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Items: 1 to 50 of 131

1.

Adaptive evolution by spontaneous domain fusion and protein relocalization.

Farr AD, Remigi P, Rainey PB.

Nat Ecol Evol. 2017 Oct;1(10):1562-1568. doi: 10.1038/s41559-017-0283-7. Epub 2017 Aug 28.

PMID:
29185504
2.

Fragmentation modes and the evolution of life cycles.

Pichugin Y, Peña J, Rainey PB, Traulsen A.

PLoS Comput Biol. 2017 Nov 22;13(11):e1005860. doi: 10.1371/journal.pcbi.1005860. eCollection 2017 Nov.

3.

Darwin was right: where now for experimental evolution?

Rainey PB, Remigi P, Farr AD, Lind PA.

Curr Opin Genet Dev. 2017 Dec;47:102-109. doi: 10.1016/j.gde.2017.09.003. Epub 2017 Oct 20. Review.

PMID:
29059583
4.

Identification and Characterization of Domesticated Bacterial Transposases.

Bertels F, Gallie J, Rainey PB.

Genome Biol Evol. 2017 Aug 1;9(8):2110-2121. doi: 10.1093/gbe/evx146.

5.

Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25.

Liu Y, Gokhale CS, Rainey PB, Zhang XX.

Mol Microbiol. 2017 Aug;105(4):589-605. doi: 10.1111/mmi.13720. Epub 2017 Jun 19.

PMID:
28557013
6.

Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas.

Gerth ML, Liu Y, Jiao W, Zhang XX, Baker EN, Lott JS, Rainey PB, Johnston JM.

Proteins. 2017 Aug;85(8):1580-1588. doi: 10.1002/prot.25303. Epub 2017 Apr 25.

PMID:
28383128
7.

Origin and Evolution of the Kiwifruit Canker Pandemic.

McCann HC, Li L, Liu Y, Li D, Pan H, Zhong C, Rikkerink EHA, Templeton MD, Straub C, Colombi E, Rainey PB, Huang H.

Genome Biol Evol. 2017 Apr 1;9(4):932-944. doi: 10.1093/gbe/evx055.

8.

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra.

Shewaramani S, Finn TJ, Leahy SC, Kassen R, Rainey PB, Moon CD.

PLoS Genet. 2017 Jan 19;13(1):e1006570. doi: 10.1371/journal.pgen.1006570. eCollection 2017 Jan.

9.

Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids.

Colombi E, Straub C, Künzel S, Templeton MD, McCann HC, Rainey PB.

Environ Microbiol. 2017 Feb;19(2):819-832. doi: 10.1111/1462-2920.13662. Epub 2017 Feb 1.

PMID:
28063194
10.

Evolutionary convergence in experimental Pseudomonas populations.

Lind PA, Farr AD, Rainey PB.

ISME J. 2017 Mar;11(3):589-600. doi: 10.1038/ismej.2016.157. Epub 2016 Dec 2.

PMID:
27911438
11.

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.

ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.

12.

Correction to 'Competition both drives and impedes diversification in a model adaptive radiation'.

Bailey SF, Dettman JR, Rainey PB, Kassen R.

Proc Biol Sci. 2016 Apr 27;283(1829). pii: 20160763. doi: 10.1098/rspb.2016.0763. No abstract available.

13.

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution.

Cottinet D, Condamine F, Bremond N, Griffiths AD, Rainey PB, de Visser JA, Baudry J, Bibette J.

PLoS One. 2016 Apr 14;11(4):e0152395. doi: 10.1371/journal.pone.0152395. eCollection 2016.

14.

The turnover of strains in intermittent and persistent nasal carriers of Staphylococcus aureus.

Ritchie SR, Isdale E, Priest P, Rainey PB, Thomas MG.

J Infect. 2016 Mar;72(3):295-301. doi: 10.1016/j.jinf.2015.12.010. Epub 2015 Dec 24.

PMID:
26724770
15.

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium.

Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore M, Winsor GL, Aaron SD, Barbeau J, Bell SC, Burns JL, Camara M, Cantin A, Charette SJ, Dewar K, Déziel É, Grimwood K, Hancock RE, Harrison JJ, Heeb S, Jelsbak L, Jia B, Kenna DT, Kidd TJ, Klockgether J, Lam JS, Lamont IL, Lewenza S, Loman N, Malouin F, Manos J, McArthur AG, McKeown J, Milot J, Naghra H, Nguyen D, Pereira SK, Perron GG, Pirnay JP, Rainey PB, Rousseau S, Santos PM, Stephenson A, Taylor V, Turton JF, Waglechner N, Williams P, Thrane SW, Wright GD, Brinkman FS, Tucker NP, Tümmler B, Winstanley C, Levesque RC.

Front Microbiol. 2015 Sep 29;6:1036. doi: 10.3389/fmicb.2015.01036. eCollection 2015.

16.

Modes of migration and multilevel selection in evolutionary multiplayer games.

Pichugin Y, Gokhale CS, Garcia J, Traulsen A, Rainey PB.

J Theor Biol. 2015 Dec 21;387:144-53. doi: 10.1016/j.jtbi.2015.09.027. Epub 2015 Oct 9.

PMID:
26456203
17.

Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol.

Liu Y, Rainey PB, Zhang XX.

Mol Microbiol. 2015 Oct;98(3):553-70. doi: 10.1111/mmi.13142. Epub 2015 Aug 16.

18.

Role of the Transporter-Like Sensor Kinase CbrA in Histidine Uptake and Signal Transduction.

Zhang XX, Gauntlett JC, Oldenburg DG, Cook GM, Rainey PB.

J Bacteriol. 2015 Sep;197(17):2867-78. doi: 10.1128/JB.00361-15. Epub 2015 Jul 6.

19.

Experimental evolution reveals hidden diversity in evolutionary pathways.

Lind PA, Farr AD, Rainey PB.

Elife. 2015 Mar 25;4. doi: 10.7554/eLife.07074.

20.

Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens.

Gallie J, Libby E, Bertels F, Remigi P, Jendresen CB, Ferguson GC, Desprat N, Buffing MF, Sauer U, Beaumont HJ, Martinussen J, Kilstrup M, Rainey PB.

PLoS Biol. 2015 Mar 12;13(3):e1002109. doi: 10.1371/journal.pbio.1002109. eCollection 2015 Mar.

21.

Precarious development: the uncertain social life of cellular slime molds.

Rainey PB.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2639-40. doi: 10.1073/pnas.1500708112. Epub 2015 Feb 23. No abstract available.

22.

Mini-Tn7 vectors for studying post-transcriptional gene expression in Pseudomonas.

Liu Y, Rainey PB, Zhang XX.

J Microbiol Methods. 2014 Dec;107:182-5.

PMID:
25447885
23.

Life cycles, fitness decoupling and the evolution of multicellularity.

Hammerschmidt K, Rose CJ, Kerr B, Rainey PB.

Nature. 2014 Nov 6;515(7525):75-9. doi: 10.1038/nature13884.

PMID:
25373677
24.

Microbes are not bound by sociobiology: response to Kümmerli and Ross-Gillespie (2013).

Rainey PB, Desprat N, Driscoll WW, Zhang XX.

Evolution. 2014 Nov;68(11):3344-55. doi: 10.1111/evo.12508. Epub 2014 Sep 29.

PMID:
25141778
25.

The genetic structure of Staphylococcus aureus populations from the Southwest Pacific.

Ritchie SR, Thomas MG, Rainey PB.

PLoS One. 2014 Jul 8;9(7):e100300. doi: 10.1371/journal.pone.0100300. eCollection 2014.

26.

Nascent multicellular life and the emergence of individuality.

De Monte S, Rainey PB.

J Biosci. 2014 Apr;39(2):237-48.

27.

The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography.

Whiteson KL, Bailey B, Bergkessel M, Conrad D, Delhaes L, Felts B, Harris JK, Hunter R, Lim YW, Maughan H, Quinn R, Salamon P, Sullivan J, Wagner BD, Rainey PB.

Am J Respir Crit Care Med. 2014 Jun 1;189(11):1309-15. doi: 10.1164/rccm.201312-2129PP.

28.

The biosurfactant viscosin produced by Pseudomonas fluorescens SBW25 aids spreading motility and plant growth promotion.

Alsohim AS, Taylor TB, Barrett GA, Gallie J, Zhang XX, Altamirano-Junqueira AE, Johnson LJ, Rainey PB, Jackson RW.

Environ Microbiol. 2014 Jul;16(7):2267-81. doi: 10.1111/1462-2920.12469. Epub 2014 Apr 29.

PMID:
24684210
29.

Automated reconstruction of whole-genome phylogenies from short-sequence reads.

Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E.

Mol Biol Evol. 2014 May;31(5):1077-88. doi: 10.1093/molbev/msu088. Epub 2014 Mar 5.

30.

Eco-evolutionary feedback and the tuning of proto-developmental life cycles.

Libby E, Rainey PB.

PLoS One. 2013 Dec 18;8(12):e82274. doi: 10.1371/journal.pone.0082274. eCollection 2013.

31.

Founder niche constrains evolutionary adaptive radiation.

Flohr RC, Blom CJ, Rainey PB, Beaumont HJ.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20663-8. doi: 10.1073/pnas.1310310110. Epub 2013 Dec 4.

32.

Urocanate as a potential signaling molecule for bacterial recognition of eukaryotic hosts.

Zhang XX, Ritchie SR, Rainey PB.

Cell Mol Life Sci. 2014 Feb;71(4):541-7. doi: 10.1007/s00018-013-1527-6. Epub 2013 Dec 5.

PMID:
24305948
33.

Exploring the sociobiology of pyoverdin-producing Pseudomonas.

Zhang XX, Rainey PB.

Evolution. 2013 Nov;67(11):3161-74. doi: 10.1111/evo.12183. Epub 2013 Jul 10.

PMID:
24152000
34.
35.

Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.

McCann HC, Rikkerink EH, Bertels F, Fiers M, Lu A, Rees-George J, Andersen MT, Gleave AP, Haubold B, Wohlers MW, Guttman DS, Wang PW, Straub C, Vanneste JL, Rainey PB, Templeton MD.

PLoS Pathog. 2013;9(7):e1003503. doi: 10.1371/journal.ppat.1003503. Epub 2013 Jul 25. Erratum in: PLoS Pathog. 2013;9(9). doi:10.1371/annotation/af157ddc-200a-4105-b243-3f01251cc677. Vanneste, Joel [corrected to Vanneste, Joel L].

36.

Competition both drives and impedes diversification in a model adaptive radiation.

Bailey SF, Dettman JR, Rainey PB, Kassen R.

Proc Biol Sci. 2013 Sep 7;280(1766):20131253. doi: 10.1098/rspb.2013.1253. Print 2013 Sep 7. Erratum in: Proc Biol Sci. 2016 Apr 27;283(1829). pii: 20160763. doi: 10.1098/rspb.2016.0763.

37.

The effect of population structure on the rate of evolution.

Frean M, Rainey PB, Traulsen A.

Proc Biol Sci. 2013 May 15;280(1762):20130211. doi: 10.1098/rspb.2013.0211. Print 2013 Jul 7.

38.

Cystic fibrosis therapy: a community ecology perspective.

Conrad D, Haynes M, Salamon P, Rainey PB, Youle M, Rohwer F.

Am J Respir Cell Mol Biol. 2013 Feb;48(2):150-6. doi: 10.1165/rcmb.2012-0059PS. Epub 2012 Oct 25. Review.

39.

Evolution: How the unicorn got its horn.

Hendrickson H, Rainey PB.

Nature. 2012 Sep 27;489(7417):504-5. doi: 10.1038/nature11487. Epub 2012 Sep 19. No abstract available.

PMID:
22992522
40.

Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting.

Kidd TJ, Ritchie SR, Ramsay KA, Grimwood K, Bell SC, Rainey PB.

PLoS One. 2012;7(9):e44199. doi: 10.1371/journal.pone.0044199. Epub 2012 Sep 6.

41.

Curiosities of REPINs and RAYTs.

Bertels F, Rainey PB.

Mob Genet Elements. 2011 Nov 1;1(4):262-268.

42.

Genome sequence of the biocontrol strain Pseudomonas fluorescens F113.

Redondo-Nieto M, Barret M, Morrisey JP, Germaine K, Martínez-Granero F, Barahona E, Navazo A, Sánchez-Contreras M, Moynihan JA, Giddens SR, Coppoolse ER, Muriel C, Stiekema WJ, Rainey PB, Dowling D, O'Gara F, Martín M, Rivilla R.

J Bacteriol. 2012 Mar;194(5):1273-4. doi: 10.1128/JB.06601-11.

43.

Variation in transport explains polymorphism of histidine and urocanate utilization in a natural Pseudomonas population.

Zhang XX, Chang H, Tran SL, Gauntlett JC, Cook GM, Rainey PB.

Environ Microbiol. 2012 Aug;14(8):1941-51. doi: 10.1111/j.1462-2920.2011.02692.x. Epub 2012 Jan 9.

PMID:
22225938
44.

The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1.

Gerth ML, Ferla MP, Rainey PB.

Environ Microbiol. 2012 Aug;14(8):1929-40. doi: 10.1111/j.1462-2920.2011.02691.x. Epub 2012 Jan 9.

PMID:
22225844
45.

The evolutionary emergence of stochastic phenotype switching in bacteria.

Rainey PB, Beaumont HJ, Ferguson GC, Gallie J, Kost C, Libby E, Zhang XX.

Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S14. doi: 10.1186/1475-2859-10-S1-S14. Epub 2011 Aug 30.

46.

Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung.

Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, Rainey PB, Schmieder R, Youle M, Conrad D, Rohwer F.

Am J Respir Cell Mol Biol. 2012 Feb;46(2):127-31. doi: 10.1165/rcmb.2011-0253OC. Epub 2011 Oct 6.

47.

Spatial distribution of microbial communities in the cystic fibrosis lung.

Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, Rohwer F, Conrad D.

ISME J. 2012 Feb;6(2):471-4. doi: 10.1038/ismej.2011.104. Epub 2011 Jul 28.

48.

Nasal carriage of Staphylococcus aureus in healthy Aucklanders.

Best N, Fraser JD, Rainey PB, Roberts SA, Thomas MG, Ritchie SR.

N Z Med J. 2011 Apr 15;124(1332):31-9.

PMID:
21747421
49.

Demographic variation in community-based MRSA skin and soft tissue infection in Auckland, New Zealand.

Ritchie SR, Fraser JD, Libby E, Morris AJ, Rainey PB, Thomas MG.

N Z Med J. 2011 Apr 15;124(1332):21-30.

PMID:
21747420
50.

Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria.

Bertels F, Rainey PB.

PLoS Genet. 2011 Jun;7(6):e1002132. doi: 10.1371/journal.pgen.1002132. Epub 2011 Jun 16.

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