Frederic Bertels

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1. Explaining REPIN distribution across bacterial strains

Bacterial genomes are almost devoid of repetitive sequences compared to their eukaryotic counterparts. Yet, there is one type of repetitive sequence called REPINs that is present in hundreds of copies in a large number of bacterial genomes. In this project we will analyze the distribution of REPINs across different bacterial species. The main aim of this analysis will be to devise a predictive model that can explain REPIN distributions across different species. This project requires a strong bioinformatics background.


  1. Park HJ, Gokhale CS, Bertels F. 2020. How sequence populations persist inside a genome. bioRxiv:2020.06.25.170514.
  2. Bertels F, Gallie J, Rainey PB. 2017. Identification and Characterization of Domesticated Bacterial Transposases. Genome Biol. Evol. 9:2110–2121.
  3. Bertels F, Gokhale CS, Traulsen A. 2017. Discovering Complete Quasispecies in Bacterial Genomes. Genetics 206:2149–2157.
  4. Bertels F, Rainey PB. 2011. Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria. PLoS Genet. 7:e1002132.
  5. Bertels F, Rainey PB. 2011. Curiosities of REPINs and RAYTs. Mob Genet Elements 1:262–268.

2. Environmental trade-offs of phage infection

We have observed that the efficiency of phage infection is strongly dependent on the environment the bacterial host is cultured in. Phages that are efficient at infecting bacteria in liquid are usually very inefficient at infecting bacteria growing on solid media. This effect is very simple to reverse. A random mutagenesis screen of a phage well adapted to infecting bacteria in liquid media will yield plenty of well-adapted phage infecting bacteria in solid media. The prospective student will investigate this phenomenon by performing evolution experiments and measure the change in the fitness landscapes between liquid and solid environment.

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