Bastien Boussau

TL;DR: The corresponding model is implemented into a method named PCOC that recovers several previously identified convergent substitutions and proposes credible new candidates and is shown to better recovers convergent shifts than existing methods in terms of sensitivity and specificity.

TL;DR: In this paper, the authors introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree and introduce modules to simplify the representation of standard components in large and complex models.

TL;DR: A method to correct gene trees, extensively test it, and apply it to the reconstruction of 64 eukaryote ancestral genomes, showing that according to several measures including running time, likelihood, stability of genome content and linearity of ancestral chromosomes, trees corrected by RefineTree are arguably more plausible than the ones stored by Ensembl.

TL;DR: The results uncovered ZIKV adaptations to the cell environment leading to an accelerated replication onset coupled with resistance to TLR3-induced antiviral response, which provides insights into viral escape mechanisms and interactions with host cell and can serve as a framework to study other viruses.

TL;DR: In this paper , the authors established a pipeline to delineate at high-resolution the genetic evolution of ZIKV in a controlled host cell environment and uncovered that serially passaged ZIKVs acquired increased infectivity and simultaneously developed a resistance to TLR3-induced restriction.