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 00 (00), e00637-22 (2023)

Bertels, F.; Rainey, P. B.: Ancient Darwinian replicators nested within eubacterial genomes. Bioessays, e2200085, pp. 1 - 13 (2022)

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

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)

Garza, D. R.; von Meijenfeldt, F. A. B.; van Dijk, B.; Boleij, A.; Huynen, M. A.; Dutilh, B. E.: Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. BMC Ecology and Evolution 22, 101 (2022)

Hugoson, E.; Guliaev, A.; Ammunét, T.; Guy, L.: Host adaptation in Legionellales Is 1.9 Ga, coincident with eukaryogenesis. Molecular Biology and Evolution 39 (3), msac037 (2022)

Juncheng, E.; Kim, Y.; Bielecki, J.; Sikorski, M.; de Wijn, R.; Fortmann-Grote, C.; Sztuk-Dambietz, J.; Koliyadu, J. C. P.; Letrun, R.; Kirkwood, H. J. et al.; Sato, T.; Bean, R.; Mancuso, A. P.; Kim, C.: Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. Structural Dynamics 9 (6), 064101 (2022)

van Dijk, B.: Cacatoo: building, exploring, and sharing spatiallystructured models of biological systems. The Journal of Open Source Software 7 (70), 3948 (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)

Park, H. J.; Gokhale, C. S.; Bertels, F.: How sequence populations persist inside bacterial genomes. Genetics 217 (7), iyab027 (2021)

E, J.; Stransky, M.; Jurek, Z.; Fortmann-Grote, C.; Juha, L.; Santra, R.; Ziaja, B.; Mancuso, A. P.: Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser. Scientific Reports 11, 17976 (2021)

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)

van Dijk, B.: Can mobile genetic elements rescue genes from extinction? Current Genetics 66 (6), pp. 1069 - 1071 (2020)

Opašić, L.; Scott, J. G.; Traulsen, A.; Fortmann-Grote, C.: CancerSim: A cancer simulation package for python 3. The Journal of Open Source Software 5 (53), 2436 (2020)

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)

Doulcier, G.; Lambert, A.; De Monte, S.; Rainey, P. B.: Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity. eLife 9, e53433 (2020)

Zhang, X.; Ritchie, S. R.; Chang, H.; Arnold, D. L.; Jackson, R. W.; Rainey, P. B.: Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet‐associatedPseudomonasin Oxford and Auckland. Ecology and Evolution 10, pp. 5963 - 5975 (2020)

Quistad, S. D.; Doulcier, G.; Rainey, P. B.: Experimental manipulation of selfish genetic elements links genes to microbial community function. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 375, 20190681 (2020)

Rainey, P. B.; Quistad, S. D.: Toward a dynamical understanding of microbial communities. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 375 (1798), 20190248 (2020)