Affiliation: McGill University
- Neighbor-net: an agglomerative method for the construction of phylogenetic networksDavid 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...
- Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysisRachel 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.]...
- Accounting for gene rate heterogeneity in phylogenetic inferenceRachel 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...
- A simple and robust statistical test for detecting the presence of recombinationTrevor 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...
- A general comparison of relaxed molecular clock modelsThomas 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...
- 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
- Site interdependence attributed to tertiary structure in amino acid sequence evolutionNicolas 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...
- DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene listsDa 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...
- Conditioned genome reconstruction: how to avoid choosing the conditioning genomeMatthew 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...
- Continuous and tractable models for the variation of evolutionary ratesThomas 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...
- Application of phylogenetic networks in evolutionary studiesDaniel 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...
- Biogeographic interpretation of splits graphs: least squares optimization of branch lengthsRichard 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...
- A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genesChristian 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...
- Parsimony via consensusTrevor 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...
- Cloning and characterization of a theta class glutathione transferase from the potato pathogen Phytophthora infestansDavid 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...
- 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...