Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J, Sebaihia M, Coulthurst SJ, Gotoh N, Thomson NR, Ewbank JJ, Hayashi T (2014) <br />Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen<br /><i>Genome Biol Evol</i> <b>6</b>: 2096<br /><br />Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcao JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR (2014) <br />Parallel independent evolution of pathogenicity within the genus Yersinia<br /><i>Proc Natl Acad Sci U S A</i> <b>111</b>: 6768<br /><br />Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR, Phiri A, Hall N, Gordon MA, Wain J, Hart CA, Wigley P, Thomson NR, Winstanley C (2013) <br />Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi<br /><i>PLoS Negl Trop Dis</i> <b>7</b>: e2557<br /><br />Dziva F, Hauser H, Connor TR, van Diemen PM, Prescott G, Langridge GC, Eckert S, Chaudhuri RR, Ewers C, Mellata M, Mukhopadhyay S, Curtiss R, 3rd, Dougan G, Wieler LH, Thomson NR, Pickard DJ, Stevens MP (2013) <br />Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms<br /><i>Infect Immun</i> <b>81</b>: 838<br /><br />Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT, Thomson NR (2013) <br />Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts<br /><i>Science</i> <b>341</b>: 1514<br /><br />Kroger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hebrard M, Handler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC (2012) <br />The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium<br /><i>Proc Natl Acad Sci U S A</i> <b>109</b>: E1277<br /><br />Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M, Petty NK, Kingsley RA, Baumler AJ, Nuccio SP, Contreras I, Santiviago CA, Maskell D, Barrow P, Humphrey T, Nastasi A, Roberts M, Frankel G, Parkhill J, Dougan G, Thomson NR (2011) <br />Salmonella bongori provides insights into the evolution of the Salmonellae<br /><i>PLoS Pathog</i> <b>7</b>: e1002191<br /><br />Richardson EJ, Limaye B, Inamdar H, Datta A, Manjari KS, Pullinger GD, Thomson NR, Joshi RR, Watson M, Stevens MP (2011) <br />Genome sequences of Salmonella enterica serovar typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well- defined virulence in food-producing animals<br /><i>Journal of Bacteriology</i> <b>193</b>: 3162<br /><br />Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM, Frankel G, Tang CM, Dudley EG, Roberts IS, Rasko DA, Pallen MJ, Parkhill J, Nataro JP, Thomson NR, Henderson IR (2010) <br />Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042<br /><i>PLoS ONE</i> <b>5</b>: e8801<br /><br />Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL, Savarino SJ, Turner SM, Pallen MJ, Penn CW, Parkhill J, Turner AK, Johnson TJ, Thomson NR, Smith SG, Henderson IR (2010) <br />A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407<br /><i>Journal of Bacteriology</i> <b>192</b>: 5822<br /><br />Petty NK, Bulgin R, Crepin VF, Cerdeno-Tarraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A, Clark L, Toribio AL, Parkhill J, Dougan G, Frankel G, Thomson NR (2010) <br />The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli<br /><i>Journal of Bacteriology</i> <b>192</b>: 525<br /><br />Schroeder GN, Petty NK, Mousnier A, Harding CR, Vogrin AJ, Wee B, Fry NK, Harrison TG, Newton HJ, Thomson NR, Beatson SA, Dougan G, Hartland EL, Frankel G (2010) <br />Legionella pneumophila strain 130b possesses a unique combination of type IV secretion systems and novel Dot/Icm secretion system effector proteins<br /><i>Journal of Bacteriology</i> <b>192</b>: 6001<br /><br />Unemo M, Seth-Smith HM, Cutcliffe LT, Skilton RJ, Barlow D, Goulding D, Persson K, Harris SR, Kelly A, Bjartling C, Fredlund H, Olcen P, Thomson NR, Clarke IN (2010) <br />The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization<br /><i>Microbiology</i> <b>156</b>: 1394<br /><br />Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeno-Tarraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J (2009) <br />The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients<br /><i>Journal of Bacteriology</i> <b>191</b>: 261<br /><br />Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Simmonds M, White B, Bason N, Mungall K, Dougan G, Parkhill J (2009) <br />Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi<br /><i>BMC Genomics</i> <b>10</b>: 36<br /><br />Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P, Kenny B, Quail MA, Thurston S, Dougan G, Hayashi T, Parkhill J, Frankel G (2009) <br />Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69<br /><i>Journal of Bacteriology</i> <b>191</b>: 347<br /><br />Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE, Gordon MA, Harris D, Clarke L, Whitehead S, Sangal V, Marsh K, Achtman M, Molyneux ME, Cormican M, Parkhill J, MacLennan CA, Heyderman RS, Dougan G (2009) <br />Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype<br /><i>Genome Res</i> <b>19</b>: 2279<br /><br />Seth-Smith HM, Harris SR, Persson K, Marsh P, Barron A, Bignell A, Bjartling C, Clark L, Cutcliffe LT, Lambden PR, Lennard N, Lockey SJ, Quail MA, Salim O, Skilton RJ, Wang Y, Holland MJ, Parkhill J, Thomson NR, Clarke IN (2009) <br />Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain<br /><i>BMC Genomics</i> <b>10</b>: 239<br /><br />Silby MW, Cerdeno-Tarraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR (2009) <br />Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens<br /><i>Genome Biol</i> <b>10</b>: R51<br /><br />Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, Thomson NR, Winsor GL, Quail MA, Lennard N, Bignell A, Clarke L, Seeger K, Saunders D, Harris D, Parkhill J, Hancock RE, Brinkman FS, Levesque RC (2009) <br />Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa<br /><i>Genome Res</i> <b>19</b>: 12<br /><br />Crossman LC, Gould VC, Dow JM, Vernikos GS, Okazaki A, Sebaihia M, Saunders D, Arrowsmith C, Carver T, Peters N, Adlem E, Kerhornou A, Lord A, Murphy L, Seeger K, Squares R, Rutter S, Quail MA, Rajandream MA, Harris D, Churcher C, Bentley SD, Parkhill J, Thomson NR, Avison MB (2008) <br />The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants<br /><i>Genome Biol</i> <b>9</b>: R74<br /><br />Hjerde E, Lorentzen MS, Holden MT, Seeger K, Paulsen S, Bason N, Churcher C, Harris D, Norbertczak H, Quail MA, Sanders S, Thurston S, Parkhill J, Willassen NP, Thomson NR (2008) <br />The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay<br /><i>BMC Genomics</i> <b>9</b>: 616<br /><br />Pearson MM, Sebaihia M, Churcher C, Quail MA, Seshasayee AS, Luscombe NM, Abdellah Z, Arrosmith C, Atkin B, Chillingworth T, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Walker D, Whithead S, Thomson NR, Rather PN, Parkhill J, Mobley HL (2008) <br />Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility<br /><i>Journal of Bacteriology</i> <b>190</b>: 4027<br /><br />Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J (2008) <br />The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates<br /><i>Journal of Bacteriology</i> <b>190</b>: 6881<br /><br />Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M, Barron A, Layton A, Pickard D, Kingsley RA, Bignell A, Clark L, Harris B, Ormond D, Abdellah Z, Brooks K, Cherevach I, Chillingworth T, Woodward J, Norberczak H, Lord A, Arrowsmith C, Jagels K, Moule S, Mungall K, Sanders M, Whitehead S, Chabalgoity JA, Maskell D, Humphrey T, Roberts M, Barrow PA, Dougan G, Parkhill J (2008) <br />Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways<br /><i>Genome Res</i> <b>18</b>: 1624<br /><br />Thomson NR, Holden MT, Carder C, Lennard N, Lockey SJ, Marsh P, Skipp P, O'Connor CD, Goodhead I, Norbertzcak H, Harris B, Ormond D, Rance R, Quail MA, Parkhill J, Stephens RS, Clarke IN (2008) <br />Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates<br /><i>Genome Res</i> <b>18</b>: 161<br /><br />Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman L, Paul CJ, Ivens A, Wells-Bennik MH, Davis IJ, Cerdeno-Tarraga AM, Churcher C, Quail MA, Chillingworth T, Feltwell T, Fraser A, Goodhead I, Hance Z, Jagels K, Larke N, Maddison M, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, White B, Whithead S, Parkhill J (2007) <br />Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes<br /><i>Genome Res</i> <b>17</b>: 1082<br /><br />Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006) <br />Escherichia coli K-12: a cooperatively developed annotation snapshot--2005<br /><i>Nucleic Acids Research</i> <b>34</b>: 1<br /><br />Sebaihia M, Preston A, Maskell DJ, Kuzmiak H, Connell TD, King ND, Orndorff PE, Miyamoto DM, Thomson NR, Harris D, Goble A, Lord A, Murphy L, Quail MA, Rutter S, Squares R, Squares S, Woodward J, Parkhill J, Temple LM (2006) <br />Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction<br /><i>Journal of Bacteriology</i> <b>188</b>: 6002<br /><br />Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeno-Tarraga AM, Wang H, Holden MT, Wright A, Churcher C, Quail MA, 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, Parkhill J (2006) <br />The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome<br /><i>Nat Genet</i> <b>38</b>: 779<br /><br />Thomson NR, Howard S, Wren BW, Holden MT, Crossman L, Challis GL, Churcher C, Mungall K, Brooks K, Chillingworth T, Feltwell T, Abdellah Z, Hauser H, Jagels K, Maddison M, Moule S, Sanders M, Whitehead S, Quail MA, Dougan G, Parkhill J, Prentice MB (2006) <br />The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081<br /><i>PLoS Genet</i> <b>2</b>: e206<br /><br />Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J (2006) <br />The genome of Rhizobium leguminosarum has recognizable core and accessory components<br /><i>Genome Biol</i> <b>7</b>: R34<br /><br />Collins NE, Liebenberg J, de Villiers EP, Brayton KA, Louw E, Pretorius A, Faber FE, van Heerden H, Josemans A, van Kleef M, Steyn HC, van Strijp MF, Zweygarth E, Jongejan F, Maillard JC, Berthier D, Botha M, Joubert F, Corton CH, Thomson NR, Allsopp MT, Allsopp BA (2005) <br />The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number<br /><i>Proc Natl Acad Sci U S A</i> <b>102</b>: 838<br /><br />Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD, Livingstone M, Cerdeno-Tarraga AM, Harris B, Doggett J, Ormond D, Mungall K, Clarke K, Feltwell T, Hance Z, Sanders M, Quail MA, Price C, Barrell BG, Parkhill J, Longbottom D (2005) <br />The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation<br /><i>Genome Res</i> <b>15</b>: 629<br /><br />Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Norbertczak H, Ormond D, Price C, Quail MA, Sanders M, Walker D, Whitehead S, Salmond GP, Birch PR, Parkhill J, Toth IK (2004) <br />Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors<br /><i>Proc Natl Acad Sci U S A</i> <b>101</b>: 11105<br /><br />Holden MT, Titball RW, Peacock SJ, Cerdeno-Tarraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J (2004) <br />Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei<br /><i>Proc Natl Acad Sci U S A</i> <b>101</b>: 14240<br /><br />Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A, Chillingworth T, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Quail MA, Rabbinowitsch E, Rutherford KM, Thomson NR, Unwin L, Whitehead S, Barrell BG, Parkhill J (2003) <br />The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129<br /><i>Nucleic Acids Research</i> <b>31</b>: 6516<br /><br />Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) <br />Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)<br /><i>Nature</i> <b>417</b>: 141<br /><br />Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG (2001) <br />Massive gene decay in the leprosy bacillus<br /><i>Nature</i> <b>409</b>: 1007<br /><br />Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MTG, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeno-Tarraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PCF, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (2001) <br />Genome sequence of Yersinia pestis, the causative agent of plague.<br /><i>Nature</i> <b>413</b>: 523<br /><br />Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (2001) <br />Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18<br /><i>Nature</i> <b>413</b>: 848<br /><br />