Parkhill J

References (78)

Title : Stepwise pathogenic evolution of Mycobacterium abscessus - Bryant_2021_Science_372_
Author(s) : Bryant JM , Brown KP , Burbaud S , Everall I , Belardinelli JM , Rodriguez-Rincon D , Grogono DM , Peterson CM , Verma D , Evans IE , Ruis C , Weimann A , Arora D , Malhotra S , Bannerman B , Passemar C , Templeton K , MacGregor G , Jiwa K , Fisher AJ , Blundell TL , Ordway DJ , Jackson M , Parkhill J , Floto RA
Ref : Science , 372 : , 2021
PubMedID: 33926925

Title : Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera - Sun_2015_Nat.Commun_6_8322
Author(s) : Sun Z , Harris HM , McCann A , Guo C , Argimon S , Zhang W , Yang X , Jeffery IB , Cooney JC , Kagawa TF , Liu W , Song Y , Salvetti E , Wrobel A , Rasinkangas P , Parkhill J , Rea MC , O'Sullivan O , Ritari J , Douillard FP , Paul Ross R , Yang R , Briner AE , Felis GE , de Vos WM , Barrangou R , Klaenhammer TR , Caufield PW , Cui Y , Zhang H , O'Toole PW
Ref : Nat Commun , 6 :8322 , 2015
PubMedID: 26415554
Gene_locus related to this paper: 9laco-a0a0r1hz65 , 9laco-a0a0r1j1t4 , 9laco-a0a0r1j3p0 , 9laco-a0a0r1k3i0 , 9laco-a0a0r1k563 , 9laco-a0a0r1kgb3 , 9laco-a0a0r1kji2 , 9laco-a0a0r1kwq5 , 9laco-a0a0r1l700 , 9laco-a0a0r1p6l8 , 9laco-a0a0r1q939 , 9laco-a0a0r1qv39 , 9laco-a0a0r1wj75 , laccl-a0a0r2bne3 , 9laco-a0a0r2dnk9 , 9laco-a0a0r2ds70 , 9laco-a0a0r2k127 , 9laco-a0a0r2lee7 , 9laco-a0a0r2lqt2 , 9laco-a0a0r2m354 , 9laco-a0a0r2n9f2 , 9laco-a0a0r2nrk2 , lacze-a0a0r1ekw6 , 9laco-a0a0r1ju11 , 9laco-a0a0r1k516 , 9laco-a0a0r1leq9 , 9laco-a0a0r1lul8 , 9laco-a0a0r1lzg4 , 9laco-a0a0r1mhp8 , 9laco-a0a0r1mjt1 , 9laco-a0a0r1nv21 , 9laco-a0a0r1q1p6 , 9laco-a0a0r1qm41 , 9laco-a0a0r1qs58 , 9laco-a0a0r1rgu0 , 9laco-a0a0r1tg12 , 9laco-a0a0r1u777 , 9laco-a0a0r1ufv3 , 9laco-a0a0r1ul77 , 9laco-a0a0r1vad0 , 9laco-a0a0r1w3f4 , 9laco-a0a0r1w9r8 , 9laco-a0a0r1wpq2 , 9laco-a0a0r1x2g3 , 9laco-a0a0r2abe6 , 9laco-a0a0r2b6w1 , 9laco-a0a0r2b8g1 , 9laco-a0a0r2ch10 , 9laco-a0a0r2cld6 , 9laco-a0a0r2cv38 , 9laco-a0a0r2d3x3 , 9laco-a0a0r2dct2 , 9laco-a0a0r2flt3 , 9laco-a0a0r2frk5 , 9laco-a0a0r2guq4 , 9firm-a0a0r2h5m0 , weivi-a0a0r2h8r4 , 9lact-a0a0r2hnx4 , 9lact-a0a0r2jkt6 , 9lact-a0a0r2jmz1 , 9laco-a0a0r2jwg5 , 9laco-a0a0r2jxu0 , 9laco-a0a0r2jxw0 , lacam-a0a0r2kgt3 , 9laco-a0a0r2kx86 , 9laco-a0a0r2mxi6 , 9laco-a0a0r1vln2 , 9laco-a0a0r2ca25 , 9laco-a0a0r1zjs2 , weipa-c5rbw8

Title : Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen - Iguchi_2014_Genome.Biol.Evol_6_2096
Author(s) : 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
Ref : Genome Biol Evol , 6 :2096 , 2014
PubMedID: 25070509
Gene_locus related to this paper: serma-a0a031rry9 , serma-a0a0a5sc46

Title : Parallel independent evolution of pathogenicity within the genus Yersinia - Reuter_2014_Proc.Natl.Acad.Sci.U.S.A_111_6768
Author(s) : 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
Ref : Proc Natl Acad Sci U S A , 111 :6768 , 2014
PubMedID: 24753568
Gene_locus related to this paper: yeren-k1bwy7

Title : A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic - Holden_2013_Genome.Res_23_653
Author(s) : Holden MT , Hsu LY , Kurt K , Weinert LA , Mather AE , Harris SR , Strommenger B , Layer F , Witte W , de Lencastre H , Skov R , Westh H , Zemlickova H , Coombs G , Kearns AM , Hill RL , Edgeworth J , Gould I , Gant V , Cooke J , Edwards GF , McAdam PR , Templeton KE , McCann A , Zhou Z , Castillo-Ramirez S , Feil EJ , Hudson LO , Enright MC , Balloux F , Aanensen DM , Spratt BG , Fitzgerald JR , Parkhill J , Achtman M , Bentley SD , Nubel U
Ref : Genome Res , 23 :653 , 2013
PubMedID: 23299977
Gene_locus related to this paper: staau-SA2240

Title : Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis - Supply_2013_Nat.Genet_45_172
Author(s) : Supply P , Marceau M , Mangenot S , Roche D , Rouanet C , Khanna V , Majlessi L , Criscuolo A , Tap J , Pawlik A , Fiette L , Orgeur M , Fabre M , Parmentier C , Frigui W , Simeone R , Boritsch EC , Debrie AS , Willery E , Walker D , Quail MA , Ma L , Bouchier C , Salvignol G , Sayes F , Cascioferro A , Seemann T , Barbe V , Locht C , Gutierrez MC , Leclerc C , Bentley SD , Stinear TP , Brisse S , Medigue C , Parkhill J , Cruveiller S , Brosch R
Ref : Nat Genet , 45 :172 , 2013
PubMedID: 23291586
Gene_locus related to this paper: mycmm-b2ht49 , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv1069c , myctu-RV1215C , myctu-RV1758 , myctu-Rv2045c , myctu-RV3452 , myctu-RV3724 , myctu-Rv3802c

Title : Description and nomenclature of Neisseria meningitidis capsule locus - Harrison_2013_Emerg.Infect.Dis_19_566
Author(s) : Harrison OB , Claus H , Jiang Y , Bennett JS , Bratcher HB , Jolley KA , Corton C , Care R , Poolman JT , Zollinger WD , Frasch CE , Stephens DS , Feavers I , Frosch M , Parkhill J , Vogel U , Quail MA , Bentley SD , Maiden MC
Ref : Emerg Infect Dis , 19 :566 , 2013
PubMedID: 23628376
Gene_locus related to this paper: neime-h6t5x5

Title : Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts - Mather_2013_Science_341_1514
Author(s) : 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
Ref : Science , 341 :1514 , 2013
PubMedID: 24030491

Title : A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus - Crossman_2013_ISME.J_7_148
Author(s) : Crossman LC , Chen H , Cerdeno-Tarraga AM , Brooks K , Quail MA , Pineiro SA , Hobley L , Sockett RE , Bentley SD , Parkhill J , Williams HN , Stine OC
Ref : Isme J , 7 :148 , 2013
PubMedID: 22955231
Gene_locus related to this paper: bacms-e1x4r0 , bacms-e1wxp3

Title : The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex - Bentley_2012_PLoS.Negl.Trop.Dis_6_e1552
Author(s) : Bentley SD , Comas I , Bryant JM , Walker D , Smith NH , Harris SR , Thurston S , Gagneux S , Wood J , Antonio M , Quail MA , Gehre F , Adegbola RA , Parkhill J , de Jong BC
Ref : PLoS Negl Trop Dis , 6 :e1552 , 2012
PubMedID: 22389744
Gene_locus related to this paper: myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv1069c , myctu-RV1215C , myctu-RV1758 , myctu-RV3452 , myctu-RV3724 , myctu-Rv3802c

Title : Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens - Park_2012_BMC.Genomics_13_545
Author(s) : Park J , Zhang Y , Buboltz AM , Zhang X , Schuster SC , Ahuja U , Liu M , Miller JF , Sebaihia M , Bentley SD , Parkhill J , Harvill ET
Ref : BMC Genomics , 13 :545 , 2012
PubMedID: 23051057
Gene_locus related to this paper: borbr-BB0273

Title : Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius - Strouts_2012_Emerg.Infect.Dis_18_449
Author(s) : Strouts FR , Power P , Croucher NJ , Corton N , Van Tonder A , Quail MA , Langford PR , Hudson MJ , Parkhill J , Kroll JS , Bentley SD
Ref : Emerg Infect Dis , 18 :449 , 2012
PubMedID: 22377449
Gene_locus related to this paper: haein-pldb , neime-ESD

Title : Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity - Mappley_2012_BMC.Genomics_13_454
Author(s) : Mappley LJ , Black ML , AbuOun M , Darby AC , Woodward MJ , Parkhill J , Turner AK , Bellgard MI , La T , Phillips ND , La Ragione RM , Hampson DJ
Ref : BMC Genomics , 13 :454 , 2012
PubMedID: 22947175
Gene_locus related to this paper: brap9-d8ife9

Title : Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study - Garcia-Alvarez_2011_Lancet.Infect.Dis_11_595
Author(s) : Garcia-Alvarez L , Holden MT , Lindsay H , Webb CR , Brown DF , Curran MD , Walpole E , Brooks K , Pickard DJ , Teale C , Parkhill J , Bentley SD , Edwards GF , Girvan EK , Kearns AM , Pichon B , Hill RL , Larsen AR , Skov RL , Peacock SJ , Maskell DJ , Holmes MA
Ref : Lancet Infect Dis , 11 :595 , 2011
PubMedID: 21641281
Gene_locus related to this paper: staau-SA0897 , staau-SA2240

Title : Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors - Heilbronner_2011_FEMS.Microbiol.Lett_322_60
Author(s) : Heilbronner S , Holden MT , Van Tonder A , Geoghegan JA , Foster TJ , Parkhill J , Bentley SD
Ref : FEMS Microbiology Letters , 322 :60 , 2011
PubMedID: 21682763
Gene_locus related to this paper: stalh-d3qdw5 , stalh-d3qhh5 , stalu-q0kkp0

Title : A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin - Holt_2011_Genome.Biol.Evol_3_881
Author(s) : Holt DC , Holden MT , Tong SY , Castillo-Ramirez S , Clarke L , Quail MA , Currie BJ , Parkhill J , Bentley SD , Feil EJ , Giffard PM
Ref : Genome Biol Evol , 3 :881 , 2011
PubMedID: 21813488
Gene_locus related to this paper: staau-SA0897 , staau-SA2240

Title : Salmonella bongori provides insights into the evolution of the Salmonellae - Fookes_2011_PLoS.Pathog_7_e1002191
Author(s) : 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
Ref : PLoS Pathog , 7 :e1002191 , 2011
PubMedID: 21876672
Gene_locus related to this paper: salbc-f8vhq9

Title : The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli - Petty_2010_J.Bacteriol_192_525
Author(s) : 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
Ref : Journal of Bacteriology , 192 :525 , 2010
PubMedID: 19897651
Gene_locus related to this paper: citk8-bioh , citk8-y1948 , citri-d2th08 , citri-d2tjf8 , citri-d2tjy8 , citri-d2tk80 , citri-d2tmm5 , citri-d2tmq5 , citri-d2tri3 , citri-d2trm8

Title : Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06 - Bennett_2010_BMC.Genomics_11_652
Author(s) : Bennett JS , Bentley SD , Vernikos GS , Quail MA , Cherevach I , White B , Parkhill J , Maiden MC
Ref : BMC Genomics , 11 :652 , 2010
PubMedID: 21092259
Gene_locus related to this paper: neigo-pip , neil0-e4zan3 , neima-metx , neime-NMB0276 , neime-NMB1877

Title : Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen - O'Toole_2010_BMC.Genomics_11_164
Author(s) : O'Toole PW , Snelling WJ , Canchaya C , Forde BM , Hardie KR , Josenhans C , Graham R , McMullan G , Parkhill J , Belda E , Bentley SD
Ref : BMC Genomics , 11 :164 , 2010
PubMedID: 20219135
Gene_locus related to this paper: helm1-d3uha6 , helm1-d3uix4

Title : A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407 - Crossman_2010_J.Bacteriol_192_5822
Author(s) : 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
Ref : Journal of Bacteriology , 192 :5822 , 2010
PubMedID: 20802035
Gene_locus related to this paper: ecoli-rutD , ecoli-bioh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-yeiG , ecoli-YFBB , ecoli-yiel , ecoli-yqia

Title : Comparative genomics of prevaccination and modern Bordetella pertussis strains - Bart_2010_BMC.Genomics_11_627
Author(s) : Bart MJ , van Gent M , van der Heide HG , Boekhorst J , Hermans P , Parkhill J , Mooi FR
Ref : BMC Genomics , 11 :627 , 2010
PubMedID: 21070624

Title : Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW) - Holden_2010_J.Bacteriol_192_888
Author(s) : Holden MT , Lindsay JA , Corton C , Quail MA , Cockfield JD , Pathak S , Batra R , Parkhill J , Bentley SD , Edgeworth JD
Ref : Journal of Bacteriology , 192 :888 , 2010
PubMedID: 19948800
Gene_locus related to this paper: staau-LIP , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2594

Title : Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946 - Sebaihia_2010_J.Bacteriol_192_2020
Author(s) : Sebaihia M , Bocsanczy AM , Biehl BS , Quail MA , Perna NT , Glasner JD , DeClerck GA , Cartinhour S , Schneider DJ , Bentley SD , Parkhill J , Beer SV
Ref : Journal of Bacteriology , 192 :2020 , 2010
PubMedID: 20118253
Gene_locus related to this paper: erwac-d4hwt0 , erwac-d4hxs4 , erwac-d4i2q5 , erwac-d4i3s4 , erwac-d4i259 , erwae-d4idw0 , erwpe-d0fwy1 , erwse-e3dex4

Title : Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042 - Chaudhuri_2010_PLoS.One_5_e8801
Author(s) : 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
Ref : PLoS ONE , 5 :e8801 , 2010
PubMedID: 20098708
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-MCMK , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yhet , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-Z0347 , ecoli-YfhR , yerpe-YBTT

Title : Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81 - Croucher_2009_J.Bacteriol_191_1480
Author(s) : Croucher NJ , Walker D , Romero P , Lennard N , Paterson GK , Bason NC , Mitchell AM , Quail MA , Andrew PW , Parkhill J , Bentley SD , Mitchell TJ
Ref : Journal of Bacteriology , 191 :1480 , 2009
PubMedID: 19114491
Gene_locus related to this paper: strpi-pepx , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-SP0614 , strpn-SP1343

Title : The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients - Holden_2009_J.Bacteriol_191_261
Author(s) : 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
Ref : Journal of Bacteriology , 191 :261 , 2009
PubMedID: 18931103
Gene_locus related to this paper: burcj-b4e794 , 9burk-a0u8m3 , burcj-b4ek59 , burcj-b4ehl7 , burca-q1bk56 , burce-a0a088tsj6 , burcj-b4ecv6

Title : Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens - Wilkinson_2009_BMC.Genomics_10_302
Author(s) : Wilkinson P , Waterfield NR , Crossman L , Corton C , Sanchez-Contreras M , Vlisidou I , Barron A , Bignell A , Clark L , Ormond D , Mayho M , Bason N , Smith F , Simmonds M , Churcher C , Harris D , Thompson NR , Quail M , Parkhill J , ffrench-Constant RH
Ref : BMC Genomics , 10 :302 , 2009
PubMedID: 19583835
Gene_locus related to this paper: phoaa-b6vks1 , phoaa-b6vmd3 , phoaa-c7bgr2 , phoaa-c7bhw5 , phoaa-c7bjq6 , phoaa-c7bk59 , phoaa-c7bnd9 , pholu-lxd2 , pholu-PLU2437 , phoaa-c7bh14 , phoaa-c7bkb9

Title : Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348\/69 - Iguchi_2009_J.Bacteriol_191_347
Author(s) : 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
Ref : Journal of Bacteriology , 191 :347 , 2009
PubMedID: 18952797
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-YfhR

Title : Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium - Stabler_2009_Genome.Biol_10_R102
Author(s) : Stabler RA , He M , Dawson L , Martin M , Valiente E , Corton C , Lawley TD , Sebaihia M , Quail MA , Rose G , Gerding DN , Gibert M , Popoff MR , Parkhill J , Dougan G , Wren BW
Ref : Genome Biol , 10 :R102 , 2009
PubMedID: 19781061
Gene_locus related to this paper: pepdi-t4eki5 , clod6-q183v0 , clodr-c9ynf2 , pepd6-pip

Title : Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens - Holden_2009_PLoS.Pathog_5_e1000346
Author(s) : Holden MT , Heather Z , Paillot R , Steward KF , Webb K , Ainslie F , Jourdan T , Bason NC , Holroyd NE , Mungall K , Quail MA , Sanders M , Simmonds M , Willey D , Brooks K , Aanensen DM , Spratt BG , Jolley KA , Maiden MC , Kehoe M , Chanter N , Bentley SD , Robinson C , Maskell DJ , Parkhill J , Waller AS
Ref : PLoS Pathog , 5 :e1000346 , 2009
PubMedID: 19325880
Gene_locus related to this paper: stre4-c0mbg3 , stre4-pepx , strem-b4u0u4 , strem-b4u3j8 , strs7-pepx

Title : Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis - Holden_2009_PLoS.One_4_e6072
Author(s) : Holden MT , Hauser H , Sanders M , Ngo TH , Cherevach I , Cronin A , Goodhead I , Mungall K , Quail MA , Price C , Rabbinowitsch E , Sharp S , Croucher NJ , Chieu TB , Mai NT , Diep TS , Chinh NT , Kehoe M , Leigh JA , Ward PN , Dowson CG , Whatmore AM , Chanter N , Iversen P , Gottschalk M , Slater JD , Smith HE , Spratt BG , Xu J , Ye C , Bentley S , Barrell BG , Schultsz C , Maskell DJ , Parkhill J
Ref : PLoS ONE , 4 :e6072 , 2009
PubMedID: 19603075
Gene_locus related to this paper: strsu-q302y4 , strsy-a4vus4 , strsy-a4vwf6

Title : Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi - Holt_2009_BMC.Genomics_10_36
Author(s) : 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
Ref : BMC Genomics , 10 :36 , 2009
PubMedID: 19159446

Title : Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain - Seth-Smith_2009_BMC.Genomics_10_239
Author(s) : 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
Ref : BMC Genomics , 10 :239 , 2009
PubMedID: 19460133
Gene_locus related to this paper: chltr-CT073 , chltr-CT136

Title : Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis - Ward_2009_BMC.Genomics_10_54
Author(s) : Ward PN , Holden MT , Leigh JA , Lennard N , Bignell A , Barron A , Clark L , Quail MA , Woodward J , Barrell BG , Egan SA , Field TR , Maskell D , Kehoe M , Dowson CG , Chanter N , Whatmore AM , Bentley SD , Parkhill J
Ref : BMC Genomics , 10 :54 , 2009
PubMedID: 19175920
Gene_locus related to this paper: stru0-b9drp1 , stru0-b9dsd7 , stru0-b9dum0 , stru0-b9dvu1 , stru0-pepx

Title : Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype - Kingsley_2009_Genome.Res_19_2279
Author(s) : 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
Ref : Genome Res , 19 :2279 , 2009
PubMedID: 19901036
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-BIOH , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-P74847 , salty-PLDB , salty-STM0332 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YHET , salty-YQIA

Title : Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis - Stinear_2008_Genome.Res_18_729
Author(s) : Stinear TP , Seemann T , Harrison PF , Jenkin GA , Davies JK , Johnson PD , Abdellah Z , Arrowsmith C , Chillingworth T , Churcher C , Clarke K , Cronin A , Davis P , Goodhead I , Holroyd N , Jagels K , Lord A , Moule S , Mungall K , Norbertczak H , Quail MA , Rabbinowitsch E , Walker D , White B , Whitehead S , Small PL , Brosch R , Ramakrishnan L , Fischbach MA , Parkhill J , Cole ST
Ref : Genome Res , 18 :729 , 2008
PubMedID: 18403782
Gene_locus related to this paper: mycmm-b2hds9 , mycmm-b2hed7 , mycmm-b2hg81 , mycmm-b2hgg2 , mycmm-b2hgg7 , mycmm-b2hhi7 , mycmm-b2hhu3 , mycmm-b2hiu3 , mycmm-b2hiu5 , mycmm-b2hiw7 , mycmm-b2hiy0 , mycmm-b2hj55 , mycmm-b2hjb4 , mycmm-b2hju3 , mycmm-b2hku1 , mycmm-b2hkw0 , mycmm-b2hlr0 , mycmm-b2hlt7 , mycmm-b2hlt8 , mycmm-b2hlt9 , mycmm-b2hlu0 , mycmm-b2hlv0 , mycmm-b2hlv1 , mycmm-b2hlv2 , mycmm-b2hlx2 , mycmm-b2hm55 , mycmm-b2hnr9 , mycmm-b2hnz5 , mycmm-b2hp80 , mycmm-b2hpp0 , mycmm-b2hq96 , mycmm-b2hr10 , mycmm-b2hsm6 , mycmm-b2hsm8 , mycmm-b2hsy0 , mycmm-b2ht06 , mycmm-b2ht20 , mycmm-b2ht49 , mycmm-dhma , mycmm-metx , mycmr-q5sdq4 , myctu-RV1683 , mycmm-b2h1k1 , mycua-a0pku2 , mycua-a0pl47 , mycua-a0plr3 , mycua-a0pm12 , mycua-a0pm14 , mycua-a0pmv0 , mycua-a0pmx9 , mycua-a0pn71 , mycua-a0ppm6 , mycua-a0pqm2 , mycua-a0pqs2 , mycua-a0prq2 , mycua-a0psb1 , mycua-a0psb4 , mycua-a0psi2 , mycua-a0pth6 , mycua-a0ptq0 , mycua-a0pu55 , mycua-a0pum4 , mycua-a0pv11 , mycua-a0pva4 , mycua-a0pwi8 , mycua-a0pwr6 , mycua-a0pwz5 , mycul-a85a , mycmm-b2hcy1 , mycua-a0pvg7 , mycmm-b2hnj4 , mycmm-b2he93 , mycua-a0pwz4 , mycmm-b2hqy3 , mycua-a0pmc3 , mycmm-b2hnn7 , mycmm-b2he68 , mycmm-b2hqm3 , mycmm-tesa

Title : The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay - Hjerde_2008_BMC.Genomics_9_616
Author(s) : 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
Ref : BMC Genomics , 9 :616 , 2008
PubMedID: 19099551
Gene_locus related to this paper: alisl-b6elz2 , alisl-b6ek45

Title : Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids - Letek_2008_J.Bacteriol_190_5797
Author(s) : Letek M , Ocampo-Sosa AA , Sanders M , Fogarty U , Buckley T , Leadon DP , Gonzalez P , Scortti M , Meijer WG , Parkhill J , Bentley S , Vazquez-Boland JA
Ref : Journal of Bacteriology , 190 :5797 , 2008
PubMedID: 18606735
Gene_locus related to this paper: coreq-e9sxw6 , coreq-e9t5k8 , coreq-e9t5k9 , coreq-e9t7v9 , coreq-d9i5p0

Title : Rapid Virulence Annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts - Waterfield_2008_Proc.Natl.Acad.Sci.U.S.A_105_15967
Author(s) : Waterfield NR , Sanchez-Contreras M , Eleftherianos I , Dowling A , Yang G , Wilkinson P , Parkhill J , Thomson N , Reynolds SE , Bode HB , Dorus S , ffrench-Constant RH
Ref : Proc Natl Acad Sci U S A , 105 :15967 , 2008
PubMedID: 18838673
Gene_locus related to this paper: phoaa-b6vks1 , phoaa-b6vmd3

Title : Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation - Bentley_2008_J.Bacteriol_190_2150
Author(s) : Bentley SD , Corton C , Brown SE , Barron A , Clark L , Doggett J , Harris B , Ormond D , Quail MA , May G , Francis D , Knudson D , Parkhill J , Ishimaru CA
Ref : Journal of Bacteriology , 190 :2150 , 2008
PubMedID: 18192393
Gene_locus related to this paper: clam3-a5cqb1 , clam3-a5crq6 , clam3-a5csc5 , clam3-a5css8 , clams-b0rcr0 , clams-b0rdd6 , clams-b0rdd7 , clams-b0rde2 , clams-b0rde3 , clams-b0rer7 , clams-b0rga8 , clams-b0riv5 , clam3-a5cp43 , clam3-a5cp56

Title : Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility - Pearson_2008_J.Bacteriol_190_4027
Author(s) : 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
Ref : Journal of Bacteriology , 190 :4027 , 2008
PubMedID: 18375554
Gene_locus related to this paper: promh-b4euu8 , promh-b4ev30 , promh-b4evj5 , promh-b4f0a1 , promh-bioh , promi-c2lhp6 , promi-c2lla8 , promi-NRPS , promi-NRPT , promi-k1gzm2 , promh-b4eve8

Title : Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates - Thomson_2008_Genome.Res_18_161
Author(s) : 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
Ref : Genome Res , 18 :161 , 2008
PubMedID: 18032721
Gene_locus related to this paper: chltr-CT073 , chltr-CT136

Title : Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287\/91 provides insights into evolutionary and host adaptation pathways - Thomson_2008_Genome.Res_18_1624
Author(s) : 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
Ref : Genome Res , 18 :1624 , 2008
PubMedID: 18583645
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-BIOH , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-P74847 , salty-PLDB , salty-STM0332 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YHET , salty-YQIA

Title : Genome evolution of Wolbachia strain wPip from the Culex pipiens group - Klasson_2008_Mol.Biol.Evol_25_1877
Author(s) : Klasson L , Walker T , Sebaihia M , Sanders MJ , Quail MA , Lord A , Sanders S , Earl J , O'Neill SL , Thomson N , Sinkins SP , Parkhill J
Ref : Molecular Biology Evolution , 25 :1877 , 2008
PubMedID: 18550617

Title : The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants - Crossman_2008_Genome.Biol_9_R74
Author(s) : 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
Ref : Genome Biol , 9 :R74 , 2008
PubMedID: 18419807
Gene_locus related to this paper: strm5-b4sjf3 , strm5-b4sly1 , strm5-b4smq6 , strm5-b4st20 , strm5-bioh , strmk-b2fhb1 , strmk-b2fju9 , strmk-b2fkx8 , strmk-b2fl50 , strmk-b2fl54 , strmk-b2flj0 , strmk-b2fnc5 , strmk-b2fre3 , strmk-b2frm1 , strmk-b2frs0 , strmk-b2fsp0 , strmk-b2ftw9 , strmk-b2fuf3 , strmk-metx , xanma-P95782 , strmk-b2fmj5 , strmk-b2fpy9 , strmk-b2ftk7 , strmk-b2frv5

Title : Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome - Hiller_2007_J.Bacteriol_189_8186
Author(s) : Hiller NL , Janto B , Hogg JS , Boissy R , Yu S , Powell E , Keefe R , Ehrlich NE , Shen K , Hayes J , Barbadora K , Klimke W , Dernovoy D , Tatusova T , Parkhill J , Bentley SD , Post JC , Ehrlich GD , Hu FZ
Ref : Journal of Bacteriology , 189 :8186 , 2007
PubMedID: 17675389
Gene_locus related to this paper: strpn-AXE1 , strpn-pepx , strpn-SP1343

Title : Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18 - Bentley_2007_PLoS.Genet_3_e23
Author(s) : Bentley SD , Vernikos GS , Snyder LA , Churcher C , Arrowsmith C , Chillingworth T , Cronin A , Davis PH , Holroyd NE , Jagels K , Maddison M , Moule S , Rabbinowitsch E , Sharp S , Unwin L , Whitehead S , Quail MA , Achtman M , Barrell B , Saunders NJ , Parkhill J
Ref : PLoS Genet , 3 :e23 , 2007
PubMedID: 17305430
Gene_locus related to this paper: neigo-pip , neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1828 , neime-NMB1877 , neimf-a1kta9

Title : Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo - Holden_2007_J.Bacteriol_189_1473
Author(s) : Holden MT , Scott A , Cherevach I , Chillingworth T , Churcher C , Cronin A , Dowd L , Feltwell T , Hamlin N , Holroyd S , Jagels K , Moule S , Mungall K , Quail MA , Price C , Rabbinowitsch E , Sharp S , Skelton J , Whitehead S , Barrell BG , Kehoe M , Parkhill J
Ref : Journal of Bacteriology , 189 :1473 , 2007
PubMedID: 17012393
Gene_locus related to this paper: strpy-ESTA , strpy-PEPXP , strpy-SPY1308 , strpy-SPYM18.1727

Title : Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes - Sebaihia_2007_Genome.Res_17_1082
Author(s) : 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
Ref : Genome Res , 17 :1082 , 2007
PubMedID: 17519437
Gene_locus related to this paper: clobh-A5I3I2 , clobh-A51055 , clob1-a7fqm2 , clob1-a7fv94 , clobl-a7gbn0 , clobh-pip , clobh-a5i3m0

Title : Genome plasticity of BCG and impact on vaccine efficacy - Brosch_2007_Proc.Natl.Acad.Sci.U.S.A_104_5596
Author(s) : Brosch R , Gordon SV , Garnier T , Eiglmeier K , Frigui W , Valenti P , Dos Santos S , Duthoy S , Lacroix C , Garcia-Pelayo C , Inwald JK , Golby P , Garcia JN , Hewinson RG , Behr MA , Quail MA , Churcher C , Barrell BG , Parkhill J , Cole ST
Ref : Proc Natl Acad Sci U S A , 104 :5596 , 2007
PubMedID: 17372194
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas2 , myctu-d5yk66 , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-Rv2045c , myctu-RV2054 , myctu-Rv2284 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-Rv3591c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28

Title : The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081 - Thomson_2006_PLoS.Genet_2_e206
Author(s) : 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
Ref : PLoS Genet , 2 :e206 , 2006
PubMedID: 17173484
Gene_locus related to this paper: yere8-a1jik0 , yere8-a1jmx1 , yere8-a1jrp7 , yere8-bioh , yere8-menh , yere8-y3204 , yeren-fes , yeren-YPLA , yeren-YqiA , yermo-c4sfz7 , yerpe-y1616 , yerpe-YPO1501 , yerbe-c4rym7

Title : The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome - Sebaihia_2006_Nat.Genet_38_779
Author(s) : 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
Ref : Nat Genet , 38 :779 , 2006
PubMedID: 16804543
Gene_locus related to this paper: pepdi-t4eki5 , clod6-q18a60 , clod6-q183v0 , clodi-HYDD , clodr-c9ynf2 , pepd6-pip , pepdi-g6brr4

Title : Multireplicon genome architecture of Lactobacillus salivarius - Claesson_2006_Proc.Natl.Acad.Sci.U.S.A_103_6718
Author(s) : Claesson MJ , Li Y , Leahy S , Canchaya C , van Pijkeren JP , Cerdeno-Tarraga AM , Parkhill J , Flynn S , O'Sullivan GC , Collins JK , Higgins D , Shanahan F , Fitzgerald GF , van Sinderen D , O'Toole PW
Ref : Proc Natl Acad Sci U S A , 103 :6718 , 2006
PubMedID: 16617113
Gene_locus related to this paper: lacs1-PEPX , lacs1-q1wrt6 , lacs1-q1ws61 , lacs1-q1wtn9 , lacs1-q1wv71

Title : The genome of Rhizobium leguminosarum has recognizable core and accessory components - Young_2006_Genome.Biol_7_R34
Author(s) : 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
Ref : Genome Biol , 7 :R34 , 2006
PubMedID: 16640791
Gene_locus related to this paper: rhiec-q2k7y0 , rhiec-q2k107 , rhiec-q2kav5 , rhiec-q2ke86 , rhil3-q1m3b7 , rhil3-q1m3u0 , rhil3-q1m4b4 , rhil3-q1m4e5 , rhil3-q1m4g3 , rhil3-q1m4h0 , rhil3-q1m5k0 , rhil3-q1m5s6 , rhil3-q1m6q0 , rhil3-q1m6u8 , rhil3-q1m6w8 , rhil3-q1m7c2 , rhil3-q1m7c3 , rhil3-q1m7i2 , rhil3-q1m7n3 , rhil3-q1m7q9 , rhil3-q1m7r8 , rhil3-q1m8d0 , rhil3-q1m8u4 , rhil3-q1m9d6 , rhil3-q1m9i6 , rhil3-q1m347 , rhil3-q1m571 , rhil3-q1m580 , rhil3-q1m672 , rhil3-q1m812 , rhil3-q1m841 , rhil3-q1m917 , rhil3-q1m919 , rhil3-q1mbv4 , rhil3-q1mbz5 , rhil3-q1mc48 , rhil3-q1mcr4 , rhil3-q1md19 , rhil3-q1mdd8 , rhil3-q1me05 , rhil3-q1mee4 , rhil3-q1mel6 , rhil3-q1men7 , rhil3-q1mf17 , rhil3-q1mf73 , rhil3-q1mf76 , rhil3-q1mfb0 , rhil3-q1mfp5 , rhil3-q1mg17 , rhil3-q1mg51 , rhil3-q1mg97 , rhil3-q1mgh3 , rhil3-q1mgh5 , rhil3-q1mgu7 , rhil3-q1mgx5 , rhil3-q1mh67 , rhil3-q1mhh7 , rhil3-q1mhz8 , rhil3-q1mi67 , rhil3-q1mi98 , rhil3-q1mia3 , rhil3-q1mig2 , rhil3-q1miz0 , rhil3-q1mj26 , rhil3-q1mj65 , rhil3-q1mjs2 , rhil3-q1mjx4 , rhil3-q1mk84 , rhil3-q1mkk8 , rhil3-q1mli7 , rhil3-q1mlj7 , rhil3-q1mm33 , rhil3-q1mmf9 , rhil3-q1mmp7 , rhil3-q1mmx0 , rhil3-q1mn42 , rhile-Q93EA8 , rhils-c6axl5 , rhils-c6b1w7 , rhilw-b5zrm4 , rhilw-b5zs97 , rhilv-j0vcs5

Title : 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 - Sebaihia_2006_J.Bacteriol_188_6002
Author(s) : 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
Ref : Journal of Bacteriology , 188 :6002 , 2006
PubMedID: 16885469
Gene_locus related to this paper: bora1-q2kti1 , bora1-q2ktw2 , bora1-q2ku63 , bora1-q2kun8 , bora1-q2kuu7 , bora1-q2kuz2 , bora1-q2kv84 , bora1-q2kvg3 , bora1-q2kw07 , bora1-q2kw58 , bora1-q2kwy4 , bora1-q2kxl0 , bora1-q2kxn8 , bora1-q2kxw5 , bora1-q2kxz8 , bora1-q2kyw6 , bora1-q2kzr8 , bora1-q2kzt4 , bora1-q2kzx4 , bora1-q2l0h1 , bora1-q2l0h9 , bora1-q2l0p4 , bora1-q2l1n9 , bora1-q2l1v4 , bora1-q2l1z1 , bora1-q2l122 , bora1-q2l209

Title : Complete genome sequence and lytic phase transcription profile of a Coccolithovirus - Wilson_2005_Science_309_1090
Author(s) : Wilson WH , Schroeder DC , Allen MJ , Holden MT , Parkhill J , Barrell BG , Churcher C , Hamlin N , Mungall K , Norbertczak H , Quail MA , Price C , Rabbinowitsch E , Walker D , Craigon M , Roy D , Ghazal P
Ref : Science , 309 :1090 , 2005
PubMedID: 16099989
Gene_locus related to this paper: 9phyc-q4a2b6 , 9phyc-q4a3c9 , ehv86-q4a332

Title : The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation - Thomson_2005_Genome.Res_15_629
Author(s) : 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
Ref : Genome Res , 15 :629 , 2005
PubMedID: 15837807
Gene_locus related to this paper: chlab-q5l5y2 , chlab-q5l6t6

Title : Extensive DNA inversions in the B. fragilis genome control variable gene expression - Cerdeno-Tarraga_2005_Science_307_1463
Author(s) : Cerdeno-Tarraga AM , Patrick S , Crossman LC , Blakely G , Abratt V , Lennard N , Poxton I , Duerden B , Harris B , Quail MA , Barron A , Clark L , Corton C , Doggett J , Holden MT , Larke N , Line A , Lord A , Norbertczak H , Ormond D , Price C , Rabbinowitsch E , Woodward J , Barrell B , Parkhill J
Ref : Science , 307 :1463 , 2005
PubMedID: 15746427
Gene_locus related to this paper: bacfn-q5l8p8 , bacfn-q5lef1 , bacfn-q5lh43 , bacfn-q5lhv2 , bacfr-q64mh3 , bacfr-q64n33 , bacfr-q64qs3 , bacfr-q64t24 , bacfr-q64uj8 , bacfr-q64vx6 , bacfr-q64wh2 , bacfr-q64xp9 , bacfr-q650j0

Title : Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
Author(s) : 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
Ref : Proc Natl Acad Sci U S A , 101 :14240 , 2004
PubMedID: 15377794
Gene_locus related to this paper: burma-a5j5w8 , burma-a5tj72 , burma-a5tq93 , burma-metx , burma-q62a61 , burma-q62ar2.1 , burma-q62ar2.2 , burma-q62ax8 , burma-q62b60 , burma-q62b79 , burma-q62bh9 , burma-q62bl4 , burma-q62bl7 , burma-q62c00 , burma-q62cg5 , burma-q62d41 , burma-q62d56 , burma-q62d83 , burma-q62dg2 , burma-q62du7 , burma-q62e67 , burma-q62eb8 , burma-q62ed8 , burma-q62f28 , burma-q62fx7 , burma-q62g26 , burma-q62gx9 , burma-q62gy2 , burma-q62hq2 , burma-q62i62 , burma-q62ib8 , burma-q62ie8 , burma-q62j07 , burma-q62j15 , burma-q62jn5 , burma-q62jy7 , burma-q62kb7 , burma-q62kg0 , burma-q62kh9 , burma-q62lp7 , burma-q62m40 , burma-q62mc3 , burma-q62mf4 , burma-q62mq7 , burma-q629m1 , burma-q629p4 , burma-q629u0 , burp1-q3jvq2 , burps-a4lm41 , burps-q3v7s4 , burps-q63hx2 , burps-q63i95 , burps-q63im5 , burps-q63is4 , burps-q63ja6 , burps-q63ja9 , burps-q63jh5 , burps-q63l17 , burps-q63l41 , burps-q63l44 , burps-q63lt9 , burps-q63me1 , burps-q63mj7 , burps-q63mj8 , burps-q63mn8 , burps-q63mr2 , burps-q63n52 , burps-q63p18 , burps-q63p99 , burps-q63ug2 , burps-q63ug5 , burps-q63xf9 , burps-q63y36 , burps-q63y45 , burps-q63y52 , burps-q63y59 , burta-q2t474 , burps-hboh

Title : Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica - Parkhill_2003_Nat.Genet_35_32
Author(s) : Parkhill J , Sebaihia M , Preston A , Murphy LD , Thomson N , Harris DE , Holden MT , Churcher CM , Bentley SD , Mungall KL , Cerdeno-Tarraga AM , Temple L , James K , Harris B , Quail MA , Achtman M , Atkin R , Baker S , Basham D , Bason N , Cherevach I , Chillingworth T , Collins M , Cronin A , Davis P , Doggett J , Feltwell T , Goble A , Hamlin N , Hauser H , Holroyd S , Jagels K , Leather S , Moule S , Norberczak H , O'Neil S , Ormond D , Price C , Rabbinowitsch E , Rutter S , Sanders M , Saunders D , Seeger K , Sharp S , Simmonds M , Skelton J , Squares R , Squares S , Stevens K , Unwin L , Whitehead S , Barrell BG , Maskell DJ
Ref : Nat Genet , 35 :32 , 2003
PubMedID: 12910271
Gene_locus related to this paper: borbr-BB0273 , borbr-BB0570 , borbr-BB0670 , borbr-BB1064 , borbr-BB1079 , borbr-BB1247 , borbr-BB1498 , borbr-BB2718 , borbr-BB4129 , borbr-BB4247 , borbr-MHPC , borbr-q7wdw1 , borbr-q7wiz8 , borbr-q7wk25 , borbr-q7wmc2 , borbr-q7wpd9 , borpa-q7w3f3 , borpa-q7w9v8 , borpe-BIOH , borpe-BP0300 , borpe-BP2114 , borpe-BP2146 , borpe-BP2511 , borpe-BP3096 , borpe-BP3623 , borpe-BP3691 , borpe-CATD2 , borpe-METX , borpe-O30449 , borpe-PHBC , borpe-q7vsl4 , borpe-q7vt07 , borpe-q7vtg0 , borpe-q7vtv2 , borpe-q7vus4 , borpe-q7vuv4 , borpe-q7vv11 , borpe-q7vv48 , borpe-q7vvf6 , borpe-q7vwu4 , borpe-q7vyn0 , borpe-q7vyq4 , borpe-q7vz26 , borpe-q7vzb4 , borpe-q7vzj6 , borpe-q7w073

Title : The complete genome sequence of Mycobacterium bovis - Garnier_2003_Proc.Natl.Acad.Sci.U.S.A_100_7877
Author(s) : Garnier T , Eiglmeier K , Camus JC , Medina N , Mansoor H , Pryor M , Duthoy S , Grondin S , Lacroix C , Monsempe C , Simon S , Harris B , Atkin R , Doggett J , Mayes R , Keating L , Wheeler PR , Parkhill J , Barrell BG , Cole ST , Gordon SV , Hewinson RG
Ref : Proc Natl Acad Sci U S A , 100 :7877 , 2003
PubMedID: 12788972
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-d5yk66 , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-MT3441 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0421C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1190 , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-Rv2045c , myctu-RV2054 , myctu-Rv2284 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-Y2307 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28

Title : Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei - Bentley_2003_Lancet_361_637
Author(s) : Bentley SD , Maiwald M , Murphy LD , Pallen MJ , Yeats CA , Dover LG , Norbertczak HT , Besra GS , Quail MA , Harris DE , von Herbay A , Goble A , Rutter S , Squares R , Squares S , Barrell BG , Parkhill J , Relman DA
Ref : Lancet , 361 :637 , 2003
PubMedID: 12606174
Gene_locus related to this paper: trowh-TW083.1 , trowh-TW083.2 , trowh-TWT693

Title : Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 - Parkhill_2000_Nature_404_502
Author(s) : Parkhill J , Achtman M , James KD , Bentley SD , Churcher C , Klee SR , Morelli G , Basham D , Brown D , Chillingworth T , Davies RM , Davis P , Devlin K , Feltwell T , Hamlin N , Holroyd S , Jagels K , Leather S , Moule S , Mungall K , Quail MA , Rajandream MA , Rutherford KM , Simmonds M , Skelton J , Whitehead S , Spratt BG , Barrell BG
Ref : Nature , 404 :502 , 2000
PubMedID: 10761919
Gene_locus related to this paper: neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1877 , neimf-a1kta9 , neime-r0tza2

Title : The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences - Parkhill_2000_Nature_403_665
Author(s) : Parkhill J , Wren BW , Mungall K , Ketley JM , Churcher C , Basham D , Chillingworth T , Davies RM , Feltwell T , Holroyd S , Jagels K , Karlyshev AV , Moule S , Pallen MJ , Penn CW , Quail MA , Rajandream MA , Rutherford KM , van Vliet AH , Whitehead S , Barrell BG
Ref : Nature , 403 :665 , 2000
PubMedID: 10688204
Gene_locus related to this paper: camco-e0qbj3 , camco-q4hhu5 , camje-a3zji1 , camje-CJ0796C , camjr-q5ht69 , camju-a3yll6 , camju-Q9ZF63

Title : Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence - Cole_1998_Nature_393_537
Author(s) : Cole ST , Brosch R , Parkhill J , Garnier T , Churcher C , Harris D , Gordon SV , Eiglmeier K , Gas S , Barry CE, 3rd , Tekaia F , Badcock K , Basham D , Brown D , Chillingworth T , Connor R , Davies R , Devlin K , Feltwell T , Gentles S , Hamlin N , Holroyd S , Hornsby T , Jagels K , Krogh A , McLean J , Moule S , Murphy L , Oliver K , Osborne J , Quail MA , Rajandream MA , Rogers J , Rutter S , Seeger K , Skelton J , Squares R , Squares S , Sulston JE , Taylor K , Whitehead S , Barrell BG
Ref : Nature , 393 :537 , 1998
PubMedID: 9634230
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-d5yk66 , myctu-ephA , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-ephF , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-MT3441 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0421C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1190 , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-RV2054 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-Rv3591c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-Y2307 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28