MAB team | LIRMM | Univ Montpellier 2 | CNRS

Vincent Berry

software

Contact

Please contact me by email for above offers or other enquiries.
( vberry AT lirmm DOT fr )

Context

Research activities are conducted in the Methods and Algorithms for Bioinformatics (MAB) group at the LIRMM lab, and in tight collaboration with several life sciences lab.

Keywords

Phylogenomics Consensus Networks Statistics Triplets and quartets

Projects

Current

2013-2017 Member of the IBC project, ie Institut de Biologie Computationnelle

2011-2014 Member of the Phylospace ANR project.

2010-2013 I'm coordinating 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.

Papers

2013

CompPhy - an online collaborative tool for visualizing and managing phylogenies
N. Fiorini, V. Lefort, F. Chevenet, A.-M. Arigon Chifolleau, V. Berry, submitted
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, submitted.
SylvX and Mowgli - reconciliation tools in the forest of gene and species trees
F. Chevenet, J.-P. Doyon, T.H. Nguyen, S. Pointet, V. Berry, to be submitted
Amalgamating Source Trees with Different Taxonomic Levels
V. Berry, O. Bininda-Emonds, C. Semple. Accepted in Systematic Biology
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.
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
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 r&ecaute;conciliation 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
- Annual Meeting of the Society for Molecular Biology and Evolution (SMBE'10) - "Integrative phylogenomics: from genes to organismal history" track, July 2010 [ slides ]
- Bertinoro Computational Biology (BCB'10), May 2010 [ slides ]

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).