F. Bertels

Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes

The paper provides empirical evidence that some insertion sequences (ISs) can repair DNA breaks in bacterial genomes by inserting without generating target site duplications (TSDs) during large-scale genome rearrangements.

Chloramphenicol and gentamicin reduce resistance evolution to phage {Phi}X174 by suppressing a subset of E. coli C LPS mutants

Rapid dissemination of host-metabolism-manipulating transposon-like entities via integrative and conjugative elements

The paper identifies a transposon-like entity in Pseudomonas syringae ICEs that manipulates bacterial metabolism, with a key regulator affecting gene expression and fitness.

Stepwise evolution of E. coli C and {varphi}X174 reveals unexpected lipopolysaccharide (LPS) diversity

This study evolves E. coli C and its phage {Phi}X174 to reveal unexpected LPS diversity and show that current LPS biology understanding is insufficient to predict phage adaptation.

Ancient Darwinian replicators nested within eubacterial genomes

The paper identifies REPINs as non-autonomous mobile genetic elements that form long-term beneficial associations with bacterial genomes, showing evidence of mutualistic relationships through population dynamics and conservation patterns.

Transposable elements drive the evolution of genome streamlining

The paper shows that transposable elements can drive genome streamlining in prokaryotes through horizontal gene transfer and rock-paper-scissors dynamics, despite being maladaptive to individual cells.

How sequence populations persist inside a genome

The paper models how sequence populations can persist in bacterial genomes by balancing benefits and costs, showing that horizontal gene transfer and population dynamics play key roles.

Convergent evolution as an indicator for selection during acute HIV-1 infection

The paper examines convergent mutations in HIV-1 env genes during early infection, finding an excess of convergent mutations indicating positive selection and purifying selection on private mutations.

Repeated phenotypic evolution by different genetic routes: the evolution of colony switching in Pseudomonas fluorescens SBW25

This study shows that two independent lineages of Pseudomonas fluorescens SBW25 evolved colony switching through different genetic mutations, with Line 6 relying on an rpoD mutation affecting ribosome expression.

Dissecting HIV Virulence: Heritability Of Setpoint Viral Load, CD4+ T Cell Decline And Per-Parasite Pathogenicity

The paper estimates heritability of HIV virulence traits using donor-recipient regression and phylogenetic models, finding moderate heritability for CD4+ T cell decline and per-parasite pathogenicity.

Identification And Characterization Of Domesticated Bacterial Transposases

The paper identifies and characterizes RAYTs, a class of bacterial transposases, showing they are domesticated and functionally integrated into host genomes.

Discovering Complete Quasispecies In Bacterial Genomes

The paper models REPIN populations in bacterial genomes as quasispecies, estimates duplication rates, and identifies trade-offs between REPIN survival and host genome mutational load.