Publications

 

Paul Rainey’s publications on Google Scholar

Steven Quistad’s publications on Google Scholar

Maxime Ardré’s publications on Goolge Scholar

Guilhem Doulcier’s publications on Google Scholar


Recent publications
Ardré, M. & Rainey P. B. (2019 under rev.). Causes and consequences of cellulose production by Pseudomonas fluorescens SBW25 at the air-liquid interface. BioRxiv. DOI:https://doi.org/10.1101/538561

Pichugin, Y., Peña, J., Rainey, P. B. & Tralusen, A. (2017). Fragmentation modes and the evolution of life cycles. PLoS Computational Biology. DOI: 10.1371/journal.pcbi.1005860

Rainey, P. B., Remigi, P., Farr, A. D. & Lind, P. A. (2017). Darwin was right: where now for experimental evolution? Current Opinion in Genetics and Development. 47, 102-109. DOI: 10.1016/j.gde.2017.09.003

Farr, A. D., Remigi, P. & Rainey, P. B. (2017). Adaptive evolution by spontaneous domain fusion and protein re-localisation. Nature Ecology and Evolution 1, 1562-1568. DOI: 10.1038/s41559-017-0283-7

Bertels, F., Gallie, J. & P. B. Rainey. (2017). Identification and characterisation of domesticated bacterial transposases. Genome Biology and Evolution 9, 2110-2121. DOI: 10.1093/gbe/evx146

Liu, Y, Gokhale, C. S., Rainey, P. B. & Zhang, X.-X. (2017). Unravelling the complexity and redundancy of carbon catabolic repression in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. Molecular Microbiology 105, 589-605. DOI: 10.1111/mmi.13720

McCann, H. C., Li, L., Liu, Y., Templeton, M., Colombi, E., Straub, C., Rainey, P. B*. & Huang, H.* (2017). Origin and evolution of the kiwifruit canker pandemic. *Joint senior authors. Genome Biology and Evolution 9, 932-944. DOI: 10.1093/gbe/evx055

Gerth, M. L., Liu, Y., Jiao, W., Zhang, X.-X., Baker, E. N., Lott, J. S., Rainey, P. B. & Johnston, J. M. (2017). Crystal structure of a bicupin protein HutD involved in histidine utilisation in Pseudomonas 85, 1580-1588. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.25303

Shewaramani, S., Finn, T. J., Leahy, S. C., Kassen, R., Rainey, P. B. & Moon, C. D. (2017). Anaerobically grown Escherichia coli has an enhanced mutation rate and distinct mutational spectra. PLoS Genetics. DOI: 10.1371/journal.pgen.1006570

Colombi, E., Straub, C., Kunzel, S., Templeton, M. D., McCann, H. C. & Rainey, P. B. (2017). Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids. Environmental Microbiology 19, 819-832. DOI: 10.1111/1462-2920.13662. See also accompanying Research Highlight by Steve Lindow (2017) Horizontal gene transfer gone wild: promiscuity in a kiwifruit pathogen leads to resistance to chemical control. Environmental Microbiology 19, 1363-1365. DOI: 10.1111/1462-2920.13717

Lind, P. A., Farr, A. D. & Rainey, P. B. (2017). Convergence in experimental Pseudomonas populations. ISME Journal 11, 589-600. DOI: 10.1038/ismej.2016.157


Selected publications

Lind, P. A., Farr, A.D. & Rainey, P. B. (2015). Experimental evolution reveals hidden diversity in evolutionary pathways. eLife 10.7554/eLife.07074. DOI: 10.7554/eLife.07074

Gallie, J., Libby, E., Bertels, F., Remigi, P., Jendresen, C. B., Ferguson, G. C., Desprat, N., Buffing, M. F., Sauer, U., Beaumont, H. J. E., Martinussen, J., Kilstrup, M. & Rainey, P. B. (2015). Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biology 13(3): e1002109. DOI: 10.1371/journal.pbio.1002109

Hammerschmidt, K., Rose, C., Kerr, B. & Rainey, P. B. (2014). Life cycles, fitness decoupling and the evolution of multicellularity. Nature 515, 75-79. DOI: 10.1038/nature13884

Rainey, P. B., Desprat, N., Driscoll, W. W. & Zhang, X.-X. (2014). Microbes are not bound by sociobiology. Evolution 68, 3344-3355. DOI: 10.1111/evo.12508

Rainey, P. B. & De Monte, S. (2014). Resolving conflicts during the transition to multicellular life. Annual Review of Ecology Evolution and Systematics 45, 599-620. DOI: 10.1146/annurev-ecolsys-120213-091740

Zhang, X.-X. & Rainey, P. B. (2013). Exploring the social biology of pyoverdin-producing Pseudomonas. Evolution 67, 3161-3174. DOI: 10.1111/evo.12183

McCann, H., Rikkerink, E. H., Bertels, F. Fiers, M., Lu, A., Rees-George, J., Andersen, M. T., Gleave, A. P., Haubold, B., Wohlers, Guttman, D. S., Wang, P., Vanneste, J., Rainey, P. B*. & Templeton, M. D*. (2013). Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insights into the origins of an emergent plant disease. PLoS Pathogens 9(7): e1003503. *Joint senior authors. DOI: 10.1371/journal.ppat.1003503

Libby, E. & Rainey, P. B. (2013). A conceptual framework for the evolutionary origins of multicellularity. Physical Biology 10, 035001. DOI: 10.1088/1478-3975/10/3/035001.

Bertels, F. & Rainey, P. B. (2011). Within genome evolution of REPINs: A new family of miniature mobile DNA in bacteria. PLoS Genetics, 7(6): e1002132.

Libby, E. & Rainey, P. B. (2011). Exclusion rules, population bottlenecks, and the evolution of stochastic switching. Proceedings of the Royal Society (London) B 278, 3574-3583. DOI:10.1098/rspb.2011.0146.

Refardt, D. & Rainey, P. B. (2010). Tuning a genetic switch: experimental evolution and natural variation of prophage induction. Evolution 64, 1086-1097.

Beaumont, H. J. E., Gallie, J., Kost, C., Ferguson, G. C. & Rainey, P. B. (2009). Experimental evolution of bet-hedging. Nature 462, 90-93.

McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X.-X. & Rainey, P. B. (2009). Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183, 1041-1053.

Silby, M. W., Cerdeno-Tarranga, A. M., Vernikos, G., Giddens, S. R., Jackson, R. W., Preston, G. M., Zhang, X.-X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M. A., Saunders, E., Anderson, I., Mavromat, K., Brettin, T. S., Bentley, S., Hothersall, J., Stephens, E., Thomas, C. M., Parkhill, J., Levy, S. B., Rainey, P. B. & Thomson, N. R. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10, R51.

Giddens, S. R., Jackson, R. W., Moon, C. D., Jacobs, M. A., Zhang, X.-X., Gehrig, S. M. & Rainey, P. B. (2007). Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proceedings of the National Academy of Sciences, USA 104, 18247-18252.

Rainey, P. B. (2007). Unity from conflict. Nature 446, 616.

Fukami, T, Beaumont, H. J. E. & Zhang, X.-X. Rainey, P. B. Immigration history controls diversification in experimental adaptive radiation. Nature 446, 436-439.

Kirkelund Hansen, S., Rainey, P. B*., Haagensen, J. A. J & Molin, S. (2007). Evolution of species interactions in a biofilm community. Nature 445, 533-536. *Corresponding author.

Knight, C. G., Zitzmann, N, Prabhakar, S, Antrobus, R, Dwek, R, Hebestreit, H., & Rainey, P. B. (2006). Unravelling adaptive evolution: how a single point mutation affects the protein co-regulation network. Nature Genetics 38, 1015-1022.

Knight, C. G., Kassen, R, Hebestreit, H. & Rainey, P. B. (2004) Global analysis of predicted proteomes: functional adaptation and physical properties. Proceedings of the National Academy of Sciences, USA 101, 8390-8395.

MacLean, C. Bell, G. & Rainey, P. B. (2004) The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proceedings of the National Academy of Sciences, USA 101, 8072-8077.

Kassen, R & Rainey, P. B. (2004). The ecology and genetics of microbial diversity. Annual Review of Microbiology 58, 207-231.

Jessup, C. M., Kassen, R., Forde, S. E., Kerr, B., Buckling, A., Rainey, P. B. & Bohannan, B. J. M. (2004) Big questions, small worlds: Microbial model systems in ecology. Trends in Ecology and Evolution 19, 189-197.

Gal, M., Preston, G. M., Massey, R. M., Spiers, A. J. & Rainey, P. B. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Molecular Ecology 12, 3109-3121.

Rainey, P. B. & Rainey. K. (2003). Evolution of co-operation and conflict in experimental bacterial populations. Nature 425, 72-74.

Buckling, A. & Rainey, P. B. (2002). The role of parasites on sympatric and allopatric diversification of hosts. Nature 420, 496-499.

D’Argenio, D. A., Calfee, M. W., Rainey, P. B. & Pesci, E. C. (2002) Autolysis and autoaggregation in Pseudomonas aeruginosa colony morphology mutants. Journal of Bacteriology 184, 6481-6489.

Buckling, A & Rainey, P. B. (2002). Antagonistic coevolution between a bacterium and a bacteriophage. Proceedings of the Royal Society (London) B 269, 931-936.

Spiers, A. J., Kahn, S. G., Bohannon, J., Travisano, M. & Rainey, P. B. (2002). Adaptive divergence in experimental populations of Pseudomonas fluorescens. 1. Genetic and phenotypic bases of wrinkly spreader fitness. Genetics 161, 33-46.

Preston, G. M. Bertrand, N. & Rainey, P. B. (2001). Type III (Hrp) secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Molecular Microbiology 41, 999-1014.

Buckling, A. Kassen, R. Bell, G. & Rainey, P. B. (2000). Diversity and disturbance in experimental microcosms. Nature 408, 961-964.

Kassen, R. Buckling, A. Bell, G. & Rainey, P. B. (2000) Diversity peaks at intermediate productivity in a laboratory microcosm. Nature 406, 508-512.

Spiers, A. J., Buckling, A. & Rainey, P. B. (2000). The causes of Pseudomonas diversity. Microbiology 146, 2345-2350.

Rainey, P. B. (1999). Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environmental Microbiology 1, 243-258.

Rainey, P. B. & Travisano, M. (1998) Adaptive radiation in a heterogeneous environment. Nature 394, 69-72.

Haubold, B. & Rainey, P. B. (1996). Genetic and ecotypic structure of a fluorescent Pseudomonas population. Molecular Ecology 5, 747-761.

Moxon, E. R., Rainey, P. B., Nowak, M. & Lenski, R. E (1994). Adaptive evolution of highly mutable loci in pathogenic bacteria. Current Biology 4, 24-33.

Rainey, P. B. & Moxon, E. R. (1993). Unusual mutational mechanisms and evolution. Science 260, 1958.


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