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Number of documents

55

Vincent Berry


Journal articles33 documents

  • 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⟩
  • Gaëtan Droc, Julie Sardos, Alberto Cenci, Björn Geigle, Mark Hibbins, 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⟩
  • 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, In Press, pp.1-3. ⟨hal-01885401⟩
  • 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 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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 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⟩
  • 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. ⟨10.1145/1497290.1497299⟩. ⟨lirmm-00324073⟩
  • Daniel Huson, Regula Rupp, Vincent Berry, Philippe Gambette, Christophe Paul. Computing Galled Networks from Real Data. Bioinformatics, Oxford University Press (OUP), 2009, 25 (12), pp.i85-i93. ⟨10.1093/bioinformatics/btp217⟩. ⟨lirmm-00368545v2⟩
  • 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⟩
  • 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. ⟨10.1016/j.dam.2008.06.007⟩. ⟨lirmm-00371209⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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 - International Journal of Organic Evolution, Wiley, 2008, 62 (7), pp.1777-1797. ⟨10.1111/j.1558-5646.2008.00406.x⟩. ⟨lirmm-00324068⟩
  • 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.798-817. ⟨10.1080/10635150701639754⟩. ⟨lirmm-00194235⟩
  • Vincent Berry, François Nicolas. Maximum Agreement and Compatible Supertrees. Journal of Discrete Algorithms, Elsevier, 2007, 5 (3), pp.564-591. ⟨10.1016/j.jda.2006.08.005⟩. ⟨lirmm-00194239⟩
  • 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⟩
  • Vincent Berry, Charles Semple. Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa. Systematic Biology, Oxford University Press (OUP), 2006, 55 (2), pp.270-288. ⟨10.1080/10635150500541649⟩. ⟨lirmm-00131854⟩

Conference papers13 documents

  • Vincent Berry, Celine Scornavacca, Mathias Weller. Scanning Phylogenetic Networks is NP-hard. SOFSEM, Jan 2020, Limassol, Cyprus. pp.519-530, ⟨10.1007/978-3-030-38919-2_42⟩. ⟨hal-02353161⟩
  • 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⟩
  • François Hubert, Alain Franc, Antoine Kremer, Vincent Berry. Phylogenetic reconstruction in Quercus based on multiple nuclear genes. IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. ⟨hal-02804068⟩
  • 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. 12th International Workshop on Algorithms in Bioinformatics (WABI 2012), Sep 2012, Ljubljana, Slovenia. pp.123-134, ⟨10.1007/978-3-642-33122-0_10⟩. ⟨hal-00718347v3⟩
  • 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, Institut National d'Etudes Supérieures Agronomiques de Montpellier (Montpellier SupAgro). Montpellier, FRA., Sep 2010, Montpellier, France. pp.8. ⟨lirmm-00833164⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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, 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, JOBIM 2016. ⟨hal-01594479⟩

Book sections2 documents

Reports5 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-00269481⟩
  • Vincent Berry. Super-Arbre d'Accord Maximum. 03040, 2003, pp.5. ⟨lirmm-00191964⟩

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⟩