Context

MAB team

My research activities are conducted in the Methods and Algorithms for Bioinformatics (MAB) group at the LIRMM lab, in the Computationnal Bioinformatics Institute. This research is most often realized in collaboration with life sciences labs. Computationnal Bioinformatics Institute

Keywords

Phylogenomics Consensus Triplets and quartets Networks Statistics Software, Website, Database

Offers

  • Post-doctoral position, in collaboration with C. Scornavacca (ISE-M) and F. Pardi (LIRMM): Methods and algorithms for recovering the phylogenetic networks of cultivated plants. See here for a description.
  • PhD proposal co-supervision with C. Scornavacca in the context of the Genome Harvest project. Subject: New computational methods to characterize inter(sub)specific crop genomes. A description and presenting slides are available.

Current projects

2016-2019 Member of the Genome Harvest flagship project, funded by the Agropolis foundation.

2013-2017   Member of the Institut de Biologie Computationnelle (IBC)

2011-2018   Member of the NumEv labex. Co-animator of the Algorithms & Computation axis (2014-)

2013-2017   Member of the ANCESTROME ANR project

Papers

    2016

    • Inferring gene duplications, transfers and losses can be done in a discrete framework
      V. Ranwez, S. Scornavacca, J.-P. Doyon, V. Berry, Journal of Mathematical Biology Volume 72, Issue 7, pp 1811-1844  

    2015

    • SylvX: a viewer for phylogenetic tree reconciliations
      F. Chevenet, J.P. Doyon, C. Scornavacca, E. Jousselin, E. Jacox, V. BerryBioinformatics (doi:10.1093/bioinformatics/btv625)  
    • Maximum Compatible Tree
      V. Berry, in book Encyclopedia of Algorithms, M.-Y. Kao Ed., Springer, version 2  
    • Ancestral gene synteny reconstruction improves extant species scaffolding
      Y. Anselmetti, V. Berry, C. Chauve, A. Chateau, E. Tannier and S. Berard BMC Genomics, 16 Suppl 10:S11, Procs of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics.  

    2014

    • CompPhy - an online collaborative tool for visualizing and managing phylogenies
      N. Fiorini, V. Lefort, F. Chevenet, A.-M. Arigon Chifolleau, V. Berry,  [ Web site free paper online]. Highly accessed paper  
    • Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus
      F. Hubert, G.W. Grimm, E. Jousselin, V. Berry, A. Franc, A. Kremer, Systematics and Biodiversity, 12(4), 405-423 [ link and supplementary data ]. Nominated by the journal for the Outstanding Paper Award for 2014.  

    2013

    • Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods
      , Nguyen T-H, Ranwez V, Berry V, Scornavacca C, PLoS ONE 8(10): e73667. [ doi]  
    • Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us
      F. El Baidouri, S. Brisse, V. Berry, F. Chevenet, L. Diancourt, F. Pratlong, P. Marty, C. Ravel, PLOS Neglected Tropical Diseases, 7(6): e2255. [ doi: 10.1371/journal.pntd.0002255 ]  
    • Reconciliation and local gene tree rearrangement can be of mutual profit.
      T.H. Nguyen, J.-P. Doyon, S. Pointet, A.-M. Arigon Chifolleau, V. Ranwez, V. Berry, Algorithms for Molecular Biology, 8:12. DOI: 10.1186/1748-7188-8-12  
    • Amalgamating Source Trees with Different Taxonomic Levels
      V. Berry, O. Bininda-Emonds, C. Semple, Systematic Biology, 62(2):231-49. DOI: 10.1093/sysbio/sys090.  
    • Representing a set of reconciliations in a compact way
      C. Scornavacca, V. Berry, V. Ranwez, Journal of Bioinformatics and Computational Biology Vol. 11, No. 2, [ DOI: 10.1142/S0219720012500254 ]   

    2012

    • Accounting for gene tree uncertainties improves gene trees and reconciliation inference
      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.  
    • Sequencing of the smallest apicomplexan genome from the human pathogen Babesia Microti
      E. Cornillot, K. Hadj-Kaddour1, A. Dassouli1, B.Noel, V. Ranwez, B. Vacherie, A. Duclos, Y. Augagneur, V. Brès, S. Randazzo1, B. Carcy, S. Delbecq, K. Moubri-Méage1, F. Debierre-Grockiego, H. Shams-Eldin, F. Bringaud, P. Wincker, C.P. Vivarès, R.T. Schwarz, T.P. Schetters, P.J. Krause, A. Gorenflot, V. Berry, V. Barbe, C. Ben Mamoun, Nucleic Acid Research, 40(18), 9102-9114, DOI: 10.1093/nar/gks700  
    • Quartets and unrooted phylogenetic networks
      P. Gambette, V. Berry, C. Paul, Journal of Bioinformatics and Computational Biology 10(4), 1250004 (23 p.) [DOI].  

    2011

    • Models, algorithms, and programs for phylogeny reconciliation
      J.P. Doyon, V. Daubin, V. Ranwez, V. Berry, accepted in Briefings in Bioinformatics,12(5): 392-400. DOI: 10.1093/bib/bbr045  
    • CompPhy a web-based collaborative plaform for phylogenetics
      N. Fiorini, M. Agbessi, A. Bisch, F. Dumond, F. Chevenet, V. Lefort, A.M. Arigon, V. Berry, 12èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), 2011. [ pdf of the poster ]  
    • Building species trees from larger parts of phylogenomic databases
      C. Scornavacca, V. Berry, V. Ranwez, Information and Computation, (209) : pp. 590-605.
      (Completed version of the extended abstract appearing in LATA'09). [ pdf draft | programs ]  

    2010

    • An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers
      J.P. Doyon, C. Scornavacca, K. Gorbunov, G. Szollosi, V. Ranwez, V. Berry, 8th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2010. [ pdf draft ]  
    • Un algorithme de parcimonie efficace pour la réconciliation d'arbres de gènes/espèces avec pertes, duplications et transferts
      J.P. Doyon, C. Scornavacca, G. Szollosi, V. Ranwez, V. Berry, 11èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), 2010. [ pdf draft ]  
    • Scriptree: scripting phylogenetic graphics
      F. Chevenet, O. Croce, M. Hebrard, R. Christen, V. Berry, Bioinformatics, 2010. [ Web site | doi]  
    • Most parsimonious reconciliation of gene and species trees with duplications, transfers and losses
      JP Doyon, S. Scornavacca, G. Szollozi, V. Ranwez, V. Berry.  
      Presented at

    2009

    • 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. [ free pdf | Web site | doi]  (3rd most viewed paper in June 09)  
    • The Structure of Level-k Phylogenetic Networks,
      P. Gambette, V. Berry & C. Paul, 20th Ann. Symp. on Combin. Pattern Matching (CPM), LNCS, 5577, 289-300, Springer.  
    • Computing Galled Networks from Real Data
      D. Huson, R. Rupp, V. Berry, P. Gambette & C. Paul, 17th Ann. Int. Conf. Intel. Syst. for Mol. Biol. (ISMB), to appear in a special issue of Bioinformatics. Implemented in Dendroscope.  
    • 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, 702-714. [ pdf | programs ]  
    • Linear time 3-approximation for the MAST problem
      V. Berry, S. Guillemot, F. Nicolas, C. Paul, ACM Transaction on Algorithms (TALG), to appear [ doi ].  
    • Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem
      S. Guillemot, V. Berry, IEEE/ACM Trans. Comp. Biol. and Bioinformatics (TCBB), to appear (journal version of the CPM'07 paper). [ doi | pdf | program used on this site]  
    • On the approximability of the Maximum Agreement SubTree and Maximum Compatible Tree problems
      S. Guillemot, F. Nicolas, V. Berry, C. Paul, Discrete Applied Mathematics, to appear in vol. 157(7), 1555-1570 [ doi ].  

    2008

    • On building and comparing trees - Application to supertrees in phylogenetics
      V. Berry, Habilitation a diriger des recherches, Univ. Montpellier 2 [ pdf | slides ]  
    • PhySIC_IST: cleaning source trees to infer more informative supertrees
      C. Scornavacca, V. Berry, E.J.P. Douzery and V. Ranwez, BMC Bioinformatics, 9:413 [ doi | free access to pdf | software page]  
    • PhySIC_IST: healing source trees to infer healthy supertrees
      C. Scornavacca, V. Berry, E.J.P. Douzery and V. Ranwez, Annual Meeting of the Society for Molecular Biology and Evolution (SMBE'08) - Bioinformatics for molecular evolution track
      [ talk presenting the Physic_IST method (see paper above)]  
    • Maximum Compatible Tree
      V. Berry, in book Encyclopedia of Algorithms, M.-Y. Kao Ed., Springer, ISBN 978-0-387-30770-1.
      [ bibTex | doi | pdf ]  
    • One fig to bind them all: host conservatism in a fig wasp community unraveled by cospeciation analyses among pollinating and nonpollinating fig wasps
      E. Jousselin, S. van Noort, V. Berry J.-Y. Rasplus, N. Rønsted, J. C. Erasmus and J.M. Greef, Evolution, 62-7: 1777--1797
      [ doi ]  
    • From constrained to unconstrained maximum agreement subtree in linear time.
      V. Berry, Z.S. Peng and H.F. Ting, Algorithmica, 50(3), 369--385, [ bibTex | doi | pdf ]  

    2007

    • Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem
      S. Guillemot, V. Berry, 18th Ann. Combinatorial Pattern Matching Symposium , LNCS 4580, pp. 274-285, (pdf version with proofs).  
    • Finding a largest subset of rooted triples identifying a tree is an NP-hard task
      S. Guillemot, V. Berry, Research report RR-LIRMM num 07010, pdf  
    • PhySIC: a Veto Supertree Method with Desirable Properties.
      V. Ranwez, V. Berry, A. Criscuolo, P.-H. Fabre, S. Guillemot, C. Scornavacca and E.J.P. Douzery, Systematic Biology, 56(5), 293-304, [ pdf | software page ]  
    • Maximum Agreement and Compatible Supertrees.
      V.Berry and F. Nicolas, Journal of Discrete Algorithms, 5(3), pp 564-591, [ link | doi ].  

    2006

    • Votez veto pour l'Arbre de la Vie
      V. Berry, V. Ranwez, P.-H. Fabre, E. Douzery, JOBIM, A. Denise, P. Durrens, S. Robin, E. Rocha, A. de Daruvar, A. Groppi, ed., p. 251-263, pdf  
    • Multipolar consensus for phylogenetic trees
      C. Bonnard, V. Berry, N. Lartillot, Systematic Biology, 55(5):837-843, pdf  
    • SDM : A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics
      A. Criscuolo, V. Berry, E.J.P. Douzery and O. Gascuel, Systematic Biology 55(5):740-755, pdf  
    • Improved parametrized complexity of Maximum Agreement Subtree and Maximum Compatible Tree problems.
      V. Berry and F. Nicolas, IEEE/ACM Trans. on Comp. Biol. and Bioinf., 3(3), 289-302 (tech. rep. version with proofs).  
    • Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa
      V. Berry, C. Semple, Systematic Biology, 55(2), U108-U126, draft version  

    Prior to 2006

    • On the Approximation of Computing Evolutionary Trees.
      V.Berry, F.Nicolas, S.Guillemot and C.Paul, COCOON'05: 11th Annual International Conference on Computing and Combinatorics, LNCS n° 3595, pp. 115-125, 2005.  
    • Approximating the Maximum Compatible Tree.
      V.Berry and F. Nicolas, tech. rep. 05019, 2005.  
    • Maximum Agreement and Compatible Supertrees.
      V.Berry and F. Nicolas, 15th Ann. Combinatorial Pattern Matching Symposium (CPM), LNCS 3109, Springer Verlag, 2004. (tech. rep. version with proofs).  
    • A Structured Family of Clustering and Tree Construction Methods.
      D.Bryant and V.Berry Advances in Applied Math, 27, pp 705-732, 2001. [ Implemented in SplitsTree ]  
    • Choosing the tree which actually best explains the data: another look at the bootstrap in phylogenetic reconstruction.
      V. Berry and O. Gascuel, Computational Statistics and Data Analysis, 2000, 38, pp 273-283. draft version (71k)  
    • Inferring Evolutionary Trees with Strong Combinatorial Evidence.
      V. Berry and O. Gascuel, Theoretical Computer Science, 2000, 240(2), pp 271-298. draft version (285k). [ software]  
    • A practical algorithm for recovering the best supported edges of an evolutionary tree.
      V. Berry, D. Bryant, T. Jiang, P. Kearney, M. Li, T. Wareham and H. Zhang, SODA 2000,287-296.
      [ bibTex ]  
    • Faster reliable phylogenetic analysis.
      V. Berry and D. Bryant, RECOMB 99. [ draft ps | Implemented in SplitsTree ]  
    • Quartet Cleaning: Improved Algorithms and Simulations.
      V. Berry, P. Kearney, M. Li, T. Jiang and T. Wareham, ESA 99.  
    • Méthodes et Algorithmes pour reconstruire les arbres de l'Évolution.
      V. Berry, Thèse de doctorat, 1997 (gzipped ps file).  
    • On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain.
      V. Berry and O. GascuelMolecular Biology and Evolution, 13(7):999-1011. 1996. draft version (306k).  

    Other documents

    • A short survey on methods for building supertrees, V.Berry, 2003 (sildes .ps.gz).
    • Introduction to the field of phylogenetic reconstruction (in french).

    Previous projects

      2011-2014   Member of the Phylospace ANR project.

      2010-2013   Principal Investigator of the ATCG research program on reconciliation methods applied to plants, host/parasites and biogeographic data. The project involves, several teams in Montpellier, located at CIRAD, ISEM, BioVersity, SupAgro. The project is funded by the Région Languedoc-Roussillon.

      2009-2012   P.I. of the PhylAriane ANR project, involving the ISEM,LBBE and LIRMM labs.

      2007-2008  Reconstructing the Tree Of Life from large tree databases.

      Funded by the CS of University Montpellier 2.

      2005-2006   Phylogenetics Funded by the BIOSTIC-LR consortium.

      2003-2006   Supertree. Funded by the ACI IMPBIO consortium.