Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads von Bertels, Frederic, Silander, Olin K., Pachkov, Mikhail, Rainey, Paul B., van Nimwegen, Erik

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Transposable elements promote the evolution of genome streamlining von van Dijk, Bram, Bertels, Frederic, Stolk, Lianne, Takeuchi, Nobuto, Rainey, Paul B

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Parallel Evolution of HIV-1 in a Long-Term Experiment von Bertels, Frederic, Leemann, Christine, Metzner, Karin J, Regoes, Roland R

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Discovering Complete Quasispecies in Bacterial Genomes von Bertels, Frederic, Gokhale, Chaitanya S, Traulsen, Arne

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Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease von McCann, Honour C, Rikkerink, Erik H A, Bertels, Frederic, Fiers, Mark, Lu, Ashley, Rees-George, Jonathan, Andersen, Mark T, Gleave, Andrew P, Haubold, Bernhard, Wohlers, Mark W, Guttman, David S, Wang, Pauline W, Straub, Christina, Vanneste, Joel L, Vanneste, Joel, Rainey, Paul B, Templeton, Matthew D

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Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria von Bertels, Frederic, Rainey, Paul B

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The perils of plenty: what are we going to do with all these genes? von Rodrigo, Allen, Bertels, Frederic, Heled, Joseph, Noder, Raphael, Shearman, Helen, Tsai, Peter

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Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens von Gallie, Jenna, Libby, Eric, Bertels, Frederic, Remigi, Philippe, Jendresen, Christian B, Ferguson, Gayle C, Desprat, Nicolas, Buffing, Marieke F, Sauer, Uwe, Beaumont, Hubertus J E, Martinussen, Jan, Kilstrup, Mogens, Rainey, Paul B

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Recombination of Virulence Genes in Divergent Acidovorax avenae Strains That Infect a Common Host von Zeng, Quan, Wang, Jie, Bertels, Frederic, Giordano, Paul R, Chilvers, Martin I, Huntley, Regan B, Vargas, Joseph M, Sundin, George W, Jacobs, Janette L, Yang, Ching-Hong

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Stepwise Evolution of E. coli C and ΦX174 Reveals Unexpected Lipopolysaccharide (LPS) Diversity von Romeyer Dherbey, Jordan, Parab, Lavisha, Gallie, Jenna, Bertels, Frederic

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Ancient Darwinian replicators nested within eubacterial genomes von Bertels, Frederic, Rainey, Paul B.

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Stepwise Evolution of E. coli C and [PHI]X174 Reveals Unexpected Lipopolysaccharide Diversity von Dherbey, Jordan Romeyer, Parab, Lavisha, Gallie, Jenna, Bertels, Frederic

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How sequence populations persist inside bacterial genomes von Park, Hye Jin, Gokhale, Chaitanya S, Bertels, Frederic

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A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes von Ngan, Wing Y, Parab, Lavisha, Bertels, Frederic, Gallie, Jenna

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Parallel evolution of HIV-1 in a long-term experiment von Bertels, Frederic, Leemann, Christine, Metzner, Karin J, Regoes, Roland

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Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements von Colombi, Elena, Bertels, Frederic, Doulcier, Guilhem, McConnell, Ellen, Pichugina, Tatyana, Sohn, Kee Hoon, Straub, Christina, McCann, Honour C, Rainey, Paul B

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The untapped potential of phage model systems as therapeutic agents von Romeyer Dherbey, Jordan, Bertels, Frederic

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Convergent evolution as an indicator for selection during acute HIV-1 infection von Bertels, Frederic, Metzner, Karin J., Regoes, Roland

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Repeated Phenotypic Evolution by Different Genetic Routes in Pseudomonas fluorescens SBW25 von Gallie, Jenna, Bertels, Frederic, Remigi, Philippe, Ferguson, Gayle C, Nestmann, Sylke, Rainey, Paul B

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Adaptive divergence in experimental populations of Pseudomonas fluorescens. V. Insight into the niche specialist fuzzy spreader compels revision of the model Pseudomonas radiation von Ferguson, Gayle C, Bertels, Frederic, Rainey, Paul B

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