Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). - Cédric Chauve; Jean-Philippe Doyon; Nadia El-Mabrouk (RECOMB-CG, 2007)

Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations. - Jean-Philippe Doyon; Cédric Chauve; Sylvie Hamel (RECOMB-CG, 2008)

Gene Family Evolution by Duplication, Speciation, and Loss. - Cédric Chauve; Jean-Philippe Doyon; Nadia El-Mabrouk (J. Comput. Biol., 2008)

Space of Gene/Species Trees Reconciliations and Parsimonious Models. - Jean-Philippe Doyon; Cédric Chauve; Sylvie Hamel (J. Comput. Biol., 2009)

An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. - Jean-Philippe Doyon; Céline Scornavacca; K. Yu. Gorbunov; Gergely J. Szöllosi; Vincent Ranwez; Vincent Berry (RECOMB-CG, 2010)

Models, algorithms and programs for phylogeny reconciliation. - Jean-Philippe Doyon; Vincent Ranwez; Vincent Daubin; Vincent Berry (Briefings Bioinform., 2011)

Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. - Thi Hau Nguyen; Jean-Philippe Doyon; Stéphanie Pointet; Anne-Muriel Arigon Chifolleau; Vincent Ranwez; Vincent Berry (WABI, 2012)

An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework. - Jean-Philippe Doyon; Sylvie Hamel; Cédric Chauve (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Reconciliation and local gene tree rearrangement can be of mutual profit. - Thi Hau Nguyen; Vincent Ranwez; Stéphanie Pointet; Anne-Muriel Arigon Chifolleau; Jean-Philippe Doyon; Vincent Berry (Algorithms Mol. Biol., 2013)

SylvX: a viewer for phylogenetic tree reconciliations. - François Chevenet; Jean-Philippe Doyon; Céline Scornavacca; Edwin Jacox; Emmanuelle Jousselin; Vincent Berry (Bioinform., 2016)