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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), S. 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, S. 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, S. 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)

Black, A. J.; Bourrat, P.; Rainey, P. B.: Ecological scaffolding and the evolution of individuality. Nature Ecology & Evolution 4, S. 426 - 436 (2020)

Bertels, F.; Leemann, C.; Metzner, K. J.; Regoes, R.: Parallel evolution of HIV-1 in a long-term experiment. Molecular Biology and Evolution 36 (11), S. 2400 - 2414 (2019)

Czuppon, P.; Rogers, D. W.: Evolution of mating types in finite populations: the precarious advantage of being rare. Journal of Evolutionary Biology 32 (11), S. 1290 - 1299 (2019)

Hugoson, E.; Lam, W. T.; Guy, L.: miComplete: weighted quality evaluation of assembled microbial genomes. Bioinformatics, btz664 (2019)

Ardré, M.; Dufour, D.; Rainey, P. B.: Causes and biophysical consequences of cellulose production by Pseudomonas fluorescens SBW25 at the air-liquid interface. Journal of Bacteriology 201 (18), e00110-19 (2019)

Gallie, J.; Bertels, F.; Remigi, P.; Ferguson, G. C.; Nestmann, S.; Rainey, P. B.: Repeated phenotypic evolution by different genetic routes in Pseudomonas fluorescens SBW25. Molecular Biology and Evolution 36 (5), S. 1071 - 1085 (2019)

Remigi, P.; Ferguson, G. C.; McConnell, E.; De Monte, S.; Rogers, D. W.; Rainey, P. B.: Ribosome provisioning activates a bistable switch coupled to fast exit from stationary phase. Molecular Biology and Evolution 36 (5), S. 1056 - 1070 (2019)