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Items: 32

1.

Functional genomics of a symbiotic community: shared traits in the olive fruit fly gut microbiota.

Blow F, Gioti A, Goodhead IB, Kalyva M, Kampouraki A, Vontas J, Darby AC.

Genome Biol Evol. 2019 Dec 12. pii: evz258. doi: 10.1093/gbe/evz258. [Epub ahead of print]

PMID:
31830246
2.

Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa.

Bricio-Moreno L, Sheridan VH, Goodhead I, Armstrong S, Wong JKL, Waters EM, Sarsby J, Panagiotou S, Dunn J, Chakraborty A, Fang Y, Griswold KE, Winstanley C, Fothergill JL, Kadioglu A, Neill DR.

Nat Commun. 2018 Jul 6;9(1):2635. doi: 10.1038/s41467-018-04996-x.

3.

Campylobacter jejuni transcriptome changes during loss of culturability in water.

Bronowski C, Mustafa K, Goodhead I, James CE, Nelson C, Lucaci A, Wigley P, Humphrey TJ, Williams NJ, Winstanley C; ENIGMA Consortium.

PLoS One. 2017 Nov 30;12(11):e0188936. doi: 10.1371/journal.pone.0188936. eCollection 2017.

4.

Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies: Spiroplasma is present in both laboratory and natural populations.

Doudoumis V, Blow F, Saridaki A, Augustinos A, Dyer NA, Goodhead I, Solano P, Rayaisse JB, Takac P, Mekonnen S, Parker AG, Abd-Alla AMM, Darby A, Bourtzis K, Tsiamis G.

Sci Rep. 2017 Jul 5;7(1):4699. doi: 10.1038/s41598-017-04740-3.

5.

Fifty important research questions in microbial ecology.

Antwis RE, Griffiths SM, Harrison XA, Aranega-Bou P, Arce A, Bettridge AS, Brailsford FL, de Menezes A, Devaynes A, Forbes KM, Fry EL, Goodhead I, Haskell E, Heys C, James C, Johnston SR, Lewis GR, Lewis Z, Macey MC, McCarthy A, McDonald JE, Mejia-Florez NL, O'Brien D, Orland C, Pautasso M, Reid WDK, Robinson HA, Wilson K, Sutherland WJ.

FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix044.

PMID:
28379446
6.

A simple procedure for directly obtaining haplotype sequences of diploid genomes.

Noyes HA, Daly D, Goodhead I, Kay S, Kemp SJ, Kenny J, Saccheri I, Schnabel RD, Taylor JF, Hall N.

BMC Genomics. 2015 Aug 28;16:642. doi: 10.1186/s12864-015-1818-4.

7.

ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata.

Pieszko M, Weir W, Goodhead I, Kinnaird J, Shiels B.

PLoS Negl Trop Dis. 2015 Aug 14;9(8):e0003933. doi: 10.1371/journal.pntd.0003933. eCollection 2015.

8.

Corrigendum: Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.

Ilott NE, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, Goodhead I, Hertz-Fowler C, Heger A, Hall N, Donnelly LE, Sims D, Lindsay MA.

Nat Commun. 2015 Apr 9;6:6814. doi: 10.1038/ncomms7814. No abstract available.

9.

Taking the pseudo out of pseudogenes.

Goodhead I, Darby AC.

Curr Opin Microbiol. 2015 Feb;23:102-9. doi: 10.1016/j.mib.2014.11.012. Epub 2014 Dec 1. Review.

PMID:
25461580
10.

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.

IIott NE, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, Goodhead I, Hertz-Fowler C, Heger A, Hall N, Donnelly LE, Sims D, Lindsay MA.

Nat Commun. 2014 Jun 9;5:3979. doi: 10.1038/ncomms4979. Erratum in: Nat Commun. 2015;6:6814.

11.

Whole-genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence.

Goodhead I, Capewell P, Bailey JW, Beament T, Chance M, Kay S, Forrester S, MacLeod A, Taylor M, Noyes H, Hall N.

MBio. 2013 Aug 20;4(4). pii: e00197-13. doi: 10.1128/mBio.00197-13.

12.

Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.

13.

Identification of a mutation associated with fatal Foal Immunodeficiency Syndrome in the Fell and Dales pony.

Fox-Clipsham LY, Carter SD, Goodhead I, Hall N, Knottenbelt DC, May PD, Ollier WE, Swinburne JE.

PLoS Genet. 2011 Jul;7(7):e1002133. doi: 10.1371/journal.pgen.1002133. Epub 2011 Jul 7.

14.

A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice.

Goodhead I, Archibald A, Amwayi P, Brass A, Gibson J, Hall N, Hughes MA, Limo M, Iraqi F, Kemp SJ, Noyes HA.

PLoS Negl Trop Dis. 2010 Nov 9;4(11):e880. doi: 10.1371/journal.pntd.0000880.

15.

Defining transcribed regions using RNA-seq.

Wilhelm BT, Marguerat S, Goodhead I, Bähler J.

Nat Protoc. 2010 Feb;5(2):255-66. doi: 10.1038/nprot.2009.229. Epub 2010 Jan 21.

PMID:
20134426
16.

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.

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.

PLoS One. 2009 Jul 15;4(7):e6072. doi: 10.1371/journal.pone.0006072.

17.

Population genomics of domestic and wild yeasts.

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743. Epub 2009 Feb 11.

18.

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.

19.

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.

20.

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing.

Campbell PJ, Pleasance ED, Stephens PJ, Dicks E, Rance R, Goodhead I, Follows GA, Green AR, Futreal PA, Stratton MR.

Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13081-6. doi: 10.1073/pnas.0801523105. Epub 2008 Aug 22.

21.

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G.

Nat Genet. 2008 Aug;40(8):987-93. doi: 10.1038/ng.195. Epub 2008 Jul 27.

22.

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.

Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J.

Nature. 2008 Jun 26;453(7199):1239-43. doi: 10.1038/nature07002. Epub 2008 May 18.

PMID:
18488015
23.

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA.

Nat Genet. 2008 Jun;40(6):722-9. doi: 10.1038/ng.128. Epub 2008 Apr 27.

24.

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.

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.

Genome Res. 2008 May;18(5):729-41. doi: 10.1101/gr.075069.107. Epub 2008 Apr 10.

25.

Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates.

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.

Genome Res. 2008 Jan;18(1):161-71. Epub 2007 Nov 21.

26.

A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

Baker S, Holt K, Whitehead S, Goodhead I, Perkins T, Stocker B, Hardy J, Dougan G.

Mol Microbiol. 2007 Dec;66(5):1207-18. Epub 2007 Nov 1.

27.

Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.

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, Cerdeño-Tárraga 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.

Genome Res. 2007 Jul;17(7):1082-92. Epub 2007 May 22.

28.

A novel linear plasmid mediates flagellar variation in Salmonella Typhi.

Baker S, Hardy J, Sanderson KE, Quail M, Goodhead I, Kingsley RA, Parkhill J, Stocker B, Dougan G.

PLoS Pathog. 2007 May 11;3(5):e59.

29.

The genome of the African trypanosome Trypanosoma brucei.

Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Böhme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM.

Science. 2005 Jul 15;309(5733):416-22.

30.

The genome of the social amoeba Dictyostelium discoideum.

Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A.

Nature. 2005 May 5;435(7038):43-57.

31.

Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptoses.

Karlyshev AV, Champion OL, Churcher C, Brisson JR, Jarrell HC, Gilbert M, Brochu D, St Michael F, Li J, Wakarchuk WW, Goodhead I, Sanders M, Stevens K, White B, Parkhill J, Wren BW, Szymanski CM.

Mol Microbiol. 2005 Jan;55(1):90-103.

32.

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R, Baker S, Barron A, Brooks K, Buckee CO, Burrows C, Cherevach I, Chillingworth C, Chillingworth T, Christodoulou Z, Clark L, Clark R, Corton C, Cronin A, Davies R, Davis P, Dear P, Dearden F, Doggett J, Feltwell T, Goble A, Goodhead I, Gwilliam R, Hamlin N, Hance Z, Harper D, Hauser H, Hornsby T, Holroyd S, Horrocks P, Humphray S, Jagels K, James KD, Johnson D, Kerhornou A, Knights A, Konfortov B, Kyes S, Larke N, Lawson D, Lennard N, Line A, Maddison M, McLean J, Mooney P, Moule S, Murphy L, Oliver K, Ormond D, Price C, Quail MA, Rabbinowitsch E, Rajandream MA, Rutter S, Rutherford KM, Sanders M, Simmonds M, Seeger K, Sharp S, Smith R, Squares R, Squares S, Stevens K, Taylor K, Tivey A, Unwin L, Whitehead S, Woodward J, Sulston JE, Craig A, Newbold C, Barrell BG.

Nature. 2002 Oct 3;419(6906):527-31.

PMID:
12368867

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