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Vincent Berry

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On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo

Charles-Elie Rabier , Vincent Berry , Marnus Stoltz , Joao D. Santos , Wensheng Wang
PLoS Computational Biology, 2021, 17 (9), pp.e1008380. ⟨10.1371/journal.pcbi.1008380⟩
Journal articles hal-03287030v2
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Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

Gaëtan Droc , Julie Sardos , Alberto A. Cenci , Björn Geigle , Mark S. Hibbins
Genome Biology and Evolution, 2018, 10 (12), pp.3129-3140. ⟨10.1093/gbe/evy227⟩
Journal articles lirmm-02097189v1
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A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactions

Vincent Berry , François Chevenet , Jean-Philippe Doyon , Emmanuelle Jousselin
Molecular Ecology Resources, 2018, 18 (5), pp.1173-1184. ⟨10.1111/1755-0998.12897⟩
Journal articles hal-01942777v1
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RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin , Guillaume Gence , Anne-Muriel Arigon Chifolleau , Lars Arvestad , Mukul Bansal
Bioinformatics, 2018, 34 (21), pp.3646-3652. ⟨10.1093/bioinformatics/bty389⟩
Journal articles lirmm-01800296v1
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Inferring gene duplications, transfers and losses can be done in a discrete framework

Vincent Ranwez , Celine Scornavacca , Jean-Philippe Doyon , Vincent Berry
Journal of Mathematical Biology, 2016, 72 (7), pp.1811-1844. ⟨10.1007/s00285-015-0930-z⟩
Journal articles hal-01370854v1
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SylvX: a viewer for phylogenetic tree reconciliations

François Chevenet , Jean-Philippe Doyon , Celine Scornavacca , Edwin Jacox , Emmanuelle Jousselin
Bioinformatics, 2016, 32 (4), pp.608-610. ⟨10.1093/bioinformatics/btv625⟩
Journal articles hal-01942605v1
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Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti , Vincent Berry , Cedric Chauve , Annie Chateau , Eric Tannier
BMC Genomics, 2015, 16 (Suppl 10), pp.S11. ⟨10.1186/1471-2164-16-S10-S11⟩
Journal articles hal-01180303v2
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CompPhy: a web-based collaborative platform for comparing phylogenies

Nicolas Fiorini , Vincent Lefort , François Chevenet , Vincent Berry , Anne-Muriel Arigon Chifolleau
BMC Evolutionary Biology, 2014, 14 (1), pp.253-255. ⟨10.1186/s12862-014-0253-5⟩
Journal articles lirmm-01140756v1

Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus

François Hubert , Guido W. Grimm , Emmanuelle Jousselin , Vincent Berry , Alain Franc
Systematics and Biodiversity, 2014, 12 (4), pp.405-423. ⟨10.1080/14772000.2014.941037⟩
Journal articles lirmm-01140770v1
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Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us

Fouad El Baidouri , Sylvain Brisse , Vincent Berry , François Chevenet , Laure Diancourt
PLoS Neglected Tropical Diseases, 2013, 7 (6), pp.e2255. ⟨10.1371/journal.pntd.0002255⟩
Journal articles lirmm-00818822v1
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Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods

Thi-Hau Nguyen , Vincent Ranwez , Vincent Berry , Celine Scornavacca
PLoS ONE, 2013, 8 (10), pp.e73667. ⟨10.1371/journal.pone.0073667⟩
Journal articles hal-01189798v1
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Representing a set of reconciliations in a compact way

Celine Scornavacca , Wojciech Paprotny , Vincent Berry , Vincent Ranwez
Journal of Bioinformatics and Computational Biology, 2013, 11 (2), pp.1250025. ⟨10.1142/S0219720012500254⟩
Journal articles lirmm-00818801v1
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Amalgamating Source Trees with Different Taxonomic Levels

Vincent Berry , Olaf Bininda-Emonds , Charles Semple
Systematic Biology, 2013, 62 (2), pp.231-249. ⟨10.1093/sysbio/sys090⟩
Journal articles lirmm-00804769v1
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Reconciliation and local gene tree rearrangement can be of mutual profit

Thi Nguyen , Vincent Ranwez , Stéphanie Pointet , Anne-Muriel Arigon Chifolleau , Jean-Philippe Doyon
Algorithms for Molecular Biology, 2013, 8 (12), ⟨10.1186/1748-7188-8-12⟩
Journal articles lirmm-00812726v1
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Quartets and Unrooted Phylogenetic Networks

Philippe Gambette , Vincent Berry , Christophe Paul
Journal of Bioinformatics and Computational Biology, 2012, 10 (4), pp.1250004.1-1250004.23. ⟨10.1142/S0219720012500047⟩
Journal articles hal-00678046v1
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Sequencing of the smallest apicomplexan genome from the human pathogen Babesia Microti

Emmanuel Cornillot , Kamel Hadj-Kaddour , Amina Dassouli , Benjamin Noel , Vincent Ranwez
Nucleic Acids Research, 2012, 40 (18), pp.9102-9114. ⟨10.1093/nar/gks700⟩
Journal articles lirmm-00818833v1
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Models, algorithms, and programs for phylogeny reconciliation

Jean-Philippe Doyon , Vincent Ranwez , Vincent Daubin , Vincent Berry
Briefings in Bioinformatics, 2011, 12 (5), pp.392-400. ⟨10.1093/bib/bbr045⟩
Journal articles lirmm-00825041v1
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Building species trees from larger parts of phylogenomic databases

Celine Scornavacca , Vincent Berry , Vincent Ranwez
Information and Computation, 2011, 209 (3), pp.590-605. ⟨10.1016/j.ic.2010.11.022⟩
Journal articles lirmm-00825050v1

ScripTree: scripting phylogenetic graphics

François Chevenet , Olivier Croce , Maxime Hebrard , Richard Christen , Vincent Berry
Bioinformatics, 2010, 26 (8), pp.1125-1126. ⟨10.1093/bioinformatics/btq086⟩
Journal articles hal-00497209v1
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Computing Galled Networks from Real Data

Daniel Huson , Regula Rupp , Vincent Berry , Philippe Gambette , Christophe Paul
Bioinformatics, 2009, 25 (12), pp.i85-i93. ⟨10.1093/bioinformatics/btp217⟩
Journal articles lirmm-00368545v2
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PhyloExplorer: a web server to validate, explore and query phylogenetic trees

Vincent Ranwez , Nicolas Clairon , Frédéric Delsuc , Saeed Pourali , Nicolas Auberval
BMC Evolutionary Biology, 2009, 9, pp.108. ⟨10.1186/1471-2148-9-108⟩
Journal articles lirmm-00396040v1
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Linear time 3-approximation for MAST problem

Vincent Berry , Sylvain Guillemot , François Nicolas , Christophe Paul
ACM Transactions on Algorithms, 2009, 5 (2), pp.1-18. ⟨10.1145/1497290.1497299⟩
Journal articles lirmm-00324073v1

On the Approximability Results for Maximum Agreement Subtree and Maximum Compatible Tree Problems

François Nicolas , Sylvain Guillemot , Vincent Berry , Christophe Paul
Discrete Applied Mathematics, 2009, 157 (7), pp.1555-1570. ⟨10.1016/j.dam.2008.06.007⟩
Journal articles lirmm-00371209v1
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Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem

Sylvain Guillemot , Vincent Berry
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, 7 (2), pp.342-353. ⟨10.1109/TCBB.2008.93⟩
Journal articles lirmm-00324055v1
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PhySIC IST : cleaning source trees to infer more informative supertrees

Celine Scornavacca , Vincent Berry , Vincent Lefort , Emmanuel J.P. Douzery , Vincent Ranwez
BMC Bioinformatics, 2008, 9 (413), pp.1471-2105. ⟨10.1186/1471-2105-9-413⟩
Journal articles lirmm-00324069v1
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One fig to bind them all: host conservatism in a fig wasp community unraveled by cospeciation analyses among pollinating and nonpollinating fig wasps.

Emmanuelle Jousselin , Simon van Noort , Vincent Berry , Jean-Yves Rasplus , Nina Rønsted
Evolution - International Journal of Organic Evolution, 2008, 62 (7), pp.1777-1797. ⟨10.1111/j.1558-5646.2008.00406.x⟩
Journal articles lirmm-00324068v1
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From constrained to Unconstrained Maximum Agreement Subtree in Linear Time

Vincent Berry , Zeshan S. Peng , Hing-Fung Ting
Algorithmica, 2008, 50 (3), pp.369-385. ⟨10.1007/s00453-007-9084-8⟩
Journal articles lirmm-00324070v1
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PhySIC: A Veto Supertree Method with Desirable Properties

Vincent Ranwez , Vincent Berry , Alexis Criscuolo , Pierre-Henri Fabre , Sylvain Guillemot
Systematic Biology, 2007, 56 (5), pp.798-817. ⟨10.1080/10635150701639754⟩
Journal articles lirmm-00194235v1
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Maximum Agreement and Compatible Supertrees

Vincent Berry , François Nicolas
Journal of Discrete Algorithms, 2007, 5 (3), pp.564-591. ⟨10.1016/j.jda.2006.08.005⟩
Journal articles lirmm-00194239v1
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Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa

Vincent Berry , Charles Semple
Systematic Biology, 2006, 55 (2), pp.270-288. ⟨10.1080/10635150500541649⟩
Journal articles lirmm-00131854v1
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SDM : A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics

Alexis Criscuolo , Vincent Berry , Emmanuel J.P. Douzery , Olivier Gascuel
Systematic Biology, 2006, 55 (5), pp.740-755. ⟨10.1080/10635150600969872⟩
Journal articles lirmm-00136655v1
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Improved Parametrized Complexity of Maximum Agreement Subtree and Maximum Compatible Tree problems

Vincent Berry , François Nicolas
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006, 3 (3), pp.289-302. ⟨10.1109/TCBB.2006.39⟩
Journal articles lirmm-00131835v1
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Multipolar Consensus for Phylogenetic Trees

Cécile Bonnard , Vincent Berry , Nicolas Lartillot
Systematic Biology, 2006, 55 (5), pp.837-843. ⟨10.1080/10635150600969880⟩
Journal articles lirmm-00126475v1
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Analyse des traces de consultations des ressources en ligne et de la réalisation des activité dans un module hybride en école d’ingénieur

Chrysta Pélissier , Vincent Berry , Jérôme Fortin
AIPU 2023 - 33e congrès de l'Association Internationale de Pédagogie Universitaire, Mar 2023, Perpignan, France
Conference papers lirmm-04027971v1
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ShellOnYou : Learning by Doing Unix Command Line

Vincent Berry , Arnaud Castelltort , Chrysta Pélissier , Marion Rousseau , Chouki Tibermacine
ITiCSE 2022 - 27th ACM Conference on on Innovation and Technology in Computer Science Education, Jul 2022, Dublin, Ireland. pp.379-385, ⟨10.1145/3502718.3524753⟩
Conference papers halshs-03726175v1
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Quand collaborer répond à une « urgence » : l'atout d'une structuration Réseau

Marion Rousseau , Nora Cherifa Abid , Vincent Berry
AIPU 2022 - 32e congrès de l'Association Internationale de Pédagogie Universitaire, May 2022, Rennes, France
Conference papers lirmm-04028069v1
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Stop Reinventing the Wheel! Promoting Community Software in Computing Education

Jeremiah Blanchard , John R. Hott , Vincent Berry , Rebecca Carroll , Bob Edmison
ITiCSE-WG 2022 - 27th ACM Conference on Innovation and Technology in Computer Science Education, Jul 2022, Dublin, Ireland. pp.261-292, ⟨10.1145/3571785.3574129⟩
Conference papers lirmm-04025606v1
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Scanning Phylogenetic Networks is NP-hard

Vincent Berry , Celine Scornavacca , Mathias Weller
SOFSEM 2020 - 46th International Conference on Current Trends in Theory and Practice of Informatics, Jan 2020, Limassol, Cyprus. pp.519-530, ⟨10.1007/978-3-030-38919-2_42⟩
Conference papers hal-02353161v2
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Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels

Yoann Anselmetti , Vincent Berry , Cedric Chauve , Annie Chateau , Eric Tannier
Journées Ouvertes Biologie Informatique Mathématiques, 2016, Lyon, France
Conference papers hal-01394409v1
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Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses predictions

Thi-Hau Nguyen , Jean-Philippe Doyon , Stéphanie Pointet , Anne-Muriel Arigon Chifolleau , Vincent Ranwez
12th International Workshop on Algorithms in Bioinformatics (WABI 2012), Sep 2012, Ljubljana, Slovenia. pp.123-134, ⟨10.1007/978-3-642-33122-0_10⟩
Conference papers hal-00718347v3

Phylogenetic reconstruction in Quercus based on multiple nuclear genes

François Hubert , Alain Franc , Antoine Kremer , Vincent Berry
IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France
Conference papers hal-02804068v1
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Un algorithme de parcimonie efficace pour la réconciliation d'arbres de gènes/espèces avec pertes, duplications et transferts

Jean-Philippe Doyon , Celine Scornavacca , Gergely J. Szöllősi , Vincent Ranwez , Vincent Berry
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
Conference papers lirmm-00833164v1
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From Gene Trees to Species Trees Through a Supertree Approach

Celine Scornavacca , Vincent Berry , Vincent Ranwez
Language and Automata Theory and Applications : LATA 2009, Apr 2009, Tarragona, Spain. pp.10-19, ⟨10.1007/978-3-642-00982-2_60⟩
Conference papers lirmm-00367086v1
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The Structure of Level-k Phylogenetic Networks

Philippe Gambette , Vincent Berry , Christophe Paul
CPM: Combinatorial Pattern Matching, Jun 2009, Lille, France. pp.289-300, ⟨10.1007/978-3-642-02441-2_26⟩
Conference papers lirmm-00371485v1
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Fixed-parameter Tractability of the Maximum Agreement Supertree Problem

Sylvain Guillemot , Vincent Berry
CPM: Combinatorial Pattern Matching, 2007, Montpellier, France. pp.274-285
Conference papers lirmm-00130406v2
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Votez veto pour l'Arbre de la Vie

Vincent Berry , Vincent Ranwez , Pierre-Henri Fabre , Emmanuel J.P. Douzery
JOBIM'06 : Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2006, Bordeaux, France, pp.251-263
Conference papers lirmm-00131866v1
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On the Approximation of Computing Evolutionary Trees

Vincent Berry , Sylvain Guillemot , Nicolas François , Christophe Paul
COCOON: Computing and Combinatorics Conference, Aug 2005, Kunming, China. pp.115-125, ⟨10.1007/11533719_14⟩
Conference papers lirmm-00106451v1
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SDM: Une Méthode de Distance Rapide pour les Etudes de Phylogénomique

Alexis Criscuolo , Vincent Berry , Emmanuel J.P. Douzery , Olivier Gascuel
JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. pp.231-244
Conference papers lirmm-00106495v1
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Maximum Agreement and Compatible Supertrees

Vincent Berry , François Nicolas
CPM: Combinatorial Pattern Matching, 2004, Istanbul, Turkey. pp.205-219, ⟨10.1007/978-3-540-27801-6_15⟩
Conference papers lirmm-00108782v1
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On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo

Charles-Elie Rabier , Vincent Berry , Jean-Christophe Glaszmann , Fabio Pardi , Celine Scornavacca
JOBIM 2020 - 20e Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier, France.
Conference poster lirmm-04027842v1

CompPhy v2 : une plate-forme collaborative pour visualiser et comparer des phylogénies

Floréal Cabanettes , Marc Chakiachvili , Vincent Lefort , Jean-François Dufayard , Frédéric F. de Lamotte
JOBIM: Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 437 p., 2016, JOBIM 2016
Conference poster hal-01594479v1

Maximum Compatible Tree

Vincent Berry
Ming-Yang Kao. Encyclopedia of Algorithms, Springer, 2016, Foundations of Computing, 978-1-4939-2863-7. ⟨10.1007/978-1-4939-2864-4⟩
Book sections lirmm-01264556v1
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An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers

Jean-Philippe Doyon , Celine Scornavacca , Yu Gorbunov , Gergely J. Szöllősi , Vincent Ranwez
Eric Tannier. Comparative Genomics. RECOMB-CG 2010, LNCS (6398), Springer Berlin Heidelberg, pp.93-108, 2010, 978-3-642-16181-0. ⟨10.1007/978-3-642-16181-0_9⟩
Book sections lirmm-00818889v1
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Maximum Compatible Tree

Vincent Berry
Ming-Yang Kao. Encyclopedia of Algorithms, Springer, pp.499-502, 2008, Foundations of Computing, 978-0-387-30770-1. ⟨10.1007/978-0-387-30162-4_223⟩
Book sections lirmm-00324061v1
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On building and comparing trees
Application to supertrees in phylogenetics

Vincent Berry
Informatique [cs]. Université Montpellier II - Sciences et Techniques du Languedoc, 2008
Habilitation à diriger des recherches tel-00360926v1