Publications:
A list of publications and public presentations of the Phyl-ARIANE project.
Affiliations: LIRMM ; ISEM ; LBBE
Journals:
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.
S. Abby, E. Tannier, M. Gouy and V. Daubin
BMC Bioinformatics. 2010 Jun 15;11:324. PubMed PMID: 20550700; PubMed Central PMCID: PMC2905365.
(Publication)
SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics.
V. Ranwez, A. Criscuolo and E. J. P. Douzery
Bioinformatics, Vol. 26, No. 12. (15 June 2010), pp. i115-123. Extended version of ISMB 2010.
(Website ; Publication)
ScripTree: scripting phylogenetic graphics.
F. Chevenet, O. Croce, M. Hebrard, R. Christen and V. Berry.
Bioinformatics. march 2010. [Epub ahead of print]. doi:10.1093/bioinformatics/btq086. PMID: 20194627.
(Website ; Publication)
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
JY. Dutheil, F. Jossinet and E. Westhof.
Mol Biol Evol. 2010 Mar 8. [Epub ahead of print]. PMID: 20211929.
(Publication)
Space of Gene/Species Trees Reconciliations and Parsimonious Models.
J-P. Doyon, C. Chauve, and S. Hamel
Journal of Comp. Biology, October 2009.
(PDF file)
Genomes as documents of evolutionary history.
B. Boussau and V. Daubin.
Trends Ecol. Evol. 2010 Apr;25(4):224-32. Epub 2009 Oct 31. Review. PubMed PMID: 19880211.
(PDF file)
PhyloExplorer: a web server to validate, explore and query phylogenetic trees.
V. Ranwez, F. Delsuc, N. Clairon, S. Pourali, N. Auberval, S. Diser and V. Berry.
BMC Evolutionary Biology, 2009, 9:108.
(PDF file)
Databases of homologous gene families for comparative genomics.
S. Penel, A-M. Arigon, J-F. Dufayard, A-S. Sertier, V. Daubin, L. Duret, M. Gouy and G. Perrière.
BMC Bioinformatics, vol. 10 pp.1-13, 2009.
(Publication)
Computing Galled Networks from Real Data.
D. Huson, R. Rupp, V. Berry, P. Gambette and C. Paul.
Bioinformatics, vol. 25, No. 12, pp. i85-i93, ISMB 2009. Implemented in Dendroscope.
(Publication)
International conferences:
Simultaneous inference of species tree and gene trees in the presence of duplications and losses.
B. Boussau, G. Szekely, L. Duret, M. Gouy, E. Tannier and V. Daubin.
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE'10) - "Integrative phylogenomics: from genes to organismal history" symposium, July 2010.
Horizontal gene transfer as a molecular clock.
G. Szöllösi, B. Boussau, E. Tannier and V. Daubin.
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE'10) - "Mathematical and computational phylogenetics" symposium, July 2010.
SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics.
V. Ranwez, A. Criscuolo and E. J. P. Douzery
ISMB 2010.
(PPT slides)
An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers.
J-P. Doyon, C. Scornavacca, K. Y. Gorbunov, G. Szöllösi, V. Ranwez and V. Berry
RECOMB Comparative Genomics, 2010.
(PDF file)
The Structure of Level-k Phylogenetic Networks.
P. Gambette, V. Berry and C. Paul
CPM 2009, LNCS 5577, pp. 289-300, Springer.
(PDF file)
Visualising a Text with a Tree Cloud.
P. Gambette and Jean Véronis
IFCS 2009, Studies in Classification, Data Analysis, and Knowledge Organization 40, pp. 561-570, Springer. Implemented in TreeCloud.
(PDF file)
From gene trees to species trees through a supertree approach.
C. Scornavacca, V. Berry, V. Ranwez
3rd Int. Conf. on Lang. and Automata Theor. and Applications (LATA), LNCS 5457, to appear.
(PDF file)
Phylogenomic analyses: dealing with incongruence.
N. Galtier, V. Daubin
SMBE 2008.
(Publication)
Others oral presentations:
Ultra-fast sequence clustering from similarity networks with SiLiX.
V. Miele, V. Miele and S. Penel
Long talk, JOBIM 2010.
Most parsimonious reconciliation of gene and species trees with duplications, transfers and losses.
J-P. Doyon, C. Scornavacca, G. Szöllösi, V. Ranwez and V. Berry
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE'10) - "Integrative phylogenomics: from genes to organismal history" track, July 2010.
(PDF slides)
An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers.
J-P. Doyon, C. Scornavacca, G. J. Szöllösi, V. Ranwez and V. Berry
JOBIM 2010.
(PDF file)
Reconstruction combinatoire de réseaux phylogénétiques.
Philippe Gambette
Journées annuelles
de la Société Française de Systématique, Angers, 2009-06-10.
(PDF file)
Space of Gene/Species Trees Reconciliations and Probabilistic Models.
Jean-Philippe Doyon, Sylvie Hamel and Cedric Chauve
Integrative Post-Genomics, Lyon, 2009-11.
(PDF file)
Méthode de construction et de comparaison d'arbres retraçant l'évolution des espèces depuis des données phylogénomiques
Yimin Shen
Stage de master, septembre 2009.
(PDF file)
Posters:
Extracting the speciation signal from multigene families
J-F. Dufayard, C. Scornavacca, V. Ranwez, V. Berry and V. Daubin
SMBE 2010, presented by C. Scornavacca.
(PDF file)
Prunier: Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.
S. Abby, E. Tannier, M. Gouy and V. Daubin
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE'10) - "Integrative phylogenomics: from genes to organismal history" symposium, July 2010.
(PDF file)
Les dates de divergence améliorent la qualité des superarbres.
Y. Shen, L. Bréhélin, E. J. P. Douzery and V. Berry
11ème congrès de la Société de Recherche Opérationnelle et d'Aide à la Décision (ROADEF), 2010.
(PDF file)
Phylogenomics - Integrated algorithms and visualizations for analyzing the evolution of life (Phylariane).
LIRMM ; ISEM ; LBBE
Présentation aux journées STIC de l'ANR : "Quelle recherche pour les STIC de demain ?", janvier 2010.
(PDF file)
Technical reports:
An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications, and Transfers.
J-P. Doyon, C. Scornavacca, G. J. Szöllösi, V. Ranwez and V. Berry
Technical report, 2010.
(Publication)
