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Items: 1 to 20 of 69

1.

The pig X and Y Chromosomes: structure, sequence, and evolution.

Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, Gilbert J, Austin-Guest S, Beal K, Carvalho-Silva D, Cheng W, Gordon D, Grafham D, Hardy M, Harley J, Hauser H, Howden P, Howe K, Lachani K, Ellis PJ, Kelly D, Kerry G, Kerwin J, Ng BL, Threadgold G, Wileman T, Wood JM, Yang F, Harrow J, Affara NA, Tyler-Smith C.

Genome Res. 2016 Jan;26(1):130-9. doi: 10.1101/gr.188839.114. Epub 2015 Nov 11.

2.

Expansion of the HSFY gene family in pig lineages : HSFY expansion in suids.

Skinner BM, Lachani K, Sargent CA, Yang F, Ellis P, Hunt T, Fu B, Louzada S, Churcher C, Tyler-Smith C, Affara NA.

BMC Genomics. 2015 Jun 9;16:442. doi: 10.1186/s12864-015-1650-x.

3.

The zebrafish reference genome sequence and its relationship to the human genome.

Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL.

Nature. 2013 Apr 25;496(7446):498-503. doi: 10.1038/nature12111. Epub 2013 Apr 17. Erratum in: Nature. 2014 Jan 9;505(7482):248. Cooper, James [corrected to Cooper, James D]; Eliott, David [corrected to Elliot, David]; Mortimer, Beverly [corrected to Mortimore, Beverley]; Begum, Sharmin [added]; Lloyd, Christine [added]; Lanz, Christa [added]; Raddatz, Günter [added]; Schuster, Stephan C [added].

4.

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.

Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.

5.

Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.

Seth-Smith HM, Fookes MC, Okoro CK, Baker S, Harris SR, Scott P, Pickard D, Quail MA, Churcher C, Sanders M, Harmse J, Dougan G, Parkhill J, Thomson NR.

J Bacteriol. 2012 Mar;194(6):1494-504. doi: 10.1128/JB.06403-11. Epub 2012 Jan 13.

6.

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL, Fookes M, Roberts K, Monson R, Nair S, Kingsley RA, Bulgin R, Wiles S, Goulding D, Keane T, Corton C, Lennard N, Harris D, Willey D, Rance R, Yu L, Choudhary JS, Churcher C, Quail MA, Parkhill J, Frankel G, Dougan G, Salmond GP, Thomson NR.

PLoS Pathog. 2011 Apr;7(4):e1002018. doi: 10.1371/journal.ppat.1002018. Epub 2011 Apr 7.

7.

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease.

Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L.

BMC Microbiol. 2011 Jan 10;11:7. doi: 10.1186/1471-2180-11-7.

8.

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.

Vu TT, Holmes EC, Duong V, Nguyen TQ, Tran TH, Quail M, Churcher C, Parkhill J, Cardosa J, Farrar J, Wills B, Lennon NJ, Birren BW, Buchy P, Henn MR, Simmons CP.

PLoS Negl Trop Dis. 2010 Jul 20;4(7):e757. doi: 10.1371/journal.pntd.0000757.

9.

Pig genome sequence--analysis and publication strategy.

Archibald AL, Bolund L, Churcher C, Fredholm M, Groenen MA, Harlizius B, Lee KT, Milan D, Rogers J, Rothschild MF, Uenishi H, Wang J, Schook LB; Swine Genome Sequencing Consortium.

BMC Genomics. 2010 Jul 19;11:438. doi: 10.1186/1471-2164-11-438.

10.

The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing.

McLaughlin SD, Walker AW, Churcher C, Clark SK, Tekkis PP, Johnson MW, Parkhill J, Ciclitira PJ, Dougan G, Nicholls RJ, Petrovska L.

Ann Surg. 2010 Jul;252(1):90-8. doi: 10.1097/SLA.0b013e3181e3dc8b.

11.

Evolutionary dynamics of Clostridium difficile over short and long time scales.

He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, Clark L, Corton C, Murray V, Rose G, Thurston S, van Tonder A, Walker D, Wren BW, Dougan G, Parkhill J.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7527-32. doi: 10.1073/pnas.0914322107. Epub 2010 Apr 5.

12.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerød A, Russnes HE, Foekens JA, Reis-Filho JS, van 't Veer L, Richardson AL, Børresen-Dale AL, Campbell PJ, Futreal PA, Stratton MR.

Nature. 2009 Dec 24;462(7276):1005-10. doi: 10.1038/nature08645.

13.

Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.

Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark R, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TP, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, Groenen MA.

PLoS One. 2009 Aug 5;4(8):e6524. doi: 10.1371/journal.pone.0006524.

14.

Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens.

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.

BMC Genomics. 2009 Jul 7;10:302. doi: 10.1186/1471-2164-10-302.

15.

The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.

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.

BMC Genomics. 2008 Dec 19;9:616. doi: 10.1186/1471-2164-9-616.

16.

Telomeric expression sites are highly conserved in Trypanosoma brucei.

Hertz-Fowler C, Figueiredo LM, Quail MA, Becker M, Jackson A, Bason N, Brooks K, Churcher C, Fahkro S, Goodhead I, Heath P, Kartvelishvili M, Mungall K, Harris D, Hauser H, Sanders M, Saunders D, Seeger K, Sharp S, Taylor JE, Walker D, White B, Young R, Cross GA, Rudenko G, Barry JD, Louis EJ, Berriman M.

PLoS One. 2008;3(10):e3527. doi: 10.1371/journal.pone.0003527. Epub 2008 Oct 27.

17.

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.

Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga 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.

J Bacteriol. 2009 Jan;191(1):261-77. doi: 10.1128/JB.01230-08. Epub 2008 Oct 17. Erratum in: J Bacteriol. 2009 Apr;191(8):2907.

18.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG, Berriman M.

Nature. 2008 Oct 9;455(7214):799-803. doi: 10.1038/nature07306.

19.

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.

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.

Genome Res. 2008 Oct;18(10):1624-37. doi: 10.1101/gr.077404.108. Epub 2008 Jun 26.

20.

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants.

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.

Genome Biol. 2008 Apr 17;9(4):R74. doi: 10.1186/gb-2008-9-4-r74.

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