Evolution of gene neighborhoods within reconciled phylogenies. - Sèverine Bérard; Coralie Gallien; Bastien Boussau; Gergely J. Szöllosi; Vincent Daubin; Eric Tannier (Bioinform., 2012)

RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

Phylogenomics, convergent evolution, and the Anthropocene. (Phylogénomique, évolution convergente, et l'Anthropocène). - Bastien Boussau (2019)

CAARS: comparative assembly and annotation of RNA-Seq data. - Carine Rey; Philippe Veber; Bastien Boussau; Marie Sémon (Bioinform., 2019)

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. - Nicolas Comte; Benoit Morel; Damir Hasic; Laurent Guéguen; Bastien Boussau; Vincent Daubin; Simon Penel; Céline Scornavacca; Manolo Gouy; Alexandros Stamatakis; Eric Tannier; David P. Parsons (Bioinform., 2020)