Julien Y Dutheil

Summary

Country: France

Publications

  1. ncbi A model-based approach for detecting coevolving positions in a molecule
    Julien Dutheil
    CNRS UMR 5171 Laboratoire Génome, Populations, Interactions, Adaptation, Universite Montpellier II, Montpellier Cedex, France
    Mol Biol Evol 22:1919-28. 2005
  2. ncbi Ancestral population genomics
    Julien Y Dutheil
    Institut des Sciences de l Évolution Montpellier ISE M, UMR 5554, CNRS, Unversité Montpellier, Montpellier, France
    Methods Mol Biol 856:293-313. 2012
  3. ncbi Detecting coevolving positions in a molecule: why and how to account for phylogeny
    Julien Y Dutheil
    Institut des Sciences de l Evolution Montpellier I S E M Unité Mixte de Recherche UMII CNRS UMR 5554 Université de Montpellier II CC 065 34095 Montpellier Cedex 05
    Brief Bioinform 13:228-43. 2012
  4. ncbi Base pairing constraints drive structural epistasis in ribosomal RNA sequences
    Julien Y Dutheil
    Bioinformatics Research Center BiRC, Aarhus University, Arhus, Denmark
    Mol Biol Evol 27:1868-76. 2010
  5. ncbi Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    Julien Dutheil
    CNRS UMR 5171 Génome, Populations, Interactions, Adaptation GPIA, Universite Montpellier 2, France
    BMC Bioinformatics 7:188. 2006
  6. ncbi Detecting groups of coevolving positions in a molecule: a clustering approach
    Julien Dutheil
    Institut des Sciences de l Evolution UM2 CNRS Université Montpellier 2 Place Eugéne Bataillon, CC064, 34 095 Montpellier Cedex 5, France
    BMC Evol Biol 7:242. 2007
  7. ncbi Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model
    Thomas Mailund
    Bioinformatics Research Centre, Aarhus University, Denmark
    PLoS Genet 7:e1001319. 2011
  8. ncbi Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, DK 8000 Aarhus C, Denmark
    Genome Res 21:349-56. 2011
  9. ncbi Ancestral population genomics: the coalescent hidden Markov model approach
    Julien Y Dutheil
    Bioinformatics Research Center, Aarhus University, C F Møllers Allé 8, Bldg 1110, DK 8000 Aarhus C, Denmark
    Genetics 183:259-74. 2009
  10. ncbi Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping
    Jonathan Romiguier
    Institut des Sciences de l Evolution de Montpellier, CNRS Universite Montpellier 2, Montpellier, France
    PLoS ONE 7:e33852. 2012

Detail Information

Publications13

  1. ncbi A model-based approach for detecting coevolving positions in a molecule
    Julien Dutheil
    CNRS UMR 5171 Laboratoire Génome, Populations, Interactions, Adaptation, Universite Montpellier II, Montpellier Cedex, France
    Mol Biol Evol 22:1919-28. 2005
    ..More than 95% of the intramolecular predicted pairs of sites correspond to known interacting site pairs...
  2. ncbi Ancestral population genomics
    Julien Y Dutheil
    Institut des Sciences de l Évolution Montpellier ISE M, UMR 5554, CNRS, Unversité Montpellier, Montpellier, France
    Methods Mol Biol 856:293-313. 2012
    ..In particular, we emphasize core assumptions and working hypothesis. Finally, we discuss computational and statistical challenges that arise in the analysis of population genomics data sets...
  3. ncbi Detecting coevolving positions in a molecule: why and how to account for phylogeny
    Julien Y Dutheil
    Institut des Sciences de l Evolution Montpellier I S E M Unité Mixte de Recherche UMII CNRS UMR 5554 Université de Montpellier II CC 065 34095 Montpellier Cedex 05
    Brief Bioinform 13:228-43. 2012
    ..I also evaluate, using rigorous statistical procedures, the best approaches to do so, and discuss several important biological aspects to consider when performing coevolution analyses...
  4. ncbi Base pairing constraints drive structural epistasis in ribosomal RNA sequences
    Julien Y Dutheil
    Bioinformatics Research Center BiRC, Aarhus University, Arhus, Denmark
    Mol Biol Evol 27:1868-76. 2010
    ..They also demonstrate that coevolutionary analysis provides almost exclusively 2D information and only little 3D signal...
  5. ncbi Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    Julien Dutheil
    CNRS UMR 5171 Génome, Populations, Interactions, Adaptation GPIA, Universite Montpellier 2, France
    BMC Bioinformatics 7:188. 2006
    ..Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications...
  6. ncbi Detecting groups of coevolving positions in a molecule: a clustering approach
    Julien Dutheil
    Institut des Sciences de l Evolution UM2 CNRS Université Montpellier 2 Place Eugéne Bataillon, CC064, 34 095 Montpellier Cedex 5, France
    BMC Evol Biol 7:242. 2007
    ....
  7. ncbi Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model
    Thomas Mailund
    Bioinformatics Research Centre, Aarhus University, Denmark
    PLoS Genet 7:e1001319. 2011
    ..We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection...
  8. ncbi Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, DK 8000 Aarhus C, Denmark
    Genome Res 21:349-56. 2011
    ..Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny...
  9. ncbi Ancestral population genomics: the coalescent hidden Markov model approach
    Julien Y Dutheil
    Bioinformatics Research Center, Aarhus University, C F Møllers Allé 8, Bldg 1110, DK 8000 Aarhus C, Denmark
    Genetics 183:259-74. 2009
    ..We expect that this framework will prove useful for population genomics and provide exciting insights into genome evolution...
  10. ncbi Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping
    Jonathan Romiguier
    Institut des Sciences de l Evolution de Montpellier, CNRS Universite Montpellier 2, Montpellier, France
    PLoS ONE 7:e33852. 2012
    ....
  11. ncbi The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species
    Eva H Stukenbrock
    Bioinformatics Research Center, Aarhus University, C F Moellers Alle, DK 8000 Aarhus C, Denmark
    Genome Res 21:2157-66. 2011
    ..The strong impact of natural selection, we document, is at odds with the small effective population sizes estimated and suggest that population sizes were historically large but likely unstable...
  12. ncbi Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
    Julien Dutheil
    BiRC Bioinformatics Research Center, University of Aarhus, C, F, Møllers Alle, DK 8000 Arhus C, Denmark
    BMC Evol Biol 8:255. 2008
    ....
  13. ncbi Recombination difference between sexes: a role for haploid selection
    Thomas Lenormand
    UMR 5175, Centre d Ecologie Fonctionnelle et Evolutive, Montpellier, France
    PLoS Biol 3:e63. 2005
    ..This finding provides strong empirical support in favour of a population genetic explanation for the evolution of heterochiasmy and, more broadly, for the evolution of sex and recombination...