Keywords

Co-authors

Number of documents

55

Vincent Berry


Journal articles32 documents

  • 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⟩
  • Vincent Berry, François Chevenet, Jean-Philippe Doyon, Emmanuelle Jousselin. A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactions. Molecular Ecology Resources, Wiley/Blackwell, 2018, 18 (5), pp.1173-1184. ⟨10.1111/1755-0998.12897⟩. ⟨hal-01942777⟩
  • Floréal Cabanettes, Jean-François Dufayard, Vincent Berry, Vincent Lefort, Frederic de Lamotte Guéry, et al.. CompPhy2: a flexible and real time collaborative web platform for editing and comparing phylogenies. Bioinformatics, Oxford University Press (OUP), In press. ⟨hal-01885401⟩
  • Gaëtan Droc, Guillaume Martin, Julie Sardos, Alberto Cenci, Björn Geigle, et al.. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2018, 10 (12), pp.3129-3140. ⟨10.1093/gbe/evy227⟩. ⟨lirmm-02097189⟩
  • 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⟩
  • 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⟩
  • Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, et al.. Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S11. ⟨10.1186/1471-2164-16-S10-S11⟩. ⟨hal-01180303v2⟩
  • François Hubert, Guido W. Grimm, Emmanuelle Jousselin, Vincent Berry, Alain Franc, et al.. Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus. Systematics and Biodiversity, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2014, 12 (4), pp.405-423. ⟨10.1080/14772000.2014.941037⟩. ⟨lirmm-01140770⟩
  • Nicolas Fiorini, Vincent Lefort, François Chevenet, Vincent Berry, Anne-Muriel Arigon Chifolleau. CompPhy: a web-based collaborative platform for comparing phylogenies. BMC Evolutionary Biology, BioMed Central, 2014, 14 (1), pp.253-255. ⟨10.1186/s12862-014-0253-5⟩. ⟨lirmm-01140756⟩
  • Thi Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Jean-Philippe Doyon, et al.. Reconciliation and local gene tree rearrangement can be of mutual profit. Algorithms for Molecular Biology, BioMed Central, 2013, 8 (12), ⟨10.1186/1748-7188-8-12⟩. ⟨lirmm-00812726⟩
  • Vincent Berry, Olaf Bininda-Emonds, Charles Semple. Amalgamating Source Trees with Different Taxonomic Levels. Systematic Biology, Oxford University Press (OUP), 2013, 62 (2), pp.231-249. ⟨10.1093/sysbio/sys090⟩. ⟨lirmm-00804769⟩
  • 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. ⟨10.1142/S0219720012500254⟩. ⟨lirmm-00818801⟩
  • Fouad El Baidouri, Sylvain Brisse, Vincent Berry, François Chevenet, Laure Diancourt, et al.. Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us. PLoS Neglected Tropical Diseases, Public Library of Science, 2013, 7 (6), pp.e2255. ⟨10.1371/journal.pntd.0002255⟩. ⟨lirmm-00818822⟩
  • 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⟩
  • Philippe Gambette, Vincent Berry, Christophe Paul. Quartets and Unrooted Phylogenetic Networks. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2012, 10 (4), pp.1250004.1-1250004.23. ⟨10.1142/S0219720012500047⟩. ⟨hal-00678046⟩
  • Emmanuel Cornillot, Kamel Hadj-Kaddour, Amina Dassouli, Benjamin Noel, Vincent Ranwez, et al.. Sequencing of the smallest apicomplexan genome from the human pathogen Babesia Microti. Nucleic Acids Research, Oxford University Press, 2012, 40 (18), pp.9102-9114. ⟨10.1093/nar/gks700⟩. ⟨lirmm-00818833⟩
  • 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. ⟨10.1016/j.ic.2010.11.022⟩. ⟨lirmm-00825050⟩
  • Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry. Models, algorithms, and programs for phylogeny reconciliation. Briefings in Bioinformatics, Oxford University Press (OUP), 2011, 12 (5), pp.392-400. ⟨10.1093/bib/bbr045⟩. ⟨lirmm-00825041⟩
  • François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen, Vincent Berry. ScripTree: scripting phylogenetic graphics. Bioinformatics, Oxford University Press (OUP), 2010, 26 (8), pp.1125-1126. ⟨10.1093/bioinformatics/btq086⟩. ⟨hal-00497209⟩
  • Vincent Berry, Sylvain Guillemot, François Nicolas, Christophe Paul. Linear time 3-approximation for MAST problem. ACM Transactions on Algorithms, Association for Computing Machinery, 2009, 5 (2), pp.1-18. ⟨lirmm-00324073⟩
  • Sylvain Guillemot, Vincent Berry. Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2009, 7 (2), pp.342-353. ⟨10.1109/TCBB.2008.93.⟩. ⟨lirmm-00324055⟩
  • Vincent Ranwez, Nicolas Clairon, Frédéric Delsuc, Saeed Pourali, Nicolas Auberval, et al.. PhyloExplorer: a web server to validate, explore and query phylogenetic trees. BMC Evolutionary Biology, BioMed Central, 2009, 9, pp.108. ⟨10.1186/1471-2148-9-108⟩. ⟨lirmm-00396040⟩
  • François Nicolas, Sylvain Guillemot, Vincent Berry, Christophe Paul. On the Approximability Results for Maximum Agreement Subtree and Maximum Compatible Tree Problems. Discrete Applied Mathematics, Elsevier, 2009, 157 (7), pp.1555-1570. ⟨lirmm-00371209⟩
  • Vincent Berry, Zeshan Peng, Hing-Fung Ting. From constrained to Unconstrained Maximum Agreement Subtree in Linear Time. Algorithmica, Springer Verlag, 2008, 50 (3), pp.369-385. ⟨lirmm-00324070⟩
  • Emmanuelle Jousselin, Simon van Noort, Vincent Berry, Jean-Yves Rasplus, Nina Rønsted, et al.. One fig to bind them all: host conservatism in a fig wasp community unraveled by cospeciation analyses among pollinating and nonpollinating fig wasps.. Evolution, Wiley, 2008, 62 (7), pp.1777-1797. ⟨10.1111/j.1558-5646.2008.00406.x⟩. ⟨lirmm-00324068⟩
  • 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. ⟨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. ⟨lirmm-00194235⟩
  • Vincent Berry, François Nicolas. Maximum Agreement and Compatible Supertrees. Journal of Discrete Algorithms, Elsevier, 2007, 5 (3), pp.564-591. ⟨lirmm-00194239⟩
  • Vincent Berry, Charles Semple. Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa. Systematic Biology, Oxford University Press (OUP), 2006, 55 (2), pp.U108-U126. ⟨lirmm-00131854⟩
  • Cécile Bonnard, Vincent Berry, Nicolas Lartillot. Multipolar Consensus for Phylogenetic Trees. Systematic Biology, Oxford University Press (OUP), 2006, 55 (5), pp.837-843. ⟨10.1080/10635150600969880⟩. ⟨lirmm-00126475⟩
  • Alexis Criscuolo, Vincent Berry, Emmanuel Douzery, Olivier Gascuel. SDM : A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics. Systematic Biology, Oxford University Press (OUP), 2006, 55 (5), pp.740-755. ⟨10.1080/10635150600969872⟩. ⟨lirmm-00136655⟩
  • Vincent Berry, François Nicolas. Improved Parametrized Complexity of Maximum Agreement Subtree and Maximum Compatible Tree problems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2006, 3 (3), pp.289-302. ⟨10.1109/TCBB.2006.39⟩. ⟨lirmm-00131835⟩

Conference papers13 documents

  • Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, et al.. Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels. Journées Ouvertes Biologie Informatique Mathématiques, 2016, Lyon, France. ⟨hal-01394409⟩
  • Thi-Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Vincent Ranwez, et al.. Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses predictions. WABI'12 : Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.N/A. ⟨hal-00718347v3⟩
  • Thi-Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Vincent Ranwez, et al.. Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses  predictions. WABI: Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.123-134, ⟨10.1007/978-3-642-33122-0_10⟩. ⟨hal-01189848⟩
  • 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-CG: Comparative Genomics, Oct 2010, Ottawa, Canada. pp.93-108, ⟨10.1007/978-3-642-16181-0_9⟩. ⟨lirmm-00818889⟩
  • 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, Montpellier, France. pp.8. ⟨lirmm-00833164⟩
  • Daniel Huson, Regula Rupp, Vincent Berry, Philippe Gambette, Christophe Paul. Computing Galled Networks from Real Data. ISMB/ECCB'09: 17th Annual Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology, Jun 2009, France. pp.i85-i93, ⟨10.1093/bioinformatics/btp217⟩. ⟨lirmm-00368545v2⟩
  • Philippe Gambette, Vincent Berry, Christophe Paul. The Structure of Level-k Phylogenetic Networks. CPM: Combinatorial Pattern Matching, Jun 2009, Lille, France. pp.289-300, ⟨10.1007/978-3-642-02441-2_26⟩. ⟨lirmm-00371485⟩
  • Celine Scornavacca, Vincent Berry, Vincent Ranwez. From Gene Trees to Species Trees Through a Supertree Approach. LATA: Language and Automata Theory and Applications, Apr 2009, Tarragone, Spain. pp.10-19, ⟨10.1007/978-3-642-00982-2_60⟩. ⟨lirmm-00367086⟩
  • Sylvain Guillemot, Vincent Berry. Fixed-parameter Tractability of the Maximum Agreement Supertree Problem. CPM: Combinatorial Pattern Matching, 2007, Montpellier, France. pp.274-285. ⟨lirmm-00130406v2⟩
  • Vincent Berry, Vincent Ranwez, Pierre-Henri Fabre, Emmanuel Douzery. Votez veto pour l'Arbre de la Vie. JOBIM'06 : Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2006, Bordeaux, France, pp.251-263. ⟨lirmm-00131866⟩
  • Alexis Criscuolo, Vincent Berry, Emmanuel Douzery, Olivier Gascuel. SDM: Une Méthode de Distance Rapide pour les Etudes de Phylogénomique. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. pp.231-244. ⟨lirmm-00106495⟩
  • Vincent Berry, Sylvain Guillemot, Nicolas François, Christophe Paul. On the Approximation of Computing Evolutionary Trees. COCOON: Computing and Combinatorics Conference, Aug 2005, Kunming, China. pp.115-125, ⟨10.1007/11533719_14⟩. ⟨lirmm-00106451⟩
  • Vincent Berry, François Nicolas. Maximum Agreement and Compatible Supertrees. CPM: Combinatorial Pattern Matching, 2004, Istanbul, Turkey. pp.205-219, ⟨10.1007/978-3-540-27801-6_15⟩. ⟨lirmm-00108782⟩

Poster communications1 document

  • Floréal Cabanettes, Marc Chakiachvili, Vincent Lefort, Jean-François Dufayard, Frederic de Lamotte Guéry, et al.. CompPhy v2 : une plate-forme collaborative pour visualiser et comparer des phylogénies. JOBIM: Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. 437 p., 2016. ⟨hal-01594479⟩

Book sections2 documents

Reports6 documents

  • Sylvain Guillemot, Vincent Berry. Finding a Largest Subset of Rooted Triples Identifying a Tree is an NP-hard task. RR-07010, 2007, pp.7. ⟨lirmm-00143208⟩
  • Vincent Berry. Improving the Reduction from the Constrained to the Unconstrained MAST. 05041, 2005, pp.2. ⟨lirmm-00106642⟩
  • Vincent Berry, François Nicolas. Approximating the Maximum Compatible Tree. 05019, 2005. ⟨lirmm-00106626⟩
  • Vincent Berry. Super-Arbre d'Accord Maximum. 03040, 2003, pp.5. ⟨lirmm-00191964⟩
  • Vincent Berry. Super-Arbre d'Accord Maximum. 03040, 2003, pp.5. ⟨lirmm-00269757⟩
  • Vincent Berry. Super-arbre d'Accord Maximum. 03040, 2003, pp.5. ⟨lirmm-00269481⟩

Habilitation à diriger des recherches1 document

  • Vincent Berry. On building and comparing trees
    Application to supertrees in phylogenetics. Informatique [cs]. Université Montpellier II - Sciences et Techniques du Languedoc, 2008. ⟨tel-00360926⟩