Since January 2013, I'm a postdoctoral researcher in the Phylogenomics Lab of David Posada.
From 2009 to 2012, I was a postdoctoral researcher in the Computational Biology (LIRMM) and Molecular Phylogeny (ISEM) groups. I
worked with Vincent Berry and Vincent Ranwez. As a member of the Phyl-ARIANE project,
my main interest is to depict gene family evolutionary scenario through
reconciliation between gene and species trees. More specifically:
combinatorial and probabilistic aspects of reconciliations, efficient
inference of reconciliation, enumerative combinatorics, the problem of
horizontal gene transfer in bacterial genomes, etc.
During my PhD in computer science at "Université de Montréal", under the supervision of Cedric Chauve, Sylvie Hamel, and Hervé Philippe, I studied the
combinatorial architecture of the space of reconciliations according to
discrete criteria and probabilistic models.
Programs and Biological Analysis
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- Mowgli: a program that computes a Most Parsimonious Reconciliation (with
Dup, Transfer and Loss) between a gene tree and a (dated) species tree
(in collaboration with C. Scornavacca): http://www.atgc-montpellier.fr/Mowgli/
Publications in Refereed Journals
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Thi Hau Nguyen, Vincent Ranwez, Stephanie Pointet, Anne-Muriel. Chifolleau, Jean-Philippe Doyon
and Vincent Berry. Reconciliation and local gene tree rearrangement can
be of mutual profit. Accepted to Algorithms for Molecular Biology.
J-P. Doyon, V. Ranwez, V.
Daubin, and V. Berry. Models, algorithms and programs for phylogeny
reconciliation. Brief Bioinform (2011) 12(5): 392-400
doi:10.1093/bib/bbr045 (link)
J-P. Doyon and C. Chauve.
Branch-and-Bound approach for parsimonious inference of a species tree
from a set of gene family trees. In: Software Tools and Algorithms for
Biological Systems. Springer
(book series, Advances in Experimental Medicine and Biology), (to appear in April 2011).
J-P. Doyon, S.
Hamel and C. Chauve. An efficient method for exploring the space of
gene tree/species tree reconciliations in a probabilistic framework. Accepted to IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011 (link)
J-P. Doyon, C. Chauve, and S. Hamel. Space of
Gene/Species Trees Reconciliations and Parsimonious Models. Journal of
Comp. Biology, October 2009. (pdf)
C. Chauve, J-P. Doyon, and N. El-Mabrouk. Gene family evolution by
duplication, speciation and loss. Journal of Comp. Biology. 15:1043-1062, 2008. (link)
Publications in Conference Proceedings
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J-P. Doyon, C. Scornavacca, K.
Y. Gorbunov, G. Szöllösi, V. Ranwez and V. Berry, An efficient
algorithm for gene/species trees parsimonious reconciliation with
losses, duplications and transfers. RCG-CG 2010 (pdf)
J-P. Doyon, C. Scornavacca, G. J. Szöllösi, V. Ranwez and V. Berry. An
efficient algorithm for gene/species trees parsimonious reconciliation
with losses, duplications, and transfers. JOBIM 2010 (pdf)
J-P. Doyon, C. Chauve, and S. Hamel. Algorithms for exploring the space
of gene tree/species tree reconciliations. LNCS/LNBI 5267:1-13, RCG-CG 2008
(pdf)
C. Chauve, J-P. Doyon, and N. El-Mabrouk. Inferring a duplication,
speciation and loss history from a gene tree. LNCS/LNBI
4751:45-57, RCG-CG 2007. (pdf)
J-P. Doyon,
C. Scornavacca, G. J. Szöllösi, V. Ranwez and V. Berry. An Efficient
Algorithm for Gene/Species Trees Parsimonious Reconciliation with
Losses, Duplications, and Transfers. LIRMM, 2010 (link)
J-P. Doyon
and C. Chauve. Branch-and-Bound Approach for Parsimonious Inference of
a Species Tree From a Set of Gene Family Trees. LIRMM, 2010 (link)
J-P. Doyon, C. Chauve, and S. Hamel. Algorithms for exploring the space
of gene tree/species tree reconciliations. 2008 (pdf)
J-P. Doyon, C. Scornavacca, K. Yu. Gorbunov, G. Szöllösi, V. Ranwez and V.
Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. RCG-CG, Ottawa, 2010. (pdf)
J-P.
Doyon, C. Scornavacca, G. J. Szöllösi, V. Ranwez and V. Berry. An
efficient algorithm for gene/species trees parsimonious reconciliation
with losses, duplications, and transfers. JOBIM 2010 (pdf)
J-P. Doyon, C. Scornavacca, G. Szöllösi, V. Ranwez and V.
Berry. Most parsimonious reconciliation of gene and species trees with
duplications, transfers and losses. SMBE 2010 (pdf)
J-P. Doyon, C. Chauve, and S. Hamel. Space of Gene/Species
Trees Reconciliations and Probabilistic Models. Integrative
Post-Genomics. France, 2009 (pdf)
J-P. Doyon, C. Chauve, and S. Hamel. Algorithms for exploring the space
of gene tree/species tree reconciliations. RCG-CG,
Paris, 2008. (pdf)
C. Chauve, J-P. Doyon, and N. El-Mabrouk. Inferring a duplication and
speciation history from a gene tree [2]. SMBE 2007. (pdf)
C. Chauve, J-P. Doyon, and N. El-Mabrouk. Inferring a duplication and
speciation history from a gene tree. Poster, RCG-CG 2006. (pdf)
J-P. Doyon. Méthode de recherche de gčnes orthologues, Réunion de Bioinformatique
Comparative et Intégrative, Canada, 2005 (ppt, pdf)
J-P. Doyon. IRIS: An Automated Nurse Scheduling System, Les Journées de
l'Optimisation, Canada, 2002
J-P. Doyon. Algorithmes pour la réconciliation d’un arbre de gčnes avec un arbre d’espčces. Ph.D. thesis. Université de Montréal (pdf)
J-P. Doyon. Algorithme de "branch-and-price" pour la confection d'horaires d'infirmičres (pdf)
