Parab, L.; Romeyer Dherbey, J.; Rivera, N.; Schwarz, M.; Gallie, J.; Bertels, F.: Chloramphenicol and gentamicin reduce the evolution of resistance to phage ΦX174 by suppressing a subset of E. coli LPS mutants. PLOS Biology 23 (1), e3002952 (2025)

Ngan, W. Y.; Parab, L. S.; Bertels, F.; Gallie, J.: A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes. mBio 16 (1), e03052-24 (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)

Romeyer Dherbey, J.; Bertels, F.: The untapped potential of phage model systems as therapeutic agents. Virus Evolution 10 (1), veae007 (2024)

Romeyer Dherbey, J.; Parab, L.; Gallie, J.; Bertels, F.: Stepwise evolution of E. coli C and ΦX174 reveals unexpected Lipopolysaccharide (LPS) diversity. Molecular Biology and Evolution 40 (7), msad154 (2023)

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)

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)

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)

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)

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

Bons, E.; Bertels, F.; Regoes, R. R.: Estimating the mutational fitness effects distribution during early HIV infection. Virus Evolution 4 (2), vey029 (2018)

Bertels, F.; Gallie, J.; Rainey, P. B.: Identification and characterization of domesticated bacterial transposases. Genome Biology and Evolution 9 (8), S. 2110 - 2121 (2017)

Bertels, F.; Gokhale, C. S.; Traulsen, A.: Discovering complete quasispecies in bacterial genomes. Genetics 206 (4), S. 2149 - 2157 (2017)

Zeng, Q.; Wang, J.; Bertels, F.; Giordano, P. R.; Chilvers, M. I.; Huntley, R. B.; Vargas, J. M.; Sundin, G. W.; Jacobs, J. L.; Yang, C.-H.: Recombination of virulence genes in divergent acidovorax avenae strains that infect a common host. Molecular Plant-Microbe Interactions 30 (10), S. 813 - 828 (2017)

Fortmann-Grote, C.; Bertels, F.; Irmer, J.: RAREFAN: a publicly accessible bioinformatic pipeline on a cloud server - Implementation and limitations. Workshop on "Life Science/Bioinformatics and HPC 2023, at GWDG (2023)

Böhmker, C.: The evolutionary dynamics and functional role of the REPIN-RAYT system in the hut locus of Pseudomonas fluorescens SBW25. Dissertation, 142 S., Christian-Albrechts-Universität, Kiel (2025)