Publications:
A list of publications and public presentations of the Phyl-ARIANE project.
Affiliations: LIRMM ; ISEM ; LBBE
Journals:
Lateral gene transfer as a support for the tree of life
S. Abby, E. Tannier, M. Gouy and V. Daubin
In revision for PNAS
(No link yet)
Quartets and unrooted phylogenetic networks
P. Gambette, V. Berry and C. Paul
Journal of Bioinformatics and Computational Biology (accepted), 2012.
(PDF file)
Conflict packing yields linear vertex-kernels for k-fast, k-dense RTI and a related problem.
C. Paul, A. Perez and S. Thomassé.
Mathematical Foundations of Computer Science (MFCS). Number 6907 in Lecture Notes in Computer Science, pages 497-507, 2011.
(PDF file)
On Encodings of Phylogenetic Networks of Bounded Level.
P. Gambette, KT. Huber
Journal of Mathematical Biology. To appear.
(PDF file)
An O(n.m) algorithm for calculating the closure of lca-type operators.
V. Ranwez, Stefan Janaqi and Sylvie Ranwez
Ars Combinatoria ( to be published in vol 104, April 2012)
(No link yet)
User Centered and Ontology Based Information Retrieval System for Life Sciences
Mohameth-François Sy, Sylvie Ranwez, Jacky Montmain, Armelle Regnault, Michel Crampes, V. Ranwez
BMC Bioinformatics accepted
(No link yet)
Ultra-fast sequence clustering from similarity networks with SiLiX.
V. Miele, S. Penel, L. Duret
BMC Bioinformatics 12:116, 2011.
(Publication)
Building species trees from larger parts of phylogenomic databases.
C. Scornavacca, V. Berry. and V. Ranwez
Information and Computation, (209): pp. 590-605, 2011
(Publication)
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
V. Ranwez, Sébastien Harispe, EJP. Douzery, EJP. Douzery
Plos One 6(9): e22594, 2011.
(Publication)
Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).
Juan S Escobar, C. Scornavacca, Alberto Cenci, Claire Guilhaumon, Sylvain Santoni, EJP. Douzery, V. Ranwez, Sylvain Glemin and Jacques David
BMC Evolutionary Biology, 11:181, 2011
(Publication)
Sub-ontology extraction using hyponym and hypernym closure on is-a directed acyclic graphs.
V. Ranwez, Sylvie Ranwez and Stefan Janaqi.
IEEE Transactions on Knowledge and Data Engineering 99, 2011.
(Publication)
Models, algorithms, and programs for phylogeny reconciliation.
J-P. Doyon, V. Ranwez, V. Daubin and V. Berry.
Briefings in Bioinformatics (2011) 12(5):392-400.
(Publication)
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.
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)
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, september 2010.
(PDF file, PDF slides)
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:
Phyl-ARIANE. Phylogénomique : Algorithmes et Représentations Intégrés pour l'ANalyse de l'Évolution du vivant
E. Tannier
Colloque ANR STIC 2012, Lyon.
(PDF slides)
Practical use of combinatorial methods for phylogenetic network reconstruction.
P. Gambette
Alphy 2011, Lyon.
(PDF slides)
Prunier: Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.
S. Abby
Alphy 2011, Lyon.
Simultaneous inference of gene trees and organism tree in the presence of duplications and losses.
B. Boussau
Alphy 2011, Lyon.
Horizontal gene transfer as a molecular clock.
G. Szöllösi
Alphy 2011, Lyon.
Quartets and unrooted phylogenetic networks.
P. Gambette
Phylogenetics: New data, new Phylogenetic challenges, Follow-up Meeting, Cambridge, June 2011.
(PDF slides)
Ultra-fast sequence clustering from similarity networks with SiLiX.
V. Miele, V. Miele and S. Penel
Long talk, JOBIM 2010.
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:
A web-based collaborative platform for comparing phylogenies
N. Fiorini, A. Bish, F. Dumond, M. Agbessi, F. Chevenet, V. Lefort, A-M. Chifolleau and V. Berry
JOBIM 2011, presented by N. Fiorini.
(PDF file)
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 method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework
J-P. Doyon, S. Hamel and C. Chauve
Technical report, 2010.
(Publication)
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, April, 10th 2010.
(Publication)
French journals and bookchapters:
Extraction de sous-ontologies autonomes par fermeture des opérateurs hyponymie et hyperonymie.
V. Ranwez, S. Ranwez, S. Janaqi.
Technique et science informatiques (to appear).
Reconstruction combinatoire de réseaux phylogénétiques.
P. Gambette
Biosystema 28 "L'arbre du vivant existe-t-il ?", pp. 85-92, 2011.
Phylogénie moléculaire (chapitre 9).
S. Blanquart, A. Criscuolo, C. Douady, EJP. Douzery, N. Lartillot, H. Philippe, V. Ranwez,
in Biologie Evolutive, (M. Raymond, T. Lefèvre, and F. Thomas, eds.), De Boek Université, Bruxelles, Belgique, 2010.
