Publications of Paul Rainey

Timmis, K.; Williams, P.; Karahan, Z. C.; López‐García, P.; Rainey, P.; Chavarria, M.; Greening, C.; Steward, K.; Hallsworth, J. E.; Pereira, C. S. et al.; Giraldo, R.; Verstraete, W.; Jonjić, S.; Ramos, J. L.; Nunes, O.; Ventosa, A.; Armstrong, R.; Sessitsch, A.; Ron, E.; Wang, H.: Journals operating predatory practices are systematically eroding the science ethos: agate and code strategy to minimise their operating space and restore research best practice. Microbial Biotechnology 18 (6), e70180 (2025)

Barnett, M.; Meister, L.; Rainey, P. B.: Experimental evolution of evolvability. Science 387 (6736), eadr2756 (2025)

Farr, A. D.; Vasileiou, C.; Lind, P. A.; Rainey, P. B.: An extreme mutational hotspot in nlpD depends on transcriptional induction of rpoS. PLOS Genetics 21 (1), e1011572 (2025)

Bourrat, P.; Takacs, P.; Doulcier, G.; Nitschke, M. C.; Black, A. J.; Hammerschmidt, K.; Rainey, P. B.: Individuality through ecology: Rethinking the evolution of complex life from an externalist perspective. PLOS Biology 14, e70661 (2024)

Colombi, E.; Bertels, F.; Doulcier, G.; McConnell, E.; Pichugina, T.; Sohn, K. H.; Straub, C.; McCann, H.; Rainey, P. B.: Rapid dissemination of host-metabolism-manipulating transposon-like entities via integrative and conjugative elements. PNAS 121 (11), e2309263121 (2024)

Moreno Fenoll, C.; Ardré, M.; Rainey, P. B.: Polar accumulation of pyoverdin facilitates rapid exit from stationary phase. microLife 5, uqae001 (2024)

Gokhale, C. S.; Frean, M.; Rainey, P. B.: Eco-evolutionary logic of mutualisms. Dynamic Games and Applications 13, pp. 1066 - 1087 (2023)

Rainey, P. B.: Major evolutionary transitions in individuality between humans and AI. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 378 (1872), 20210408 (2023)

Fortmann-Grote, C.; Hugoson, E.; Summers, J.; Theodosiou, L.; Rainey, P. B.: Genome update for Pseudomonas fluorescens isolate SBW25. Microbiology Resource Announcements 12 (2), e00637-22 (2023)

Bertels, F.; Rainey, P. B.: Ancient Darwinian replicators nested within eubacterial genomes. Bioessays 45 (2), 2200085 (2023)

Nitschke, M. C.; Black, A. J.; Bourrat, P.; Rainey, P. B.: The effect of bottleneck size on evolution in nested Darwinian populations. Journal of Theoretical Biology 561, 111414 (2023)

Rainey, P. B.: Humans and AI - on the way to symbiosis? Max Planck Research: the science magazine of the Max Planck Society 3, pp. 16 - 21 (2023)

van Dijk, B.; Buffard, P.; Farr, A. D.; Giersdorf, F.; Meijer, J.; Dutilh, B. E.; Rainey, P. B.: Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME Communications 3, 90 (2023)

Wortel, M. T.; Agashe, D.; Bailey, S. F.; Bank, C.; Bisschop, K.; Blankers, T.; Cairns, J.; Colizzi, E. S.; Cusseddu, D.; Desai, M. M. et al.; van Dijk, B.; Egas, M.; Ellers, J.; Groot, A. T.; Heckel , D. G.; Johnson, M. L.; Kraaijeveld, K.; Krug, J.; Laan, L.; Lässig, M.; Lind, P. A.; Meijer, J.; Noble, L. M.; Okasha, S.; Rainey, P. B.; Rozen, D. E.; Shitut, S.; Tans, S. J.; Tenaillon, O.; Teotónio, H.; de Visser, J. A. G. M.; Visser, M. E.; Vroomans, R. M. A.; Werner, G. D. A.; Wertheim, B.; Pennings, P. S.: Towards evolutionary predictions: current promises and challenges. Evolutionary Applications 16 (1), pp. 3 - 21 (2023)

Ardré, M.; Doulcier, G.; Brenner, N.; Rainey, P. B.: A leader cell triggers end of lag phase in populations of Pseudomonas fluorescens. microLife 3, uqac022 (2022)

Bourrat, P.; Doulcier, G.; Rose, C. J.; Rainey, P. B.; Hammerschmidt, K.: Tradeoff breaking as a model of evolutionary transitions in individuality and limits of the fitness-decoupling metaphor. eLife 11, e73715 (2022)

Theodosiou, L.; Farr, A.; Rainey, P. B.: Barcoding populations of Pseudomonas fluorescens SBW25. Journal of Molecular Evolution: the Journal of the International Society of Molecular Evolution 91, pp. 254 - 262 (2022)

van Dijk, B.; Bertels, F.; Stolk, L.; Takeuchi, N.; Rainey, P. B.: Transposable elements promote the evolution of genome streamlining. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 377 (1842), 20200477 (2022)

Paulson, A. R.; O’Callaghan, M.; Zhang, X.-X.; Rainey, P. B.; Hurst, M. R. H.: In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella. G3: Genes, Genomes, Genetics 11 (1), jkaa024 (2021)

Rose, C. J.; Hammerschmidt, K.; Pichugin, Y.; Rainey, P. B.: Meta-population structure and the evolutionary transition to multicellularity. Ecology Letters 23, pp. 1380 - 1390 (2020)