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Publications


Journal articles28 documents

  • Rémi Allio, Celine Scornavacca, Benoit Nabholz, Anne-Laure Clamens, Felix A. H. Sperling, et al.. Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution. Systematic Biology, Oxford University Press (OUP), In press, ⟨10.1093/sysbio/syz030⟩. ⟨hal-02125214⟩
  • Laurent Brottier, Clémence Chaintreuil, Paul Simion, Celine Scornavacca, Ronan Rivallan, et al.. A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses. BMC Plant Biology, BioMed Central, 2018, 18 (1), ⟨10.1186/s12870-018-1567-z⟩. ⟨hal-01961745⟩
  • Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, et al.. RecPhyloXML: a format for reconciled gene trees. Bioinformatics, Oxford University Press (OUP), 2018, 34 (21), pp.3646-3652. ⟨10.1093/bioinformatics/bty389⟩. ⟨lirmm-01800296⟩
  • Steven Kelk, Fabio Pardi, Celine Scornavacca, Leo Van Iersel. Finding a most parsimonious or likely tree in a network with respect to an alignment. Journal of Mathematical Biology, Springer Verlag (Germany), 2018, ⟨10.1007/s00285-018-1282-2⟩. ⟨lirmm-01964467⟩
  • Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, et al.. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Research, Oxford University Press, 2017, ⟨10.1093/nar/gkx1108⟩. ⟨hal-01636650⟩
  • Philippe Gambette, Leo Van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, et al.. Rearrangement Moves on Rooted Phylogenetic Networks. PLoS Computational Biology, Public Library of Science, 2017, 13 (8), pp.e1005611.1-21. ⟨10.1371/journal.pcbi.1005611⟩. ⟨hal-01572624v2⟩
  • Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, et al.. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2017, 9 (5), pp.1312-1319. ⟨10.1093/gbe/evx069⟩. ⟨hal-01503766v2⟩
  • Celine Scornavacca, Nicolas Galtier. Incomplete Lineage Sorting in Mammalian Phylogenomics. Systematic Biology, Oxford University Press (OUP), 2016, 66, pp.112 - 120. ⟨10.1093/sysbio/syw082⟩. ⟨hal-01815360⟩
  • Edwin Jacox, Cedric Chauve, Gergely J Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.. Bioinformatics (Oxford, England), 2016, pp.2056-8. ⟨hal-01276903⟩
  • François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin, et al.. SylvX: a viewer for phylogenetic tree reconciliations. Bioinformatics, Oxford University Press (OUP), 2016, 32 (4), pp.608-610. ⟨10.1093/bioinformatics/btv625⟩. ⟨hal-01942605⟩
  • Steven Kelk, Leo Van Iersel, Celine Scornavacca, Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. Journal of Graph Algorithms and Applications (JGAA), Brown University, 2016, 20 (2), pp.189-215. ⟨10.7155/jgaa.00390⟩. ⟨lirmm-01348425⟩
  • Mark Jones, Christophe Paul, Celine Scornavacca. On the consistency of orthology relationships. BMC Bioinformatics, BioMed Central, 2016, 17 (S14), ⟨10.1186/s12859-016-1267-3⟩. ⟨lirmm-01481206⟩
  • Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio Pardi. Fast and accurate branch lengths estimation for phylogenomic trees. BMC Bioinformatics, BioMed Central, 2016, 17 (23), ⟨10.1186/s12859-015-0821-8⟩. ⟨lirmm-01236485⟩
  • Magnus Bordewich, Celine Scornavacca, Nihan Tokac, Mathias Weller. On the fixed parameter tractability of agreement-based phylogenetic distances. Journal of Mathematical Biology, Springer Verlag (Germany), 2016, In press. ⟨10.1007/s00285-016-1023-3⟩. ⟨lirmm-01348420⟩
  • Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon, Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. Journal of Mathematical Biology, Springer Verlag (Germany), 2016, 72 (7), pp.1811-1844. ⟨10.1007/s00285-015-0930-z⟩. ⟨hal-01370854⟩
  • Philippe Gambette, Leo Van Iersel, Steven Kelk, Fabio Pardi, Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network?. Bulletin of Mathematical Biology, Springer Verlag, 2016, 78 (9), pp.1773-1795. ⟨10.1007/s11538-016-0199-4⟩. ⟨hal-01372824⟩
  • Matija Brozovic, Cyril Martin, Christelle Dantec, Delphine Dauga, Mickäel Mendez, et al.. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Research, Oxford University Press, 2016, 44 (D1), pp.D808-D818. ⟨10.1093/nar/gkv966⟩. ⟨hal-01295171⟩
  • Yao-Ban Chan, Vincent Ranwez, Céline Scornavacca. Exploring the space of gene/species reconciliations with transfers. Journal of Mathematical Biology, Springer Verlag (Germany), 2015, 71 (5), pp.1179-1209. ⟨10.1007/s00285-014-0851-2⟩. ⟨hal-01268903⟩
  • Fabio Pardi, Celine Scornavacca. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable. PLoS Computational Biology, Public Library of Science, 2015, 11 (4), pp.e1004135. ⟨10.1371/journal.pcbi.1004135⟩. ⟨lirmm-01194638⟩
  • Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, et al.. Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution. Molecular Biology and Evolution, Oxford University Press (OUP), 2013, 30 (8), pp.1745 - 1750. ⟨10.1093/molbev/mst097⟩. ⟨hal-01209906⟩
  • Yao-Ban Chan, Vincent Ranwez, Celine Scornavacca. Reconciliation-based detection of co-evolving gene families. BMC Bioinformatics, BioMed Central, 2013, 14, 15 p. ⟨10.1186/1471-2105-14-332⟩. ⟨hal-01189789⟩
  • Celine Scornavacca, Wojciech Paprotny, Vincent Berry, Vincent Ranwez. Representing a set of reconciliations in a compact way. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2013, 11 (2), pp.1250025. ⟨http://www.worldscientific.com/doi/abs/10.1142/S0219720012500254⟩. ⟨10.1142/S0219720012500254⟩. ⟨lirmm-00818801⟩
  • Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry, Celine Scornavacca. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PLoS ONE, Public Library of Science, 2013, 8 (10), pp.e73667. ⟨10.1371/journal.pone.0073667 ⟩. ⟨hal-01189798⟩
  • Steven Kelk, Leo Van Iersel, Nela Lekic, Simone Linz, Celine Scornavacca, et al.. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. Siam Journal on Discrete Mathematics, Society for Industrial and Applied Mathematics, 2012, 26 (4), pp.1635-1656. ⟨hal-00765019⟩
  • Celine Scornavacca, Vincent Berry, Vincent Ranwez. Building species trees from larger parts of phylogenomic databases. Information and Computation, Elsevier, 2011, 209 (3), pp.590-605. ⟨http://www.sciencedirect.com/science/article/pii/S0890540110002087⟩. ⟨10.1016/j.ic.2010.11.022⟩. ⟨lirmm-00825050⟩
  • M.D.V. Braga, M.-F. Sagot, C. Scornavacca, E. Tannier. Exploring the Solution Space of Sorting by Reversals with Experiments and an Application to Evolution. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2008, 5 - n°3, pp.348-356. ⟨hal-00428206⟩
  • Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel Douzery, Vincent Ranwez. PhySIC IST : cleaning source trees to infer more informative supertrees. BMC Bioinformatics, BioMed Central, 2008, 9 (413), pp.1471-2105. ⟨http://www.atgc-montpellier.fr/physic ist/⟩. ⟨10.1186/1471-2105-9-413⟩. ⟨lirmm-00324069⟩
  • Vincent Ranwez, Vincent Berry, Alexis Criscuolo, Pierre-Henri Fabre, Sylvain Guillemot, et al.. PhySIC: A Veto Supertree Method with Desirable Properties. Systematic Biology, Oxford University Press (OUP), 2007, 56 (5), pp.293-304. ⟨http://www.atgc-montpellier.fr/physic/⟩. ⟨lirmm-00194235⟩

Conference papers10 documents

  • Julien Baste, Christophe Paul, Ignasi Sau, Celine Scornavacca. Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees. AAIM: Algorithmic Aspects in Information and Management, Jul 2016, Bergamo, Italy. pp.53-64, ⟨10.1007/978-3-319-41168-2_5⟩. ⟨lirmm-01481368⟩
  • Fabio Pardi, Celine Scornavacca. Reconstructible phylogenetic networks: do not distinguish the indistinguishable. Evolution, Jun 2015, Guarujà, Brazil. ⟨lirmm-01237428⟩
  • Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio Pardi. Fast and accurate branch length estimation for phylogenomic trees: ERaBLE (Evolutionary Rates and Branch Length Estimation). Rencontres ALPHY - Génomique Evolutive, Bioinformatique, Alignement et Phylogénie, Mar 2015, Montpellier, France. ⟨lirmm-01237447⟩
  • Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio Pardi. Fast and accurate branch lengths estimation for phylogenomic trees. Evolution, Jun 2015, Guarujà, Brazil. ⟨lirmm-01237507⟩
  • Fabio Pardi, Celine Scornavacca. Reconstructible phylogenetic networks: no need to distinguish the indistinguishable. Waiheke: The Interface of Mathematics and Biology - New Zealand Phylogenomics Meeting, Feb 2014, Waiheke, New Zealand. ⟨lirmm-01237408⟩
  • Fabio Pardi, Celine Scornavacca. Identifiability of phylogenetic networks. MCEB: Mathematical and Computational Evolutionary Biology, Jun 2014, Hameau de l'Etoile, St Martin de Londres, France. ⟨lirmm-01237418⟩
  • Jean-Philippe Doyon, Celine Scornavacca, Gergely J. Szöllősi, Vincent Ranwez, Vincent Berry. Un algorithme de parcimonie efficace pour la réconciliation d'arbres de gènes/espèces avec pertes, duplications et transferts. Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, France. pp.8. ⟨lirmm-00833164⟩
  • Jean-Philippe Doyon, Celine Scornavacca, Yu Gorbunov, Gergely Szöllősi, Vincent Ranwez, et al.. An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. RECOMB'10: Comparative Genomics, Oct 2010, Ottawa, Canada. pp.93-108, ⟨10.1007/978-3-642-16181-0_9⟩. ⟨lirmm-00818889⟩
  • Celine Scornavacca, Vincent Berry, Vincent Ranwez. From Gene Trees to Species Trees Through a Supertree Approach. LATA'09: Third International Conference on Language and Automata Theory and Applications, Apr 2009, Tarragone, Espagne, pp.10-19. ⟨lirmm-00367086⟩
  • M.D.V. Braga, M.-F. Sagot, C. Scornavacca, E. Tannier. The solution space of sorting by reversals. ISBRA 2007, May 2007, Atlanta, United States. pp.293-304, ⟨10.1007/978-3-540-72031-7_27⟩. ⟨hal-00434566⟩

Other publications1 document

  • Cédric Chauve, Akbar Rafiey, Adrian Davin, Celine Scornavacca, Philippe Veber, et al.. MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers. 2017, ⟨10.1101/127548⟩. ⟨hal-01532738v3⟩

Theses1 document

  • Celine Scornavacca. Supertree methods for phylogenomics. Bioinformatics [q-bio.QM]. Université Montpellier II - Sciences et Techniques du Languedoc, 2009. English. ⟨tel-00842893⟩