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Publications:

A list of publications and public presentations of the Phyl-ARIANE project.
Affiliations: LIRMM ; ISEM ; LBBE

Journals:

Representing a set of reconciliations in a compact way.
C. Scornavacca, W. Paprotny, V. Berry, V. Ranwez
In revision for Journal of Bioinformatics and Computational Biology, 2012.

Amalgamating Source Trees with Different Taxonomic Levels.
V. Berry, O. Bininda-Emonds, C. Semple
In revision for Systematic Biology, 2012.

User centered and ontology based information retrieval system for life sciences.
M.F. Sy, S. Ranwez, J. Montmain, A. Regnault, M. Crampes, V. Ranwez
BMC Informatics 13(Suppl 1):S4, 2012.
(Website ; Publication)

ANGES: reconstructing ANcestral GEnomeS maps.
B.R. Jones, A. Rajaraman, E. Tannier, C. Chauve
Bioinformatics vol. 28(18) pp.2388-2390, 2012.
(Publication)

Lateral gene transfer as a support for the tree of life.
S. Abby, E. Tannier, M. Gouy, V. Daubin
PNAS 2012 109 (13) 4962-4967; published ahead of print March 13, 2012.
(Publication)

Quartets and unrooted phylogenetic networks.
P. Gambette, V. Berry, C. Paul
Journal of Bioinformatics and Computational Biology Vol. 10, No. 04, 2012.
(PDF file)

Conflict packing yields linear vertex-kernels for k-fast, k-dense RTI and a related problem.
C. Paul, A. Perez, 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, K. Huber
Journal of Mathematical Biology Volume 65, Number 1, Pages 157-180, 2012.
(PDF file)

An O(n.m) algorithm for calculating the closure of lca-type operators.
V. Ranwez, S. Janaqi, S. Ranwez
Ars Combinatoria Volume 104, 107-128, 2012.
(No link yet)

Mapping ancestral genomes with massive gene loss : A matrix sandwich problem.
H. Gavranovic, C. Chauve, J. Salse, E. Tannier
Bioinformatics, vol. 27(13) pp.i257-i265, 2011.
(Publication)

Reconstructing the architecture of the ancestral amniote genome.
A. Ouangraoua, E. Tannier, C. Chauve
Bioinformatics, vol. 27(19) pp.2664-2671, 2011.
(Publication)

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, 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, S. Harispe, F. Delsuc, E.J.P. Douzery
Plos One 6(9): e22594, 2011.
(Publication)

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).
J.S. Escobar, C. Scornavacca, A. Cenci, C. Guilhaumon, S. Santoni, E.J.P. Douzery, V. Ranwez, S. Glemin, J. David
BMC Evolutionary Biology, 11:181, 2011.
(Publication)

Sub-ontology extraction using hyponym and hypernym closure on is-a directed acyclic graphs.
V. Ranwez, S. Ranwez, S. 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, V. Berry
Briefings in Bioinformatics (2011) 12(5):392-400.
(Publication)

Bayesian sampling of genomic rearrangement scenarios via double cut and join.
I. Miklós, E. Tannier
Bioinformatics, vol. 26(24) pp.3012-3019, 2010.
(Publication)

The origin of eukaryotes and their evolutionary relationship with the Archaea: have we reached a phylogenomic impasse?
S. Gribaldo, A.M. Poole, V. Daubin, P. Forterre, C. Brochier-Armanet
Nature Review Microbiology, vol. 8(10) pp.743-52, 2010.
(PDF file)

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.
S. Abby, E. Tannier, M. Gouy, 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, 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, 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.
J.Y. 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, S. Hamel
Journal of Comp. Biology, October 2009.
(PDF file)

Genomes as documents of evolutionary history.
B. Boussau, 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, 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, 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, C. Paul
Bioinformatics, vol. 25, No. 12, pp. i85-i93, ISMB 2009. Implemented in Dendroscope.
(Publication)

International conferences:

Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses predictions.
T.H. Nguyen, J.P. Doyon, S. Pointet, A.M. Arigon Chifolleau, V. Ranwez, V. Berry
Proc. of the 12th Workshop on Algorithms in Bioinformatics (WABI'12), LNBI, Springer.
(Publication)

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, 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.J. Szöllösi, B. Boussau, E. Tannier, 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.J. Szöllösi, V. Ranwez, 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, 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.J. Szöllösi, V. Ranwez, V. Berry
RECOMB Comparative Genomics, september 2010.
(PDF file, PDF slides)

The Structure of Level-k Phylogenetic Networks.
P. Gambette, V. Berry, C. Paul
CPM 2009, LNCS 5577, pp. 289-300, Springer.
(PDF file)

Visualising a Text with a Tree Cloud.
P. Gambette, J. 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)

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.J. 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)

CompPhy: a web-based collaborative platform for comparing phylogenies.
N. Fiorini
JOBIM 2011.

Utilisation de proximités sémantiques pour améliorer la recherche et le rendu d'information.
S. Ranwez, V. Ranwez, M.F. Sy, J. Montmain, M. Crampes
21es Journées Francophones d'Ingénierie des Connaissances - IC2010, Nîmes.

OrthoMaM et PhyloExplorer : deux outils pour l'exploration et l'exploitation des marqueurs et arbres phylogénétiques.
E.J.P. Douzery
Alphy 2010, Marseille.

Ultra-fast sequence clustering from similarity networks with SiLiX.
V. Miele, V. Miele, 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, V. Berry
JOBIM 2010.
(PDF file)

Reconstruction combinatoire de réseaux phylogénétiques.
P. Gambette
Journées annuelles de la Société Française de Systématique, Angers, 2009-06-10.
(PDF file)

Space of Gene/Species Trees Reconciliations and Probabilistic Models.
J.P. Doyon, S. Hamel, C. 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
Y. 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, 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, 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, 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, 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, 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, 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, volume 31/1, pp. 11-38, 2012.

Reconstruction combinatoire de réseaux phylogénétiques.
P. Gambette
Biosystema 28 "L'arbre du vivant existe-t-il ?", pp. 85-92, 2011.

Des séquences moléculaires à l'Arbre de la Vie : résultats théoriques, algorithmes et outils pour la phylogénomique.
V. Ranwez
HDR soutenues le 6 décembre 2010.
(PDF file and abstract)

Phylogénie moléculaire (chapitre 9).
S. Blanquart, A. Criscuolo, C. Douady, E.J.P. Douzery, N. Lartillot, H. Philippe, V. Ranwez
in Biologie Evolutive, (M. Raymond, T. Lefèvre, and F. Thomas, eds.), De Boek Université, Bruxelles, Belgique, 2010.



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