., Gundogdu O., Wren B.W., Dorrell N., Karlyshev A.V. and Bourke B. (2009)
Campylobacter jejuni cocultured with epithelial cells reduces surface capsular polysaccharide expression. Infect Immun. 77(5):1959-67.
PubMed
 
Doyle M., Feuerbaum E.A., Fox K.R., Hinds J., Thurston D.E. and Taylor PW. (2009)
Response of Staphylococcus aureus to subinhibitory concentrations of a sequence-selective, DNA minor groove cross-linking pyrrolobenzodiazepine dimer. J Antimicrob Chemother. 64(5):949-59.
PubMed
 
Makarov V., Manina G., Mikusova K., Möllmann U., Ryabova O., Saint-Joanis B., Dhar N., Pasca M.R., Buroni S., Lucarelli A.P., Milano A., De Rossi E., Belanova M., Bobovska A., Dianiskova P., Kordulakova J., Sala C., Fullam E., Schneider P., McKinney J.D., Brodin P., Christophe T., Waddell S., Butcher P., Albrethsen J., Rosenkrands I., Brosch R., Nandi V., Bharath S., Gaonkar S., Shandil R.K., Balasubramanian V., Balganesh T., Tyagi S., Grosset J., Riccardi G. and Cole S.T. (2009)
Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis. Science. 324(5928):801-4.
PubMed
 
Kenny J.G., Ward D., Josefsson E., Jonsson I.M., Hinds J., Rees H.H., Lindsay J.A., Tarkowski A. and Horsburgh M.J. (2009)
The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications. PLoS One. 4(2):e4344.
PubMed
 
O'Neill A.J., Lindsay J.A., Gould K., Hinds J. and Chopra I. (2009)
Transcriptional signature following inhibition of early-stage cell wall biosynthesis in Staphylococcus aureus. Antimicrob Agents Chemother. 53(4):1701-4.
PubMed
 
Beste D.J., Espasa M., Bonde B., Kierzek A.M., Stewart G.R. and McFadden J. (2009)
The genetic requirements for fast and slow growth in mycobacteria. PLoS One. 4(4):e5349.
PubMed
 
Castellanos E., Aranaz A., Gould K.A., Linedale R., Stevenson K., Alvarez J., Dominguez L., de Juan L., Hinds J. and Bull T.J. (2009)
Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis. Appl Environ Microbiol. 75(3):676-86.
PubMed
 
Garcia Pelayo M.C., Garcia J.N., Golby P., Pirson C., Ewer K., Vordermeier M., Hewinson R.G. and Gordon S.V. (2009)
Gene expression profiling and antigen mining of the tuberculin production strain Mycobacterium bovis AN5. Vet Microbiol. 133(3):272-7.
PubMed
 
Li M.S., Chow N.Y., Sinha S., Halliwell D., Finney M., Gorringe A.R., Watson M.W., Kroll J.S., Langford P.R. and Webb S.A. (2009)
A Neisseria meningitidis NMB1966 mutant is impaired for invasion of respiratory epithelial cells, survival in human blood and for virulence in vivo. Med Microbiol Immunol. 198(1):57-67.
PubMed
 
Phan M.D., Kidgell C., Nair S., Holt K.E., Turner A.K., Hinds J., Butcher P., Cooke F.J., Thomson N.R., Titball R., Bhutta Z.A., Hasan R., Dougan G. and Wain J. (2008)
Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever. Antimicrob Agents Chemother. 53(2):716-27.
PubMed
 
Axler-DiPerte G.L., Hinchliffe S.J., Wren B.W., Darwin A.J. (2009)
YtxR acts as an overriding transcriptional off switch for the Yersinia enterocolitica Ysc-Yop type 3 secretion system. J Bacteriol. 191(2):514-24.
PubMed

2008
 
O'Sullivan D.M., Hinds J., Butcher P.D., Gillespie S.H. and McHugh T.D. (2008)
Mycobacterium tuberculosis DNA repair in response to subinhibitory concentrations of ciprofloxacin. J. Antimicrob. Chemother. 62(6):1199-202.
PubMed
 
Douillard F.P., Ryan K.A., Caly D.L., Hinds J., Witney A.A., Husain S.E. and O'Toole P.W. (2008)
Post-transcriptional regulation of flagellin synthesis in Helicobacter pylori by the RpoN chaperone HP0958. J. Bacteriol. 190(24):7975-84.
PubMed
 
Stabler R.A., Dawson L.F., Oyston P.C., Titball R.W., Wade J., Hinds J., Witney A.A. and Wren B.W. (2008)
Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux. BMC Microbiol. 8(1):177.
PubMed
 
Sung J.M., Lloyd D.H. and Lindsay J.A. (2008)
Staphylococcus aureus host specificity: comparative genomics of human versus animal isolates by multi-strain microarray. Microbiology. 154(7):1949-59.
PubMed
 
Andreu N and Gibert I. (2008)
Cell population heterogeneity in Mycobacterium tuberculosis H37Rv. Tuberculosis 88(6):553-9.
PubMed
 
Emerson J. E., Stabler R. A., Wren B. W. and Fairweather N. F. (2008)
Microarray analysis of the transcriptional responses of Clostridium difficile to environmental and antibiotic stress. J Med Microbiol. 57(6):757-764/
PubMed
 
Hunt D.M., Saldanha J.W., Brennan J.F., Benjamin P., Strom M., Cole J.A., Spreadbury C.L. and Buxton R.S. (2008)
Single nucleotide polymorphisms that cause structural changes in the cyclic AMP receptor protein transcriptional regulator of the tuberculosis vaccine strain Mycobacterium bovis BCG alter global gene expression without attenuating growth. Infect Immun. 76(5):2227-34.
PubMed
 
Stavrum R., Valvatne H., Bø T.H., Jonassen I., Hinds J., Butcher P.D. and Grewal H.M. (2008)
Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar. PLoS ONE. 3(4):e1973.
PubMed
 
Garton N.J., Waddell S.J., Sherratt A.L., Lee S.M., Smith R.J., Senner C., Hinds J., Rajakumar K., Adegbola R.A., Besra G.S., Butcher P.D. and Barer M.R. (2008)
Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum. PLoS Med. 5(4):e75.
PubMed
 
Hinchliffe S.J., Howard S.L., Huang Y.H., Clarke D.J. and Wren B.W. (2008)
The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae. Microbiology. 154(4):1117-31.
PubMed
 
Golby P., Nunez J., Cockle P.J., Ewer K., Logan K., Hogarth P., Vordermeier H.M., Hinds J., Hewinson R.G. and Gordon S.V. (2008)
Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology 154(4):1059-67.
PubMed
 
Waddell S.J., Laing K., Senner C. and Butcher P.D. (2008)
Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies. BMC Genomics 9:94.
PubMed
 
Zhang Y., Hatch K.A., Wernisch L. and Bacon J. (2008)
A Bayesian change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis. BMC Genomics. 9:87.
PubMed
 
Tailleux L., Waddell S.J., Pelizzola M., Mortellaro A., Withers M., Tanne A., Castagnoli P.R., Gicquel B., Stoker N.G., Butcher P.D., Foti M. and Neyrolles O. (2008)
Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE 3(1):e1403.
PubMed

2007
 
Sidders B., Withers M., Kendall S.L., Bacon J., Waddell S.J., Hinds J., Golby P., Movahedzadeh F., Cox R.A., Frita R., Ten Bokum A.M., Wernisch L. and Stoker N.G. (2007)
Quantification of global transcription patterns in prokaryotes using spotted microarrays. Genome Biol. 8(12):R265.
PubMed
 
Campbell D.R., Chapman K.E., Waldron K.J., Tottey S., Kendall S., Cavallaro G., Andreini C., Hinds J., Stoker N.G., Robinson N.J. and Cavet J.S. (2007)
Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J Biol Chem. 282(44):32298-310.
PubMed
 
Golby P., Hatch K.A., Bacon J., Cooney R., Riley P., Allnutt J., Hinds J., Nunez J., Marsh P.D., Hewinson R.G. and Gordon S.V. (2007)
Comparative transcriptomics reveals key gene expression differences between the human and bovine pathogens of the Mycobacterium tuberculosis complex. Microbiology 153(10):3323-36.
PubMed
 
Cathelyn J.S., Ellison D.W., Hinchliffe S.J., Wren B.W. and Miller V.L. (2007)
The RovA regulons of Yersinia enterocolitica and Yersinia pestis are distinct: evidence that many RovA-regulated genes were acquired more recently than the core genome. Mol Microbiol. 2007 66(1):189-205.
PubMed
 
Tang C.T., Nguyen D.T., Ngo T.H., Nguyen T.M., Le V.T., To S.D., Lindsay J., Nguyen T.D., Bach V.C., Le Q.T., Le T.H., Le D.L., Campbell J., Nguyen T.K., Nguyen VV., Cockfield J., Le T.G., Phan V.N., Le H.S., Huynh T.S., Le V.P., Counahan M., Bentsi-Enchill A., Brown R., Simmerman J., Nguyen T.C., Tran T.H., Farrar J. and Schultsz C. (2007)
An outbreak of severe infections with community-acquired MRSA carrying the Panton-Valentine leukocidin following vaccination. PLoS ONE 2(9):e822.
PubMed
 
Kamal N., Dorrell N., Jagannathan A., Turner S.M., Constantinidou C., Studholme D.J., Marsden G., Hinds J., Laing K.G., Wren B.W. and Penn C.W. (2007)
Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni. Microbiology 153(9):3099-111.
PubMed
 
Kendall S.L., Withers M., Soffair C.N., Moreland N.J., Gurcha S., Sidders B., Frita R., Ten Bokum A., Besra G.S., Lott J.S. and Stoker N.G. (2007)
A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol Microbiol. 65(3):684-99.
PubMed
 
Menéndez M.C., Buxton R.S., Evans J.T., Gascoyne-Binzi D., Barlow R.E., Hinds J., Hawkey P.M. and Colston M.J. (2007)
Genome analysis shows a common evolutionary origin for the dominant strains of Mycobacterium tuberculosis in a UK South Asian community. Tuberculosis 87(5):426-36.
PubMed
 
Standish A.J., Stroeher U.H. and Paton J.C. (2007)
The pneumococcal two-component signal transduction system RR/HK06 regulates CbpA and PspA by two distinct mechanisms. J Bacteriol. 189(15):5591-600.
PubMed
 
Garbom S., Olofsson M., Björnfot A.C., Srivastava M.K., Robinson V.L., Oyston P.C., Titball R.W. and Wolf-Watz H. (2007)
Phenotypic characterization of a virulence-associated protein, VagH, of Yersinia pseudotuberculosis reveals a tight link between VagH and the type III secretion system. Microbiology. 153(5):1464-73.
PubMed
 
Waddell S.J., Butcher P.D. and Stoker N.G. (2007)
RNA profiling in host-pathogen interactions. Curr Opin Microbiol. 10(3):297-302.
PubMed
 
Beste D.J., Laing E., Bonde B., Avignone-Rossa C., Bushell M.E. and McFadden J.J. (2007)
Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage. J Bacteriol. 189(11):3969-76.
PubMed
 
Waddell S.J and Butcher P.D. (2007)
Microarray analysis of whole genome expression of intracellular Mycobacterium tuberculosis. Curr Mol Med. 7(3):287-96.
PubMed
 
Bacon J., Dover L.G., Hatch K.A., Zhang Y., Gomes J.M., Kendall S., Wernisch L., Stoker N.G., Butcher P.D., Besra G.S. and Marsh P.D. (2007)
Lipid composition and transcriptional response of Mycobacterium tuberculosis grown under iron-limitation in continuous culture: identification of a novel wax ester. Microbiology. 153(5):1435-44.
PubMed
 
Brosch R., Gordon S.V., Garnier T., Eiglmeier K., Frigui W., Valenti P., Dos Santos S., Duthoy S., Lacroix C., Garcia-Pelayo C., Inwald J.K., Golby P., Garcia J.N., Hewinson R.G., Behr M.A., Quail M.A., Churcher C., Barrell B.G., Parkhill J. and Cole S.T. (2007)
Genome plasticity of BCG and impact on vaccine efficacy. Proc Natl Acad Sci USA. 104(13):5596-601.
PubMed
 
Cuccui J., Easton A., Chu K.K., Bancroft G.J., Oyston P.C., Titball R.W. and Wren B.W. (2007)
Development of signature-tagged mutagenesis in Burkholderia pseudomallei to identify genes important in survival and pathogenesis. Infect Immun. 75(3):1186-95.
PubMed
 
Bennett H.J., Pearce D.M., Glenn S., Taylor C.M., Kuhn M., Sonenshein A.L., Andrew P.W. and Roberts I.S. (2007)
Characterization of relA and codY mutants of Listeria monocytogenes: identification of the CodY regulon and its role in virulence. Mol Microbiol. 63(5):1453-67.
PubMed
 
Edgeworth J.D., Yadegarfar G., Pathak S., Batra R., Cockfield J.D., Wyncoll D., Beale R. and Lindsay J.A. (2007)
An outbreak in an intensive care unit of a strain of methicillin-resistant Staphylococcus aureus sequence type 239 associated with an increased rate of vascular access device-related bacteremia. Clin Infect Dis. 44(4):493-501.
PubMed

2006
 
Newton R., Hinds J. and Wernisch L. (2006)
A hidden markov model web application for analysing bacterial genomotyping DNA microarray experiments. Appl. Bioinformatics. 5(4):211-8.
PubMed
 
On S.L., Dorrell N., Petersen L., Bang D.D., Morris S., Forsythe S.J. and Wren B.W. (2006)
Numerical analysis of DNA microarray data of Campylobacter jejuni strains correlated with survival, cytolethal distending toxin and haemolysin analyses. Int J Med Microbiol. 296(6):353-63.
PubMed
 
Stabler R.A., Gerding D.N., Songer J.G., Drudy D., Brazier J.S., Trinh H.T., Witney A.A., Hinds J. and Wren B.W. (2006)
Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol. 188(20):7297-305.
PubMed
 
Sebaihia M., Wren B.W., Mullany P., Fairweather N.F., Minton N., Stabler R., Thomson N.R., Roberts A.P., Cerdeño-Tárraga A.M., Wang H., Holden M.T., Wright A., Churcher C., Quail M.A., Baker S., Bason N., Brooks K., Chillingworth T., Cronin A., Davis P., Dowd L., Fraser A., Feltwell T., Hance Z., Holroyd S., Jagels K., Moule S., Mungall K., Price C., Rabbinowitsch E., Sharp S., Simmonds M., Stevens K., Unwin L., Whithead S., Dupuy B., Dougan G., Barrell B. and Parkhill J. (2006)
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet. 38(7):779-86.
PubMed
 
O'Connor J.R., Lyras D., Farrow K.A., Adams V., Powell D.R., Hinds J., Cheung J.K. and Rood J.I. (2006)
Construction and analysis of chromosomal Clostridium difficile mutants. Mol Microbiol. 61(5):1335-51.
PubMed
 
Stabler R. and Hinds J. (2006)
The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as virulence genes: response. BMC Genomics. 7(1):129.
PubMed
 
Silva N.A., McCluskey J., Jefferies J.M., Hinds J., Smith A., Clarke S.C., Mitchell T.J., Paterson G.K. (2006)
Genomic diversity between strains of the same serotype and multilocus sequence type among pneumococcal clinical isolates. Infect Immun. 74(6):3513-8.
PubMed
 
Howard S.L., Gaunt M.W., Hinds J., Witney A.A., Stabler R. and Wren B.W. (2006)
Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J Bact. 188(10) 3645-53.
PubMed
 
Lindsay J.A., Moore C.E., Day N.P., Peacock S.J., Witney A.A., Stabler R.A., Husain S.E., Butcher P.D. and Hinds J. (2006)
Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes. J. Bact. 188(2) 669-76.
PubMed
 
Brodin P., Majlessi L., Marsollier L., de Jonge MI., Bottai D., Demangel C., Hinds J., Neyrolles O., Butcher P.D., Leclerc C., Cole S.T. and Brosch R. (2006)
Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence. Infect. Immun. 74(1) 88-98.
PubMed

2005
 
Witney A.A., Marsden G.L., Holden M.T.G., Stabler R.A., Husain S.E., Vass J.K., Butcher P.D. Hinds J., and Lindsay J.A. (2005)
Design, validation and application of a seven strain Staphylococcus aureus microarray for comparative genomics. Appl. Environ. Microbiol. 71(11) 7504-14.
PubMed
 
Champion O.L., Gaunt M.W., Gundogdu O., Elmi A., Witney A.A., Hinds J., Dorrell N., Wren B.W. (2005)
Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc Natl Acad Sci U S A. Oct 17; [Epub ahead of print]
PubMed
 
Stabler R.A., Marsden G.L., Witney A.A., Li Y., Bentley S.D., Tang C.M., Hinds J. (2005)
Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species. Microbiology. 151(9) 2907-22.
PubMed
 
Elvers K.T., Turner S.M., Wainwright L.M., Marsden G.L., Hinds J., Cole J.A., Poole R.K., Penn C.W. and Park S.F. (2005)
NssR, a member of the Crp-Fnr superfamily from Campylobacter jejuni, regulates a nitrosative stress-responsive regulon that includes both a single-domain and a truncated haemoglobin. Mol. Microbiol. 57(3) 735-50.
PubMed
 
Woodall C.A., Jones M.A., Barrow P.A., Kelly D.J., Marsden G.L., Hinds J., Dorrell N., Wren B.W. and Maskell D.J. (2005)
Campylobacter jejuni gene expression in chick cecum: evidence for adaptation to a low oxygen environment. Infect. Immun. 73(8) 5278-85.
PubMed
 
Taylor V.L., Titball R.W. and Oyston P.C. (2005)
Oral immunization with a dam mutant of Yersinia pseudotuberculosis protects against plague. Microbiology 151(6) 1919-26.
PubMed
 
Newcombe J., Jeynes J.C., Mendoza E., Hinds J., Marsden G.L., Stabler R.A., Marti M., and McFadden J.J. (2005)
Phenotypic and transcriptional characterization of the meningococcal PhoPQ system, a magnesium-sensing two-component regulatory system that controls genes involved in remodeling the meningococcal cell surface J. Bact. 187(14) 4967-75.
PubMed
 
Bigi F., Garcia-Pelayo M.C., Nunez-García J., Peralta A., Caimi K.C., Golby P., Hinds J., Cataldi A., Gordon S.V. and Romano M.I. (2005)
Identification of genetic markers for Mycobacterium pinnipedii through genome analysis. FEMS Microbiol. Lett. 248(2) 147-52.
PubMed
 
Rickman L.l., Scott C., Hunt D.M., Hutchinson T., Menendez M.C., Whalan R., Hinds J., Colston M.J., Green J. and Buxton R.S. (2005)
A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor. Mol. Microbiol. 56(5) 1274-86.
PubMed
 
Moen B., Oust A., Langsrud O., Dorrell N., Marsden G.L., Hinds J., Kohler A., Wren B.W. and Rudi K. (2005)
Explorative multifactor approach for investigating global survival mechanisms of Campylobacter jejuni under environmental conditions. Appl. Environ. Microbiol. 71(4) 2086-94.
PubMed
 
Redfield R.J., Cameron A.D., Qian Q., Hinds J., Ali T.R., Kroll J.S. and Langford P.R. (2005)
A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae. J. Mol. Biol. 347(4) 735-47.
PubMed

2004
 
Boriskin Y.S., Rice P.S., Stabler R.A., Hinds J., Al-Ghusein H., Vass K. and Butcher P.D. (2004)
DNA microarrays for virus detection in cases of central nervous system infection. J. Clin. Microbiol. 42(12) 5811-8.
PubMed
 
Jones M.A., Marston K.L., Woodall C.A., Maskell D.J., Linton D., Karlyshev A.V., Dorrell N., Wren B.W. and Barrow P.A. (2004)
Adaptation of Campylobacter jejuni NCTC11168 to high-level colonization of the avian gastrointestinal tract. Infect. Immun. 72(7) 3769-76.
PubMed
 
Bacon J., James B.W., Wernisch L., Williams A., Morley K.A., Hatch G.J., Mangan J.A., Hinds J., Stoker N.G., Butcher P.D. and Marsh P.D. (2004)
The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis. Tuberculosis. 84(3-4) 205-17.
PubMed
 
Butcher P.D. (2004)
Microarrays for Mycobacterium tuberculosis. Tuberculosis 84(3-4) 131-7.
PubMed
 
Garcia-Pelayo M.C., Caimi K.C., Inwald J.K., Hinds J., Bigi F., Romano M.I., van Soolingen D., Hewinson R.G., Cataldi A. and Gordon S.V. (2004)
Microarray analysis of Mycobacterium microti reveals deletion of genes encoding PE-PPE proteins and ESAT-6 family antigens. Tuberculosis 84(3-4) 159-66.
PubMed
 
Hampshire T., Soneji S., Bacon J., James B.W., Hinds J., Laing K., Stabler R.A., Marsh P.D. and Butcher P.D. (2004)
Stationary phase gene expression of Mycobacterium tuberculosis following a progressive nutrient depletion: a model for persistent organisms. Tuberculosis 84(3-4) 228-38.
PubMed
 
Muttucumaru D.G.N., Roberts G., Hinds J., Stabler R.A. and Parish T. (2004)
Gene expression profile of Mycobacterium tuberculosis in a non-replicating state. Tuberculosis 84(3-4) 239-46.
PubMed
 
Waddell S.J., Stabler R.A., Laing K., Kremer L., Reynolds R.C. and Besra G.S. (2004)
The use of microarray analysis to determine the gene expression profiles of Mycobacterium tuberculosis in response to anti-bacterial compounds. Tuberculosis 84(3-4) 263-74.
PubMed
 
Rajakumar K., Shafi J., Smith R.J., Stabler R.A., Andrew P.W., Modha D., Bryant G., Monk P., Hinds J., Butcher P.D. and Barer M.R. (2004)
Use of genome level-informed PCR as a new investigational approach for analysis of outbreak-associated Mycobacterium tuberculosis isolates. J. Clin. Microbiol. 42 1890-1896.
PubMed
 
Frota C.C., Hunt D.M., Buxton R.S., Rickman L., Hinds J., Kremer K., van Soolingen D. and Colston M.J. (2004)
Genome structure in the vole bacillus, Mycobacterium microti, a member of the Mycobacterium tuberculosis complex with a low virulence for humans. Microbiology 150(5) 1519-1527.
PubMed
 
McCluskey J., Hinds J., Husain S.E., Witney A.A. and Mitchell T.J. (2004)
A two-component system that controls the expression of pneumococcal surface antigen A (PsaA) and regulates virulence and resistance to oxidative stress in Streptococcus pneumoniae. Mol. Microbiol. 51(6) 1661-75.
PubMed
 
Kutalik Z., Inwald J., Gordon S.V., Hewinson R.G., Butcher P., Hinds J., Cho K.H., Wolkenhauer O. (2004)
Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis. Bioinformatics 20(3) 357-63.
PubMed

2003
 
Rand L., Hinds J., Springer B., Sander P., Buxton R.S. and Davis E.O. (2003)
The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. Mol. Microbiol. 50(3) 1031-1042.
PubMed
 
Stefanova T., Chouchkova M., Hinds J., Butcher P., Inwald J., Dale J., Palmer S., Hewinson G. and Gordon S. (2003)
Genetic composition of Mycobacterium bovis BCG substrain Sofia. J. Clin. Microbiol. 41(11) 5349.
PubMed
 
Schnappinger D., Ehrt S., Voskuil M.I., Liu Y., Mangan J.A., Monahan I.M., Dolganov G., Efron B., Butcher P.D., Nathan C. and Schoolnik G.K. (2003)
Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J. Exp. Med. 198(5) 693-704.
PubMed
 
Hinchliffe S.J., Isherwood K.E., Stabler R.A., Prentice M.B., Rakin A., Nichols R.A., Oyston P.C.F, Hinds J., Titball R.W. and Wren B.W. (2003)
Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 13(9) 2018-2029.
PubMed
 
Inwald J., Hinds J., Palmer S., Dale J., Butcher P.D., Hewinson R.G. and Gordon S.V. (2003)
Genomic analysis of Mycobacterium tuberculosis complex strains used for production of purified protein derivative. J Clin Microbiol 41(8) 3929-32.
PubMed
 
Marokhazi J., Waterfield N., LeGoff G., Feil E., Stabler R., Hinds J., Fodor A., and ffrench-Constant R.H. (2003)
Using a DNA microarray to investigate the distribution of insect virulence factors in strains of Photorhabdus bacteria. J Bacteriol 185(15) 4648-56.
PubMed
 
Stabler R.A., Hinds J., Witney A.A., Isherwood K., Oyston P., Titball R., Wren B., Hinchliffe S., Prentice M., Mangan J.A. and Butcher P.D. (2003)
Construction of a Yersinia pestis microarray. Adv Exp Med Biol. 529 47-9.
PubMed
 
Wernisch L., Kendall S.L., Soneji S., Wietzorrek A., Parish T., Hinds J., Butcher P.D. and Stoker N.G. (2003)
Analysis of whole-genome microarray replicates using mixed models. Bioinformatics 19(1) 53-61.
PubMed

2002
 
Hinds J., Witney A.A. and Vass J.K. (2002)
Microarray design for bacterial genomes, p67-82. In: Wren B.W. and Dorrell N. (eds.), Methods in Microbiology: Functional Microbial Genomics. Academic Press, London.
 
Hinds J., Laing K.G., Mangan J.A. and Butcher P.D. (2002)
Glass slide microarrays for bacterial genomes, p83-99. In: Wren B.W. and Dorrell N. (eds.), Methods in Microbiology: Functional Microbial Genomics. Academic Press, London.
 
Hinds J., Laing K.G., Mangan J.A. and Butcher P.D. (2002)
Microarrays for microbes: the BµG@S approach. Comparative and Functional Genomics 3(4) 333-337.
 
Inwald J., Hinds J., Dale J., Palmer S., Butcher P., Hewinson R.G., Gordon S.V. (2002)
Microarray-based comparative genomics: genome plasticity in Mycobacterium bovis. Comparative and Functional Genomics 3(4) 342-344.
 
Stewart G.R., Wernisch L., Stabler R., Mangan J.A., Hinds J., Laing K.G., Butcher P.D. and Young D.B. (2002)
The heat shock response of Mycobacterium tuberculosis: linking gene expression, immunology and pathogenesis. Comparative and Functional Genomics 3(4) 348-351.
 
Witney A.A. and Hinds J. (2002)
BµG@Sbase - a microarray database and analysis tool. Comparative and Functional Genomics 3(4) 369-371.
 
Stewart G.R., Wernisch L., Stabler R., Mangan J.A., Hinds J., Laing K.G., Young D.B. and Butcher P.D. (2002)
Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology 148(10) 3129-38.
PubMed

2001
 
Dorrell N., Mangan J.A., Laing K.G., Hinds J., Linton D., Al-Ghusein H., Barrell B.G., Parkhill J., Stoker N.G., Karlyshev A.V., Butcher P.D. and Wren B.W. (2001)
Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Research 11(10) 1706-15.
PubMed