SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. - Filip Bielejec; Andrew Rambaut; Marc A. Suchard; Philippe Lemey (Bioinform., 2011)

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. - Philippe Lemey; Vladimir N. Minin; Filip Bielejec; Sergei L. Kosakovsky Pond; Marc A. Suchard (Bioinform., 2012)

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. - Filip Bielejec; Philippe Lemey; Luiz Carvalho; Guy Baele; Andrew Rambaut; Marc A. Suchard (BMC Bioinform., 2014)

Virus genomes reveal factors that spread and sustained the Ebola epidemic. - Gytis Dudas; Luiz Max Carvalho; Trevor Bedford; Andrew J. Tatem; Guy Baele; Nuno R. Faria; Daniel J. Park; Jason T. Ladner; Armando Arias; Danny Asogun; Filip Bielejec; Sarah L. Caddy; et al. (Nat., 2017)