Fortmann-Grote, C.; von Irmer, J.; Bertels, F.: RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes. Peer Community Journal 3, e19 (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, S. 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), S. 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)

Hernandez-Beltran, J. C. R.; Miró Pina, V.; Siri‐Jégousse, A.; Palau, S.; Peña‐Miller, R.; González Casanova, A.: Segregational instability of multicopy plasmids: a population genetics approach. Ecology and Evolution 12 (12), e9469 (2022)

Parab, L.; Pal, S.; Dhar, R.: Transcription factor binding process is the primary driver of noise in gene expression. PLoS Genetics 18 (12), e1010535 (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)

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)

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, S. 254 - 262 (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)

Bertels, F.; Metzner, K. J.; Regoes, R. R.: Convergent evolution as an indicator for selection during acute HIV-1 infection. Peer Community Journal 1, e4 (2021)

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)