O Gascuel

Summary

Affiliation: Laboratoire d'Informatique
Country: France

Publications

  1. pmc Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum
    Nicolas Terrapon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Universite Montpellier 2, France
    BMC Bioinformatics 13:67. 2012
  2. pmc Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum
    Laurent Bréhélin
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Univ, Montpellier 2, CNRS 161 rue Ada, 34392 Montpellier, France
    BMC Genomics 11:35. 2010
  3. pmc A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism
    Isabelle Florent
    FRE3206 CNRS MNHN, USM504, Biologie Fonctionnelle des Protozoaires, RDDM, Museum national d histoire naturelle, Paris, France
    BMC Genomics 10:235. 2009
  4. pmc FLU, an amino acid substitution model for influenza proteins
    Cuong Cao Dang
    College of Technology, Vietnam National University Hanoi, Cau Giay, Hanoi, Vietnam
    BMC Evol Biol 10:99. 2010
  5. pmc PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
    Laurent Bréhélin
    Projet Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Univ, Montpellier 2, CNRS, 161 rue Ada, 34392 Montpellier, France
    BMC Bioinformatics 9:440. 2008
  6. pmc Fast NJ-like algorithms to deal with incomplete distance matrices
    Alexis Criscuolo
    Equipe Méthodes et Algorithmes pour Bioinformatique, LIRMM, CNRS Universite Montpellier 2, 161 rue Ada, 34392 Montpellier Cedex 05, France
    BMC Bioinformatics 9:166. 2008
  7. doi request reprint Inferring ancestral sequences in taxon-rich phylogenies
    Olivier Gascuel
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS Université de Montpellier, 161 rue Ada, 34392 Montpellier, France
    Math Biosci 227:125-35. 2010
  8. ncbi request reprint BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
    O Gascuel
    GERAD, Ecole des HEC, Montreal, Quebec, Canada
    Mol Biol Evol 14:685-95. 1997
  9. ncbi request reprint Neighbor-joining revealed
    Olivier Gascuel
    LIRMM, Montpellier, France
    Mol Biol Evol 23:1997-2000. 2006
  10. ncbi request reprint On the optimization principle in phylogenetic analysis and the minimum-evolution criterion
    O Gascuel
    Département Informatique Fondamentale et Applications, LIRMM, Montpellier, France
    Mol Biol Evol 17:401-5. 2000

Collaborators

Detail Information

Publications38

  1. pmc Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum
    Nicolas Terrapon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Universite Montpellier 2, France
    BMC Bioinformatics 13:67. 2012
    ..falciparum, the main causal agent of human malaria. In this context, fitting HMMs to the specificities of the target proteome can help identify additional domains...
  2. pmc Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum
    Laurent Bréhélin
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Univ, Montpellier 2, CNRS 161 rue Ada, 34392 Montpellier, France
    BMC Genomics 11:35. 2010
    ..Gene expression data have been widely used in the recent years to help functional annotation in an intra-species way via the so-called Guilt By Association (GBA) principle...
  3. pmc A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism
    Isabelle Florent
    FRE3206 CNRS MNHN, USM504, Biologie Fonctionnelle des Protozoaires, RDDM, Museum national d histoire naturelle, Paris, France
    BMC Genomics 10:235. 2009
    ..falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains...
  4. pmc FLU, an amino acid substitution model for influenza proteins
    Cuong Cao Dang
    College of Technology, Vietnam National University Hanoi, Cau Giay, Hanoi, Vietnam
    BMC Evol Biol 10:99. 2010
    ..We propose an influenza-specific amino acid substitution model to enhance the understanding of the evolution of influenza viruses...
  5. pmc PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
    Laurent Bréhélin
    Projet Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Univ, Montpellier 2, CNRS, 161 rue Ada, 34392 Montpellier, France
    BMC Bioinformatics 9:440. 2008
    ..Non-homology methods are thus needed to obtain functional clues for these uncharacterized genes...
  6. pmc Fast NJ-like algorithms to deal with incomplete distance matrices
    Alexis Criscuolo
    Equipe Méthodes et Algorithmes pour Bioinformatique, LIRMM, CNRS Universite Montpellier 2, 161 rue Ada, 34392 Montpellier Cedex 05, France
    BMC Bioinformatics 9:166. 2008
    ..But available agglomerative algorithms cannot deal with incomplete matrices...
  7. doi request reprint Inferring ancestral sequences in taxon-rich phylogenies
    Olivier Gascuel
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS Université de Montpellier, 161 rue Ada, 34392 Montpellier, France
    Math Biosci 227:125-35. 2010
    ..i.d. models may no longer be valid. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases...
  8. ncbi request reprint BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
    O Gascuel
    GERAD, Ecole des HEC, Montreal, Quebec, Canada
    Mol Biol Evol 14:685-95. 1997
    ..0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%...
  9. ncbi request reprint Neighbor-joining revealed
    Olivier Gascuel
    LIRMM, Montpellier, France
    Mol Biol Evol 23:1997-2000. 2006
    ..The origins of this story lie in a paper by Pauplin (2000) though its continuation has unfolded in more mathematically inclined literature. Our aim here is to make these findings more widely accessible...
  10. ncbi request reprint On the optimization principle in phylogenetic analysis and the minimum-evolution criterion
    O Gascuel
    Département Informatique Fondamentale et Applications, LIRMM, Montpellier, France
    Mol Biol Evol 17:401-5. 2000
    ..Simulations show that BIONJ significantly outperforms NJ...
  11. doi request reprint Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial
    Si Quang Le
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS Universite Montpellier II, 161 rue Ada, Montpellier Cedex 5, France
    Syst Biol 59:277-87. 2010
    ..Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/...
  12. ncbi request reprint Topological rearrangements and local search method for tandem duplication trees
    Denis Bertrand
    Projet Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, CNRS Univ Montpellier 2, 161 rue Ada, 34392 Montpellier 5, France
    IEEE/ACM Trans Comput Biol Bioinform 2:15-28. 2005
    ..We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our method than using any other program...
  13. doi request reprint An improved general amino acid replacement matrix
    Si Quang Le
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS, Universite Montpellier II, Montpellier, France
    Mol Biol Evol 25:1307-20. 2008
    ..Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG...
  14. ncbi request reprint Efficient biased estimation of evolutionary distances when substitution rates vary across sites
    Stephane Guindon
    LIRMM, UMR 9928 Université Montpellier II CNRS, 161 rue Ada, 34392 Montpellier Cedex 5, France
    Mol Biol Evol 19:534-43. 2002
    ..Finally, a data set of Maoricicada species sequences is analyzed, which confirms the advantage of our method...
  15. ncbi request reprint An efficient and accurate distance based algorithm to reconstruct tandem duplication trees
    Olivier Elemento
    Département d Informatique Fondamentale et Applications, LIRMM, Montpellier, France
    Bioinformatics 18:S92-9. 2002
    ..The results clearly show that DTSCORE is more accurate than all the other methods we studied. Finally, we report the results of DTSCORE on a real dataset. Supplementary information: http://www.lirmm.fr/w3ifa/MAAS/..
  16. ncbi request reprint A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    Stephane Guindon
    LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
    Syst Biol 52:696-704. 2003
    ..This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/...
  17. doi request reprint Robustness of phylogenetic inference based on minimum evolution
    Fabio Pardi
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS Université de Montpellier, 161 rue Ada, 34392 Montpellier, France
    Bull Math Biol 72:1820-39. 2010
    ..This difference may explain the gap in reconstruction accuracy observed in practice between OLS + ME and BME (which forms the basis of popular programs such as NJ and FastME)...
  18. ncbi request reprint Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
    Wim Hordijk
    Projet Méthodes et Algorithmes pour la Bioinformatique, LIRMM, UMR CNRS 5506, Université Montpellier 2 161 rue Ada, 34392 Montpellier, France
    Bioinformatics 21:4338-47. 2005
    ..When this occurs, the resulting trees may still show some of the defects (e.g. long branch attraction) of starting trees obtained using fast distance or parsimony programs...
  19. doi request reprint Using repeated measurements to validate hierarchical gene clusters
    Laurent Bréhélin
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS University Montpellier II, France
    Bioinformatics 24:682-8. 2008
    ..In this work, we propose an approach to evaluate the stability of clusters derived from hierarchical clustering by taking repeated measurements into account...
  20. doi request reprint Empirical profile mixture models for phylogenetic reconstruction
    Le Si Quang
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS UM2, Montpellier Cedex 5, France
    Bioinformatics 24:2317-23. 2008
    ..We apply it, learning on the HSSP database, and observe that a set of 20 profiles is enough to provide a better statistical fit than currently available empirical matrices (WAG, JTT), in particular on saturated data...
  21. doi request reprint Detection of new protein domains using co-occurrence: application to Plasmodium falciparum
    Nicolas Terrapon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Universite Montpellier 2, CNRS, 161 rue Ada, 34392 Montpellier Cedex 5, France
    Bioinformatics 25:3077-83. 2009
    ..However, numerous domains may be missed in highly divergent proteins. This is the case for Plasmodium falciparum proteins, the main causal agent of human malaria...
  22. pmc Phylogenetic mixture models for proteins
    Si Quang Le
    Méthodes et Algorithmes pour Bioinformatique, LIRMM, CNRS Universite Montpellier II, 161 rue Ada, 34392 Montpellier Cedex 5, France
    Philos Trans R Soc Lond B Biol Sci 363:3965-76. 2008
    ..All our models and a PhyML implementation are available from http://atgc.lirmm.fr/mixtures...
  23. ncbi request reprint Reconstructing the duplication history of tandemly repeated genes
    Olivier Elemento
    Département d Informatique Fondamentale et Applications, LIRMM, 161 rue Ada, 34392 Montpellier, France
    Mol Biol Evol 19:278-88. 2002
    ....
  24. ncbi request reprint SDM: a fast distance-based approach for (super) tree building in phylogenomics
    Alexis Criscuolo
    Groupe Phylogénie Moléculaire, ISEM, Universite Montpellier 2, Montpellier, France
    Syst Biol 55:740-55. 2006
    ..2002, Syst. Biol. 51: 652-664) that involves 48 genes of 75 placental mammals. The results indicate that these genes have strong rate heterogeneity and confirm the simulation conclusions...
  25. ncbi request reprint Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets
    Vincent Ranwez
    Département Informatique Fondamentale et Applications, LIRMM, Montpellier Cedex 5, France
    Mol Biol Evol 19:1952-63. 2002
    ..5% for BioNJ and Weighbor, respectively). Moreover, this combination requires only about 1.5 min to infer a phylogeny of 96 sequences composed of 1,200 nucleotides, as compared with 6.5 h for FastDNAml on the same machine (PC 466 MHz)...
  26. ncbi request reprint The combinatorics of tandem duplication trees
    Olivier Gascuel
    Département d Informatique Fondamentale et Applications, LIRMM, 161 rue Ada, 34392 Montpellier, France
    Syst Biol 52:110-8. 2003
    ..The recurrence relation also suggests efficient algorithms to recognize duplication trees and to generate random duplication trees for simulation. We present a linear-time recognition algorithm...
  27. doi request reprint Estimating maximum likelihood phylogenies with PhyML
    Stephane Guindon
    Laboratoire d Informatique, de Robotique et de Microélectronique de Montpellier LIRMM, UMR 5506 CNRS, Universite Montpellier II, Montpellier, France
    Methods Mol Biol 537:113-37. 2009
    ..We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from (http://atgc_montpellier.fr/phyml/)...
  28. doi request reprint New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    Stephane Guindon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Centre National de la Recherche Scientifique, Universite de Montpellier, Montpellier Cedex 5, France
    Syst Biol 59:307-21. 2010
    ..Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/...
  29. doi request reprint Getting a tree fast: Neighbor Joining, FastME, and distance-based methods
    Richard Desper
    Department of Biology, University College, London, United Kingdom
    Curr Protoc Bioinformatics . 2006
    ..It also describes how to estimate evolutionary distances from DNA and proteins, how to perform bootstrap analysis, and how to use CLUSTAL to compute both a sequence alignment and a phylogenetic tree...
  30. pmc PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
    Stephane Guindon
    Bioinformatics Institute and Allan Wilson Centre, University of Auckland Private Bag 92019, Auckland, New Zealand
    Nucleic Acids Res 33:W557-9. 2005
    ..The server and its documentation are available at http://atgc.lirmm.fr/phyml...
  31. ncbi request reprint A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin
    Elodie Duprat
    Laboratoire d ImmunoGénétique Moléculaire IGH UPR CNRS 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
    Bioinformatics 22:453-9. 2006
    ..IMGT standardization of MhcSF protein domains provides a unique numbering of the multiple alignment positions, and conditions to develop such predictive tool...
  32. ncbi request reprint Duplication and inversion history of a tandemly repeated genes family
    Mathieu Lajoie
    DIRO, Universite de Montreal, Montreal H3C 3J7, QC, Canada
    J Comput Biol 14:462-78. 2007
    ..We show, on simulated data, that those algorithms can be used to improve phylogenetic inference of tandemly repeated gene families. An application on a published phylogeny of KRAB zinc finger genes is presented...
  33. pmc Identification of novel peptide hormones in the human proteome by hidden Markov model screening
    Olivier Mirabeau
    Mouse Biology Unit, EMBL, 00016 Monterotondo, Italy
    Genome Res 17:320-7. 2007
    ..Peptide hormones and their receptors are important diagnostic and therapeutic targets, and our results suggest that spexin and augurin are novel peptide hormones likely to be involved in physiological homeostasis...
  34. ncbi request reprint Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle
    Richard Desper
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    J Comput Biol 9:687-705. 2002
    ..Moreover, this BME scheme yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy...
  35. ncbi request reprint Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting
    Richard Desper
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Mol Biol Evol 21:587-98. 2004
    ..Interestingly, the covarion parameter has little effect on the tree quality for any of the algorithms. FASTME is freely available on the web...
  36. pmc Genomics, biogeography, and the diversification of placental mammals
    Derek E Wildman
    Perinatology Research Branch, National Institute of Child Health and Human Development National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 104:14395-400. 2007
    ..Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades...
  37. ncbi request reprint Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs
    Didier Gonze
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, CP 263, Campus Plaine, Blvd du Triomphe, B 1050 Bruxelles, Belgium
    Bioinformatics 21:3490-500. 2005
    ..We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus...
  38. ncbi request reprint Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    Maria Anisimova
    Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM CNRS, Universite Montpellier II, Montpellier 34392, France
    Syst Biol 55:539-52. 2006
    ..The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003)...