David Bryant

Summary

Affiliation: McGill University
Country: Canada

Publications

  1. ncbi request reprint Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    David Bryant
    McGill Centre for Bioinformatics, Montreal, Quebec, Canada
    Mol Biol Evol 21:255-65. 2004
  2. ncbi request reprint Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis
    Rachel B Bevan
    McGill Centre for Bioinformatics, Duff Medical Building, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada
    Syst Biol 54:900-15. 2005
  3. ncbi request reprint Accounting for gene rate heterogeneity in phylogenetic inference
    Rachel B Bevan
    McGill Centre for Bioinformatics, McGill University, Duff Medical Building, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada
    Syst Biol 56:194-205. 2007
  4. 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
  5. 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
  6. ncbi request reprint Matrix representations with parsimony or with distances: two sides of the same coin?
    Francois Joseph Lapointe
    Departement de sciences biologiques, Universite de Montreal, C P 6128, Succ Centre Ville, Montreal, Quebec H3C 3J7, Canada
    Syst Biol 52:865-8. 2003
  7. 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
  8. pmc DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, SAIC Frederick, Inc, National Cancer Institute at Frederick, MD 21702, USA
    Nucleic Acids Res 35:W169-75. 2007
  9. ncbi request reprint Conditioned genome reconstruction: how to avoid choosing the conditioning genome
    Matthew Spencer
    Department of Mathematics and Statistics, Dalhousie University, Hali, Nova Scotia, B3H 3J5, Canada
    Syst Biol 56:25-43. 2007
  10. ncbi request reprint Continuous and tractable models for the variation of evolutionary rates
    Thomas Lepage
    Department of Mathematics and Statistics, McGill University, Montreal, Canada
    Math Biosci 199:216-33. 2006

Collaborators

Detail Information

Publications16

  1. ncbi request reprint Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    David Bryant
    McGill Centre for Bioinformatics, Montreal, Quebec, Canada
    Mol Biol Evol 21:255-65. 2004
    ..and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package...
  2. ncbi request reprint Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis
    Rachel B Bevan
    McGill Centre for Bioinformatics, Duff Medical Building, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada
    Syst Biol 54:900-15. 2005
    ..e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.]...
  3. ncbi request reprint Accounting for gene rate heterogeneity in phylogenetic inference
    Rachel B Bevan
    McGill Centre for Bioinformatics, McGill University, Duff Medical Building, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada
    Syst Biol 56:194-205. 2007
    ..Furthermore, improved model fit over the concatenated model is highly correlated with the presence of a gene with a slow relative rate of evolution...
  4. 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...
  5. 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...
  6. ncbi request reprint Matrix representations with parsimony or with distances: two sides of the same coin?
    Francois Joseph Lapointe
    Departement de sciences biologiques, Universite de Montreal, C P 6128, Succ Centre Ville, Montreal, Quebec H3C 3J7, Canada
    Syst Biol 52:865-8. 2003
  7. 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...
  8. pmc DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, SAIC Frederick, Inc, National Cancer Institute at Frederick, MD 21702, USA
    Nucleic Acids Res 35:W169-75. 2007
    ..With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists...
  9. ncbi request reprint Conditioned genome reconstruction: how to avoid choosing the conditioning genome
    Matthew Spencer
    Department of Mathematics and Statistics, Dalhousie University, Hali, Nova Scotia, B3H 3J5, Canada
    Syst Biol 56:25-43. 2007
    ..However, an analysis of 40 bacterial genomes using this method supports an incorrect clade of parasites. This is a common feature of model-based gene content methods and is due to parallel gene loss...
  10. ncbi request reprint Continuous and tractable models for the variation of evolutionary rates
    Thomas Lepage
    Department of Mathematics and Statistics, McGill University, Montreal, Canada
    Math Biosci 199:216-33. 2006
    ..We provide here an exact formula for the likelihood of a three-taxon tree. The likelihoods of larger trees can be evaluated using Monte-Carlo methods...
  11. ncbi request reprint Application of phylogenetic networks in evolutionary studies
    Daniel H Huson
    Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
    Mol Biol Evol 23:254-67. 2006
    ..Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees...
  12. ncbi request reprint Biogeographic interpretation of splits graphs: least squares optimization of branch lengths
    Richard Winkworth
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Syst Biol 54:56-65. 2005
    ..We also discuss the biogeographic interpretation and limitations of splits graphs...
  13. ncbi request reprint A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
    Christian Esser
    Institute of Botany III, University of Dusseldorf, Dusseldorf, Germany
    Mol Biol Evol 21:1643-60. 2004
    ..Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed...
  14. doi request reprint Parsimony via consensus
    Trevor C Bruen
    Department of Mathematics, University of California, Berkeley, USA
    Syst Biol 57:251-6. 2008
    ..We discuss implications of this connection for the debate over the use of consensus trees or total evidence and show how it provides a link between incongruence of characters and recombination...
  15. ncbi request reprint Cloning and characterization of a theta class glutathione transferase from the potato pathogen Phytophthora infestans
    David Bryant
    School of Biological and Biomedical Sciences, Crop Protection Group, Durham University, South Road, Durham DH1 3LE, UK
    Phytochemistry 67:1427-34. 2006
    ..An antiserum was raised to PiGSTT1-1 and used to demonstrate that the respective enzyme was abundantly expressed in P. infestans both cultured on pea agar and during the infection of potato plants...
  16. pmc High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Bioinformatics 6:168. 2005
    ..We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations...