Hervé Philippe

Summary

Country: Canada

Publications

  1. pmc State-of the art methodologies dictate new standards for phylogenetic analysis
    Maria Anisimova
    Department of Computer Science, Swiss Federal Institute of Technology ETH, Zurich 8092, Switzerland
    BMC Evol Biol 13:161. 2013
  2. pmc Cnidarian phylogenetic relationships as revealed by mitogenomics
    Ehsan Kayal
    Dept, Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, IA, USA
    BMC Evol Biol 13:5. 2013
  3. pmc Origin of land plants: do conjugating green algae hold the key?
    Sabina Wodniok
    Biozentrum Köln, Botanik, Universitat zu Koln, Zülpicher Strasse 47b, 50674 Koln, Germany
    BMC Evol Biol 11:104. 2011
  4. pmc Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
    Nicolas Lartillot
    Laboratoire d Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS Université de Montpellier 2, Montpellier Cedex 5, France
    BMC Evol Biol 7:S4. 2007
  5. ncbi request reprint Heterotachy and functional shift in protein evolution
    Hervé Philippe
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    IUBMB Life 55:257-65. 2003
  6. doi request reprint Less is more: decreasing the number of scientific conferences to promote economic degrowth
    Hervé Philippe
    Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Montreal, Quebec H3T1J4, Canada
    Trends Genet 24:265-7. 2008
  7. pmc Acoel flatworms are not platyhelminthes: evidence from phylogenomics
    Hervé Philippe
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    PLoS ONE 2:e717. 2007
  8. pmc Heterotachy and long-branch attraction in phylogenetics
    Hervé Philippe
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    BMC Evol Biol 5:50. 2005
  9. pmc Difficult phylogenetic questions: more data, maybe; better methods, certainly
    Hervé Philippe
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada
    BMC Biol 9:91. 2011
  10. ncbi request reprint Phylogenomics of eukaryotes: impact of missing data on large alignments
    Hervé Philippe
    School of Animal and Microbial Sciences, The University of Reading, Reading, UK
    Mol Biol Evol 21:1740-52. 2004

Detail Information

Publications48

  1. pmc State-of the art methodologies dictate new standards for phylogenetic analysis
    Maria Anisimova
    Department of Computer Science, Swiss Federal Institute of Technology ETH, Zurich 8092, Switzerland
    BMC Evol Biol 13:161. 2013
    ..The rapid pace at which sequence data accumulate quickly outdates such publications. Although clearly, discoveries stemming from data mining, reports of new tools and databases and review papers are also desirable. ..
  2. pmc Cnidarian phylogenetic relationships as revealed by mitogenomics
    Ehsan Kayal
    Dept, Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, IA, USA
    BMC Evol Biol 13:5. 2013
    ..Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution...
  3. pmc Origin of land plants: do conjugating green algae hold the key?
    Sabina Wodniok
    Biozentrum Köln, Botanik, Universitat zu Koln, Zülpicher Strasse 47b, 50674 Koln, Germany
    BMC Evol Biol 11:104. 2011
    ....
  4. pmc Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
    Nicolas Lartillot
    Laboratoire d Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS Université de Montpellier 2, Montpellier Cedex 5, France
    BMC Evol Biol 7:S4. 2007
    ....
  5. ncbi request reprint Heterotachy and functional shift in protein evolution
    Hervé Philippe
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    IUBMB Life 55:257-65. 2003
    ....
  6. doi request reprint Less is more: decreasing the number of scientific conferences to promote economic degrowth
    Hervé Philippe
    Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Montreal, Quebec H3T1J4, Canada
    Trends Genet 24:265-7. 2008
  7. pmc Acoel flatworms are not platyhelminthes: evidence from phylogenomics
    Hervé Philippe
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    PLoS ONE 2:e717. 2007
    ....
  8. pmc Heterotachy and long-branch attraction in phylogenetics
    Hervé Philippe
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    BMC Evol Biol 5:50. 2005
    ....
  9. pmc Difficult phylogenetic questions: more data, maybe; better methods, certainly
    Hervé Philippe
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada
    BMC Biol 9:91. 2011
    ....
  10. ncbi request reprint Phylogenomics of eukaryotes: impact of missing data on large alignments
    Hervé Philippe
    School of Animal and Microbial Sciences, The University of Reading, Reading, UK
    Mol Biol Evol 21:1740-52. 2004
    ....
  11. ncbi request reprint Horizontal gene transfer and phylogenetics
    Hervé Philippe
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, QC, H3C 3J7, Montreal, Canada
    Curr Opin Microbiol 6:498-505. 2003
    ..This history, even if horizontal gene transfers are rare, should be represented by a network surrounding the core phylogeny...
  12. ncbi request reprint Large-scale sequencing and the new animal phylogeny
    Hervé Philippe
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, QC, Canada, H3C 3J7
    Trends Ecol Evol 21:614-20. 2006
    ..This approach counters both sources of error, gives the best hope of a well-resolved phylogeny of the animals and will act as a central resource for a carefully targeted genome sequencing programme...
  13. ncbi request reprint Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models
    Nicolas Rodrigue
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, C P 6821, Succ Centre Ville, Montreal, Quebec Canada
    Bioinformatics 24:56-62. 2008
    ..However, current probabilistic methods for generating such mappings are ill-suited to certain types of evolutionary models, in particular, the widely used models of codon substitution...
  14. ncbi request reprint An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics
    Henner Brinkmann
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    Syst Biol 54:743-57. 2005
    ....
  15. ncbi request reprint Statistical potentials for improved structurally constrained evolutionary models
    Claudia L Kleinman
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 27:1546-60. 2010
    ....
  16. ncbi request reprint Assessing site-interdependent phylogenetic models of sequence evolution
    Nicolas Rodrigue
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 23:1762-75. 2006
    ....
  17. ncbi request reprint Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles
    Denis Baurain
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 27:1698-709. 2010
    ..Therefore, we reject the chromalveolate hypothesis as falsified in favor of more complex evolutionary scenarios involving multiple higher order eukaryote-eukaryote endosymbioses...
  18. pmc Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support
    Yu Liu
    Robert Cedergren Centre, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    BMC Evol Biol 9:272. 2009
    ..Yet, published phylogenies with up to five genes are without compelling statistical support, and genome-level data should be used to resolve this question with confidence...
  19. doi request reprint A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests
    Yan Zhou
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Quebec, Canada
    Mol Biol Evol 27:371-84. 2010
    ..We describe posterior predictive discrepancy tests and use these to demonstrate the importance of these different elements of the models...
  20. ncbi request reprint Detecting and overcoming systematic errors in genome-scale phylogenies
    Naiara Rodriguez-Ezpeleta
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3T 1J4, Canada
    Syst Biol 56:389-99. 2007
    ..Finally, our results allow us to formulate guidelines for detecting and overcoming phylogenetic artefacts in genome-scale phylogenetic analyses...
  21. ncbi request reprint Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta
    Naiara Rodriguez-Ezpeleta
    Department de Biochimie, Centre Robert Cedergren, Canadian Institute of Advanced Research, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 24:723-31. 2007
    ..Importantly, we demonstrate that using an increased taxon sampling as well as more realistic models of evolution allows increasing congruence among the nuclear, mitochondrial, and plastid data sets...
  22. ncbi request reprint Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes
    Naiara Rodriguez-Ezpeleta
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3T 1J4, Canada
    Curr Biol 15:1325-30. 2005
    ....
  23. pmc An unusual choanoflagellate protein released by Hedgehog autocatalytic processing
    Elizabeth A Snell
    School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK
    Proc Biol Sci 273:401-7. 2006
    ..Since Hh-C and Hoglet-C are homologous, but Hh-N and Hoglet-N are not, we argue that metazoan hedgehog genes evolved by fusion of two distinct genes...
  24. ncbi request reprint Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans
    Naiara Rodriguez-Ezpeleta
    Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Curr Biol 17:1420-5. 2007
    ..We discuss the implications of these results for the concept of "excavates" and for the elucidation of eukaryotic phylogeny in general...
  25. pmc A maximum likelihood framework for protein design
    Claudia L Kleinman
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    BMC Bioinformatics 7:326. 2006
    ....
  26. pmc Evaluation of the models handling heterotachy in phylogenetic inference
    Yan Zhou
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    BMC Evol Biol 7:206. 2007
    ....
  27. ncbi request reprint Site interdependence attributed to tertiary structure in amino acid sequence evolution
    Nicolas Rodrigue
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Canada
    Gene 347:207-17. 2005
    ..We propose such a combination as a useful way of capturing the complexity of protein evolution. Finally, we outline features of the model using three datasets and show the approach's sensitivity to different tree topologies...
  28. doi request reprint Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts
    Yu Liu
    Robert Cedergren Centre, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 26:27-34. 2009
    ....
  29. doi request reprint Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
    Béatrice Roure
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 30:197-214. 2013
    ..g., the site-heterogeneous CAT model instead of the site-homogeneous WAG model) is more beneficial to phylogenetic accuracy than reducing the level of missing data...
  30. ncbi request reprint Inferring and validating horizontal gene transfer events using bipartition dissimilarity
    Alix Boc
    Departement d informatique, Universite du Quebec a Montreal, C P 8888, Succ Centre Ville, Montreal, Quebec, Canada
    Syst Biol 59:195-211. 2010
    ..Finally, a statistical framework for assessing the reliability of obtained HGTs by bootstrap analysis is also presented...
  31. pmc Bayesian comparisons of codon substitution models
    Nicolas Rodrigue
    Canadian Institute for Advanced Research, Départementde Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Genetics 180:1579-91. 2008
    ..Altogether, the framework presented here suggests a broad modeling project in the MG style, stressing the importance of combining and contrasting available model formulations and grounding developments in a sound probabilistic paradigm...
  32. ncbi request reprint Exploring fast computational strategies for probabilistic phylogenetic analysis
    Nicolas Rodrigue
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Quebec, Canada
    Syst Biol 56:711-26. 2007
    ....
  33. ncbi request reprint Tunicates and not cephalochordates are the closest living relatives of vertebrates
    Frédéric Delsuc
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    Nature 439:965-8. 2006
    ....
  34. ncbi request reprint Phylogenomics and the reconstruction of the tree of life
    Frédéric Delsuc
    Canadian Institute for Advanced Research, Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C3J7, Canada
    Nat Rev Genet 6:361-75. 2005
    ..The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence...
  35. ncbi request reprint Plastid origin: replaying the tape
    Naiara Rodriguez-Ezpeleta
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3T 1J4, Canada
    Curr Biol 16:R53-6. 2006
  36. pmc SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics
    Béatrice Roure
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Montreal, Quebec H3C3J7, Canada
    BMC Evol Biol 7:S2. 2007
    ..A tool that selects sequences, species, and genes, while dealing with these issues, is needed in a phylogenomics context...
  37. pmc Acoelomorph flatworms are deuterostomes related to Xenoturbella
    Hervé Philippe
    Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada
    Nature 470:255-8. 2011
    ....
  38. ncbi request reprint Phylogenomics: the beginning of incongruence?
    Olivier Jeffroy
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec, Canada, H3C3J7
    Trends Genet 22:225-31. 2006
    ..We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence...
  39. pmc A simple and robust statistical test for detecting the presence of recombination
    Trevor C Bruen
    McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
    Genetics 172:2665-81. 2006
    ..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
  40. ncbi request reprint Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
    Hervé Philippe
    Canadian Institute for Advanced Research and Département de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 22:1246-53. 2005
    ..These findings have important implications for the interpretation of morphological and genomic data...
  41. pmc Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference
    Béatrice Roure
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Quebec, Canada
    BMC Evol Biol 11:17. 2011
    ..However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations...
  42. doi request reprint Phylogenomics revives traditional views on deep animal relationships
    Hervé Philippe
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec, Canada
    Curr Biol 19:706-12. 2009
    ..This new phylogeny provides a stimulating framework for exploring the important changes that shaped the body plans of the early diverging phyla...
  43. ncbi request reprint The diversity of eukaryotes and the root of the eukaryotic tree
    Henner Brinkmann
    Canadian Institute for Advanced Research, Evolutionary Biology Program, Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Succursale Centreville, 2900 Edouard Montpetit, Montreal, Quebec H3C3J7, Canada
    Adv Exp Med Biol 607:20-37. 2007
    ..Therefore it is time to reevaluate the origin and evolution of eukaryotes, in light of the newly established phylogeny, by further integrating secondary simplification as an equal partner to complexification...
  44. ncbi request reprint A general comparison of relaxed molecular clock models
    Thomas Lepage
    Department of Mathematics and Statistics, McGill University, Montreal, Quebec, Canada
    Mol Biol Evol 24:2669-80. 2007
    ..Altogether, our results provide useful guidelines for model choice in the field of molecular dating while opening the way to more extensive model comparisons...
  45. ncbi request reprint A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    Nicolas Lartillot
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec Canada
    Mol Biol Evol 21:1095-109. 2004
    ....
  46. ncbi request reprint Origin of land plants revisited in the light of sequence contamination and missing data
    Simon Laurin-Lemay
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Montreal Quebec, Canada
    Curr Biol 22:R593-4. 2012
    ..The use of a carefully checked and almost complete dataset suggests that land plants are closely related to a group composed of Zygnematales and Coleochaetales...